Comparative genomics using Fugu reveals insights into regulatory subfunctionalization

Fish-mammal genomic alignments were used to compare over 800 conserved non-coding elements that associate with genes that have undergone fish-specific duplication and retention, revealing a pattern of element retention and loss between paralogs indicative of subfunctionalization

Genomic features defining exonic variants that modulate splicing

A comparative analysis of SNPs and their exonic and intronic environments identifies the features predictive of splice affecting variants

CONDOR: a database resource of developmentally associated conserved non-coding elements

<p>Abstract</p> <p>Background</p> <p>Comparative genomics is currently one of the most popular approaches to study the regulatory architecture of vertebrate genomes. Fish-mammal genomic comparisons have proved powerful in identifying conserved non-coding elements likely to be distal <it>cis-</it>regulatory modules such as enhancers, silencers or insulators that control the expression of genes involved in the regulation of early development. The scientific community is showing increasing interest in characterizing the function, evolution and language of these sequences. Despite this, there remains little in the way of user-friendly access to a large dataset of such elements in conjunction with the analysis and the visualization tools needed to study them.</p> <p>Description</p> <p>Here we present CONDOR (COnserved Non-coDing Orthologous Regions) available at: <url>http://condor.fugu.biology.qmul.ac.uk</url>. In an interactive and intuitive way the website displays data on > 6800 non-coding elements associated with over 120 early developmental genes and conserved across vertebrates. The database regularly incorporates results of ongoing <it>in vivo </it>zebrafish enhancer assays of the CNEs carried out in-house, which currently number ~100. Included and highlighted within this set are elements derived from duplication events both at the origin of vertebrates and more recently in the teleost lineage, thus providing valuable data for studying the divergence of regulatory roles between paralogs. CONDOR therefore provides a number of tools and facilities to allow scientists to progress in their own studies on the function and evolution of developmental <it>cis</it>-regulation.</p> <p>Conclusion</p> <p>By providing access to data with an approachable graphics interface, the CONDOR database presents a rich resource for further studies into the regulation and evolution of genes involved in early development.</p

Early Evolution of Conserved Regulatory Sequences Associated with Development in Vertebrates

Comparisons between diverse vertebrate genomes have uncovered thousands of highly conserved non-coding sequences, an increasing number of which have been shown to function as enhancers during early development. Despite their extreme conservation over 500 million years from humans to cartilaginous fish, these elements appear to be largely absent in invertebrates, and, to date, there has been little understanding of their mode of action or the evolutionary processes that have modelled them. We have now exploited emerging genomic sequence data for the sea lamprey, Petromyzon marinus, to explore the depth of conservation of this type of element in the earliest diverging extant vertebrate lineage, the jawless fish (agnathans). We searched for conserved non-coding elements (CNEs) at 13 human gene loci and identified lamprey elements associated with all but two of these gene regions. Although markedly shorter and less well conserved than within jawed vertebrates, identified lamprey CNEs are able to drive specific patterns of expression in zebrafish embryos, which are almost identical to those driven by the equivalent human elements. These CNEs are therefore a unique and defining characteristic of all vertebrates. Furthermore, alignment of lamprey and other vertebrate CNEs should permit the identification of persistent sequence signatures that are responsible for common patterns of expression and contribute to the elucidation of the regulatory language in CNEs. Identifying the core regulatory code for development, common to all vertebrates, provides a foundation upon which regulatory networks can be constructed and might also illuminate how large conserved regulatory sequence blocks evolve and become fixed in genomic DNA

VISTA plot of an MLAGAN alignment of orthologous regions surrounding two co-orthologs in (Fr) and in chicken (Gg), rat (Rn) and human

<p><b>Copyright information:</b></p><p>Taken from "Comparative genomics using reveals insights into regulatory subfunctionalization"</p><p>Genome Biology 2007;8(4):R53-R53.</p><p>Published online 11 Apr 2007</p><p>PMCID:PMC1896008.</p><p></p> The baseline is 268 kb of human sequence. Conservation between human and each sequence is shown as a peak. Peaks that represent conservation in a non-coding region of at least 65% over 40 bp are shaded pink with coding exons shaded purple and peaks located within untranslated regions shaded light-blue. All CNEs conserved in at least one of the co-orthologs are color-coded. CNEs in both co-orthologs that overlap the same region in human are shaded yellow while CNEs that are 'distinct' (or conserved solely) in are shaded red and CNEs distinct to are shaded green. Peaks marked with a double-headed arrow are conserved in in the opposite orientation (and therefore do not show up in the VISTA plot). A number of the CNEs around are also duplicated CNEs (dCNEs) that are located elsewhere in the genome in the vicinity of paralogs. CNEs marked with an orange box have another dCNE family member in the vicinity of and the CNE marked with a blue box has a dCNE family member conserved upstream of

Proportion of each CNE sequence that overlaps the counterpart co-ortholog CNE

<p><b>Copyright information:</b></p><p>Taken from "Comparative genomics using reveals insights into regulatory subfunctionalization"</p><p>Genome Biology 2007;8(4):R53-R53.</p><p>Published online 11 Apr 2007</p><p>PMCID:PMC1896008.</p><p></p> Main graph: for each overlapping pair of co-orthologous CNEs (involving just two sequences), the proportion of the full length of each CNE (P1-P2) made up by the overlap was calculated using the human sequence as the reference. The larger of the two proportions was always plotted as P1 to simplify analysis. Inset bar chart: summary of the number of overlapping CNE pairs falling into three main proportion categories: P1 ≥ 0.8, P2 ≥ 0.8 - pairs that overlapped over the majority of both elements, suggesting little evolution of element length since duplication; P1 ≥ 0.8, P2 < 0.8 - pairs that have undergone significant degeneration in element length in one of the copies compared to its counterpart; P1 < 0.8, P2 < 0.8 - pairs that have undergone a level of degeneration in element length in both copies at their edges

Significant change in element length and substitution rate in overlapping CNEs upstream of and

<p><b>Copyright information:</b></p><p>Taken from "Comparative genomics using reveals insights into regulatory subfunctionalization"</p><p>Genome Biology 2007;8(4):R53-R53.</p><p>Published online 11 Apr 2007</p><p>PMCID:PMC1896008.</p><p></p> CNEs (filled blue boxes) were identified around each co-ortholog (A1, top) and (A2, bottom) (gene exons are shown in the coding sequence (CDS) track as filled red boxes). The scale at the top represents positions along the sequence used in the multiple alignment. Two CNEs, highlighted in pink boxes, one upstream of (CRCNEAC00031954 [53], referred to as CNE_A1) and one upstream of (CRCNEAC00032205 [53], referred to as CNE_A2) are conserved to part of the same sequence in human upstream of . The overlap region is 126 bp in length and encompasses all of the CNE_A2 but only 35% of CNE_A1 (which is 360 bp long), indicating a significant loss of element length in CNE_A2. A relative rate test of the CNEs across the overlapping region using human as the outgroup reveals a highly significant number of independent substitutions (26) in CNE_A2 with no independent substitutions in CNE_A1 (< 0.001). This suggests CNE_A1 is likely to have retained the ancestral function while CNE_A2 may have evolved to have a different function