BACKGROUND
long non-coding rnas  were firstly reported as transcripts expressed in large numbers in mammalian transcriptomes  <cit> .
they were shown to constitute more than half of all the transcriptional outputs of mammalian genomes  <cit> .
prior to these reports xist in mammals and xlsirt in amphibians were the only well characterized lncrnas described to function in Χ; chromosome inactivation and the formation of cytoskeleton  <cit> .
recently, several aspects of development and disease have been associated with lncrnas function albeit to a small proportion of them.
processes associated with lncrnas include epigenetic regulation of multi-gene loci  <cit> , apoptosis and cell cycle  <cit> , regulation of gene splicing  <cit>  and tumor suppressor activity  <cit> .
there are also examples of lncrnas playing a role in the adaptive immunity of mammals  <cit> , being differentially expressed in response to carcinogens  <cit>  and functioning as enhancers  <cit> .
a probe into the functional role of lncrnas requires knowledge of the specificity of their expression across developmental stages and different tissues.
microarray technology was initially used to detect lncrnas in differentiating mouse embryonic stem cells.
many lncrnas showed correlation of expression with the flanking protein-coding genes that associated with developmental functions  <cit> .
similar transcriptomics studies identified many lncrnas expressed in cd8+ cells and during neuronal lineage specification in mouse  <cit> .
however, cross-hybridization, background noise and limited genome coverage associated to array based detection techniques were often used as arguments against the pervasive existence of lncrnas.
today these problems have been solved thanks to the advent of the rna sequencing technology   <cit> .
rnaseq deals with direct quantification of a cdna population and is not limited to transcripts mapped to known genomic sequences.
an rnaseq experiment on differentiating human neurons led to the identification of about  <dig>  lncrnas with dynamical expression levels  <cit> .
recently, sequencing studies have even identified hundreds of lncrnas expressed during early developmental stages in zebrafish and c. elegans finally demonstrating that the pervasiveness of non-coding transcription is not an exclusive feature of mammalian transcriptomes.
pauli et al identified about  <dig>  non-coding rnas expressed during embryogenesis in zebrafish  <cit> .
ulitsky et al reported a set of about  <dig> long intergenic non-coding rnas  expressed during zebrafish development; they show low sequence similarity but conserved genomic locations with their mammalian counterparts  <cit> .
finally nam et al reported a catalog of  <dig> lncrnas in c.elegans  <cit>  which show similar features to vertebrate lncrnas in terms of lack of general sequence conservation as well as stage specific expression patterns.
the execution of large-scale studies about the discovery and characterization of candidate lncrnas is facilitating the establishment of a catalog of these important molecular players which, in turn, permit to annotate them with specific biological validations and comparative analyses improving our knowledge of the lncrnaome  <cit> .
however, lack of sequence homology and lack of deep tissue and stage specific expression data have been one of the obstacles in defining a proper catalog of lncrnas among different species.
computational methods for the discovery and the annotation of lncrnas are sparse and mainly limited to mammalian genomes.
parameters like open reading frame length, lack of homology to protein-coding genes and protein domains, nucleotide composition and substitution rates have been used previously to define computational lncrna discovery pipelines  <cit> .
sequence conservation has not been often used as support to justify the presence of lncrnas in an organism because the lncrnas identified in human, mouse, zebrafish and c. elegans showed little or no sequence conservation in the majority of the population  <cit> .
in addition, pauli et al stated that the level of conservation for the majority of zebrafish lncrna is comparable to that of introns and that only few of them are really conserved  <cit> .
however, short spans of sequence conservation for specific lncrnas were reported  <cit> .
four evolutionary constrained mouse lncrnas were shown to be conserved in sequence and expression between mouse, opossum and chicken  <cit> .
forty three putative long non-coding sequences from chicken ests were found to share sequence homology with human, rat and mouse transcripts  <cit> .
xist, the lncrna responsible for the Χ chromosome inactivation in eutherian mammals shares sequence homology in  <dig> vertebrates  <cit> .
sox2ot  and har1f  are conserved amongst vertebrates  <cit> .
the biggest group of lncrnas constrained in terms of their nucleotide substitution rates between mouse and human is represented by a set of  <dig> mouse transcripts  <cit> .
this set showed a tendency to juxtapose genes involved in the regulation of transcription and development.
a subset of these lncrnas expressed in the mouse brain and defined as cns-specific appear to show tissue specific expression pattern similar to their proximal protein coding genes.
despite these evidences, a lack of general sequence conservation associated with lncrnas has been proposed and this becomes more evident when considering long evolutionary distances such as the one separating mammals from fishes, even if fragments of sequence conservation have been detected  <cit> .
despite these evidences, a systematic analysis of sequence conservation of vertebrate lncrnas is still lacking and it remains unclear whether and to what extent there is general sequence conservation of lncrnas between mammals and fishes.
in order to fulfill this lack, the work here presented tries to define the level of conservation of mouse lncrnas in the zebrafish genome using an unbiased choice for the comparison parameters, taking advantage of randomizations and receiver operating characteristic  analyses.
our approach is centered around subsets of mouse constrained and/or well annotated lncrnas, based on the assumption that such transcripts constitute a representative set of lncrnas ideally containing small amounts of transcriptional noise.
we would like to specify that, although our analysis consider a subset of already published and very well annotated lncrnas, we cannot rule out the possibility that some of them might actually be coding for short peptides.
recent studies suggest that few candidate lncrnas can produce short peptides and there may exist a class of bifunctional rnas encoding both mrnas and functional noncoding transcripts  <cit> .
therefore, specific biological validations remain a fundamental step for a proper characterization of these elements.
nevertheless, the special care taken in the choice of the datasets to analyze and the literature about them, makes us confident that we are currently using, the best sets of candidate lncrnas.
we compared these transcripts against the set of zebrafish phastcons elements  <cit>  reported to be significantly conserved among fishes.
the phastcons program uses a hidden markov model-based method that estimates the probability that each nucleotide belongs to a conserved element, based on multiple alignments of selected species.
we used the phastcons6way track to select elements conserved among fishes.
these are based on scores built on multiple alignment of the zebrafish genome with tetraodon, stickleback, human, mouse and western clawed frog.
it is important to point out here that, considering the way in which they are built, these elements represent the best selection of sequences conserved, in first instance, among fishes, but many of them can also result conserved among vertebrates.
this choice implicitly adds more genomes to our analyses and is based on the assumption that lncrnas conserved between mouse and zebrafish are expected to be primarily conserved among teleosts.
for this pilot study, the reduction in the dataset dimension, given by such choice, limited the zebrafish genomic search space to the phastcons sequences, rather than to the full genome, making it feasible to use several randomizations steps  to specifically identify the levels of conservation proper of lncrnas.
here we show that the usage of the blastn e-value and alignment length as cut-offs is sufficient to distinguish conservation of mouse lncrnas against zebrafish phastcons elements as compared to shuffled sequences.
from an initial dataset of about  <dig>  mouse lncrnas we demonstrate that between  <dig> and 11% of them contain fragments significantly conserved in zebrafish in agreement with the results by ulitsky et al  <cit>  on a smaller dataset.
gene ontology enrichment analyses of protein-coding genes flanking the conserved elements, identified similar functional classes significantly enriched in both species, such as regulation of transcription and development.
these coding genes exhibited enrichment for expression in the brain in both mouse as well as zebrafish.
the lncrnas shown to be conserved are deemed to be functionally important and suggested for further experimental validation of their function.
RESULTS
selection of conservation parameters to select significantly conserved lncrnas
we developed a pipeline to identify conserved mouse lncrna fragments in zebrafish using sequence identity, randomization and the identification of an unbiased threshold to detect significant levels of conservation .
in order to identify the optimal parameters capable to select conserved lncrna sequences, we used receiver operating characteristic  like analyses on the distribution of the following blastn alignments result measures: 1) query coverage, 2) query alignment length, 3) percentage identity and 4) e-value.
roc like analyses were performed on the results of the following blastn searches: 1) mouse lncrna against zebrafish phastcons elements , 2) shuffled mouse lncrna sequences against zebrafish phastcons elements .
in order to select significant results we defined a specific cut-off showing less than  <dig> % false discovery rate  for each parameter.
the analysis was applied to different datasets and, after the application of the identified filter, between  <dig> to 11% of the sequences in the true positive datasets resulted to be significantly conserved.
conserved fragments show a mean length of about  <dig> nucleotides and an average identity of about 80% with their corresponding mouse lncrna fragments .
specifically, mouse candidates lncrnas from two sources representing three datasets, were used to determine sequence conservation.
mammalian constrained lncrnas from mouse   <cit>  were divided into central nervous system specific  and non-cns specific  giving rise to the first and second datasets.
lncrnas identified in the mouse genome by the ensembl lincrna annotation pipeline  <cit>   formed the third dataset.
an initial exploratory analysis was performed by using blastn with word lengths ranging from  <dig> to  <dig> nucleotides on the cns dataset.
roc curves, plotting the distributions of the indicated measures  suggest that the reciprocal of the e-value  is the factor capable to better segregate results between the true positive and false positive sets .
we plot the reciprocal of the e-value  because plotting the e-value produced curves significantly skewed below the diagonal line  <cit> .
in addition, alignment length presents an auc of  <dig>  and, at a manual inspection of results, we noticed that this measure is capable to filter out low complexity  regions that, in few results, show multiple hits with a small e-value and are hence retained by the exclusive e-value filter.
it is now becoming evident that repeats are enriched in lncrnas  <cit>  at the light of such considerations, we decided to combine the  <dig> measures in order to select significantly conserved lncrnas, avoiding to obtain low complexity regions in the set of results.
combining the two parameters for filtration gave us zero false positives for each dataset.
interestingly, the change in word size does not affect the performance of the classifier .
therefore, word size of  <dig> nucleotides is used in all subsequent analyses.
we selected as significantly conserved, lncrnas sequences showing < <dig> % fdr for each of the  <dig> parameter .
cut-off values were calculated in order to consider significant a percentage of false positives smaller than  <dig> % when the same filter is applied to the randomized data.
an e-value cutoff of 5e- <dig> and an alignment length cut-off of  <dig> nucleotides satisfied this criteria resulting in  <dig> lncrnas from the cns dataset significantly conserved within the zebrafish phastcons elements .
the blastn search was repeated for the ncns and the ensembl datasets .
roc curves  and manual inspection of data confirmed the e-value and query alignment length as the best parameters to successfully identify significantly conserved lncrnas .
the identified cutoffs are as follows: ncns) e-value 1e- <dig>  alignment length 66; ensembl) e-value 2e- <dig>  alignment length  <dig>  the results and the annotations of the homology searches for all  <dig> datasets can be found in additional file  <dig>  we also performed secondary structure analyses to test if we could segregate the false and true positives more efficiently using rnaz on the blastn alignments.
rnaz is an efficient method for detecting functional rnas combining comparative sequence analysis and structure prediction.
the program performs two basic calculation: 1) the measure for rna secondary structure conservation and 2) the measure for thermodynamic stability  <cit> .
the  <dig> rnaz result parameters used to build the roc curves were: ratio of pairwise identity by sequence conservation index, z score and p value  .
the sequence conservation index demonstrated a positive performance  in agreement with previous reports about structural conservation of conserved lncrnas  <cit> .
however, its performance is lower than the e-value and it is not able to filter out low complexity regions.
therefore, we did not use this measure in the rest of the analyses.
the number of lncrna putatively conserved in each dataset  after applying the query alignment length and e-value cutoffs on the produced alignments.
comparison of the genomic contexts of mouse lncrna and fish phastcons pairs predicted to be conserved
in order to evaluate the locations and shed light on the putative functions of each conserved fragment, we mapped and compared each element in the respective genic context of both analyzed organisms.
the  <dig> putatively conserved lncrnas in the cns dataset showed homology to  <dig> phastcons elements.
the ncns dataset had  <dig> lncrnas showing homology to  <dig> phastcons and the  <dig> conserved ensembl lincrnas showed homology to  <dig> fragments from  <dig> phastcons elements.
the conserved regions in zebrafish were checked for overlapping features .
the fragments from the cns dataset show  <dig> out of  <dig> elements overlapping non-coding regions  in zebrafish and  <dig> out of  <dig> in mouse.
regarding the ncns dataset,  <dig> out of  <dig> conserved sequences are present in a non-coding region in zebrafish and  <dig> out of  <dig> in mouse.
the situation for the conserved ensembl dataset is different as a minor fraction of elements is present in non-coding regions in zebrafish and in mouse .
such difference with the ensembl data may be explained by considering that cns and ncns lncrnas are curated for being mainly intergenic as compared to the ensembl lncrnas.
therefore, in the ensembl dataset, candidate lncrna fragments may overlap an external exon of a coding gene in the same chromosomal domain more frequently.
however, they must still be considered non-coding because the orientation of the transcripts is in antisense to the protein coding genes they partially overlap  and they do not show any significant open reading frame .
antisense transcripts are reported to be present in large numbers in mammalian genomes and often linked to the regulation of neighboring or overlapping protein-coding genes  <cit> .
indeed, long non-coding rnas can influence the expression of protein coding genes in cis as suggested in a previous report  <cit> .
they are also reported to be associated with enhancers of neighboring coding genes in mouse neurons  <cit>  and human  <cit> .
in order to test if the function of flanking coding genes corroborates the functional conservation suggested for each mouse and zebrafish conserved non-coding pair we identified the coding genes flanking and overlapping the aligned region in zebrafish and their mouse counterparts and evaluated their homology relationships.
the search for orthologs was performed scanning a window of  <dig> megabase flanking the conserved elements in either direction in the  <dig> genomes .
results are depicted in
<dig>  the figure shows the percentages of conserved mouse lncrnas sharing orthologous coding gene in the corresponding zebrafish genomic context.
all the lncrna conserved fragments showed at least one ortholog pair from the cns, the ncns along with 80% of the ensembl datasets supporting the hypothesis of syntenic conservation.
the genomic locations for the number of mouse lncrna fragments found to be conserved.
the location is deduced with respect to the coding region of the mouse genome in the area of alignment.
the genomic location for the number of phastcons fragments found to be conserved.
the location is deduced with respect to the coding region of the zebrafish genome in the area of alignment.
functional enrichment analyses of the protein coding genes proximal to the conserved regions
in order to understand the potential biological role of the identified sequences we performed gene ontology and tissue specific expression enrichment analyses on the coding genes flanking the conserved fragments for the ensembl dataset.
the coding genes flanking and eventually overlapping the conserved regions were considered to be the putative lncrnas associated genes.
significantly enriched go biological process categories and tissue of expression for the conserved lncrnas of the ensembl dataset in zebrafish and mouse were considered for the analysis using david  <cit>  and an ease score cutoff of  <dig> .
the ease score is a p-value adjustment method specifically designed for biological large-scale studies.
it penalizes the significance of categories supported by few genes and favors more robust categories in respect to the fisher exact probability.
it is more conservative than the pure fisher exact probability and less conservative than the benjamini and hochberg fdr  <cit> .
for genes associated to the conserved lncrnas of the ensembl dataset, the enriched go terms included development, regulation of transcription and nucleic acid metabolism in both the organisms  in agreement with previous reports in mouse  <cit> .
tissue enrichment analyses were also performed to check if the selected genes showed an enrichment for being expressed in similar specific tissues.
from this analysis neural and developmental related tissues resulted to be enriched in both the species .
these results are consistent with previous studies showing that lncrnas play an important role in regulation, neural development and plasticity  <cit> .
it is important to point out that, in mouse, the genes associated to the conserved lncrnas show the most significant enrichments for expression in the nervous tissues but also a significant enrichment in lung indicating either a possible sub-functionalization of subgroups of lncrnas or a richer annotation of the mouse transcriptome in terms of domains of expression.
taken together, these analyses highlight a conserved pattern of functions and expression domains of coding genes associated with conserved lncrna fragments.
cns and ncns datasets were not used independently because they are not of reasonable dimensions to perform enrichment analysis, however, if we join the  <dig> datasets together, similar enrichments are obtained .
in  <dig> the presence of ultra conserved elements  in the human genome was discovered.
these elements show about 100% of sequence identity with mouse and many of them are conserved also in fishes.
uces are greater than  <dig> nucleotides in length and observed to lie proximal to coding genes related to development, regulation of transcription  <cit>  and cancer related loci  <cit> .
a small fraction of them overlap protein coding exon, however uces are mainly non-coding in nature and, although a large fraction seems to be transcribed and/or to function as enhancer they do not overlap current collections of transcripts  <cit> .
in order to check if the identified sequences might belong to the ultraconserved family of elements we checked their overlap with uces  <cit> .
in total four uces were found to overlap conserved regions from lncrnas of the ensembl dataset while a single lncrna from the ncns dataset showed overlap with a single uce.
we conclude that the conserved regions identified in this study are not enriched for and do not correspond to uces elements.
therefore, they have not to be considered ultraconserved.
potential of expression of conserved regions in zebrafish
the presence of expressed sequence tags  overlapping the region of conservation might support an active transcriptional output in the given region.
in this context we chose to check for the overlap of zebrafish ests in the region of conservation.
respectively 60%, 45% and 70% of the predicted cns, ncns and ensembl conserved regions are covered by at least one est in zebrafish .
interestingly, by randomly selecting ~ <dig>  non-repeated genomic regions of the same extension from the zebrafish genome we obtained a percentage as small as 8% in overlap with ests .
the results are consistent with the possibility that the majority of the conserved regions predicted in the analysis represent actively transcribed regions of the zebrafish genome.
further, in order to add supporting evidences to the potential of expression of the zebrafish conserved fragments herein isolated we performed overlap analysis with the recently published zebrafish candidate lncrnas resulting from rnaseq experiments  <cit> .
the comparison of all the predicted conserved regions with the published lncrnas resulted in 6% of our conserved regions showing overlap with at least one reported lncrnas.
it is important to point out that no definitive estimation of the number of lncrnas expressed in an organism is currently possible.
such uncertainty arises from the fact that non-coding rnas are expressed at lower levels as compared to coding genes  <cit> .
computational identification of lncrna transcripts from next-generation sequencing data remains a "work in progress" in terms of mapping reads to the genome, assembly of new transcripts, definition of background noise and cut-off parameters.
hence, in our analysis a lack of overlap does not signify an absence of transcribed elements in zebrafish, but may reflect on undetected transcripts.
in order to test this hypothesis we mapped the raw reads from the study  <cit>   on the zebrafish genome and computed the overlap between the mapped reads and all the conserved fragments.
interestingly, more than 90% of the predicted conserved regions in the zebrafish genome show overlap with at least one mapped read while only 25% of a set of randomly chosen genomic regions overlap at least one read .
checking for regions with more than  <dig>  reads overlap, we found that 20% of the conserved regions resulted positive while only 4% of random regions showed such an overlap .
the highly significant differences between the conserved regions and the random sequences indicate that the rnaseq data supports transcriptional evidences in zebrafish for most of the regions predicted to be conserved lncrnas.
finally, in order to get information about the expression domains for the conserved sequences we took advantage of the publicly available rnaseq study srp <dig>  this study contains rna samples from nine different tissues  of gasterosteus aculeatus  a sequenced teleost fish.
first, we mapped the conserved zebrafish fragments on the stickleback genome and, as expected, all the zebrafish sequences were mapped.
then, we mapped all the raw reads from the srp <dig> study on the stickleback genome and calculated the overlap with the conserved fragments.
again, more than 85% of conserved elements resulted to overlap raw reads  consistently with what we observed in zebrafish using the data from pauli et al.
the stickleback data were generated and made publicly available by the broad institute.
in agreement with the mouse expression data of the corresponding lncrnas, the conserved cns sequences show high levels of expression in the brain  also in stickleback.
conversely, the ncns data result to be transcribed at very low or even background levels , while the ensembl dataset shows low but widespread expression .
based on these results we can confirm that the mouse cns elements are likely to be cns specific also in fishes.
regarding the ncns dataset we cannot propose conservation of expression between mouse and stickleback, more and deeper sequencing data will probably clarify this aspect.
finally, the observation that the ensembl sequences show positive expression levels in several tissues is consistent with the fact that the corresponding mouse transcript models are based on transcriptional evidences from multiple tissues and cell cultures  <cit> .
we conclude that the analyses of reads coming from teleost fishes provides supporting evidences for the transcription and, at least for the cns specific elements, the tissue specific expression of the predicted conserved regions.
as long as new sequencing datasets will become available further light can be shed to improve our knowledge about the similarity of the transcriptional outputs among different vertebrate species.
number of conserved fragments overlapping ests in the zebrafish genome.
cns specific lncrna
to better demonstrate the utility of our analysis we focused on  <dig> conserved cns lncrnas and selected a candidate element ideal for further functional validations.
each phastcons element was given a unique id at the start of the analysis which is used here as reference .
the majority of elements show evidence of transcription by overlap with est sequences in zebrafish and mouse.
many elements also overlap utrs of protein coding genes pointing towards a putative regulatory function.
the conserved element  <dig>  belongs to the cns dataset, it falls completely in an intergenic region in zebrafish and a small part of the lncrna in mouse overlaps the utr intron of the coding gene lmo <dig>  the zebrafish sequence shows a conservation of  <dig> base pairs with the murine lncrna ak <dig> at an e-value of 4e- <dig> and 88% identity.
the lmo <dig> gene flanks the region of conservation in zebrafish too.
this gene is known to be a transcriptional regulator  <cit>  and is reported to be involved in cell proliferation and differentiation during embryonic development  <cit> .
it is also implicated in neuroblastoma through its interaction with the neuronal transcription factor hen <dig>  <cit> .
the dataset of conserved elements isolated in our analysis will be of help in focusing on specific sets of elements that might have an evolutionary conserved role in development and differentiation which led to their sequence conservation across species.
the genomic features for each of the  <dig> conserved phastcons fragments  and their mouse lncrna homologs.
to be noted that while for zebrafish only the region of alignment is considered not the whole phastcons element, in case of mouse the complete lncrna was used to perform the analysis.
each region is classified in terms of it being overlapped by a utr, exon or intron of an annotated protein coding gene, or an est.
CONCLUSIONS
long non-coding rnas are not characterized by the same sequence conservation properties as protein coding genes.
however, in our analysis we demonstrated a systematic procedure to identify significant sequence conservation of candidate lncrnas in vertebrates.
it resulted in the selection of a set of mouse lncrna fragments significantly conserved in fish genomes demonstrating that a proportion of up to 11% of mouse lncrnas contains fragments conserved across vertebrates.
the candidate lncrnas reflect a sub-population of the mouse lncrnaome sharing sequence homology with zebrafish phastcons elements.
the addition of annotation layers on top of sequence conservation statistics provides biological significance to the results obtained.
go enrichment analyses of coding genes flanking the conserved sequences showed striking similarity at the functional level in both species.
in addition, significant neural expression enrichments in both mouse and zebrafish are consistent with previous observations that lncrnas play an important role in neural development, differentiation and functions.
the presence of overlapping ests and the significant overlap with developmental zebrafish rnaseq reads provide further support that these fragments produce transcriptional output in fishes.
finally, the rnaseq reads from multiple tissues of the stickleback throw light on the tissue specificity of the conserved regions as well as add additional evidences in support of their expression in fishes.
the dataset presented constitute a valuable starting point for future studies aimed at functional characterization of specific lncrnas.
in summary, this work represents a proof of principle showing that a portion between  <dig> and 11% of lncrnas retains short regions of conservation between mammals and fishes and the cutoffs to use to efficiently look for such elements.
the analyses can result especially useful as a reference to analyze the conservation of lncrnas in newly sequenced genomes and transcriptomes.

 long non-coding rnas were firstly reported as transcripts expressed in large numbers in mammalian transcriptomes. they were shown to constitute more than half of all the transcriptional outputs of mammalian genomes. prior to these reports xist in mammals and xlsirt in amphibians were the only well characterized lncrnas described to function in Χ; chromosome inactivation and the formation of cytoskeleton. recently, several aspects of development and disease have been associated with lncrnas function albeit to a small proportion of them. processes associated with lncrnas include epigenetic regulation of multi-gene loci, apoptosis and cell cycle, regulation of gene splicing and tumor suppressor activity. there are also examples of lncrnas playing a role in the adaptive immunity of mammals, being differentially expressed in response to carcinogens and functioning as enhancers. a probe into the functional role of lncrnas requires knowledge of the specificity of their expression across developmental stages and different tissues. microarray technology was initially used to detect lncrnas in differentiating mouse embryonic stem cells. many lncrnas showed correlation of expression with the flanking protein-coding genes that associated with developmental functions. similar transcriptomics studies identified many lncrnas expressed in cd8+ cells and during neuronal lineage specification in mouse. however, cross-hybridization, background noise and limited genome coverage associated to array based detection techniques were often used as arguments against the pervasive existence of lncrnas. today these problems have been solved thanks to the advent of the rna sequencing technology. rnaseq deals with direct quantification of a cdna population and is not limited to transcripts mapped to known genomic sequences. an rnaseq experiment on differentiating human neurons led to the identification of about lncrnas with dynamical expression levels. recently, sequencing studies have even identified hundreds of lncrnas expressed during early developmental stages in zebrafish and c. elegans finally demonstrating that the pervasiveness of non-coding transcription is not an exclusive feature of mammalian transcriptomes. pauli et al identified about non-coding rnas expressed during embryogenesis in zebrafish. ulitsky et al reported a set of about long intergenic non-coding rnas expressed during zebrafish development; they show low sequence similarity but conserved genomic locations with their mammalian counterparts. finally nam et al reported a catalog of lncrnas in c.elegans which show similar features to vertebrate lncrnas in terms of lack of general sequence conservation as well as stage specific expression patterns. the execution of large-scale studies about the discovery and characterization of candidate lncrnas is facilitating the establishment of a catalog of these important molecular players which, in turn, permit to annotate them with specific biological validations and comparative analyses improving our knowledge of the lncrnaome. however, lack of sequence homology and lack of deep tissue and stage specific expression data have been one of the obstacles in defining a proper catalog of lncrnas among different species. computational methods for the discovery and the annotation of lncrnas are sparse and mainly limited to mammalian genomes. parameters like open reading frame length, lack of homology to protein-coding genes and protein domains, nucleotide composition and substitution rates have been used previously to define computational lncrna discovery pipelines. sequence conservation has not been often used as support to justify the presence of lncrnas in an organism because the lncrnas identified in human, mouse, zebrafish and c. elegans showed little or no sequence conservation in the majority of the population. in addition, pauli et al stated that the level of conservation for the majority of zebrafish lncrna is comparable to that of introns and that only few of them are really conserved. however, short spans of sequence conservation for specific lncrnas were reported. four evolutionary constrained mouse lncrnas were shown to be conserved in sequence and expression between mouse, opossum and chicken. forty three putative long non-coding sequences from chicken ests were found to share sequence homology with human, rat and mouse transcripts. xist, the lncrna responsible for the Χ chromosome inactivation in eutherian mammals shares sequence homology in vertebrates. sox2ot and har1f are conserved amongst vertebrates. the biggest group of lncrnas constrained in terms of their nucleotide substitution rates between mouse and human is represented by a set of mouse transcripts. this set showed a tendency to juxtapose genes involved in the regulation of transcription and development. a subset of these lncrnas expressed in the mouse brain and defined as cns-specific appear to show tissue specific expression pattern similar to their proximal protein coding genes. despite these evidences, a lack of general sequence conservation associated with lncrnas has been proposed and this becomes more evident when considering long evolutionary distances such as the one separating mammals from fishes, even if fragments of sequence conservation have been detected. despite these evidences, a systematic analysis of sequence conservation of vertebrate lncrnas is still lacking and it remains unclear whether and to what extent there is general sequence conservation of lncrnas between mammals and fishes. in order to fulfill this lack, the work here presented tries to define the level of conservation of mouse lncrnas in the zebrafish genome using an unbiased choice for the comparison parameters, taking advantage of randomizations and receiver operating characteristic analyses. our approach is centered around subsets of mouse constrained and/or well annotated lncrnas, based on the assumption that such transcripts constitute a representative set of lncrnas ideally containing small amounts of transcriptional noise. we would like to specify that, although our analysis consider a subset of already published and very well annotated lncrnas, we cannot rule out the possibility that some of them might actually be coding for short peptides. recent studies suggest that few candidate lncrnas can produce short peptides and there may exist a class of bifunctional rnas encoding both mrnas and functional noncoding transcripts. therefore, specific biological validations remain a fundamental step for a proper characterization of these elements. nevertheless, the special care taken in the choice of the datasets to analyze and the literature about them, makes us confident that we are currently using, the best sets of candidate lncrnas. we compared these transcripts against the set of zebrafish phastcons elements reported to be significantly conserved among fishes. the phastcons program uses a hidden markov model-based method that estimates the probability that each nucleotide belongs to a conserved element, based on multiple alignments of selected species. we used the phastcons6way track to select elements conserved among fishes. these are based on scores built on multiple alignment of the zebrafish genome with tetraodon, stickleback, human, mouse and western clawed frog. it is important to point out here that, considering the way in which they are built, these elements represent the best selection of sequences conserved, in first instance, among fishes, but many of them can also result conserved among vertebrates. this choice implicitly adds more genomes to our analyses and is based on the assumption that lncrnas conserved between mouse and zebrafish are expected to be primarily conserved among teleosts. for this pilot study, the reduction in the dataset dimension, given by such choice, limited the zebrafish genomic search space to the phastcons sequences, rather than to the full genome, making it feasible to use several randomizations steps to specifically identify the levels of conservation proper of lncrnas. here we show that the usage of the blastn e-value and alignment length as cut-offs is sufficient to distinguish conservation of mouse lncrnas against zebrafish phastcons elements as compared to shuffled sequences. from an initial dataset of about mouse lncrnas we demonstrate that between and 11% of them contain fragments significantly conserved in zebrafish in agreement with the results by ulitsky et al on a smaller dataset. gene ontology enrichment analyses of protein-coding genes flanking the conserved elements, identified similar functional classes significantly enriched in both species, such as regulation of transcription and development. these coding genes exhibited enrichment for expression in the brain in both mouse as well as zebrafish. the lncrnas shown to be conserved are deemed to be functionally important and suggested for further experimental validation of their function.  selection of conservation parameters to select significantly conserved lncrnas we developed a pipeline to identify conserved mouse lncrna fragments in zebrafish using sequence identity, randomization and the identification of an unbiased threshold to detect significant levels of conservation. in order to identify the optimal parameters capable to select conserved lncrna sequences, we used receiver operating characteristic like analyses on the distribution of the following blastn alignments result measures: 1) query coverage, 2) query alignment length, 3) percentage identity and 4) e-value. roc like analyses were performed on the results of the following blastn searches: 1) mouse lncrna against zebrafish phastcons elements, 2) shuffled mouse lncrna sequences against zebrafish phastcons elements. in order to select significant results we defined a specific cut-off showing less than % false discovery rate for each parameter. the analysis was applied to different datasets and, after the application of the identified filter, between to 11% of the sequences in the true positive datasets resulted to be significantly conserved. conserved fragments show a mean length of about nucleotides and an average identity of about 80% with their corresponding mouse lncrna fragments. specifically, mouse candidates lncrnas from two sources representing three datasets, were used to determine sequence conservation. mammalian constrained lncrnas from mouse were divided into central nervous system specific and non-cns specific giving rise to the first and second datasets. lncrnas identified in the mouse genome by the ensembl lincrna annotation pipeline formed the third dataset. an initial exploratory analysis was performed by using blastn with word lengths ranging from to nucleotides on the cns dataset. roc curves, plotting the distributions of the indicated measures suggest that the reciprocal of the e-value is the factor capable to better segregate results between the true positive and false positive sets. we plot the reciprocal of the e-value because plotting the e-value produced curves significantly skewed below the diagonal line. in addition, alignment length presents an auc of and, at a manual inspection of results, we noticed that this measure is capable to filter out low complexity regions that, in few results, show multiple hits with a small e-value and are hence retained by the exclusive e-value filter. it is now becoming evident that repeats are enriched in lncrnas at the light of such considerations, we decided to combine the measures in order to select significantly conserved lncrnas, avoiding to obtain low complexity regions in the set of results. combining the two parameters for filtration gave us zero false positives for each dataset. interestingly, the change in word size does not affect the performance of the classifier. therefore, word size of nucleotides is used in all subsequent analyses. we selected as significantly conserved, lncrnas sequences showing < % fdr for each of the parameter. cut-off values were calculated in order to consider significant a percentage of false positives smaller than % when the same filter is applied to the randomized data. an e-value cutoff of 5e- and an alignment length cut-off of nucleotides satisfied this criteria resulting in lncrnas from the cns dataset significantly conserved within the zebrafish phastcons elements. the blastn search was repeated for the ncns and the ensembl datasets. roc curves and manual inspection of data confirmed the e-value and query alignment length as the best parameters to successfully identify significantly conserved lncrnas. the identified cutoffs are as follows: ncns) e-value 1e- alignment length 66; ensembl) e-value 2e- alignment length the results and the annotations of the homology searches for all datasets can be found in additional file we also performed secondary structure analyses to test if we could segregate the false and true positives more efficiently using rnaz on the blastn alignments. rnaz is an efficient method for detecting functional rnas combining comparative sequence analysis and structure prediction. the program performs two basic calculation: 1) the measure for rna secondary structure conservation and 2) the measure for thermodynamic stability. the rnaz result parameters used to build the roc curves were: ratio of pairwise identity by sequence conservation index, z score and p value. the sequence conservation index demonstrated a positive performance in agreement with previous reports about structural conservation of conserved lncrnas. however, its performance is lower than the e-value and it is not able to filter out low complexity regions. therefore, we did not use this measure in the rest of the analyses. the number of lncrna putatively conserved in each dataset after applying the query alignment length and e-value cutoffs on the produced alignments. comparison of the genomic contexts of mouse lncrna and fish phastcons pairs predicted to be conserved in order to evaluate the locations and shed light on the putative functions of each conserved fragment, we mapped and compared each element in the respective genic context of both analyzed organisms. the putatively conserved lncrnas in the cns dataset showed homology to phastcons elements. the ncns dataset had lncrnas showing homology to phastcons and the conserved ensembl lincrnas showed homology to fragments from phastcons elements. the conserved regions in zebrafish were checked for overlapping features. the fragments from the cns dataset show out of elements overlapping non-coding regions in zebrafish and out of in mouse. regarding the ncns dataset, out of conserved sequences are present in a non-coding region in zebrafish and out of in mouse. the situation for the conserved ensembl dataset is different as a minor fraction of elements is present in non-coding regions in zebrafish and in mouse. such difference with the ensembl data may be explained by considering that cns and ncns lncrnas are curated for being mainly intergenic as compared to the ensembl lncrnas. therefore, in the ensembl dataset, candidate lncrna fragments may overlap an external exon of a coding gene in the same chromosomal domain more frequently. however, they must still be considered non-coding because the orientation of the transcripts is in antisense to the protein coding genes they partially overlap and they do not show any significant open reading frame. antisense transcripts are reported to be present in large numbers in mammalian genomes and often linked to the regulation of neighboring or overlapping protein-coding genes. indeed, long non-coding rnas can influence the expression of protein coding genes in cis as suggested in a previous report. they are also reported to be associated with enhancers of neighboring coding genes in mouse neurons and human. in order to test if the function of flanking coding genes corroborates the functional conservation suggested for each mouse and zebrafish conserved non-coding pair we identified the coding genes flanking and overlapping the aligned region in zebrafish and their mouse counterparts and evaluated their homology relationships. the search for orthologs was performed scanning a window of megabase flanking the conserved elements in either direction in the genomes. results are depicted in the figure shows the percentages of conserved mouse lncrnas sharing orthologous coding gene in the corresponding zebrafish genomic context. all the lncrna conserved fragments showed at least one ortholog pair from the cns, the ncns along with 80% of the ensembl datasets supporting the hypothesis of syntenic conservation. the genomic locations for the number of mouse lncrna fragments found to be conserved. the location is deduced with respect to the coding region of the mouse genome in the area of alignment. the genomic location for the number of phastcons fragments found to be conserved. the location is deduced with respect to the coding region of the zebrafish genome in the area of alignment. functional enrichment analyses of the protein coding genes proximal to the conserved regions in order to understand the potential biological role of the identified sequences we performed gene ontology and tissue specific expression enrichment analyses on the coding genes flanking the conserved fragments for the ensembl dataset. the coding genes flanking and eventually overlapping the conserved regions were considered to be the putative lncrnas associated genes. significantly enriched go biological process categories and tissue of expression for the conserved lncrnas of the ensembl dataset in zebrafish and mouse were considered for the analysis using david and an ease score cutoff of. the ease score is a p-value adjustment method specifically designed for biological large-scale studies. it penalizes the significance of categories supported by few genes and favors more robust categories in respect to the fisher exact probability. it is more conservative than the pure fisher exact probability and less conservative than the benjamini and hochberg fdr. for genes associated to the conserved lncrnas of the ensembl dataset, the enriched go terms included development, regulation of transcription and nucleic acid metabolism in both the organisms in agreement with previous reports in mouse. tissue enrichment analyses were also performed to check if the selected genes showed an enrichment for being expressed in similar specific tissues. from this analysis neural and developmental related tissues resulted to be enriched in both the species. these results are consistent with previous studies showing that lncrnas play an important role in regulation, neural development and plasticity. it is important to point out that, in mouse, the genes associated to the conserved lncrnas show the most significant enrichments for expression in the nervous tissues but also a significant enrichment in lung indicating either a possible sub-functionalization of subgroups of lncrnas or a richer annotation of the mouse transcriptome in terms of domains of expression. taken together, these analyses highlight a conserved pattern of functions and expression domains of coding genes associated with conserved lncrna fragments. cns and ncns datasets were not used independently because they are not of reasonable dimensions to perform enrichment analysis, however, if we join the datasets together, similar enrichments are obtained. in the presence of ultra conserved elements in the human genome was discovered. these elements show about 100% of sequence identity with mouse and many of them are conserved also in fishes. uces are greater than nucleotides in length and observed to lie proximal to coding genes related to development, regulation of transcription and cancer related loci. a small fraction of them overlap protein coding exon, however uces are mainly non-coding in nature and, although a large fraction seems to be transcribed and/or to function as enhancer they do not overlap current collections of transcripts. in order to check if the identified sequences might belong to the ultraconserved family of elements we checked their overlap with uces. in total four uces were found to overlap conserved regions from lncrnas of the ensembl dataset while a single lncrna from the ncns dataset showed overlap with a single uce. we conclude that the conserved regions identified in this study are not enriched for and do not correspond to uces elements. therefore, they have not to be considered ultraconserved. potential of expression of conserved regions in zebrafish the presence of expressed sequence tags overlapping the region of conservation might support an active transcriptional output in the given region. in this context we chose to check for the overlap of zebrafish ests in the region of conservation. respectively 60%, 45% and 70% of the predicted cns, ncns and ensembl conserved regions are covered by at least one est in zebrafish. interestingly, by randomly selecting ~ non-repeated genomic regions of the same extension from the zebrafish genome we obtained a percentage as small as 8% in overlap with ests. the results are consistent with the possibility that the majority of the conserved regions predicted in the analysis represent actively transcribed regions of the zebrafish genome. further, in order to add supporting evidences to the potential of expression of the zebrafish conserved fragments herein isolated we performed overlap analysis with the recently published zebrafish candidate lncrnas resulting from rnaseq experiments. the comparison of all the predicted conserved regions with the published lncrnas resulted in 6% of our conserved regions showing overlap with at least one reported lncrnas. it is important to point out that no definitive estimation of the number of lncrnas expressed in an organism is currently possible. such uncertainty arises from the fact that non-coding rnas are expressed at lower levels as compared to coding genes. computational identification of lncrna transcripts from next-generation sequencing data remains a "work in progress" in terms of mapping reads to the genome, assembly of new transcripts, definition of background noise and cut-off parameters. hence, in our analysis a lack of overlap does not signify an absence of transcribed elements in zebrafish, but may reflect on undetected transcripts. in order to test this hypothesis we mapped the raw reads from the study on the zebrafish genome and computed the overlap between the mapped reads and all the conserved fragments. interestingly, more than 90% of the predicted conserved regions in the zebrafish genome show overlap with at least one mapped read while only 25% of a set of randomly chosen genomic regions overlap at least one read. checking for regions with more than reads overlap, we found that 20% of the conserved regions resulted positive while only 4% of random regions showed such an overlap. the highly significant differences between the conserved regions and the random sequences indicate that the rnaseq data supports transcriptional evidences in zebrafish for most of the regions predicted to be conserved lncrnas. finally, in order to get information about the expression domains for the conserved sequences we took advantage of the publicly available rnaseq study srp this study contains rna samples from nine different tissues of gasterosteus aculeatus a sequenced teleost fish. first, we mapped the conserved zebrafish fragments on the stickleback genome and, as expected, all the zebrafish sequences were mapped. then, we mapped all the raw reads from the srp study on the stickleback genome and calculated the overlap with the conserved fragments. again, more than 85% of conserved elements resulted to overlap raw reads consistently with what we observed in zebrafish using the data from pauli et al. the stickleback data were generated and made publicly available by the broad institute. in agreement with the mouse expression data of the corresponding lncrnas, the conserved cns sequences show high levels of expression in the brain also in stickleback. conversely, the ncns data result to be transcribed at very low or even background levels, while the ensembl dataset shows low but widespread expression. based on these results we can confirm that the mouse cns elements are likely to be cns specific also in fishes. regarding the ncns dataset we cannot propose conservation of expression between mouse and stickleback, more and deeper sequencing data will probably clarify this aspect. finally, the observation that the ensembl sequences show positive expression levels in several tissues is consistent with the fact that the corresponding mouse transcript models are based on transcriptional evidences from multiple tissues and cell cultures. we conclude that the analyses of reads coming from teleost fishes provides supporting evidences for the transcription and, at least for the cns specific elements, the tissue specific expression of the predicted conserved regions. as long as new sequencing datasets will become available further light can be shed to improve our knowledge about the similarity of the transcriptional outputs among different vertebrate species. number of conserved fragments overlapping ests in the zebrafish genome. cns specific lncrna to better demonstrate the utility of our analysis we focused on conserved cns lncrnas and selected a candidate element ideal for further functional validations. each phastcons element was given a unique id at the start of the analysis which is used here as reference. the majority of elements show evidence of transcription by overlap with est sequences in zebrafish and mouse. many elements also overlap utrs of protein coding genes pointing towards a putative regulatory function. the conserved element belongs to the cns dataset, it falls completely in an intergenic region in zebrafish and a small part of the lncrna in mouse overlaps the utr intron of the coding gene lmo the zebrafish sequence shows a conservation of base pairs with the murine lncrna ak at an e-value of 4e- and 88% identity. the lmo gene flanks the region of conservation in zebrafish too. this gene is known to be a transcriptional regulator and is reported to be involved in cell proliferation and differentiation during embryonic development. it is also implicated in neuroblastoma through its interaction with the neuronal transcription factor hen. the dataset of conserved elements isolated in our analysis will be of help in focusing on specific sets of elements that might have an evolutionary conserved role in development and differentiation which led to their sequence conservation across species. the genomic features for each of the conserved phastcons fragments and their mouse lncrna homologs. to be noted that while for zebrafish only the region of alignment is considered not the whole phastcons element, in case of mouse the complete lncrna was used to perform the analysis. each region is classified in terms of it being overlapped by a utr, exon or intron of an annotated protein coding gene, or an est.  long non-coding rnas are not characterized by the same sequence conservation properties as protein coding genes. however, in our analysis we demonstrated a systematic procedure to identify significant sequence conservation of candidate lncrnas in vertebrates. it resulted in the selection of a set of mouse lncrna fragments significantly conserved in fish genomes demonstrating that a proportion of up to 11% of mouse lncrnas contains fragments conserved across vertebrates. the candidate lncrnas reflect a sub-population of the mouse lncrnaome sharing sequence homology with zebrafish phastcons elements. the addition of annotation layers on top of sequence conservation statistics provides biological significance to the results obtained. go enrichment analyses of coding genes flanking the conserved sequences showed striking similarity at the functional level in both species. in addition, significant neural expression enrichments in both mouse and zebrafish are consistent with previous observations that lncrnas play an important role in neural development, differentiation and functions. the presence of overlapping ests and the significant overlap with developmental zebrafish rnaseq reads provide further support that these fragments produce transcriptional output in fishes. finally, the rnaseq reads from multiple tissues of the stickleback throw light on the tissue specificity of the conserved regions as well as add additional evidences in support of their expression in fishes. the dataset presented constitute a valuable starting point for future studies aimed at functional characterization of specific lncrnas. in summary, this work represents a proof of principle showing that a portion between and 11% of lncrnas retains short regions of conservation between mammals and fishes and the cutoffs to use to efficiently look for such elements. the analyses can result especially useful as a reference to analyze the conservation of lncrnas in newly sequenced genomes and transcriptomes. 
indeed, starting from ~ mouse lncrnas we could predict that between and 11% present conserved sequence fragments in fish genomes. our results show that a subset of mouse candidate lncrnas could be distinguished from random sequences based on their alignment with zebrafish phastcons elements. in summary, we show that interesting genomic regions in zebrafish could be marked based on their sequence homology to a mouse lncrna, overlap with ests and proximity to genes involved in nervous system development. low sequence conservation and lack of functional annotations make it difficult to identify homologs of mammalian lncrnas in other vertebrates.
 long non-coding rnas are a major class of non-coding rnas. they are involved in diverse intra-cellular mechanisms like molecular scaffolding, splicing and dna methylation. through these mechanisms they are reported to play a role in cellular differentiation and development. they show an enriched expression in the brain where they are implicated in maintaining cellular identity, homeostasis, stress responses and plasticity. low sequence conservation and lack of functional annotations make it difficult to identify homologs of mammalian lncrnas in other vertebrates. a computational evaluation of the lncrnas through systematic conservation analyses of both sequences as well as their genomic architecture is required.  our results show that a subset of mouse candidate lncrnas could be distinguished from random sequences based on their alignment with zebrafish phastcons elements. using roc analyses we were able to define a measure to select significantly conserved lncrnas. indeed, starting from ~ mouse lncrnas we could predict that between and 11% present conserved sequence fragments in fish genomes. gene ontology enrichment analyses of protein coding genes, proximal to the region of conservation, in both organisms highlighted similar go classes like regulation of transcription and central nervous system development. the proximal coding genes in both the species show enrichment of their expression in brain. in summary, we show that interesting genomic regions in zebrafish could be marked based on their sequence homology to a mouse lncrna, overlap with ests and proximity to genes involved in nervous system development.  conservation at the sequence level can identify a subset of putative lncrna orthologs. the similar protein-coding neighborhood and transcriptional information about the conserved candidates provide support to the hypothesis that they share functional homology. the pipeline herein presented represents a proof of principle showing that a portion between and 11% of lncrnas retains region of conservation between mammals and fishes. we believe this study will result useful as a reference to analyze the conservation of lncrnas in newly sequenced genomes and transcriptomes. 2- may ninth annual meeting of the italian society of bioinformatics catania, sicily 