BACKGROUND
with the advent of high-throughput rna sequencing  it has become increasingly popular to define the genetic expression profile of a cell by its transcriptome  <cit> .
an approach in which the expression of a gene is estimated as a number of sequence reads aligning to that gene assumes a linear  <dig> gene- <dig> transcript- <dig> protein information transfer relay , a scenario that is evidently a gross simplification.
if one accepts that the end readout of the genetic program, as manifested as the cellular phenotype, is dictated in large part by the proteome, it would appear more judicious to directly characterise the cells protein composition, however, this remains technically difficult.
nonetheless, such switches in the cellular phenotype are at the core of the non-tumoural to tumoural changes observed in cancer.
the non-linear information transfer from genome to proteome arises due to multiple layers of complexity.
at the mrna level, this includes alternative splicing, multiple transcriptional start sites  and polyadenylation sites all of which show cell-specific regulation, and all of which serve to couple events in the nucleus to the proteomic readout in the cytoplasm .
it is evident that alternative splicing within the open reading frame  can alter the protein readout.
however, this is not so intuitive with regards to alternative tsss which invariably change the nature of the first exon and, as a consequence, the sequence of the mrnas 5′ untranslated region ; for why see below).
nonetheless, the tl contains multiple elements that can modulate the translational readout both quantitatively  and qualitatively , and all are hard-wired into cellular signalling pathways regulating proliferation, survival and development  <cit> .
these include rna structure, internal ribosome entry sites , protein binding sites, upstream aug codons  which may be responsible for the translation of upstream open reading frames    <cit> .
the complexity within the tl is further increased by the use of non-aug start codons.
these are frequently evolutionarily conserved and can generate n-terminal extensions in coding sequences that impact on function and cellular localisation  <cit> .
such elements are frequently observed in gene transcripts that are under tight translational control.
recent ribosomal profiling studies also indicate that the uorfs are frequently expressed, an observation that calls into question the use of the term 5′utr   <cit> .
between  <dig> and 50 % of human protein coding genes have been reported to use alternative promoters, and alterations in promoter usage within particular genes have been associated with human pathologies, including cancer .
however, the impact of global changes on tss selection  on the mammalian proteome remains unclear despite evidence from yeast that such changes correlate with a major shift in translational activity  <cit> .fig.
<dig> translationally profiling in mcf <dig> and mcf10a cells.
a organisation of a mammalian mrna.
the m7gpppn 5′ cap is indicated as are potential rna structural elements within the tl.
the brown ovals indicate rna binding proteins that modulate expression by binding to regions outside the principle orf.
the 3′ polya tail n is also indicated.
b representative polysome profiles for mcf <dig> and mcf10a cells.
equivalent amounts of protein were loaded onto each gradient.
note that the polysomal fraction is considerably smaller in the non-tumoural mcf10a cell line.
c plot of the differential transcript levels  in total versus polysomal rna.
the green dots indicate the up-regulated genes, the red dots the down-regulated genes.
the spearman correlation is indicated.
d go analysis of the translationally regulated genes from the refseq annotations.
the go pie charts, which represent the percentage of gene hits against the total number of genes, were built using the panther  classification system  <cit>
rna structure impacts on translation at multiple levels: when positioned proximal to the 5′ cap it can render it less accessible for 43s ribosome loading.
such rnas therefore compete poorly for the limiting amounts of cap binding protein, eif4e   <cit> .
moreover, bioinformatic studies suggest that structure near the 5′ cap may also play a role in mirna mediated regulation possibly via the initiation factor eif4a <dig>  <cit> .
structure can also act post-43s recruitment, as a thermodynamic barrier that impedes ribosome movement during the 5′ → 3′ scanning of the tl used to locate the initiation codon.
as such it serves to repress translational expression from the main orf.
this is further highlighted by the role of rna helicases in human pathologies in which translational control is perturbed  <cit> .
approximately 40 % of mammalian mrnas carry uorfs and like rna structure, uorfs/uaugs are generally perceived to function as translational repressors  <cit> .
the magnitude of the repression is in large part determined by the nature of the sequences flanking the uaug, with the effect being the most marked when they approach the ideal “kozak context” for initiation   <cit> .
despite their apparent abundance, uaugs are less frequent than would be predicted by mere chance, yet aug is the most conserved triplet within tls pointing to a strong evolutionary selection  <cit> .
however, small uorfs can also couple the readout to eif <dig> gtp.trnaimet ternary complex  levels in the cell  <cit>  and, via a process referred to as delayed reinitiation, can permit access to start codons downstream of the aug of the principle orf  <cit> .
during translation of small uorfs not all the initiation factors are released prior to termination.
post 40s ribosomes carrying eif <dig> can remain attached to the rna and continue scanning  <cit> .
the aug codon at which they subsequently reinitiate translation is determined both by the cellular tc levels  and the distance in nucleotides that the ribosome must scan  <cit> .
the quantitative and qualitative changes in the protein readout that can arise due to the presence of small uorfs can serve as a proliferation/differentiation switch that is coupled to changes in tc levels, as observed with the transcription factor ccaat/enhancer binding protein β   <cit> .
not all the information for mrna decoding resides within its nucleotide sequence.
indeed, the translational readout from a unique transcript can exhibit considerable cell-type specificity.
in part, this is explained by the activity/availability of key trans-acting factors such as the eifs and rna helicases.
however, in recent years it has become increasingly evident that the ribosome machine itself can operate as a filter, differentially selecting specific transcript sub-populations to seed the polysome  <cit> .
in part, the filter operates via rna:rna interactions between the ribosome and its target transcript.
such interactions would be modulated by rna binding proteins that serve either to mask a site or chaperone a correct rna fold.
this latter feature explains the function of ires trans-acting factors  during the internal ribosome recruitment by cellular ireses  <cit> .
filtering would respond to proliferative, developmental and environmental signals and its dysfunctioning could potentially be at the core of a number of physiological disorders   <cit> .
indeed, in a transcriptome/translatome analysis using a glioblastoma model the authors concluded that the selective polysomal recruitment of specific mrna populations could initiate and drive tumour formation  <cit> .
the filter would also be regulated by features within the core ribosomal machine.
these could arise as a result of heterogeneity in the cellular ribosomal protein levels, which may reflect transcriptional and/or post-transcriptional changes, in combination with covalent modifications of the ribosomal proteins and rrna  <cit> .
in this model, the pool of cellular ribosomes is not homogeneous but consists of heterogeneous assemblies of varying composition each with a preference with regards to features within its mrna target.
in this article, we have applied high-throughput rnaseq technology to characterise both the transcriptome and translatome of two human cell lines, mcf <dig>  and mcf10a .
the results indicate significant cell-type specific translational control.
in addition, we observed distinct cell-type specific heterogeneity in gene-specific tss variants within both the transcriptome and translatome.
by focusing on a number of genes, selected because of their reported roles in human cancer , we demonstrate the potential impact of this on the translational readout in each cellular context.
the results serve to highlight the limitations of extrapolating from transcriptional landscape to cellular phenotype, and the implications of this are discussed both in the context of the ribosome filter hypothesis and its potential utility as a novel disease biomarker.
RESULTS
comparison of total and polysomal mrna populations in mcf <dig> and mcf10a cells reveals signs of translational regulation
biological triplicates of the polysomal  and total rnas from each cell line were processed for rnaseq .
we obtained between  <dig> and  <dig> million unambiguous alignments per sample.
the number of alignments mapped per gene was found to be strongly correlated among all three replicas .
the cell lines displayed a significantly altered transcriptome with over  <dig> genes being differentially expressed in both the total and polysomal rna.
this difference was striking for some genes, for example tgfb <dig>  and mmp <dig> , were found to be over one thousand fold lower expressed in mcf <dig> compared to mcf10a .
the fold change in polysomal rna mirrored that observed with the total rna  consistent with a limited cell-specific translational control.
we took the ratio of polysomal to total mapped reads for each gene as a measure of its translational efficiency .
a z-score transformation was used to identify the best candidates of te regulation  <cit> .
using the refseq annotations,  <dig> genes were assigned as up-regulated in mcf <dig> cells relative to mcf10a , whereas  <dig> were down-regulated .
the z-score transformation is based on comparing expression fold changes among the genes expressed at a similar level.
it allows us to compare how much the change of te for individual genes deviates from what may be expected due to stochastic variation .
gene ontology analysis indicated that the translationally regulated gene set impacted on a significant number of biological processes and molecular functions .
further data mining revealed a list of cellular genes implicated in growth control, dna repair and cell cycle regulation .
one intriguing grouping was a selection of genes that impacted directly on the translational machinery of the cell.
these took the form of ribosomal protein genes, translation initiation factors, genes implicated in ribosome biogenesis, rna helicases and amino-acyl trna synthetases .
this pointed to cell-type modifications of the “ribosome machine”.
we reasoned that in line with the ribosome filter model this was impacting on the translational read-out.
as a novel means of examining this we focused on genes already documented to exhibit alternative promoter usage.
promoter switches will change the nature of the first exon and hence the 5′ tl of the mrna.
the 5′ tl carries much of the sequence information required for loading onto ribosomes.
it therefore seemed reasonable to assume that if the filter hypothesis is operating one would observe cell specific differential recruitment of tss variants onto polysomes.
consequently, genes using multiple promoters will generate multiple transcripts with 5′ tl heterogeneity.
we therefore asked if the differential heterogeneity arising from the use of multiple promoters observed within the transcriptome influenced the translatome.
the results produced with cuffdiff revealed  <dig> genes showing differential promoter usage in the total rna,  <dig> in the polysomal with  <dig> common to both .
only three of these genes scored as translationally regulated as determined in fig.
1c, namely, mospd <dig> from the polysomal rna fraction, and ev15l and ggt <dig> from the total rna.
indeed the majority of genes found with differential promoter usage appear to have a te profile similar to the background .table  <dig> list of translationally regulated genes whose protein products impact directly on protein synthesis.
these genes scored in both the refseq and ensembl databases.
the gene names and functions, as extracted from the genecard database , are listed
fig.
<dig> differential promoter usage within the transcriptome and translatome.
venn diagram representing genes exhibiting differential promoter usage in the polysomal rna , total rna  and those common to both .
the selected five genes exhibiting differential promoter usage are detailed.
the colour coding corresponds to that depicted in the venn diagram.
the name of the each 5′ tl variant and its corresponding tss identifier are indicated.
features within the tl of each variant that have been reported to impact on the translational readout are detailed
in order to examine the robustness of these findings with regards to the alignment and normalisation approaches employed, we repeated the full workflow multiple times using different parameters.
we found that the genes found to have differential promoter usage were relatively insensitive to changes in the alignment and normalisation parameters.
however, they were sensitive to the reference transcriptome, with the regulated genes found based on the ensembl annotation differing from that obtained from refseq or ucsc.
.
the genes found to be te regulated were less affected by changes in the supplied annotation with ~70 % of the genes assigned as te using the refseq also scoring using the ensembl annotation.
.
in the additional file  <dig> we list the genes both from the refseq and ensembl annotations.
what is the potential impact of differential promoter usage for the proteome?
changes in promoter selection alter the nature of the first exon and invariably alter the tl.
if the tl is composed of multiple exons the complexity can be further increased by alternative splicing.
to experimentally test the impact of tl heterogeneity on the protein readout in each cell background we selected  <dig> genes that exhibited differential promoter usage as determined from the refseq annotations .
camkk <dig>  ccnd <dig>  wnt5b were from the polysomal grouping and 53bp <dig>  cldn <dig> from the total.
this selection was not totally arbitrary.
camkk <dig> has been reported to be involved in apoptosis in mcf <dig> cells  <cit> , ccnd <dig> is linked to her <dig> status in breast tumours  <cit> , cldn <dig> expression levels have been correlated with the metastatic potential of breast carcinomas  <cit> , 53bp <dig> has been proposed as a breast cancer biomarker  <cit>  and wnt5b gene expression is regulated by β-estradiol in mcf <dig> cells  <cit>  and the wnt family play an important role in several human cancers .
in addition, no gene has more than  <dig> annotated tsss and elements within the tls pointed to translational control  .
furthermore, the proteins expressed from the different tsss could be different.
for example, camkk <dig> and ccnd <dig> have each two tss which generate mrnas with different 5′ tls: the position of the first aug start codon is different in each variant .
consequently, these transcripts can potentially express proteins with distinct n-termini.
further complexity arises because one tss transcript from each gene can undergo alternative splicing within the orf .
the tls of wnt5b and cldn <dig> span multiple exons of which only the first is variable.
in the latter gene, the tss <dig> gives rise to the transcript variants v <dig> and v <dig> due to alternative splicing within the orf .
finally, the tls of 53bp <dig> are totally different, are both predicted to be highly structured but only the v <dig>  carries a small,  <dig> codon uorf, positioned  <dig> nucleotides upstream of the 53bp <dig> start codon  .
to examine the quantitative impact of these tl variants on expression from the aug of the principle orf, they were rt-pcr cloned and inserted upstream of the firefly  reporter in a bicistronic vector   <cit> .
these were transiently expressed in both mcf <dig> and mcf10a, and normalised firefly/renilla  activities recorded.
what was immediately striking was the repression of fluc activity with the 53bp <dig> v <dig> and ccnd <dig> v <dig>  presumably due to the presence of uorf .
although the overall behaviour of the tls was similar in both cellular backgrounds, a statistically significant difference was repeatedly observed with the cldn <dig> v1/ <dig> variant  whose expression was enhanced in mcf <dig> cells .
the tl is long  and predicted to be highly structured, but possesses no uaug/uorf .
this difference in observed reporter activity may arise due to variation in the repertoire of rna helicases expressed in each cell background.
alternatively, the long highly structured tl may have ires-activity that is enhanced in the mcf <dig> background due to the cell specific expression of ires trans-activating factors  .fig.
<dig> the gene tss variants quantitatively modulate the translational readout.
the upper image depicts schematically the bicistronic reporter construct in which the gene 5′tl is fused to the firefly  first cistron and second cistron renilla  expression is assured by the emcv ires position inter-cistronically.
panels a-e: bicistronic reporter assays performed in both mcf10a  and mcf <dig> cells  to measure the impact of the tl variants on translation initiation events at the auggene start.
the upper image in each panel depicts the organisation of the various tl variants generated in the reporter.
the positions  and length  of the uorfs are indicated.
red stars in panels c/d indicate uaugs followed immediately by a stop codon and the arrow in panel d at the aug <dig> indicates that this potential start codon is in the camkk <dig> orf.
the lower image in each panel graphically represents the normalised fluc/rluc ratios measured for each tl.
bars indicate the sem for the biological triplicates.
experiments were repeated at least three times for each gene set.
only the cldn <dig> v1/ <dig> gave a statistically significant  cell type variation in all three independent experiments .
f an in-silico rna fold of the cldn <dig> v1/ <dig> tl .
the predicted gibbs free energy is also indicated
the presence of uorfs in a number of the selected tls opened the possibility of delayed reinitiation events occurring downstream of the principle start codon.
using a bicistronic reporter developed in the lab we could indeed demonstrate significant reinitiation occurring in both cell backgrounds .
in addition, immunoblots indicated that phospho-eif2α levels were higher  in mcf <dig> cells compared to mcf10a, an observation that could impact on the behaviour of the reinitiating ribosome, particularly with regard to start site selection   <cit> .
to evaluate qualitative changes we employed a novel lp/sp reporter system that allows monitoring of initiation events not only at the principle aug of the gene  but also at a series of downstream aug codons   <cit> .
earlier studies performed in a number of mammalian cell lines indicated that the proteins expressed from this reporter  have a similar t1/ <dig>  hence the steady-state levels as determined by immunoblotting reflect relative initiation frequency at each aug codon  <cit> .
because the distance between these multiple augs and the tl is variable, there pattern of expression serves as a very sensitive readout for the behaviour of initiating ribosomes in each cellular context .
initially, we focused on the 53bp <dig> gene because the small uorf in the v <dig> positioned just upstream of the aug53bp <dig> mirrored very closely the organisation of the mammalian elk <dig> gene that we have extensively studied in the lab   <cit> .
in the elk <dig> context, all initiation events downstream of the augelk1arose due to delayed reinitiation from a small uorf .
using this reporter, the anti-ha immunoblots confirmed the earlier bicistronic assays with regards to the repressive nature of the v <dig> tl relative to v1/ <dig> for initiation events at the aug53bp <dig> .
however, what was remarkable was the frequency of initiation events observed downstream of the aug53bp <dig>  this was particularly evident with v <dig>  quantification of the immunoblots revealed that >90 % of the proteins generated from this variant arose from initiation downstream of the aug53bp <dig> in both cell backgrounds, a result reminiscent of that previously observed with the elk <dig> gene .
initiation events downstream of aug53bp <dig> were less evident with v1/ <dig> and probably arose due to leaky ribosome scanning.
what is also striking is the pattern of initiation events from the v <dig> transcript in the two cell backgrounds.
in mcf <dig> cells, initiation events were readily detected on the most 3′ augs , whereas in mcf10a cells the major protein product observed arose from auga.
based upon current models for reinitiation this could reflect the higher phospho-eif2α levels observed in the tumoural cell line the consequence of which would be to displace the optimal reinitiation window towards the 3′ .fig.
<dig> analysis of the tss variants of 53bp <dig>  a organisation of the lp/sp reporter .
the reporter carries two overlapping orfs, lp  and sp  each carrying a ha epitope tag .
the tl variant was inserted upstream of the auggene.
immunoblotting with the anti-ha ab permits monitoring of multiple independent initiation events at the aug codons indicated.
b lp/sp reporters carrying the 53bp <dig> tl variants v1/ <dig> and v <dig> were transiently expressed in both mcf <dig> and mcf10a cells .
proteins were resolved by sds-page and analysed by immunoblotting using the anti-ha ab .
the blots were quantitated and the intensity of the protein band corresponding to each initiation site was evaluated.
this is plotted in the lower image as the average of the duplicate values .
each aug codon in each cellular context is colour coded .
the pattern of initiation events measured for the two variants in the same cell background, or the same variant in the different cell backgrounds are indicated.
c the upper image indicates polysomal profiles for the two cell types with the light and heavy polysomal fractions indicated.
rt-pcr was performed across the gradient using primer sets specific for each tl variant plus total 53bp <dig>  the amplicons were resolved on a polyacrylamide gel  which was then quantitated and plotted graphically .
d schematic representation indicating the positioning of aug codons within the 5′ end of the 53bp <dig> transcript.
the blue rectangle represents the 53bp <dig> orf.
the green rectangle represents an internal overlapping orf located within the 5′ end of the transcript.
the location of aug initiation codons whose positions relative to the aug53bp <dig> roughly correspond to the auga/b/c and auglp sites in the reporter  are also indicated.
the brackets indicate the number of amino acids  deleted from the 53bp <dig> protein should these initiation codons drive expression.
the 5′ tl is indicated as a horizontal red line upstream of the aug53bp <dig>  the positioning of the small uorf in v <dig>  is indicated as a grey rectangle below the red line since it is not in the same reading frame as 53bp <dig>  the length of the uorf is indicated as number of codons.
note that the 5′ tl of v1/ <dig> possesses no uorfs
although polysomal profiling studies provide insights into the ribosome-associated mrna population, they remain somewhat myopic in that they provide no information on the efficiency at which a particular transcript variant is being translated.
this is not a moot point since mrna movement within the polysomes can represent a significant shift in the protein readout.
the technique of ribosomal profiling  <cit> , whilst providing quantitative information on the extent of the readout from all expressed orfs, is unable to assign this readout to a specific transcript variant .
in addition, because it follows only the 80s ribosome protected rna fragment it does not provide information on the nature of 5′tl sequences whose function are regulatory .
to realise this at a global level, one could independently characterise the light  and heavy  polysomal transcript populations  <cit> .
alternatively, one can use rt-pcr to map the endogenous transcript variants within the polysomal profile of the cell.
when this was performed with 53bp <dig>  we observed that v <dig> was associated with polysomes only in mcf <dig>  whereas in mcf10a it was exclusively in the rnp  fraction.
furthermore, a greater fraction of v1/ <dig> was associated with heavy polysomes in mcf <dig> cells .
a similar analysis was performed with the wnt5b and cldn <dig> genes .
with regards to initiation events at the augwnt5b, the v <dig> tl was highly repressive in both cell backgrounds probably due to the presence of the two short uorfs .
nonetheless, significant amounts of protein products were expressed from the downstream start sites, particularly in the mcf <dig> background .
the failure to observe significant reinitiation events at the augwnt5b was somewhat surprising considering the relatively long distance between it and the second uorf  and the fact that it has a relatively strong kozak context .
this strong context also indicates that few ribosomes are in the leaky scanning mode downstream of the second uorf , suggesting that the proteins we observed are mainly the product of delayed reinitiation.
the wnt5b v <dig> tl contains a single uorf .
however, with the aug codon positioned just  <dig> nucleotides from the 5′ end it is unlikely that this site is efficiently recognised by the 43s ribosome that is recruited onto the cap  <cit> .
during cloning into the expression plasmid additional vector-derived sequences were added 5′, as a consequence the v <dig> uorf expression was probably enhanced.
the protein pattern observed from the v <dig> and v <dig> variants was strikingly different, particularly in the mcf <dig> background .
mapping the endogenous cellular transcripts back onto polysomes revealed a small enrichment of both within the polysomal fraction of mcf <dig> cells.
in the cldn <dig> gene, the two tls are organised very differently.
the v1/ <dig> is  <dig> nucleotides long, contains no uaug/uorfs and is predicted to fold into a very thermodynamically stable structure , whereas v <dig> is much shorter and possesses a uorf of  <dig> codons.
such a long uorf would be considered sub-optimal for promoting reinitiation  <cit> .
both tls were equally repressive independent of the cell context .
however, polysomal mapping revealed a shift of the v1/ <dig> transcript into the heavy fraction in mcf <dig> cells , an observation that may explain the significant increase in the fluc reporter observed previously .fig.
<dig> analysis of the tss variants from wnt5b and cldn <dig>  the experiments performed with the 5′tl variants of the wnt5b  and cldn <dig>  genes were performed as outlined in fig.
<dig>  the panels also contain schematic images of the respective gene transcripts with the 5′ tl indicated as a red line.
the presence of uorfs within the respective variants is indicated by a grey rectangle.
putative aug start codons are marked.
encircled are regions within the n-terminal extremity of each protein which have been assigned specific biological functions.
the natures of these are also indicated
when the results from the lp/sp reporter assays are evaluated globally one striking observation emerges.
whereas small uorfs are clearly repressive for initiation events at the downstream auggene, probably coupling its expression to intracellular tc levels, they are not repressive with regards to the overall polypeptide readout  .
this suggests that very few 40s subunits detach from the mrna post-uorf termination and, as a consequence, indicate that the quantitative impact of reinitiation events downstream of the auggene  may be more important for the proteome than initially suspected.
discussion
the cellular phenotype is in large part determined by protein composition and events such as proliferation, differentiation, response to external stress, apoptosis and even regulation of the circadian clock  <cit>  involve a re-seeding of cellular polysomes with specific mrna populations.
this dynamic nature of the polysomal-associated mrna populations has been known for some time  <cit> .
more recently its characterisation  has even been exploited for comparative cell typing in the cns  <cit> .
modulation of the translational program in the cytoplasm can be rapid, proceeding and, in large part dictating the subsequent transcriptional response in the nucleus.
it is, nonetheless, limited by the complexity of the existing transcriptome since it is from this pool that the mrna will be recruited.
in this article, we have compared the transcriptome and translatome of two human cell lines of tumoural and non-tumoural origin and identified changes in the relative te of nearly  <dig> genes.
a number of these modulate directly the translational readout because they encode ribosomal proteins, initiation factors, aminoacyl-trna synthetases , helicases that impact on rrna biogenesis and mrna translation and enzymes involved in ribosome maturation.
with regards to the tumoural origin of the mcf <dig> cell line, some hits were particularly intriguing.
for example, eif3e, which was also translationally down-regulated in mcf <dig> cells, has been proposed to function as a tumour suppressor and reduced expression has been reported in ~37 % of human breast cancers  <cit> .
mammalian arss are known to have functions supplementary to their role in protein synthesis.
in our analysis, three arss were translationally down-regulated .
they form part of the mammalian multi-trna synthetase complex .
aberrant expression of components of the msc has been associated with cancers and are known to affect responses coupled to angiogenesis, inflammation and apoptosis  <cit> .
a number of the genes exhibiting differential translational expression play central roles in the assembly of the active ribosome, suggesting differences in the translational machinery in each cell type.
such ribosomal heterogeneity was proposed to modulate both quantitatively and qualitatively the translational readout from as far back as the early 1970s  <cit> , and is now considered an important component of the filter hypothesis  <cit> .
many of the key features within an mrna that impact recruitment by the ribosome reside with the tl.
mammalian tls show extensive heterogeneity in large part due to multiple tsss  <cit> .
for example, the number of transcripts detected by rnaseq is at least one order of magnitude greater than the ~ <dig>  genes of the mouse genome  <cit> .
complete switches in the dominant tss were reported to occur in over  <dig> genes during differentiation with more subtle shifts being detected in over  <dig> others  <cit> , suggesting that the tss fingerprint  within the transcriptome is a genetic marker for cellular type .
however, the impact of this heterogeneity within the translatome had been in large part overlooked.
using the mcf7/mcf10a model we observed distinct differential tss fingerprints within the total  and polysomal .
the gene list from this analysis was sensitive to the reference transcriptome, a result that may reflect the fact that 5′tls are generally poorly annotated.
earlier reports have already suggested that 5′ end incompleteness may be a potential source of error in the assignment of the translation initiation codon in human mrnas  <cit> .
this arises due to variabilities in the methods employed to construct the cdna libraries combined with differences in the normalisation and subtraction procedures all of which serve to distort the readout.
this is underscored by the results of a genome-wide characterisation of transcriptional start site clusters  which reported that thousands of these tscs were not annotated in any database  <cit> , and the on-going efforts to improve methods of generating 5′ end libraries  <cit> .
most of the genes exhibiting differential promoter usage did not fall into the translationally regulated gene list as depicted in fig.
1c.
as such they were not scored as genes undergoing cell-type specific translational control.
nonetheless, by focusing on only a limited number exhibiting differential promoter usage in both the total and polysomal rna we were able to demonstrate that tl variants can modulate the protein readout both quantitatively and qualitatively, and frequently in a manner specific to each cellular background.
promoter switches within a gene expressing multiple tss variants has already been linked to a number of human pathologies  <cit> .
frequently these changes modulate the protein readout due to the presence of uorf/uaug in one of the variants.
for example, the mdm <dig> gene, whose product regulates cellular p <dig> levels, is expressed from two alternative promoters that generate a long and a short tl.
initiation at the augmdm <dig> in the long tl is repressed due to the presence of two uorfs absent in the short.
in certain tumours, mdm <dig> over-expression is due to an enrichment of the short form.
furthermore, polysomal gradient analysis indicated that this form was also more efficiently translated in tumoural compared to non-tumoural cells  <cit> , demonstrating that the effect of a promoter switch can be further amplified by the cell-specific recruitment of a tl variant onto ribosomes.
other studies have indicated that the uorfs present in the long form may also promote delayed reinitiation events that could qualitatively modulate the protein read-out  <cit> .
n-terminal deletions arising due to alternative start site selection can generate protein isoforms with opposing biological functions, as observed with c/ebpβ  <cit> .
this can also be coupled to the use of alternative promoters as reported for lef <dig>  and ctnna <dig>  amongst others  <cit> .
likewise, many of the most marked changes that we observed occurred in tl variants carrying uorfs.
whilst these were globally negative for initiation events at the auggene, significant delayed reinitiation events were detectable downstream.
in the case of 53bp <dig>  wnt5b and cldn <dig> this has the clear potential to generate n-terminal nested sets of protein products .
whilst little is known about the structure-functional organisation of the n-terminus of 53bp <dig>  n-terminal truncations arising due to downstream initiation would remove the signal peptide sequence of wnt5b generating an intracellular protein isoform, and would impact on the multiple transmembrane domains of cldn <dig>  reinitiation events mediated by the small uorf of the 53bp <dig> v <dig> tl would also permit the expression of an internal orf of as yet unknown function.
since the endogenous v <dig> transcript was associated with polysomes only in mcf <dig>  this protein product would be specific to the tumoural cell background.
CONCLUSIONS
as proposed recently in yeast, we postulate that major changes in the mammalian translational readout, changes that ultimately determine the cellular phenotype, can arise due to the selective recruitment of tl variants onto polysomes without the requirement for an overall change in mrna levels or even a change in the transcriptional program of the cell  <cit> .
we envisage cellular tl heterogeneity within the transcriptome as a tss “quasi-species” in line with the idea that it is dynamic and will respond to the changing physiological settings that the cell encounters.
as with the “quasi-species” defined for rna viruses  <cit> , this gives the cell the potential to respond rapidly to a changing environment via the selective ribosomal recruitment  of pre-existing transcripts variants that modulate and “fine-tune” the translational readout and hence the proteome.
in line with this model, not all tl variants within the quasi-species will necessarily be found on polysomes, as is the case with the v <dig> of 53bp <dig> in mcf10a cells.
however, the potential to recruit these onto the translatome allows a rapid cell response without altering the transcriptional program.
in a similar vein, aberrant ribosome selection from the quasi-species may be at the heart of a number of human pathologies including cancer.
such changes could occur in the absence of any marked alteration in the transcriptional landscape.
as a consequence, it is possible that the tl fingerprint of the translatome may contain novel biomarkers for human disease.

 with the advent of high-throughput rna sequencing it has become increasingly popular to define the genetic expression profile of a cell by its transcriptome. an approach in which the expression of a gene is estimated as a number of sequence reads aligning to that gene assumes a linear gene- transcript- protein information transfer relay, a scenario that is evidently a gross simplification. if one accepts that the end readout of the genetic program, as manifested as the cellular phenotype, is dictated in large part by the proteome, it would appear more judicious to directly characterise the cells protein composition, however, this remains technically difficult. nonetheless, such switches in the cellular phenotype are at the core of the non-tumoural to tumoural changes observed in cancer. the non-linear information transfer from genome to proteome arises due to multiple layers of complexity. at the mrna level, this includes alternative splicing, multiple transcriptional start sites and polyadenylation sites all of which show cell-specific regulation, and all of which serve to couple events in the nucleus to the proteomic readout in the cytoplasm. it is evident that alternative splicing within the open reading frame can alter the protein readout. however, this is not so intuitive with regards to alternative tsss which invariably change the nature of the first exon and, as a consequence, the sequence of the mrnas 5′ untranslated region; for why see below). nonetheless, the tl contains multiple elements that can modulate the translational readout both quantitatively and qualitatively, and all are hard-wired into cellular signalling pathways regulating proliferation, survival and development. these include rna structure, internal ribosome entry sites, protein binding sites, upstream aug codons which may be responsible for the translation of upstream open reading frames. the complexity within the tl is further increased by the use of non-aug start codons. these are frequently evolutionarily conserved and can generate n-terminal extensions in coding sequences that impact on function and cellular localisation. such elements are frequently observed in gene transcripts that are under tight translational control. recent ribosomal profiling studies also indicate that the uorfs are frequently expressed, an observation that calls into question the use of the term 5′utr. between and 50 % of human protein coding genes have been reported to use alternative promoters, and alterations in promoter usage within particular genes have been associated with human pathologies, including cancer. however, the impact of global changes on tss selection on the mammalian proteome remains unclear despite evidence from yeast that such changes correlate with a major shift in translational activity.fig. translationally profiling in mcf and mcf10a cells. a organisation of a mammalian mrna. the m7gpppn 5′ cap is indicated as are potential rna structural elements within the tl. the brown ovals indicate rna binding proteins that modulate expression by binding to regions outside the principle orf. the 3′ polya tail n is also indicated. b representative polysome profiles for mcf and mcf10a cells. equivalent amounts of protein were loaded onto each gradient. note that the polysomal fraction is considerably smaller in the non-tumoural mcf10a cell line. c plot of the differential transcript levels in total versus polysomal rna. the green dots indicate the up-regulated genes, the red dots the down-regulated genes. the spearman correlation is indicated. d go analysis of the translationally regulated genes from the refseq annotations. the go pie charts, which represent the percentage of gene hits against the total number of genes, were built using the panther classification system rna structure impacts on translation at multiple levels: when positioned proximal to the 5′ cap it can render it less accessible for 43s ribosome loading. such rnas therefore compete poorly for the limiting amounts of cap binding protein, eif4e. moreover, bioinformatic studies suggest that structure near the 5′ cap may also play a role in mirna mediated regulation possibly via the initiation factor eif4a. structure can also act post-43s recruitment, as a thermodynamic barrier that impedes ribosome movement during the 5′ → 3′ scanning of the tl used to locate the initiation codon. as such it serves to repress translational expression from the main orf. this is further highlighted by the role of rna helicases in human pathologies in which translational control is perturbed. approximately 40 % of mammalian mrnas carry uorfs and like rna structure, uorfs/uaugs are generally perceived to function as translational repressors. the magnitude of the repression is in large part determined by the nature of the sequences flanking the uaug, with the effect being the most marked when they approach the ideal “kozak context” for initiation. despite their apparent abundance, uaugs are less frequent than would be predicted by mere chance, yet aug is the most conserved triplet within tls pointing to a strong evolutionary selection. however, small uorfs can also couple the readout to eif gtp.trnaimet ternary complex levels in the cell and, via a process referred to as delayed reinitiation, can permit access to start codons downstream of the aug of the principle orf. during translation of small uorfs not all the initiation factors are released prior to termination. post 40s ribosomes carrying eif can remain attached to the rna and continue scanning. the aug codon at which they subsequently reinitiate translation is determined both by the cellular tc levels and the distance in nucleotides that the ribosome must scan. the quantitative and qualitative changes in the protein readout that can arise due to the presence of small uorfs can serve as a proliferation/differentiation switch that is coupled to changes in tc levels, as observed with the transcription factor ccaat/enhancer binding protein β. not all the information for mrna decoding resides within its nucleotide sequence. indeed, the translational readout from a unique transcript can exhibit considerable cell-type specificity. in part, this is explained by the activity/availability of key trans-acting factors such as the eifs and rna helicases. however, in recent years it has become increasingly evident that the ribosome machine itself can operate as a filter, differentially selecting specific transcript sub-populations to seed the polysome. in part, the filter operates via rna:rna interactions between the ribosome and its target transcript. such interactions would be modulated by rna binding proteins that serve either to mask a site or chaperone a correct rna fold. this latter feature explains the function of ires trans-acting factors during the internal ribosome recruitment by cellular ireses. filtering would respond to proliferative, developmental and environmental signals and its dysfunctioning could potentially be at the core of a number of physiological disorders. indeed, in a transcriptome/translatome analysis using a glioblastoma model the authors concluded that the selective polysomal recruitment of specific mrna populations could initiate and drive tumour formation. the filter would also be regulated by features within the core ribosomal machine. these could arise as a result of heterogeneity in the cellular ribosomal protein levels, which may reflect transcriptional and/or post-transcriptional changes, in combination with covalent modifications of the ribosomal proteins and rrna. in this model, the pool of cellular ribosomes is not homogeneous but consists of heterogeneous assemblies of varying composition each with a preference with regards to features within its mrna target. in this article, we have applied high-throughput rnaseq technology to characterise both the transcriptome and translatome of two human cell lines, mcf and mcf10a. the results indicate significant cell-type specific translational control. in addition, we observed distinct cell-type specific heterogeneity in gene-specific tss variants within both the transcriptome and translatome. by focusing on a number of genes, selected because of their reported roles in human cancer, we demonstrate the potential impact of this on the translational readout in each cellular context. the results serve to highlight the limitations of extrapolating from transcriptional landscape to cellular phenotype, and the implications of this are discussed both in the context of the ribosome filter hypothesis and its potential utility as a novel disease biomarker.  comparison of total and polysomal mrna populations in mcf and mcf10a cells reveals signs of translational regulation biological triplicates of the polysomal and total rnas from each cell line were processed for rnaseq. we obtained between and million unambiguous alignments per sample. the number of alignments mapped per gene was found to be strongly correlated among all three replicas. the cell lines displayed a significantly altered transcriptome with over genes being differentially expressed in both the total and polysomal rna. this difference was striking for some genes, for example tgfb and mmp, were found to be over one thousand fold lower expressed in mcf compared to mcf10a. the fold change in polysomal rna mirrored that observed with the total rna consistent with a limited cell-specific translational control. we took the ratio of polysomal to total mapped reads for each gene as a measure of its translational efficiency. a z-score transformation was used to identify the best candidates of te regulation. using the refseq annotations, genes were assigned as up-regulated in mcf cells relative to mcf10a, whereas were down-regulated. the z-score transformation is based on comparing expression fold changes among the genes expressed at a similar level. it allows us to compare how much the change of te for individual genes deviates from what may be expected due to stochastic variation. gene ontology analysis indicated that the translationally regulated gene set impacted on a significant number of biological processes and molecular functions. further data mining revealed a list of cellular genes implicated in growth control, dna repair and cell cycle regulation. one intriguing grouping was a selection of genes that impacted directly on the translational machinery of the cell. these took the form of ribosomal protein genes, translation initiation factors, genes implicated in ribosome biogenesis, rna helicases and amino-acyl trna synthetases. this pointed to cell-type modifications of the “ribosome machine”. we reasoned that in line with the ribosome filter model this was impacting on the translational read-out. as a novel means of examining this we focused on genes already documented to exhibit alternative promoter usage. promoter switches will change the nature of the first exon and hence the 5′ tl of the mrna. the 5′ tl carries much of the sequence information required for loading onto ribosomes. it therefore seemed reasonable to assume that if the filter hypothesis is operating one would observe cell specific differential recruitment of tss variants onto polysomes. consequently, genes using multiple promoters will generate multiple transcripts with 5′ tl heterogeneity. we therefore asked if the differential heterogeneity arising from the use of multiple promoters observed within the transcriptome influenced the translatome. the results produced with cuffdiff revealed genes showing differential promoter usage in the total rna, in the polysomal with common to both. only three of these genes scored as translationally regulated as determined in fig. 1c, namely, mospd from the polysomal rna fraction, and ev15l and ggt from the total rna. indeed the majority of genes found with differential promoter usage appear to have a te profile similar to the background.table list of translationally regulated genes whose protein products impact directly on protein synthesis. these genes scored in both the refseq and ensembl databases. the gene names and functions, as extracted from the genecard database, are listed fig. differential promoter usage within the transcriptome and translatome. venn diagram representing genes exhibiting differential promoter usage in the polysomal rna, total rna and those common to both. the selected five genes exhibiting differential promoter usage are detailed. the colour coding corresponds to that depicted in the venn diagram. the name of the each 5′ tl variant and its corresponding tss identifier are indicated. features within the tl of each variant that have been reported to impact on the translational readout are detailed in order to examine the robustness of these findings with regards to the alignment and normalisation approaches employed, we repeated the full workflow multiple times using different parameters. we found that the genes found to have differential promoter usage were relatively insensitive to changes in the alignment and normalisation parameters. however, they were sensitive to the reference transcriptome, with the regulated genes found based on the ensembl annotation differing from that obtained from refseq or ucsc.. the genes found to be te regulated were less affected by changes in the supplied annotation with ~70 % of the genes assigned as te using the refseq also scoring using the ensembl annotation.. in the additional file we list the genes both from the refseq and ensembl annotations. what is the potential impact of differential promoter usage for the proteome? changes in promoter selection alter the nature of the first exon and invariably alter the tl. if the tl is composed of multiple exons the complexity can be further increased by alternative splicing. to experimentally test the impact of tl heterogeneity on the protein readout in each cell background we selected genes that exhibited differential promoter usage as determined from the refseq annotations. camkk ccnd wnt5b were from the polysomal grouping and 53bp cldn from the total. this selection was not totally arbitrary. camkk has been reported to be involved in apoptosis in mcf cells, ccnd is linked to her status in breast tumours, cldn expression levels have been correlated with the metastatic potential of breast carcinomas, 53bp has been proposed as a breast cancer biomarker and wnt5b gene expression is regulated by β-estradiol in mcf cells and the wnt family play an important role in several human cancers. in addition, no gene has more than annotated tsss and elements within the tls pointed to translational control. furthermore, the proteins expressed from the different tsss could be different. for example, camkk and ccnd have each two tss which generate mrnas with different 5′ tls: the position of the first aug start codon is different in each variant. consequently, these transcripts can potentially express proteins with distinct n-termini. further complexity arises because one tss transcript from each gene can undergo alternative splicing within the orf. the tls of wnt5b and cldn span multiple exons of which only the first is variable. in the latter gene, the tss gives rise to the transcript variants v and v due to alternative splicing within the orf. finally, the tls of 53bp are totally different, are both predicted to be highly structured but only the v carries a small, codon uorf, positioned nucleotides upstream of the 53bp start codon. to examine the quantitative impact of these tl variants on expression from the aug of the principle orf, they were rt-pcr cloned and inserted upstream of the firefly reporter in a bicistronic vector. these were transiently expressed in both mcf and mcf10a, and normalised firefly/renilla activities recorded. what was immediately striking was the repression of fluc activity with the 53bp v and ccnd v presumably due to the presence of uorf. although the overall behaviour of the tls was similar in both cellular backgrounds, a statistically significant difference was repeatedly observed with the cldn v1/ variant whose expression was enhanced in mcf cells. the tl is long and predicted to be highly structured, but possesses no uaug/uorf. this difference in observed reporter activity may arise due to variation in the repertoire of rna helicases expressed in each cell background. alternatively, the long highly structured tl may have ires-activity that is enhanced in the mcf background due to the cell specific expression of ires trans-activating factors.fig. the gene tss variants quantitatively modulate the translational readout. the upper image depicts schematically the bicistronic reporter construct in which the gene 5′tl is fused to the firefly first cistron and second cistron renilla expression is assured by the emcv ires position inter-cistronically. panels a-e: bicistronic reporter assays performed in both mcf10a and mcf cells to measure the impact of the tl variants on translation initiation events at the auggene start. the upper image in each panel depicts the organisation of the various tl variants generated in the reporter. the positions and length of the uorfs are indicated. red stars in panels c/d indicate uaugs followed immediately by a stop codon and the arrow in panel d at the aug indicates that this potential start codon is in the camkk orf. the lower image in each panel graphically represents the normalised fluc/rluc ratios measured for each tl. bars indicate the sem for the biological triplicates. experiments were repeated at least three times for each gene set. only the cldn v1/ gave a statistically significant cell type variation in all three independent experiments. f an in-silico rna fold of the cldn v1/ tl. the predicted gibbs free energy is also indicated the presence of uorfs in a number of the selected tls opened the possibility of delayed reinitiation events occurring downstream of the principle start codon. using a bicistronic reporter developed in the lab we could indeed demonstrate significant reinitiation occurring in both cell backgrounds. in addition, immunoblots indicated that phospho-eif2α levels were higher in mcf cells compared to mcf10a, an observation that could impact on the behaviour of the reinitiating ribosome, particularly with regard to start site selection. to evaluate qualitative changes we employed a novel lp/sp reporter system that allows monitoring of initiation events not only at the principle aug of the gene but also at a series of downstream aug codons. earlier studies performed in a number of mammalian cell lines indicated that the proteins expressed from this reporter have a similar t1/ hence the steady-state levels as determined by immunoblotting reflect relative initiation frequency at each aug codon. because the distance between these multiple augs and the tl is variable, there pattern of expression serves as a very sensitive readout for the behaviour of initiating ribosomes in each cellular context. initially, we focused on the 53bp gene because the small uorf in the v positioned just upstream of the aug53bp mirrored very closely the organisation of the mammalian elk gene that we have extensively studied in the lab. in the elk context, all initiation events downstream of the augelk1arose due to delayed reinitiation from a small uorf. using this reporter, the anti-ha immunoblots confirmed the earlier bicistronic assays with regards to the repressive nature of the v tl relative to v1/ for initiation events at the aug53bp. however, what was remarkable was the frequency of initiation events observed downstream of the aug53bp this was particularly evident with v quantification of the immunoblots revealed that >90 % of the proteins generated from this variant arose from initiation downstream of the aug53bp in both cell backgrounds, a result reminiscent of that previously observed with the elk gene. initiation events downstream of aug53bp were less evident with v1/ and probably arose due to leaky ribosome scanning. what is also striking is the pattern of initiation events from the v transcript in the two cell backgrounds. in mcf cells, initiation events were readily detected on the most 3′ augs, whereas in mcf10a cells the major protein product observed arose from auga. based upon current models for reinitiation this could reflect the higher phospho-eif2α levels observed in the tumoural cell line the consequence of which would be to displace the optimal reinitiation window towards the 3′.fig. analysis of the tss variants of 53bp a organisation of the lp/sp reporter. the reporter carries two overlapping orfs, lp and sp each carrying a ha epitope tag. the tl variant was inserted upstream of the auggene. immunoblotting with the anti-ha ab permits monitoring of multiple independent initiation events at the aug codons indicated. b lp/sp reporters carrying the 53bp tl variants v1/ and v were transiently expressed in both mcf and mcf10a cells. proteins were resolved by sds-page and analysed by immunoblotting using the anti-ha ab. the blots were quantitated and the intensity of the protein band corresponding to each initiation site was evaluated. this is plotted in the lower image as the average of the duplicate values. each aug codon in each cellular context is colour coded. the pattern of initiation events measured for the two variants in the same cell background, or the same variant in the different cell backgrounds are indicated. c the upper image indicates polysomal profiles for the two cell types with the light and heavy polysomal fractions indicated. rt-pcr was performed across the gradient using primer sets specific for each tl variant plus total 53bp the amplicons were resolved on a polyacrylamide gel which was then quantitated and plotted graphically. d schematic representation indicating the positioning of aug codons within the 5′ end of the 53bp transcript. the blue rectangle represents the 53bp orf. the green rectangle represents an internal overlapping orf located within the 5′ end of the transcript. the location of aug initiation codons whose positions relative to the aug53bp roughly correspond to the auga/b/c and auglp sites in the reporter are also indicated. the brackets indicate the number of amino acids deleted from the 53bp protein should these initiation codons drive expression. the 5′ tl is indicated as a horizontal red line upstream of the aug53bp the positioning of the small uorf in v is indicated as a grey rectangle below the red line since it is not in the same reading frame as 53bp the length of the uorf is indicated as number of codons. note that the 5′ tl of v1/ possesses no uorfs although polysomal profiling studies provide insights into the ribosome-associated mrna population, they remain somewhat myopic in that they provide no information on the efficiency at which a particular transcript variant is being translated. this is not a moot point since mrna movement within the polysomes can represent a significant shift in the protein readout. the technique of ribosomal profiling, whilst providing quantitative information on the extent of the readout from all expressed orfs, is unable to assign this readout to a specific transcript variant. in addition, because it follows only the 80s ribosome protected rna fragment it does not provide information on the nature of 5′tl sequences whose function are regulatory. to realise this at a global level, one could independently characterise the light and heavy polysomal transcript populations. alternatively, one can use rt-pcr to map the endogenous transcript variants within the polysomal profile of the cell. when this was performed with 53bp we observed that v was associated with polysomes only in mcf whereas in mcf10a it was exclusively in the rnp fraction. furthermore, a greater fraction of v1/ was associated with heavy polysomes in mcf cells. a similar analysis was performed with the wnt5b and cldn genes. with regards to initiation events at the augwnt5b, the v tl was highly repressive in both cell backgrounds probably due to the presence of the two short uorfs. nonetheless, significant amounts of protein products were expressed from the downstream start sites, particularly in the mcf background. the failure to observe significant reinitiation events at the augwnt5b was somewhat surprising considering the relatively long distance between it and the second uorf and the fact that it has a relatively strong kozak context. this strong context also indicates that few ribosomes are in the leaky scanning mode downstream of the second uorf, suggesting that the proteins we observed are mainly the product of delayed reinitiation. the wnt5b v tl contains a single uorf. however, with the aug codon positioned just nucleotides from the 5′ end it is unlikely that this site is efficiently recognised by the 43s ribosome that is recruited onto the cap. during cloning into the expression plasmid additional vector-derived sequences were added 5′, as a consequence the v uorf expression was probably enhanced. the protein pattern observed from the v and v variants was strikingly different, particularly in the mcf background. mapping the endogenous cellular transcripts back onto polysomes revealed a small enrichment of both within the polysomal fraction of mcf cells. in the cldn gene, the two tls are organised very differently. the v1/ is nucleotides long, contains no uaug/uorfs and is predicted to fold into a very thermodynamically stable structure, whereas v is much shorter and possesses a uorf of codons. such a long uorf would be considered sub-optimal for promoting reinitiation. both tls were equally repressive independent of the cell context. however, polysomal mapping revealed a shift of the v1/ transcript into the heavy fraction in mcf cells, an observation that may explain the significant increase in the fluc reporter observed previously.fig. analysis of the tss variants from wnt5b and cldn the experiments performed with the 5′tl variants of the wnt5b and cldn genes were performed as outlined in fig.  the panels also contain schematic images of the respective gene transcripts with the 5′ tl indicated as a red line. the presence of uorfs within the respective variants is indicated by a grey rectangle. putative aug start codons are marked. encircled are regions within the n-terminal extremity of each protein which have been assigned specific biological functions. the natures of these are also indicated when the results from the lp/sp reporter assays are evaluated globally one striking observation emerges. whereas small uorfs are clearly repressive for initiation events at the downstream auggene, probably coupling its expression to intracellular tc levels, they are not repressive with regards to the overall polypeptide readout. this suggests that very few 40s subunits detach from the mrna post-uorf termination and, as a consequence, indicate that the quantitative impact of reinitiation events downstream of the auggene may be more important for the proteome than initially suspected. discussion the cellular phenotype is in large part determined by protein composition and events such as proliferation, differentiation, response to external stress, apoptosis and even regulation of the circadian clock involve a re-seeding of cellular polysomes with specific mrna populations. this dynamic nature of the polysomal-associated mrna populations has been known for some time. more recently its characterisation has even been exploited for comparative cell typing in the cns. modulation of the translational program in the cytoplasm can be rapid, proceeding and, in large part dictating the subsequent transcriptional response in the nucleus. it is, nonetheless, limited by the complexity of the existing transcriptome since it is from this pool that the mrna will be recruited. in this article, we have compared the transcriptome and translatome of two human cell lines of tumoural and non-tumoural origin and identified changes in the relative te of nearly genes. a number of these modulate directly the translational readout because they encode ribosomal proteins, initiation factors, aminoacyl-trna synthetases, helicases that impact on rrna biogenesis and mrna translation and enzymes involved in ribosome maturation. with regards to the tumoural origin of the mcf cell line, some hits were particularly intriguing. for example, eif3e, which was also translationally down-regulated in mcf cells, has been proposed to function as a tumour suppressor and reduced expression has been reported in ~37 % of human breast cancers. mammalian arss are known to have functions supplementary to their role in protein synthesis. in our analysis, three arss were translationally down-regulated. they form part of the mammalian multi-trna synthetase complex. aberrant expression of components of the msc has been associated with cancers and are known to affect responses coupled to angiogenesis, inflammation and apoptosis. a number of the genes exhibiting differential translational expression play central roles in the assembly of the active ribosome, suggesting differences in the translational machinery in each cell type. such ribosomal heterogeneity was proposed to modulate both quantitatively and qualitatively the translational readout from as far back as the early 1970s, and is now considered an important component of the filter hypothesis. many of the key features within an mrna that impact recruitment by the ribosome reside with the tl. mammalian tls show extensive heterogeneity in large part due to multiple tsss. for example, the number of transcripts detected by rnaseq is at least one order of magnitude greater than the ~ genes of the mouse genome. complete switches in the dominant tss were reported to occur in over genes during differentiation with more subtle shifts being detected in over others, suggesting that the tss fingerprint within the transcriptome is a genetic marker for cellular type. however, the impact of this heterogeneity within the translatome had been in large part overlooked. using the mcf7/mcf10a model we observed distinct differential tss fingerprints within the total and polysomal. the gene list from this analysis was sensitive to the reference transcriptome, a result that may reflect the fact that 5′tls are generally poorly annotated. earlier reports have already suggested that 5′ end incompleteness may be a potential source of error in the assignment of the translation initiation codon in human mrnas. this arises due to variabilities in the methods employed to construct the cdna libraries combined with differences in the normalisation and subtraction procedures all of which serve to distort the readout. this is underscored by the results of a genome-wide characterisation of transcriptional start site clusters which reported that thousands of these tscs were not annotated in any database, and the on-going efforts to improve methods of generating 5′ end libraries. most of the genes exhibiting differential promoter usage did not fall into the translationally regulated gene list as depicted in fig. 1c. as such they were not scored as genes undergoing cell-type specific translational control. nonetheless, by focusing on only a limited number exhibiting differential promoter usage in both the total and polysomal rna we were able to demonstrate that tl variants can modulate the protein readout both quantitatively and qualitatively, and frequently in a manner specific to each cellular background. promoter switches within a gene expressing multiple tss variants has already been linked to a number of human pathologies. frequently these changes modulate the protein readout due to the presence of uorf/uaug in one of the variants. for example, the mdm gene, whose product regulates cellular p levels, is expressed from two alternative promoters that generate a long and a short tl. initiation at the augmdm in the long tl is repressed due to the presence of two uorfs absent in the short. in certain tumours, mdm over-expression is due to an enrichment of the short form. furthermore, polysomal gradient analysis indicated that this form was also more efficiently translated in tumoural compared to non-tumoural cells, demonstrating that the effect of a promoter switch can be further amplified by the cell-specific recruitment of a tl variant onto ribosomes. other studies have indicated that the uorfs present in the long form may also promote delayed reinitiation events that could qualitatively modulate the protein read-out. n-terminal deletions arising due to alternative start site selection can generate protein isoforms with opposing biological functions, as observed with c/ebpβ. this can also be coupled to the use of alternative promoters as reported for lef and ctnna amongst others. likewise, many of the most marked changes that we observed occurred in tl variants carrying uorfs. whilst these were globally negative for initiation events at the auggene, significant delayed reinitiation events were detectable downstream. in the case of 53bp wnt5b and cldn this has the clear potential to generate n-terminal nested sets of protein products. whilst little is known about the structure-functional organisation of the n-terminus of 53bp n-terminal truncations arising due to downstream initiation would remove the signal peptide sequence of wnt5b generating an intracellular protein isoform, and would impact on the multiple transmembrane domains of cldn reinitiation events mediated by the small uorf of the 53bp v tl would also permit the expression of an internal orf of as yet unknown function. since the endogenous v transcript was associated with polysomes only in mcf this protein product would be specific to the tumoural cell background.  as proposed recently in yeast, we postulate that major changes in the mammalian translational readout, changes that ultimately determine the cellular phenotype, can arise due to the selective recruitment of tl variants onto polysomes without the requirement for an overall change in mrna levels or even a change in the transcriptional program of the cell. we envisage cellular tl heterogeneity within the transcriptome as a tss “quasi-species” in line with the idea that it is dynamic and will respond to the changing physiological settings that the cell encounters. as with the “quasi-species” defined for rna viruses, this gives the cell the potential to respond rapidly to a changing environment via the selective ribosomal recruitment of pre-existing transcripts variants that modulate and “fine-tune” the translational readout and hence the proteome. in line with this model, not all tl variants within the quasi-species will necessarily be found on polysomes, as is the case with the v of 53bp in mcf10a cells. however, the potential to recruit these onto the translatome allows a rapid cell response without altering the transcriptional program. in a similar vein, aberrant ribosome selection from the quasi-species may be at the heart of a number of human pathologies including cancer. such changes could occur in the absence of any marked alteration in the transcriptional landscape. as a consequence, it is possible that the tl fingerprint of the translatome may contain novel biomarkers for human disease. 
however, the transcriptional landscape is complex and it is unclear as to what extent it reflects the ribosome associated mrna population. nonetheless, reporter assays demonstrated that the tss variants impacted on the translational readout both quantitatively and qualitatively. indeed, promoter switches have been reported in pathologies such as cancer. since characterisation of the proteome remains technically laborious it is attractive to define the genetic expression profile using the transcriptome. in this article, we have characterised both the transcriptome and translatome of the mcf and mcf10a cell lines. the results point to considerable and distinct cell-specific 5′tl heterogeneity within both the transcriptome and translatome of the two cell lines analysed. the genetic program, as manifested as the cellular phenotype, is in large part dictated by the cell’s protein composition. this is not a moot point because the 5′tl plays a key role in regulating mrna recruitment onto polysomes. this observation is in-line with the ribosome filter hypothesis which posits that the ribosomal machine can selectively filter information from within the transcriptome. this is particularly pertinent for genes using multiple transcriptional start sites generating mrnas with heterogeneous 5′ transcript leaders.
 the genetic program, as manifested as the cellular phenotype, is in large part dictated by the cell’s protein composition. since characterisation of the proteome remains technically laborious it is attractive to define the genetic expression profile using the transcriptome. however, the transcriptional landscape is complex and it is unclear as to what extent it reflects the ribosome associated mrna population. this is particularly pertinent for genes using multiple transcriptional start sites generating mrnas with heterogeneous 5′ transcript leaders. furthermore, the relative abundance of the tss gene variants is frequently cell-type specific. indeed, promoter switches have been reported in pathologies such as cancer. the consequences of this 5′tl heterogeneity within the transcriptome for the translatome remain unresolved. this is not a moot point because the 5′tl plays a key role in regulating mrna recruitment onto polysomes.  in this article, we have characterised both the transcriptome and translatome of the mcf and mcf10a cell lines. we identified ~ genes exhibiting differential translation efficiency. in itself, this is maybe not surprising. however, by focusing on genes exhibiting tss heterogeneity we observed distinct differential promoter usage patterns in both the transcriptome and translatome. only a minor fraction of these genes belonged to those exhibiting differential te. nonetheless, reporter assays demonstrated that the tss variants impacted on the translational readout both quantitatively and qualitatively.  the results point to considerable and distinct cell-specific 5′tl heterogeneity within both the transcriptome and translatome of the two cell lines analysed. this observation is in-line with the ribosome filter hypothesis which posits that the ribosomal machine can selectively filter information from within the transcriptome. as such it cautions against the simple extrapolation transcriptome → proteome. furthermore, polysomal occupancy of specific gene 5′tl variants may also serve as novel disease biomarkers. electronic supplementary material the online version of this article contains supplementary material, which is available to authorized users. keywords translatometranscriptomeproteome5′ mrna heterogeneity5′ transcript leadertranslationcancerissue-copyright-statement© the author 2015 