BACKGROUND
most eukaryotic gene regulation occurs at the level of transcription  <cit> .
this form of regulation involves the interaction of transcription factors  with element and function specific dna sequences, referred to as cis-regulatory modules .
their modular organization allows for elaborate regulatory mechanisms and fine control of gene expression  <cit> .
evolutionary changes in crms have a profound effect on species divergence.
many studies suggest that species specific crms are the defining factor for species identity  <cit> .
differences in human and chimpanzee, for example, are almost completely due to changes in functional noncoding sequence  <cit> .
efforts to locate the “human gene” have only revealed differences in a small number of genes  <cit> .
moreover, comparisons of organisms at the extremes of eukaryotes show that the genes encoding tfs and signaling components  are largely conserved  <cit> .
taken together, this evidence suggests a hierarchical organization of regulatory networks.
modules at the top, performing essential upstream functions, span large evolutionary distances virtually unchanged, while lower level modules, involved in peripheral sub-networks, show a higher level of adaptation  <cit> .
under this model, part of the regulatory material must be under purifying selection and thus conserved between any two species of sufficiently small evolutionary divergence.
evidence of conservation of regulatory sequence among species has inspired a series of computational methods.
some of these methods use machine learning and phylogenetic profiling to discover crms , others use comparative analysis to identify genomic material under purifying evolutionary constraint as a representative of the functional genome .
at the same time, a number of experimental studies suggest that while sequence might encode enough information to drive tf binding  <cit> , the way this information is encoded is not trivial – similar sequence does not necessarily translate in similar function and vice versa.
for example, regulatory elements have been found to tolerate sequence rearrangements  <cit>  or even be under positive selection while maintaining the downstream regulatory machinery unchanged  <cit> .
recently, it was found that gata <dig> changes its motif preferences during cell differentiation  <cit> , serving as an example of tfs having multiple preferred motif sequences  <cit>  while maintaining a regulatory function.
both computational and experimental approaches have provided valuable insight into the regulatory portion of the genome, but they have limitations.
computational methods are biased toward well-annotated and evolutionarily conserved genomic regions, indeed comparative analyses based on evolutionary conservation alone ignore species-specific functional elements.
experimental approaches based on direct genome wide measurements of tfos are a powerful resource for the identification and analysis of tf binding sites.
however, the number of cell types and tfs assessed so far has often been limited.
with some studies pointing at conservation, others at divergence, and others yet at turnover of motifs and the importance of occupancy, the level of constraint on the crms is still an open question.
this apparently contradicting evidence can be reconciled by considering conservation as specific to the tf or the cell type.
in this study, we combined several types of function-associated datasets from a large number of tfs from a wide variety of tissues and cell lines in both mouse and human.
our main data source is chip-seq experiments performed by the mouse and human encode projects.
these data give evidence on the locations where tf have come close enough to the dna to cross-link in cells.
the question remains whether these locations, termed tfos  <cit> , could represent direct binding to a specific motif in the dna or co-association with another tf.
however, there is evidence that the tfos are active in assays for regulatory function at a far higher rate than non-occupied dna segments, or dna segments predicted as regulatory based on sequence motifs or conservation making them likely to have regulatory function.
we also used dnase i hypersensitive sites  generated by the human  <cit>  and the mouse encode  <cit>  projects.
dhs regions are markers of regulatory dna and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers and locus control regions.
we conduced a comparative analysis, by integrating tfos with human-mouse wga, gene annotations, and tf-gene associations.
we have also compiled the data and annotations derived from this study into a database to serve as a resource in exploring the relationship between sequence evolution and function of regulatory elements .
RESULTS
an alignment based map for human-mouse tfos
differences between present day genomes are the result of a series of evolutionary events originating on their most recent common ancestor  <cit> .
many of these events can be explained under probability models and represented in the form of wga .
sequence that has undergone a moderate number of evolutionary events will appear aligned, while highly divergent regions will usually be left un-aligned.
we used wga to obtain a consistent map for tfos across human and mouse ).
these alignments provide long, inferred homologous regions in the form of chains of gapless blocks.
they can account for inversions, translocations, duplications, large-scale deletions, and overlapping independent deletions.
we considered chained blastz  <cit>  alignments available from the ucsc browser  <cit>  and the 12-way mammalian wga from the epo pipeline  <cit>  available from ensembl version  <dig>  <cit> .
to choose the most appropriate alignment for our mappings we used several criteria: symmetry, coverage, feature enrichment, and other method specific properties.figure  <dig>
we built a one to one map between the human and mouse genomes from their wga.
the track diagram shows tfos  and how they map to the other species .
the thick part of the middle track is the mappable dna.
the features on the middle track can be mapped on the other species and are: seqcons if not overlapping features from the other species , or funccons or functactive otherwise .
the venn diagrams use the same color code to show the amount  of mappable material from one species to the other for dna sequence, tfos, and dhs.
for example, human tfos cover 121 mb of the human genome.
when mapped to mouse, these tfos cover 83 mb of the mouse genome and 12 mb of the sequence covered also by mouse tfos.
the diagram for dhs is labeled in a similar fashion.
the distribution of mappable tfos nucleotides across cell types.
the box-plot for each cell type summarizes the distribution of values for the fraction of nucleotides covered by tfos that can be mapped on the other species.
symmetry is important for unambiguously mapping features from one genome to the other and back.
the epo based map is inherently symmetric; we only need to extract human-mouse alignments.
we remove segmental duplications based on criteria such as the score or the length of the alignment to obtain an unambiguous map.
ucsc alignments, on the other hand, are based on blastz pairwise alignments, which are not symmetric – a human-mouse alignment is different from a mouse-human alignment in general.
however, it is possible to circumvent the problem by using a netting procedure and chaining again only the first layer in the resulting net.
this corresponds to heuristically cleaning overlapping chains based on their score.
the resulting reciprocal map is identical to the one derived from the mouse-human alignments at the cost of losing around 10% sequence coverage on both species  <cit> .
ucsc alignments align a slightly larger fraction of the mouse genome  to human.
however, epo alignments can assign a substantially higher amount of inserted mouse sequence .
in total  <dig> % of the mouse genome remains unmapped by ucsc alignments and  <dig> % by epo alignments.
next, we computed the number of features that each alignment could map on the other species for all available cell types in human and mouse.
we found that ucsc alignments mapped more features on the other species .
based on the above considerations, we adopted the reciprocal ucsc alignments.
the alignments and the comparative pipeline described here were adopted by the mouse encode consortium for the cross-species mapping of tfos.
function and sequence conservation of tfos
we processed tfos generated by chip-seq for  <dig> human and  <dig> mouse cell lines and tissues  <cit> , with a variable number of factors for each cell or tissue .
the data were generated by the human and the mouse encode projects.
the chip-seq experiments on mouse were conducted following the human encode guidelines  <cit> .
data processing, including irreproducible discovery rate  analysis, was done using a uniform data processing pipeline for both datasets.
elements recovered by the chip-seq experiments and the subsequent peak-calling pipeline were subjected to thresholds for false discovery rate at 1% and idr at 2%.
we then filtered these sets to retain only those tfos showing dhs enrichment, thereby increasing our confidence in the functional role of the filtered elements.
roughly  <dig> % of chip-seq peaks were filtered out from each species by dhs filtering.
the resulting data contained  <dig> and  <dig> elements covering  <dig>  mb and  <dig>  mb of the genome for human and mouse respectively .
the higher human coverage is due to the larger number of assays available in human.
we asked whether the selected putative regulatory material is significantly conserved.
at the sequence level, we find that the fraction of tfos intersecting homologous regions is higher than one would expect by chance  and  <dig> % ci:  with expected values of  <dig>  and  <dig>  for human and mouse respectively).
at the tf-binding activity level , mapped human and mouse tfos overlapped tfos on the other species more often than expected by chance  and  <dig> % ci:  with expected values  <dig>  and  <dig>  for human and mouse respectively).
significant conservation at the tf-binding activity level continues to hold largely for individual tfs-cell pairs .
these results indicate that most of these human and mouse regulatory regions have been under selective pressure both at the sequence and functional level.
despite the selective pressure on the tfos, the data suggest extensive evolution of the regulatory material between human and mouse.
on average  <dig> % and  <dig> % of tfos can be mapped on the other species resulting in a  <dig> % and  <dig> % of regulatory sequence coverage that is lineage-specific for human and mouse respectively  and additional file 1: s5-s12).
importantly, we found that the extent to which the remaining regulatory material is conserved varies substantially between species and among cell types and tfs.
the variability fits with previous studies on smaller numbers of tfs and cell types, which have emphasized both, conservation of tfos  <cit>  and extensive regulatory sequence evolution  <cit> .
binding signal differences between functionally and sequence conserved tfos
we focus our tfos comparative analysis on two tier  <dig> encode cell lines and their mouse analogs as chosen by the mouse encode consortium.
the data consist of  <dig> tfs from human chronic myelogenous leukemia cell line  and mouse erythroleukemia cell line ; and  <dig> tfs from lymphoblast cell lines  .
in total we have thus selected  <dig> and  <dig> tfos covering  <dig>  mb and  <dig>  mb on human and mouse respectively.
we mapped tfos of a species to homologous locations in the other and asked what function do those sites show.
the homologous site of a tfos can be:  not occupied by tfs, in which case we call the tfos seqcons;  repurposed, thus active in another cell or bound by another factor in the same cell type, in which case we call the tfos functactive; or  bound by the same factor on the same cell type, in which case the tfos is called functcons.
seqcons and functactive elements represent differences in human and mouse tf binding patterns due to tfos loss, gain, or both.
turnover occurs in the case of loss and gain of the same tfos at different, but nearby, positions.
however, more complex differences can arise when the loss of one tfos is followed by compensatory gains of tfos of other tfs.
for the pairs of analogous cell types in human and mouse, the largest proportion of tfos  are functactive, while the relative proportions of functcons and seqcons vary between cell types and species ).figure  <dig>
conservation and re-use of tfos.
the distribution of seqcons, functactive, and functcons regulatory elements summarized for all human mouse analogous cell lines .
in both cell lines, a small fraction of mappable regulatory elements is functcons .
a larger fraction  is functactive .
loss and gain of tf binding sites.
we used tfos in our data to discover tf binding sites  on both species.
we mapped human  tfbs to mouse  and computed their distance to the closest mouse  tfbs of the same tf on an analogous cell.
among these tfbs those with a positive distance but less than 150 bp contribute to the corresponding bar in the human  subplot.
in other words, each bar is the count of tfbs that were lost and gained within a 150 bp window of the original site.
reuse of functactive tfos between different cells and factors.
a point on the scatterplot indicates the number of tfos of the corresponding assay in the reference species that can be classified as functcons or functactive when considering a fixed size set of randomly chosen assays in the comparison species.
we performed multiple computations for each chosen size of such sets.
lines indicate the accumulated number of functcons, functactive, and seqcons tfos.
in this figure, about 93% of the  assay is covered by tfos from just 35% of the query assays .
conservation of occupancy in the other species was associated with peak signal strength for several cell type-tf pairs.
for example, binding signal on functcons or functactive elements was higher than that on seqcons elements for 59% and 50% of cell type-tf combinations for human and mouse respectively .
overall, functcons peak signal is on average  <dig>  and  <dig>  times larger than seqcons peak signal on human and mouse respectively .
tf binding site turnover and tfos repurposing
if seqcons and functactive elements are the result of turnover of tf binding sites  in human and mouse, then we should observe tfbs close to regions orthologous to tfbs on the other species.
we discovered tfbs using motif discovery and motif matching on tfos for both species and analyzed their alignment.
we found that for several tfs, seqcons tfbs map within 150 bp of a tfbs on the other species.
on average, 51% and 48% of seqcons tfbs have been subject to turnover in a 150 bp neighborhood for human and mouse respectively ).
the large number of functactive elements  and additional file 1: s <dig>  s16) suggests recycling of tfos among cells and tfs.
we examined this more carefully with a novel approach, based on the intuition that extensive recycling would allow any set of tfos in a comparison species to identify the occurrence of specific tfos in the reference species .
to conduct this analysis, we sampled  mapped tfos from k assays from the comparison species, took the union of these tfos, and computed the number of tfos a given assay  shares with this union.
the results strongly support extensive recycling of tfos.
specifically, we find that about 93% of the  assay is covered by tfos from just 35% of the query assays.
as k increases, coverage saturates  and additional file 1: s <dig>  s18).
this ability of different assays in the comparison species to capture tfos in the reference species is substantially different than what is obtained by simulating non-associated assays .
we tested the hypothesis that new tfos tend to arise over existing tfos – active in other cells or occupied by other factors.
under the null hypothesis, the fraction of functactive elements with respect to the non-functcons elements should not be significantly higher than the fraction of the genome that can turn into a functactive tfos, should a new tfos occur .
we found that fraction to be higher than expected  and  with expected values  <dig>  and  <dig>  for human and mouse respectively), suggesting that existing crms are sites where new tfbs are likely to arise.
turnover events or the appearance of novel tfbs lead to compositional changes in crms.
however, these changes do not always reflect downstream in, for example, the set of target genes.
following  <cit>  we extracted a set of tss-enhancer connections based on synchronized dhs activity during the transcription of a gene.
restricting on  <dig>  human-mouse orthologous genes  <cit> , we were thus able to define putative target genes for  <dig> and  <dig> tfos for human and mouse respectively.
we observe that, similarly to functcons tfos, about 39% and 43% of functactive tfos retained at least one putative target gene for human and mouse respectively.
furthermore, the amount at which the set of target genes is conserved across species is not significantly different between the two classes of tfos .
the example of the candidate enhancer linked to the acap <dig> gene in human illustrates this situation .
the dna segment in mouse that is orthologous to the human enhancer has been repurposed such that it binds different tfs, but the mouse acap <dig> gene is still the presumptive target.figure  <dig>
conservation of presumptive gene targets for a repurposed tfos.
we combined cross-species gene-gene and tfos-tfos associations and gene-tfos associations to determine whether the sets of target genes of functcons and functactive tfos differ significantly.
gene-gene association data are based on a set of orthologous genes between human and mouse produced by the mouse encode consortium, gene-tfos data are based on synchronized dhs activity during gene transcription  <cit> , and tfos-tfos associations are based on our cross-species map.
in the figure, we show a human tfos of mxi on k <dig>  associated with pusl <dig> and acap <dig>  this tfos is functactive, since its analogous location  in mouse is bound by other tfs on other cell types .
however, its analogous site in mouse is linked to gene acap <dig>  incidentally, acap <dig> and acap <dig> are orthologous and in our gene-gene association set.
the human tfos and its analogous site in mouse bind different tfs and are active in different cell types, but they share a target gene.
discussion
we reported on the construction and use of a map of functional elements between human and mouse based on wga.
this map is consistent and symmetrical in that it provides a one to one correspondence between genome elements in both directions.
furthermore, it constitutes an improvement over aligning tfos directly on the other species guided by gene orthology; this approach is likely to deteriorate with the distance of an element from the nearest gene with an ortholog on the other species.
using this mapping approach, we were able to recover, on average, 75% and 73% of tfos in the other species, of which 63% and 78% are bound by any tfs and 13% and 25% by the same tf for human and mouse respectively.
the rest of the regulatory material is species-specific either at the sequence or functional level and is likely to account for the phenotypic differences between human and mouse  <cit> .
however, some of the species-specific material retains target genes suggesting that crms buffer changes toward downstream regulation  <cit> .
one potential difficulty, which affects this analysis, is the variation that can be introduced by technical factors such as signal thresholding or by differences in the environment of the cells being compared.
by using data processed for reproducibility under the stringent standards developed by the human and mouse encode projects, restricting to regions overlapping dhs for greater confidence, considering the tf activity on analogous cell types, and employing statistical controls we hope to have ameliorated these issues.
previous studies have mapped the binding patterns of tfs between species, including mouse and human, by focusing on a single cell type and a few tfs .
while these important studies have revealed substantial divergence in the binding patterns of tfs between species, they do not explore functactive elements or related dynamics such as repurposing.
one important conclusion in our study is that the evolution of regulatory sequences varies considerably among tfs and cell types, and furthermore we document which tfos fall into the various evolutionary categories.
the traffic between noncoding functional and nonfunctional dna in a genome is two-way.
on the one hand, loss of a tfos can increase fitness, as dramatically illustrated by changes in the regulation of pitx <dig> in three-spined stickleback that lead to advantageous anatomical changes in a new environment.
on the other hand, new functional noncoding sequence can arise from nonfunctional sequence through turnover  <cit> .
the differences between the sizes of functactive and functcons pools suggests another source of functional noncoding material traffic, characterized by the exaptation of tfos into functional noncoding material with novel tf or cell type activity  <cit> .
with a partial catalog of regulatory elements it is hard to distinguish the newly created functional material from the exapted one.
however with ever-increasing numbers of experimental assays the picture should become more clear.
CONCLUSIONS
despite previous elegant studies, the level of constraint on crms remains controversial.
we provide further evidence that tfos are more conserved than random sequence and that conservation is cell and tf specific.
furthermore, we study the type of conservation of tfos and observe that  <dig> % and  <dig> % of tfos conserved at the sequence level for human and mouse respectively have been repurposed and are active in cell types or bind different tfs.
we show how this sequence makes a case for tfos exaptation into new function.
finally, we find that repurposing does not necessarily lead to changes in the tfos – target gene association.
comparative studies of crms involve a mapping strategy of regulatory elements, often by aligning elements or reads on both genomes, possibly guiding mapping with gene homologies.
we implemented a multiple wga based process for tfos mapping.
using multiple wga we should have a more sensitive and consistent mapping process.
importantly, the mapper can provide one-to-one mappings between species, which is very useful during analysis.

 most eukaryotic gene regulation occurs at the level of transcription. this form of regulation involves the interaction of transcription factors with element and function specific dna sequences, referred to as cis-regulatory modules. their modular organization allows for elaborate regulatory mechanisms and fine control of gene expression. evolutionary changes in crms have a profound effect on species divergence. many studies suggest that species specific crms are the defining factor for species identity. differences in human and chimpanzee, for example, are almost completely due to changes in functional noncoding sequence. efforts to locate the “human gene” have only revealed differences in a small number of genes. moreover, comparisons of organisms at the extremes of eukaryotes show that the genes encoding tfs and signaling components are largely conserved. taken together, this evidence suggests a hierarchical organization of regulatory networks. modules at the top, performing essential upstream functions, span large evolutionary distances virtually unchanged, while lower level modules, involved in peripheral sub-networks, show a higher level of adaptation. under this model, part of the regulatory material must be under purifying selection and thus conserved between any two species of sufficiently small evolutionary divergence. evidence of conservation of regulatory sequence among species has inspired a series of computational methods. some of these methods use machine learning and phylogenetic profiling to discover crms, others use comparative analysis to identify genomic material under purifying evolutionary constraint as a representative of the functional genome. at the same time, a number of experimental studies suggest that while sequence might encode enough information to drive tf binding, the way this information is encoded is not trivial – similar sequence does not necessarily translate in similar function and vice versa. for example, regulatory elements have been found to tolerate sequence rearrangements or even be under positive selection while maintaining the downstream regulatory machinery unchanged. recently, it was found that gata changes its motif preferences during cell differentiation, serving as an example of tfs having multiple preferred motif sequences while maintaining a regulatory function. both computational and experimental approaches have provided valuable insight into the regulatory portion of the genome, but they have limitations. computational methods are biased toward well-annotated and evolutionarily conserved genomic regions, indeed comparative analyses based on evolutionary conservation alone ignore species-specific functional elements. experimental approaches based on direct genome wide measurements of tfos are a powerful resource for the identification and analysis of tf binding sites. however, the number of cell types and tfs assessed so far has often been limited. with some studies pointing at conservation, others at divergence, and others yet at turnover of motifs and the importance of occupancy, the level of constraint on the crms is still an open question. this apparently contradicting evidence can be reconciled by considering conservation as specific to the tf or the cell type. in this study, we combined several types of function-associated datasets from a large number of tfs from a wide variety of tissues and cell lines in both mouse and human. our main data source is chip-seq experiments performed by the mouse and human encode projects. these data give evidence on the locations where tf have come close enough to the dna to cross-link in cells. the question remains whether these locations, termed tfos, could represent direct binding to a specific motif in the dna or co-association with another tf. however, there is evidence that the tfos are active in assays for regulatory function at a far higher rate than non-occupied dna segments, or dna segments predicted as regulatory based on sequence motifs or conservation making them likely to have regulatory function. we also used dnase i hypersensitive sites generated by the human and the mouse encode projects. dhs regions are markers of regulatory dna and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers and locus control regions. we conduced a comparative analysis, by integrating tfos with human-mouse wga, gene annotations, and tf-gene associations. we have also compiled the data and annotations derived from this study into a database to serve as a resource in exploring the relationship between sequence evolution and function of regulatory elements.  an alignment based map for human-mouse tfos differences between present day genomes are the result of a series of evolutionary events originating on their most recent common ancestor. many of these events can be explained under probability models and represented in the form of wga. sequence that has undergone a moderate number of evolutionary events will appear aligned, while highly divergent regions will usually be left un-aligned. we used wga to obtain a consistent map for tfos across human and mouse ). these alignments provide long, inferred homologous regions in the form of chains of gapless blocks. they can account for inversions, translocations, duplications, large-scale deletions, and overlapping independent deletions. we considered chained blastz alignments available from the ucsc browser and the 12-way mammalian wga from the epo pipeline available from ensembl version. to choose the most appropriate alignment for our mappings we used several criteria: symmetry, coverage, feature enrichment, and other method specific properties.figure we built a one to one map between the human and mouse genomes from their wga. the track diagram shows tfos and how they map to the other species. the thick part of the middle track is the mappable dna. the features on the middle track can be mapped on the other species and are: seqcons if not overlapping features from the other species, or funccons or functactive otherwise. the venn diagrams use the same color code to show the amount of mappable material from one species to the other for dna sequence, tfos, and dhs. for example, human tfos cover 121 mb of the human genome. when mapped to mouse, these tfos cover 83 mb of the mouse genome and 12 mb of the sequence covered also by mouse tfos. the diagram for dhs is labeled in a similar fashion. the distribution of mappable tfos nucleotides across cell types. the box-plot for each cell type summarizes the distribution of values for the fraction of nucleotides covered by tfos that can be mapped on the other species. symmetry is important for unambiguously mapping features from one genome to the other and back. the epo based map is inherently symmetric; we only need to extract human-mouse alignments. we remove segmental duplications based on criteria such as the score or the length of the alignment to obtain an unambiguous map. ucsc alignments, on the other hand, are based on blastz pairwise alignments, which are not symmetric – a human-mouse alignment is different from a mouse-human alignment in general. however, it is possible to circumvent the problem by using a netting procedure and chaining again only the first layer in the resulting net. this corresponds to heuristically cleaning overlapping chains based on their score. the resulting reciprocal map is identical to the one derived from the mouse-human alignments at the cost of losing around 10% sequence coverage on both species. ucsc alignments align a slightly larger fraction of the mouse genome to human. however, epo alignments can assign a substantially higher amount of inserted mouse sequence. in total % of the mouse genome remains unmapped by ucsc alignments and % by epo alignments. next, we computed the number of features that each alignment could map on the other species for all available cell types in human and mouse. we found that ucsc alignments mapped more features on the other species. based on the above considerations, we adopted the reciprocal ucsc alignments. the alignments and the comparative pipeline described here were adopted by the mouse encode consortium for the cross-species mapping of tfos. function and sequence conservation of tfos we processed tfos generated by chip-seq for human and mouse cell lines and tissues, with a variable number of factors for each cell or tissue. the data were generated by the human and the mouse encode projects. the chip-seq experiments on mouse were conducted following the human encode guidelines. data processing, including irreproducible discovery rate analysis, was done using a uniform data processing pipeline for both datasets. elements recovered by the chip-seq experiments and the subsequent peak-calling pipeline were subjected to thresholds for false discovery rate at 1% and idr at 2%. we then filtered these sets to retain only those tfos showing dhs enrichment, thereby increasing our confidence in the functional role of the filtered elements. roughly % of chip-seq peaks were filtered out from each species by dhs filtering. the resulting data contained and elements covering  mb and  mb of the genome for human and mouse respectively. the higher human coverage is due to the larger number of assays available in human. we asked whether the selected putative regulatory material is significantly conserved. at the sequence level, we find that the fraction of tfos intersecting homologous regions is higher than one would expect by chance and % ci: with expected values of and for human and mouse respectively). at the tf-binding activity level, mapped human and mouse tfos overlapped tfos on the other species more often than expected by chance and % ci: with expected values and for human and mouse respectively). significant conservation at the tf-binding activity level continues to hold largely for individual tfs-cell pairs. these results indicate that most of these human and mouse regulatory regions have been under selective pressure both at the sequence and functional level. despite the selective pressure on the tfos, the data suggest extensive evolution of the regulatory material between human and mouse. on average % and % of tfos can be mapped on the other species resulting in a % and % of regulatory sequence coverage that is lineage-specific for human and mouse respectively and additional file 1: s5-s12). importantly, we found that the extent to which the remaining regulatory material is conserved varies substantially between species and among cell types and tfs. the variability fits with previous studies on smaller numbers of tfs and cell types, which have emphasized both, conservation of tfos and extensive regulatory sequence evolution. binding signal differences between functionally and sequence conserved tfos we focus our tfos comparative analysis on two tier encode cell lines and their mouse analogs as chosen by the mouse encode consortium. the data consist of tfs from human chronic myelogenous leukemia cell line and mouse erythroleukemia cell line; and tfs from lymphoblast cell lines. in total we have thus selected and tfos covering  mb and  mb on human and mouse respectively. we mapped tfos of a species to homologous locations in the other and asked what function do those sites show. the homologous site of a tfos can be: not occupied by tfs, in which case we call the tfos seqcons; repurposed, thus active in another cell or bound by another factor in the same cell type, in which case we call the tfos functactive; or bound by the same factor on the same cell type, in which case the tfos is called functcons. seqcons and functactive elements represent differences in human and mouse tf binding patterns due to tfos loss, gain, or both. turnover occurs in the case of loss and gain of the same tfos at different, but nearby, positions. however, more complex differences can arise when the loss of one tfos is followed by compensatory gains of tfos of other tfs. for the pairs of analogous cell types in human and mouse, the largest proportion of tfos are functactive, while the relative proportions of functcons and seqcons vary between cell types and species ).figure conservation and re-use of tfos. the distribution of seqcons, functactive, and functcons regulatory elements summarized for all human mouse analogous cell lines. in both cell lines, a small fraction of mappable regulatory elements is functcons. a larger fraction is functactive. loss and gain of tf binding sites. we used tfos in our data to discover tf binding sites on both species. we mapped human tfbs to mouse and computed their distance to the closest mouse tfbs of the same tf on an analogous cell. among these tfbs those with a positive distance but less than 150 bp contribute to the corresponding bar in the human subplot. in other words, each bar is the count of tfbs that were lost and gained within a 150 bp window of the original site. reuse of functactive tfos between different cells and factors. a point on the scatterplot indicates the number of tfos of the corresponding assay in the reference species that can be classified as functcons or functactive when considering a fixed size set of randomly chosen assays in the comparison species. we performed multiple computations for each chosen size of such sets. lines indicate the accumulated number of functcons, functactive, and seqcons tfos. in this figure, about 93% of the assay is covered by tfos from just 35% of the query assays. conservation of occupancy in the other species was associated with peak signal strength for several cell type-tf pairs. for example, binding signal on functcons or functactive elements was higher than that on seqcons elements for 59% and 50% of cell type-tf combinations for human and mouse respectively. overall, functcons peak signal is on average and times larger than seqcons peak signal on human and mouse respectively. tf binding site turnover and tfos repurposing if seqcons and functactive elements are the result of turnover of tf binding sites in human and mouse, then we should observe tfbs close to regions orthologous to tfbs on the other species. we discovered tfbs using motif discovery and motif matching on tfos for both species and analyzed their alignment. we found that for several tfs, seqcons tfbs map within 150 bp of a tfbs on the other species. on average, 51% and 48% of seqcons tfbs have been subject to turnover in a 150 bp neighborhood for human and mouse respectively ). the large number of functactive elements and additional file 1: s s16) suggests recycling of tfos among cells and tfs. we examined this more carefully with a novel approach, based on the intuition that extensive recycling would allow any set of tfos in a comparison species to identify the occurrence of specific tfos in the reference species. to conduct this analysis, we sampled mapped tfos from k assays from the comparison species, took the union of these tfos, and computed the number of tfos a given assay shares with this union. the results strongly support extensive recycling of tfos. specifically, we find that about 93% of the assay is covered by tfos from just 35% of the query assays. as k increases, coverage saturates and additional file 1: s s18). this ability of different assays in the comparison species to capture tfos in the reference species is substantially different than what is obtained by simulating non-associated assays. we tested the hypothesis that new tfos tend to arise over existing tfos – active in other cells or occupied by other factors. under the null hypothesis, the fraction of functactive elements with respect to the non-functcons elements should not be significantly higher than the fraction of the genome that can turn into a functactive tfos, should a new tfos occur. we found that fraction to be higher than expected and with expected values and for human and mouse respectively), suggesting that existing crms are sites where new tfbs are likely to arise. turnover events or the appearance of novel tfbs lead to compositional changes in crms. however, these changes do not always reflect downstream in, for example, the set of target genes. following we extracted a set of tss-enhancer connections based on synchronized dhs activity during the transcription of a gene. restricting on human-mouse orthologous genes, we were thus able to define putative target genes for and tfos for human and mouse respectively. we observe that, similarly to functcons tfos, about 39% and 43% of functactive tfos retained at least one putative target gene for human and mouse respectively. furthermore, the amount at which the set of target genes is conserved across species is not significantly different between the two classes of tfos. the example of the candidate enhancer linked to the acap gene in human illustrates this situation. the dna segment in mouse that is orthologous to the human enhancer has been repurposed such that it binds different tfs, but the mouse acap gene is still the presumptive target.figure conservation of presumptive gene targets for a repurposed tfos. we combined cross-species gene-gene and tfos-tfos associations and gene-tfos associations to determine whether the sets of target genes of functcons and functactive tfos differ significantly. gene-gene association data are based on a set of orthologous genes between human and mouse produced by the mouse encode consortium, gene-tfos data are based on synchronized dhs activity during gene transcription, and tfos-tfos associations are based on our cross-species map. in the figure, we show a human tfos of mxi on k associated with pusl and acap this tfos is functactive, since its analogous location in mouse is bound by other tfs on other cell types. however, its analogous site in mouse is linked to gene acap incidentally, acap and acap are orthologous and in our gene-gene association set. the human tfos and its analogous site in mouse bind different tfs and are active in different cell types, but they share a target gene. discussion we reported on the construction and use of a map of functional elements between human and mouse based on wga. this map is consistent and symmetrical in that it provides a one to one correspondence between genome elements in both directions. furthermore, it constitutes an improvement over aligning tfos directly on the other species guided by gene orthology; this approach is likely to deteriorate with the distance of an element from the nearest gene with an ortholog on the other species. using this mapping approach, we were able to recover, on average, 75% and 73% of tfos in the other species, of which 63% and 78% are bound by any tfs and 13% and 25% by the same tf for human and mouse respectively. the rest of the regulatory material is species-specific either at the sequence or functional level and is likely to account for the phenotypic differences between human and mouse. however, some of the species-specific material retains target genes suggesting that crms buffer changes toward downstream regulation. one potential difficulty, which affects this analysis, is the variation that can be introduced by technical factors such as signal thresholding or by differences in the environment of the cells being compared. by using data processed for reproducibility under the stringent standards developed by the human and mouse encode projects, restricting to regions overlapping dhs for greater confidence, considering the tf activity on analogous cell types, and employing statistical controls we hope to have ameliorated these issues. previous studies have mapped the binding patterns of tfs between species, including mouse and human, by focusing on a single cell type and a few tfs. while these important studies have revealed substantial divergence in the binding patterns of tfs between species, they do not explore functactive elements or related dynamics such as repurposing. one important conclusion in our study is that the evolution of regulatory sequences varies considerably among tfs and cell types, and furthermore we document which tfos fall into the various evolutionary categories. the traffic between noncoding functional and nonfunctional dna in a genome is two-way. on the one hand, loss of a tfos can increase fitness, as dramatically illustrated by changes in the regulation of pitx in three-spined stickleback that lead to advantageous anatomical changes in a new environment. on the other hand, new functional noncoding sequence can arise from nonfunctional sequence through turnover. the differences between the sizes of functactive and functcons pools suggests another source of functional noncoding material traffic, characterized by the exaptation of tfos into functional noncoding material with novel tf or cell type activity. with a partial catalog of regulatory elements it is hard to distinguish the newly created functional material from the exapted one. however with ever-increasing numbers of experimental assays the picture should become more clear.  despite previous elegant studies, the level of constraint on crms remains controversial. we provide further evidence that tfos are more conserved than random sequence and that conservation is cell and tf specific. furthermore, we study the type of conservation of tfos and observe that % and % of tfos conserved at the sequence level for human and mouse respectively have been repurposed and are active in cell types or bind different tfs. we show how this sequence makes a case for tfos exaptation into new function. finally, we find that repurposing does not necessarily lead to changes in the tfos – target gene association. comparative studies of crms involve a mapping strategy of regulatory elements, often by aligning elements or reads on both genomes, possibly guiding mapping with gene homologies. we implemented a multiple wga based process for tfos mapping. using multiple wga we should have a more sensitive and consistent mapping process. importantly, the mapper can provide one-to-one mappings between species, which is very useful during analysis. 
this sequence, fueled by turnover events, provides a strong case for exaptation in regulatory elements. we compared transcription factor occupied segments for human and mouse tfs in human and mouse cell types and tissues from the human and the mouse encode projects. our analysis shows that tfos are under evolutionary constraint, but a substantial portion of the tfos does not have a homologous sequence on the other species; this portion varies among cell types and tfs. we mapped regulatory sequences from an extensive number of tfs and cell types between human and mouse using wga. a comparative analysis of this correspondence unveiled the extent of the shared regulatory sequence across tfs and cell types under study. despite tfos repurposing, we did not find substantial changes in their predicted target genes, suggesting that crms buffer evolutionary events allowing little or no change in the tfos – target gene associations. however, % and % is repurposed such that it binds the same tf in different cells or different tfs in the same cells. these events suggest exaptation of some functional regulatory sequences into new function. importantly, a large part of the shared regulatory sequence is repurposed on the other species. mouse encoderegulatory sequencescomparative genomicsissue-copyright-statement© the author 2015 we based the map between human and mouse tfos on a one-to-one nucleotide cross-species mapper, bnmapper, that utilizes whole genome alignments.
 because species-specific gene expression is driven by species-specific regulation, understanding the relationship between sequence and function of the regulatory regions in different species will help elucidate how differences among species arise. despite active experimental and computational research, relationships among sequence, conservation, and function are still poorly understood.  we compared transcription factor occupied segments for human and mouse tfs in human and mouse cell types and tissues from the human and the mouse encode projects. we based the map between human and mouse tfos on a one-to-one nucleotide cross-species mapper, bnmapper, that utilizes whole genome alignments. our analysis shows that tfos are under evolutionary constraint, but a substantial portion of the tfos does not have a homologous sequence on the other species; this portion varies among cell types and tfs. furthermore, % and % of the homologous tfos sequence shows binding activity on the other species for human and mouse respectively. however, % and % is repurposed such that it binds the same tf in different cells or different tfs in the same cells. remarkably, within the set of repurposed tfos, the corresponding genome regions in the other species are preferred locations of novel tfos. these events suggest exaptation of some functional regulatory sequences into new function. despite tfos repurposing, we did not find substantial changes in their predicted target genes, suggesting that crms buffer evolutionary events allowing little or no change in the tfos – target gene associations. thus, the small portion of tfos with strictly conserved occupancy underestimates the degree of conservation of regulatory interactions.  we mapped regulatory sequences from an extensive number of tfs and cell types between human and mouse using wga. a comparative analysis of this correspondence unveiled the extent of the shared regulatory sequence across tfs and cell types under study. importantly, a large part of the shared regulatory sequence is repurposed on the other species. this sequence, fueled by turnover events, provides a strong case for exaptation in regulatory elements. electronic supplementary material the online version of this article contains supplementary material, which is available to authorized users. keywords mouse encoderegulatory sequencescomparative genomicsissue-copyright-statement© the author 2015 