BACKGROUND
high-throughput transcriptome data obtained in particular using tiling arrays  <cit>  and cdna sequencing  <cit>  in conjunction with detailed functional studies of individual genes have profoundly changed our picture of eukaryotic gene regulation by emphasizing multiple regulatory layers, many of which involve non-protein-coding rnas .
in contrast to protein-coding genes, however, ncrnas do not form a homogeneous group of transcripts but rather belong to a diverse array of classes with vastly different structures, functions, and evolutionary patterns  <cit> .
efficient computational methods  <cit>  have recently been developed to determine the genomic inventory of a large subgroup of ncrnas, namely those that exhibit evolutionarily conserved secondary structures.
as stabilizing selection acts to preserve structure in the presence of sequence variation, these transcripts are very likely to have discernible biological function – as opposed to being a mere byproduct of transcriptional noise  <cit>  or gene regulation by transcriptional interference  <cit> .
the group of structured rnas that we are considering here consequently includes the classical families of small ncrnas  as well as structured, usually regulatory, motifs associated with larger coding or non-coding transcripts, such as internal ribosomal entry sites, ire, and secis signals see e.g.
<cit> .
the rnaz approach  <cit>  has proven to produce rather high quality predictions.
in particular, as part of the detailed analysis of the encode regions  <cit> , the verification of many unannotated rnaz predictions by means of rt-pcr has been reported, and for a substantial fraction of rnaz predictions corroborating evidence from high-throughput experiments has been obtained.
computational screens for structured rnas have been reported so far for mammalian  <cit> , urochordate  <cit> , nematode  <cit> , and yeast  <cit>  genomes.
however, no comprehensive analysis of structured ncrnas in insect genomes has been published so far, even though there is statistical evidence for an enrichment of structured rnas within highly conserved non-coding elements of drosophilids  <cit> .
drosophilids, which have been deeply sequenced by a consortium coordinated by the nhgri  <cit> , provide an ideal model system for this task, since their evolutionary divergence is comparable to those of mammals.
as a consequence, large portions of their genomes are alignable, while at the same time there is substantial sequence variation.
both are necessary prerequisites for currently available ncrna detection tools.
in addition to the statistical evidence for wide-spread structured rnas in insects, two recent genome-wide experimental studies provide evidence of a large reservoir of novel ncrnas in drosophila melanogaster: isogai et al.
<cit>  mapped trf <dig> and brf binding sites in the d. melanogaster genome and showed that, unlike most other eukaryotes, trf1/brf binding appears responsible for the initiation of all classes of polymerase-iii  transcription.
as the known pol iii transcripts are small ncrnas, their data suggests that drosophilids are likely to have a large set of previously unannotated small ncrnas.
a large-scale tiling array study of transcription in the early development of d. melanogaster  <cit>  found that about 20% of the observed transcripts in d. melanogaster come from stand-alone intergenic or intronic sources and may constitute new types of rnas, including a substantial fraction of ncrnas.
RESULTS
we report here on a computational screen for structured rna motifs in drosophilids based on 12-species pecan alignments provided by the consortium.
the detected rnaz hits are either  independently transcribed non-coding rnas with evolutionarily conserved secondary structures, or they are structured elements that are parts of coding transcripts such as secis or ire elements.
sensitivity and specificity
overall,  <dig>  <dig> rnaz hits corresponding to roughly  <dig> mb in the d. melanogaster genome show evidence of evolutionarily conserved rna secondary structure.
about 20% of these overlap existing annotation.
the  <dig>  <dig> loci of the high confidence set covers approximately  <dig>  mb of dna, see tab.
<dig>
in total,  <dig> hits correspond to known non-coding rnas according to at least one source of annotation .
tab.
<dig> summarizes the recall of the screen on several "classical" ncrnas families.
note that some classes of ncrnas were deliberately removed already in the pecan alignments, notably the 5s rrna sequences.
we recovered 96% of the known d. melanogaster mirnas.
a blast search of the drosophilid rnaz hits against the results of prior rnaz surveys of mammals  <cit> , urochordates  <cit> , and nematodes  <cit>  yielded the following pattern of conservation:  <dig> trna hits and  <dig> snrnas associated with the major spliceosome.
furthermore, we recover the u6atac snrna  and  <dig> micrornas.
in order to estimate the false discovery rate , we repeated the screen with shuffled alignments as described in  <cit> .
alignments are shuffled such that two alignment columns are swapped only if both their gap pattern and their sequence conservation pattern is the same.
this amounts to a very "gentle" shuffling that in particular preserves pairwise sequence divergence within any given window.
this gentle shuffling procedure may fail to remove the secondary structure signal in some cases because too few pairs of alignment columns satisfy the stringent conditions for shuffling.
this is at least one reason why we observe  <dig>  <dig>  hits in which true and shuffled screen intersect, including  <dig> of the  <dig> annotated d. melanogaster ncrnas, almost exclusively trnas.
the estimated fdr of roughly 50% for p >  <dig>  and 40% for the high quality set in tab.
<dig> should therefore be regarded as pessimistic estimates.
the results of a second, more "vigorous" shuffling approach lead to much more optimistic estimates: shuffling of the columns without considering their sequence conservation or gap pattern reduces the estimated fdr by factor of  <dig> to only a 1–2%.
one may argue, of course, that shuffling columns independently will change the gap pattern of the alignment .
hence, this procedure may well underestimate the fdr.
the dramatic difference in the result highlights a general problem that so far has not been solved in a satisfactory way, namely how to systematically construct randomized alignments that preserve all correlation features of the genomic background except the one under consideration.
one important feature which must be mentioned at this point is dinucleotide content.
due to the stacking energy contributions in the folding model, dinucleotide content can affect folding energies and thus fdr estimates considerably.
since there is still no way of randomizing alignments preserving dinucleotide content, we cannot control for this effect.
however, we found that, in contrast to mammalian genomes  <cit> , there is no strong dinucleotide bias in the genomic background of d. melanogaster that effects folding energies.
therefore, our estimates from mononucleotide shuffled alignments will not differ dramatically from estimates one would obtain from controls with the same dinucleotide content.
in contrast to most previous rnaz screens, we have not removed coding sequences from the input alignments.
notably,  <dig>  <dig> hits for p >  <dig>  and  <dig> hits for p >  <dig>  overlap with annotated coding regions, accounting for 19% and 13% of the rnaz hits, respectively.
these fractions are much smaller than the expected fdrs; we therefore expect that most of these signals are indeed false positives.
interestingly, if we base our analysis on the number of nucleotides that are predicted to lie in regions with conserved structures instead of counting the rnaz hits the estimates are reduced to 15%, and  <dig> %, respectively .
conversely, only 12%  at p >  <dig>  and less than 4%  at p >  <dig>  of the annotated coding regions are detected by rnaz.
note that  <dig>  <dig> rnaz hits overlap more than one annotated coding region.
the small percentage of rnaz hits in annotated cds indicates that even a possibly large number of unannotated coding sequences will not have a significant impact on the interpretation of the rnaz results in the sense that only a small fraction of the rnaz hits may be previously unannotated cds.
to further corroborate this point we have computed the overlap of the rnaz predictions with various gene prediction tracks available in the ucsc table browser, yielding no significant increase in the number of rnaz hits located in putative cds: in total only  <dig>  <dig>  and  <dig>  <dig>  rnaz hits lie in regions with any evidence for coding capacity.
genomic distribution
the genomic distribution of structured rna candidates in d. melanogaster is comparable to the observations in previous rnaz-based screens, see fig.
<dig>  as in the encode data  <cit> , the distribution of rnaz hits largely follows the patterns of sequence conservation.
in the fly data, only 5'utrs show a substantial enrichment relative to the input data.
in contrast, the largest enrichment in the human encode data was observed from 3'utrs  <cit> .
the most striking difference between fly and human data is that the relative fraction of both intronic rnaz hits and intronic sequence conservation is twice as large in human.
in a recent article manak and colleagues  <cit>  describe widespread transcriptional activity in the d. melanogaster genome during  <dig> timepoints of early embryonic development detected by genomic tiling arrays.
when comparing the rnaz hits to this data, we identify  <dig>  <dig>  and  <dig>  <dig>  hits that overlap a transfrag in any of the  <dig> timepoints.
a comparison of the fractions of rnaz hits from normal and control screen which overlap transfrags in one, several or all timepoints yields, however, no significant enrichments .
the distance distribution of intergenic rnaz hits reveals a striking difference between the situation in the human and the fly genome, fig.
<dig>  since the d. melanogaster genome is much more compact than the human one, we need to compare the distribution of the distances between rnaz hits and the nearest coding sequence relative to the length distribution of the intergenic regions .
in fig.
<dig> we plot the relative frequency of igr with a length exceeding a given distance d, and the relative frequency of rnaz hits with a distance larger than d from the nearest coding region.
if intergenic rnaz hits are uniformly distributed within the igr, the distribution of rnaz-cds distances looks like the distribution of igr distances, just shifted to the left by a factor of  <dig>  indeed, this is observed in the human data, albeit the shift is a factor between  <dig> and  <dig>  indicating that the placement of intergenic rnaz hits in human is nearly uniform, with a small tendency of avoiding the proximity of coding genes.
in contrast, about 40% of the d. melanogaster rnaz hits in intergenic regions are located adjacent to coding sequences.
this may indicate that current annotation of the fly genome lists boundaries of protein coding genes that systematically truncate the utrs.
if this is the case, however, then we would have to interpret more than 15% of the total rnaz hits as located in utrs.
our data could be explained if a situation similar to the minifly gene is prevalent in the fly: for this gene a recent study  <cit>  described several alternative poly-a sites and multiple small ncrnas that are processed from the alternative 3'utrs.
at least one of these ncrnas is structured: the snorna h <dig> was also detected in our screen.
in any case, the structured rnas by rnaz are on average much more closely linked to protein coding genes in flies than in human.
on the other hand, a small fraction  of the intergenic rnaz hits, i.e., the tail in fig.
<dig>  is located much further away from cds than expected for random placement.
this suggests the existence of a distinct class of rnaz hits with a propensity for large igrs.
most likely, these signals correspond to independently transcribed ncrnas.
about 20% of the unannotated transcripts observed in d. melanogaster early development arise from stand-alone intergenic or intronic sources   <cit> .
only a relatively small fraction of the novel independent transcripts  had intergenic origin.
in comparison, more than 13%  of the transcriptional output recorded by comparable methods from the encode regions has a distal intergenic source   <cit> .
this difference is in agreement with closer association of most rnaz hits with protein coding genes in the fly.
further annotation of rnaz predictions
in a recent study, isogai et al.
<cit>  identified trf <dig> and brf binding sites using high-resolution genome tiling microarrays and provided evidence that in drosophila the alternative trf1/brf complex appears responsible for the initiation of all known classes of pol iii transcription.
at the p >  <dig>  significance level rnaz hits are about three-fold enriched in these regions.
we have therefore analyzed the distribution of rnaz hits within the experimentally determined trf <dig> and brf binding regions.
as reported in  <cit> , most of the sites correspond to trnas, 7sl rnas, and a subset of snornas.
in addition to these known ncrnas, the loci contain  <dig> unannotated rnaz hits, which are prime candidates for novel pol iii transcripts.
in order to identify putative micrornas, we screened all rnaz hits with rnamicro  <cit> .
this results in  <dig> candidates, of which  <dig> are unannotated so far.
<dig> of these signals are located in annotated cds and are therefore most likely false positives, leaving  <dig> plausible microrna candidates.
the recent discovery of hundreds of new human micrornas that are not conserved beyond primates strongly suggests that "evolution of mirnas is an ongoing process and that along with ancient, highly conserved mirnas, there are a number of emerging mirnas"  <cit> .
in the light of these data, a large number of drosophilid-specific micrornas does not come unexpected.
using snoreport  <cit> ,  rnaz hits are classified as putative box h/aca snornas, of which  <dig> intersect with previously annotated snornas.
taking into account that for only  <dig> of the  <dig> annotated snornas the annotation distinguishes between box h/aca , box c/d , and scarnas , the small overlap with the existing annotation is not surprising.
again, recent experimental surveys in other species, including nematodes  <cit>  and mammals  <cit>  have discovered a substantial number of previously unannotated snornas in these species, suggesting that the current annotation of snornas in d. melanogaster is also far from complete.
finally,  <dig>  <dig> rnaz hits have direct evidence for expression through ests that are not related to protein coding genes, i.e., through ests that do not intersect with the flybase, refseq, n-scan, genscan, human proteins gene prediction and mrna tracks of the ucsc table browser.
structure-based clustering
since the  <dig> rnaz hits that overlap trf <dig> or brf binding regions  <cit>  are good candidates without annotation for bona fide ncrnas, we applied structure-based clustering to this small subset of our predictions to identify common secondary structures and, hence, putative novel functional rnas.
the complete clustering tree as well as a table of the most prominent clusters is given in the additional file  <dig>  since all clusters have a mean pairwise identity less than 45%, structurally related candidates are typically highly diverged at sequence level.
in fig.
<dig> an example cluster of complex structures is given.
clusters  <dig>   <dig> and  <dig> have a structure with two stem loops in common.
all consensus structures show compensatory mutations.
fig.
<dig> depicts a large cluster of simple hairpin structures.
they show a relatively high structural conservation  whereas the sequence similarity  is small.
phylogenetic distribution
in order to study the phylogenetic distribution of the rnaz prediction we determine the last common ancestor for each rnaz hit that contains the corresponding sequence in the input alignment.
fig.
<dig> summarizes these results for both the true data and the "gentle" control screen.
more than 50% of the rnaz hits are found only within the melanogaster subgroup.
to interpret this result we compute the ratio of newly appearing rnaz hits and the branch length for each branch in the tree leading to d. melanogaster.
we observe little variation in the data, with the exception of a reduced rate of innovation along the most recent branch.
this reduction is, however, most likely a methodological artefact, since the pairwise mutation distances between d. melanogaster, d. simulans, and d. sechellia are only about  <dig>  and rnaz is known to be less sensitive for highly similar sequences.
approximately 12% of the rnaz hits are conserved throughout all drosophilids.
in comparison, a screen of vertebrate genomes  <cit>  found about 3% of mammalian rnaz candidates  to be conserved throughout vertebrates.
a comparison of true and shuffled screens furthermore indicates a small but significant decrease of the fdr with phylogenetic age of the rnaz hit.
CONCLUSIONS
the present computational survey of drosophilid genomes yields about  <dig>  <dig> high quality predictions.
taking into account the  false discovery rate of about 40%, this implies that at least some ten thousand loci in the drosophila genome show the hallmarks of stabilizing selection acting on rna structure, and hence are most likely functional at the rna level.
the elucidation of these functions, however, remains elusive in many cases.
here, we have studied a small subset in more detail.
almost  <dig> rnaz hits overlap with loci that are likely to be transcribed by pol iii, strongly suggesting that these are bona fide ncrnas.
using structural clustering, we discovered several groups of structural similar ncrna candidates in these regions.
this number of putative ncrnas and a regulatory rna element is not unexpected given that about  <dig>  <dig> high quality rnaz hits have been found by a similar procedure in a screen of mammalian genomes  <cit> , which was based on a comparable size of the input set comprising about  <dig> mb of the human genome and a similar number of putative ncrnas was reported using the scfg-based evofold approach  <cit> .
a comparison with the results from a similar rnaz screen of the human genome  <cit>  and with an analysis of encode regions  <cit> , shows many similarities and several striking differences.
we observe a smaller fraction of intronic and larger fraction of protein coding hits  in flies.
a comparison of the distances between rnaz hits and their nearest annotated protein coding sequence shows that structured rnas are concentrated much more strongly around known genes in flies than in human, even when accounting for the much more compact d. melanogaster genome.
this observation agrees with recent tiling array data  <cit>  which showed that a much smaller fraction of intergenic transcription is truly independent from surrounding protein coding genes in flies compared to human  <cit> .
the inventory of structurally conserved rnas is only a very small subset of the total non-coding transcriptional output, which covers most of the non-repetitive genome  <cit> .
the current computational approach relies on substantial sequence conservation.
indeed many of the known ncrnas that were missed in our survey were not in the input set.
in fact, rnaz explicitly requires two independent signals for stabilizing selection:  sequence conservation so that a good alignment can be computed as input, and  stabilizing selection on rna secondary structure in the presence of sequence variation.
rnaz hits are therefore subject to specific selection pressures that make it highly likely that rnaz predictions have distinctive biological function.
in contrast, it has been shown recently, that in some cases, such as the bithoraxoid ncrnas of the drosophila bithorax complex, ncrna transcription itself, acting in cis, represses a target gene   <cit> .
in such a scenario, however, we do not expect to observe high levels of sequence conservation of the non-coding transcripts or the tell-tale substitution patterns of conserved secondary structures.

 high-throughput transcriptome data obtained in particular using tiling arrays and cdna sequencing in conjunction with detailed functional studies of individual genes have profoundly changed our picture of eukaryotic gene regulation by emphasizing multiple regulatory layers, many of which involve non-protein-coding rnas. in contrast to protein-coding genes, however, ncrnas do not form a homogeneous group of transcripts but rather belong to a diverse array of classes with vastly different structures, functions, and evolutionary patterns. efficient computational methods have recently been developed to determine the genomic inventory of a large subgroup of ncrnas, namely those that exhibit evolutionarily conserved secondary structures. as stabilizing selection acts to preserve structure in the presence of sequence variation, these transcripts are very likely to have discernible biological function – as opposed to being a mere byproduct of transcriptional noise or gene regulation by transcriptional interference. the group of structured rnas that we are considering here consequently includes the classical families of small ncrnas as well as structured, usually regulatory, motifs associated with larger coding or non-coding transcripts, such as internal ribosomal entry sites, ire, and secis signals see e.g.. the rnaz approach has proven to produce rather high quality predictions. in particular, as part of the detailed analysis of the encode regions, the verification of many unannotated rnaz predictions by means of rt-pcr has been reported, and for a substantial fraction of rnaz predictions corroborating evidence from high-throughput experiments has been obtained. computational screens for structured rnas have been reported so far for mammalian, urochordate, nematode, and yeast genomes. however, no comprehensive analysis of structured ncrnas in insect genomes has been published so far, even though there is statistical evidence for an enrichment of structured rnas within highly conserved non-coding elements of drosophilids. drosophilids, which have been deeply sequenced by a consortium coordinated by the nhgri, provide an ideal model system for this task, since their evolutionary divergence is comparable to those of mammals. as a consequence, large portions of their genomes are alignable, while at the same time there is substantial sequence variation. both are necessary prerequisites for currently available ncrna detection tools. in addition to the statistical evidence for wide-spread structured rnas in insects, two recent genome-wide experimental studies provide evidence of a large reservoir of novel ncrnas in drosophila melanogaster: isogai et al. mapped trf and brf binding sites in the d. melanogaster genome and showed that, unlike most other eukaryotes, trf1/brf binding appears responsible for the initiation of all classes of polymerase-iii transcription. as the known pol iii transcripts are small ncrnas, their data suggests that drosophilids are likely to have a large set of previously unannotated small ncrnas. a large-scale tiling array study of transcription in the early development of d. melanogaster found that about 20% of the observed transcripts in d. melanogaster come from stand-alone intergenic or intronic sources and may constitute new types of rnas, including a substantial fraction of ncrnas.  we report here on a computational screen for structured rna motifs in drosophilids based on 12-species pecan alignments provided by the consortium. the detected rnaz hits are either independently transcribed non-coding rnas with evolutionarily conserved secondary structures, or they are structured elements that are parts of coding transcripts such as secis or ire elements. sensitivity and specificity overall, rnaz hits corresponding to roughly mb in the d. melanogaster genome show evidence of evolutionarily conserved rna secondary structure. about 20% of these overlap existing annotation. the loci of the high confidence set covers approximately mb of dna, see tab. in total, hits correspond to known non-coding rnas according to at least one source of annotation. tab. summarizes the recall of the screen on several "classical" ncrnas families. note that some classes of ncrnas were deliberately removed already in the pecan alignments, notably the 5s rrna sequences. we recovered 96% of the known d. melanogaster mirnas. a blast search of the drosophilid rnaz hits against the results of prior rnaz surveys of mammals, urochordates, and nematodes yielded the following pattern of conservation: trna hits and snrnas associated with the major spliceosome. furthermore, we recover the u6atac snrna and micrornas. in order to estimate the false discovery rate, we repeated the screen with shuffled alignments as described in. alignments are shuffled such that two alignment columns are swapped only if both their gap pattern and their sequence conservation pattern is the same. this amounts to a very "gentle" shuffling that in particular preserves pairwise sequence divergence within any given window. this gentle shuffling procedure may fail to remove the secondary structure signal in some cases because too few pairs of alignment columns satisfy the stringent conditions for shuffling. this is at least one reason why we observe hits in which true and shuffled screen intersect, including of the annotated d. melanogaster ncrnas, almost exclusively trnas. the estimated fdr of roughly 50% for p > and 40% for the high quality set in tab. should therefore be regarded as pessimistic estimates. the results of a second, more "vigorous" shuffling approach lead to much more optimistic estimates: shuffling of the columns without considering their sequence conservation or gap pattern reduces the estimated fdr by factor of to only a 1–2%. one may argue, of course, that shuffling columns independently will change the gap pattern of the alignment. hence, this procedure may well underestimate the fdr. the dramatic difference in the result highlights a general problem that so far has not been solved in a satisfactory way, namely how to systematically construct randomized alignments that preserve all correlation features of the genomic background except the one under consideration. one important feature which must be mentioned at this point is dinucleotide content. due to the stacking energy contributions in the folding model, dinucleotide content can affect folding energies and thus fdr estimates considerably. since there is still no way of randomizing alignments preserving dinucleotide content, we cannot control for this effect. however, we found that, in contrast to mammalian genomes, there is no strong dinucleotide bias in the genomic background of d. melanogaster that effects folding energies. therefore, our estimates from mononucleotide shuffled alignments will not differ dramatically from estimates one would obtain from controls with the same dinucleotide content. in contrast to most previous rnaz screens, we have not removed coding sequences from the input alignments. notably, hits for p > and hits for p > overlap with annotated coding regions, accounting for 19% and 13% of the rnaz hits, respectively. these fractions are much smaller than the expected fdrs; we therefore expect that most of these signals are indeed false positives. interestingly, if we base our analysis on the number of nucleotides that are predicted to lie in regions with conserved structures instead of counting the rnaz hits the estimates are reduced to 15%, and %, respectively. conversely, only 12% at p > and less than 4% at p > of the annotated coding regions are detected by rnaz. note that rnaz hits overlap more than one annotated coding region. the small percentage of rnaz hits in annotated cds indicates that even a possibly large number of unannotated coding sequences will not have a significant impact on the interpretation of the rnaz results in the sense that only a small fraction of the rnaz hits may be previously unannotated cds. to further corroborate this point we have computed the overlap of the rnaz predictions with various gene prediction tracks available in the ucsc table browser, yielding no significant increase in the number of rnaz hits located in putative cds: in total only and rnaz hits lie in regions with any evidence for coding capacity. genomic distribution the genomic distribution of structured rna candidates in d. melanogaster is comparable to the observations in previous rnaz-based screens, see fig. as in the encode data, the distribution of rnaz hits largely follows the patterns of sequence conservation. in the fly data, only 5'utrs show a substantial enrichment relative to the input data. in contrast, the largest enrichment in the human encode data was observed from 3'utrs. the most striking difference between fly and human data is that the relative fraction of both intronic rnaz hits and intronic sequence conservation is twice as large in human. in a recent article manak and colleagues describe widespread transcriptional activity in the d. melanogaster genome during timepoints of early embryonic development detected by genomic tiling arrays. when comparing the rnaz hits to this data, we identify and hits that overlap a transfrag in any of the timepoints. a comparison of the fractions of rnaz hits from normal and control screen which overlap transfrags in one, several or all timepoints yields, however, no significant enrichments. the distance distribution of intergenic rnaz hits reveals a striking difference between the situation in the human and the fly genome, fig. since the d. melanogaster genome is much more compact than the human one, we need to compare the distribution of the distances between rnaz hits and the nearest coding sequence relative to the length distribution of the intergenic regions. in fig. we plot the relative frequency of igr with a length exceeding a given distance d, and the relative frequency of rnaz hits with a distance larger than d from the nearest coding region. if intergenic rnaz hits are uniformly distributed within the igr, the distribution of rnaz-cds distances looks like the distribution of igr distances, just shifted to the left by a factor of indeed, this is observed in the human data, albeit the shift is a factor between and indicating that the placement of intergenic rnaz hits in human is nearly uniform, with a small tendency of avoiding the proximity of coding genes. in contrast, about 40% of the d. melanogaster rnaz hits in intergenic regions are located adjacent to coding sequences. this may indicate that current annotation of the fly genome lists boundaries of protein coding genes that systematically truncate the utrs. if this is the case, however, then we would have to interpret more than 15% of the total rnaz hits as located in utrs. our data could be explained if a situation similar to the minifly gene is prevalent in the fly: for this gene a recent study described several alternative poly-a sites and multiple small ncrnas that are processed from the alternative 3'utrs. at least one of these ncrnas is structured: the snorna h was also detected in our screen. in any case, the structured rnas by rnaz are on average much more closely linked to protein coding genes in flies than in human. on the other hand, a small fraction of the intergenic rnaz hits, i.e., the tail in fig. is located much further away from cds than expected for random placement. this suggests the existence of a distinct class of rnaz hits with a propensity for large igrs. most likely, these signals correspond to independently transcribed ncrnas. about 20% of the unannotated transcripts observed in d. melanogaster early development arise from stand-alone intergenic or intronic sources. only a relatively small fraction of the novel independent transcripts had intergenic origin. in comparison, more than 13% of the transcriptional output recorded by comparable methods from the encode regions has a distal intergenic source. this difference is in agreement with closer association of most rnaz hits with protein coding genes in the fly. further annotation of rnaz predictions in a recent study, isogai et al. identified trf and brf binding sites using high-resolution genome tiling microarrays and provided evidence that in drosophila the alternative trf1/brf complex appears responsible for the initiation of all known classes of pol iii transcription. at the p > significance level rnaz hits are about three-fold enriched in these regions. we have therefore analyzed the distribution of rnaz hits within the experimentally determined trf and brf binding regions. as reported in, most of the sites correspond to trnas, 7sl rnas, and a subset of snornas. in addition to these known ncrnas, the loci contain unannotated rnaz hits, which are prime candidates for novel pol iii transcripts. in order to identify putative micrornas, we screened all rnaz hits with rnamicro. this results in candidates, of which are unannotated so far. of these signals are located in annotated cds and are therefore most likely false positives, leaving plausible microrna candidates. the recent discovery of hundreds of new human micrornas that are not conserved beyond primates strongly suggests that "evolution of mirnas is an ongoing process and that along with ancient, highly conserved mirnas, there are a number of emerging mirnas". in the light of these data, a large number of drosophilid-specific micrornas does not come unexpected. using snoreport, rnaz hits are classified as putative box h/aca snornas, of which intersect with previously annotated snornas. taking into account that for only of the annotated snornas the annotation distinguishes between box h/aca, box c/d, and scarnas, the small overlap with the existing annotation is not surprising. again, recent experimental surveys in other species, including nematodes and mammals have discovered a substantial number of previously unannotated snornas in these species, suggesting that the current annotation of snornas in d. melanogaster is also far from complete. finally, rnaz hits have direct evidence for expression through ests that are not related to protein coding genes, i.e., through ests that do not intersect with the flybase, refseq, n-scan, genscan, human proteins gene prediction and mrna tracks of the ucsc table browser. structure-based clustering since the rnaz hits that overlap trf or brf binding regions are good candidates without annotation for bona fide ncrnas, we applied structure-based clustering to this small subset of our predictions to identify common secondary structures and, hence, putative novel functional rnas. the complete clustering tree as well as a table of the most prominent clusters is given in the additional file since all clusters have a mean pairwise identity less than 45%, structurally related candidates are typically highly diverged at sequence level. in fig. an example cluster of complex structures is given. clusters and have a structure with two stem loops in common. all consensus structures show compensatory mutations. fig. depicts a large cluster of simple hairpin structures. they show a relatively high structural conservation whereas the sequence similarity is small. phylogenetic distribution in order to study the phylogenetic distribution of the rnaz prediction we determine the last common ancestor for each rnaz hit that contains the corresponding sequence in the input alignment. fig. summarizes these results for both the true data and the "gentle" control screen. more than 50% of the rnaz hits are found only within the melanogaster subgroup. to interpret this result we compute the ratio of newly appearing rnaz hits and the branch length for each branch in the tree leading to d. melanogaster. we observe little variation in the data, with the exception of a reduced rate of innovation along the most recent branch. this reduction is, however, most likely a methodological artefact, since the pairwise mutation distances between d. melanogaster, d. simulans, and d. sechellia are only about and rnaz is known to be less sensitive for highly similar sequences. approximately 12% of the rnaz hits are conserved throughout all drosophilids. in comparison, a screen of vertebrate genomes found about 3% of mammalian rnaz candidates to be conserved throughout vertebrates. a comparison of true and shuffled screens furthermore indicates a small but significant decrease of the fdr with phylogenetic age of the rnaz hit.  the present computational survey of drosophilid genomes yields about high quality predictions. taking into account the false discovery rate of about 40%, this implies that at least some ten thousand loci in the drosophila genome show the hallmarks of stabilizing selection acting on rna structure, and hence are most likely functional at the rna level. the elucidation of these functions, however, remains elusive in many cases. here, we have studied a small subset in more detail. almost rnaz hits overlap with loci that are likely to be transcribed by pol iii, strongly suggesting that these are bona fide ncrnas. using structural clustering, we discovered several groups of structural similar ncrna candidates in these regions. this number of putative ncrnas and a regulatory rna element is not unexpected given that about high quality rnaz hits have been found by a similar procedure in a screen of mammalian genomes, which was based on a comparable size of the input set comprising about mb of the human genome and a similar number of putative ncrnas was reported using the scfg-based evofold approach. a comparison with the results from a similar rnaz screen of the human genome and with an analysis of encode regions, shows many similarities and several striking differences. we observe a smaller fraction of intronic and larger fraction of protein coding hits in flies. a comparison of the distances between rnaz hits and their nearest annotated protein coding sequence shows that structured rnas are concentrated much more strongly around known genes in flies than in human, even when accounting for the much more compact d. melanogaster genome. this observation agrees with recent tiling array data which showed that a much smaller fraction of intergenic transcription is truly independent from surrounding protein coding genes in flies compared to human. the inventory of structurally conserved rnas is only a very small subset of the total non-coding transcriptional output, which covers most of the non-repetitive genome. the current computational approach relies on substantial sequence conservation. indeed many of the known ncrnas that were missed in our survey were not in the input set. in fact, rnaz explicitly requires two independent signals for stabilizing selection: sequence conservation so that a good alignment can be computed as input, and stabilizing selection on rna secondary structure in the presence of sequence variation. rnaz hits are therefore subject to specific selection pressures that make it highly likely that rnaz predictions have distinctive biological function. in contrast, it has been shown recently, that in some cases, such as the bithoraxoid ncrnas of the drosophila bithorax complex, ncrna transcription itself, acting in cis, represses a target gene. in such a scenario, however, we do not expect to observe high levels of sequence conservation of the non-coding transcripts or the tell-tale substitution patterns of conserved secondary structures. 
a subset of rnaz predictions overlapping with trf and brf binding sites, which are plausible candidates of pol iii transcripts, have been studied in more detail. taking a pessimistically estimated false discovery rate of 40% into account, this implies that at least some ten thousand loci in the drosophila genome show the hallmarks of stabilizing selection action of rna structure, and hence are most likely functional at the rna level. the deep-sequencing of drosophilid species coordinated by the nhgri provides an ideal data set of comparative computational approaches to determine those genomic loci that code for evolutionarily conserved rna motifs. this class of loci includes the majority of the known small ncrnas as well as structured rna motifs in mrnas. one subclass consists of those rnas that require distinctive secondary structure motifs to exert their biological function and hence exhibit distinctive patterns of sequence conservation characteristic for positive selection on rna secondary structure. the intergenic rna structures, however, are concentrated much more closely around known protein-coding loci, suggesting that flies have significantly smaller complement of independent structured ncrnas compared to mammals. the statistical evaluation of the rnaz predictions in comparison with a similar analysis of vertebrate genomes shows that qualitatively similar fractions of structured rnas are found in introns, utrs, and intergenic regions.
 recent experimental and computational studies have provided overwhelming evidence for a plethora of diverse transcripts that are unrelated to protein-coding genes. one subclass consists of those rnas that require distinctive secondary structure motifs to exert their biological function and hence exhibit distinctive patterns of sequence conservation characteristic for positive selection on rna secondary structure. the deep-sequencing of drosophilid species coordinated by the nhgri provides an ideal data set of comparative computational approaches to determine those genomic loci that code for evolutionarily conserved rna motifs. this class of loci includes the majority of the known small ncrnas as well as structured rna motifs in mrnas. we report here on a genome-wide survey using rnaz.  we obtain high quality predictions among which we recover the majority of the known ncrnas. taking a pessimistically estimated false discovery rate of 40% into account, this implies that at least some ten thousand loci in the drosophila genome show the hallmarks of stabilizing selection action of rna structure, and hence are most likely functional at the rna level. a subset of rnaz predictions overlapping with trf and brf binding sites, which are plausible candidates of pol iii transcripts, have been studied in more detail. among these sequences we identify several "clusters" of ncrna candidates with striking structural similarities.  the statistical evaluation of the rnaz predictions in comparison with a similar analysis of vertebrate genomes shows that qualitatively similar fractions of structured rnas are found in introns, utrs, and intergenic regions. the intergenic rna structures, however, are concentrated much more closely around known protein-coding loci, suggesting that flies have significantly smaller complement of independent structured ncrnas compared to mammals. 