Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development

By Adam Woolfe, Martin Goodson, D. Goode, Philip Snell, Gayle K McEwen, Tanya Vavouri, Sarah F. Smith, P. North, Heather Callaway, Krys Kelly and 6 more. PLoS Biology, 2004

1,008 citations recorded by the source corpus.

In addition to protein coding sequence, the human genome contains a significant amount of regulatory DNA, the identification of which is proving somewhat recalcitrant to both in silico and functional methods. An approach that has been used with some success is comparative sequence analysis, whereby equivalent genomic regions from different organisms are compared in order to identify both similarities and differences. In general, similarities in sequence between highly divergent organisms imply functional constraint. We have used a whole-genome comparison between humans and the pufferfish, Fugu rubripes, to identify nearly 1,400 highly conserved non-coding sequences. Given the evolutionary divergence between these species, it is likely that these sequences are found in, and furthermore are essential to, all vertebrates. Most, and possibly all, of these sequences are located in and around genes that act as developmental regulators. Some of these sequences are over 90% identical across more than 500 bases, being more highly conserved than coding sequence between these two species. Despite this, we cannot find any similar sequences in invertebrate genomes. In order to begin to functionally test this set of sequences, we have used a rapid in vivo assay system using zebrafish embryos that allows tissue-specific enhancer activity to be identified. Functional data is presented for highly conserved non-coding sequences associated with four unrelated developmental regulators (SOX21, PAX6, HLXB9, and SHH), in order to demonstrate the suitability of this screen to a wide range of genes and expression patterns. Of 25 sequence elements tested around these four genes, 23 show significant enhancer activity in one or more tissues. We have identified a set of non-coding sequences that are highly conserved throughout vertebrates. They are found in clusters across the human genome, principally around genes that are implicated in the regulation of development, including many transcription factors. These highly conserved non-coding sequences are likely to form part of the genomic circuitry that uniquely defines vertebrate development.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/59797cfe154705428e6f19d3e0a320144faca1da

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Citations in the corpus

28-way vertebrate alignment and conservation track in the UCSC Genome Browser. (2007, background): “As expected, the deeply conserved UCEs are near genes enriched in GO categories for transcription factors and developmental regulatory genes (Woolfe et al. 2005).”
High-Throughput Genomic Data in Systematics and Phylogenetics (2013, background): “UCEs are thought to be involved in gene regulation and development (e.g., Woolfe et al. 2005, Pennacchio et al. 2006) and to experience strong purifying selection (e.g., Katzman et al. 2007).”
Control of developmental regulators by Polycomb in human embryonic stem cells. (2006, background): “described by Woolfe and colleagues (Woolfe et al., 2005) were found to be associated with the SUZ12 bound developmental regulators (p-value 10 (14)).”
Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. (2012, background): “2010), and UCEs may be regulators and/or enhancers of gene expression (Woolfe et al. 2004; Sandelin et al. 2004; Pennacchio et al. 2006; Lindblad-Toh et al. 2011).”
Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains (2008, background): “Mammalian genomes contain ,200 large regions characterized by striking enrichment for highly conserved noncoding elements [30,31] and exceptionally low CpG divergence rates [32].”
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. (2008, background): “Previous studies have identified highly conserved elements within the promoters of important developmental proteincoding genes (Bejerano et al. 2004; Siepel et al. 2005; Woolfe et al. 2005).”
Transcriptional regulatory elements in the human genome. (2006, neutral): “First, although there is ample evidence that conserved regions do, indeed, often contain functional regulatory motifs (121, 139, 193), this correlation does not always hold (10), and other explanations for observed conservation have been suggested (26).”
Genomic Views of Distant-Acting Enhancers (2009, background): “The observation that DNA conservation identified many of these complex regulatory elements encouraged investigators to move away from blind studies of regions flanking genes of interest towards focusing specifically on non-coding sequences constrained across vertebrate species, culminating in whole-”
A bivalent chromatin structure marks key developmental genes in embryonic stem cells. (2006, background): “Recent studies have revealed that the most highly conserved noncoding elements (HCNEs) in mammalian genomes cluster within 200 HCNE-rich genomic loci, which include all four Hox clusters (Nobrega et al., 2003; Bejerano et al., 2004; Lindblad-Toh et al., 2005; Woolfe et al., 2005).”
The mammalian epigenome. (2007, background): “However, highly conserved elements in mammals are distributed across vast genomic regions much larger than the chromatin domains, and thus are likely to have additional functions (Lindblad-Toh et al., 2005; Woolfe et al., 2005).”
Distribution and intensity of constraint in mammalian genomic sequence. (2005, background): “…such as chicken (Hillier et al. 2004) and Fugu (Aparicio et al. 2002) may also uncover critically important functional elements in the human genome (Nobrega et al. 2003; Woolfe et al. 2004), these approaches will miss many elements, including all of those that specify unique mammalian traits.”
The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. (2006, background): “…of Air (a 108-kb polyadenylated, nonspliced ncRNA) transcription to an imprinting control element (ICE) and antisense transcription to the Igf2r promoter (Wutz et al. 2001; Zwart et al. 2001) may be similar to the relationship between Evf-2, the Dlx-5/6 enhancer, and the Dlx-6 promoter.”
Comparative Genomics (2007, positive): “Some of the DNA sequences that regulate genes encoding developmental regulatory proteins are conserved from mammals to fish, indicative of strong constraint (Nobrega et al. 2003; Woolfe et al. 2005).”