ArticleNucleic acids research2010
Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 54 citations in OpenAlex.
- CRM-TI: an enhanced pipeline for computationally assigning the target genes of cis-regulatory modules by considering comprehensive long-range regulation mechanisms.BioData mining · 2026Article
- Exonic enhancers are a widespread class of dual-function regulatory elements.Nature communications · 2026Article
- Review
- Characterization of Two Transposable Elements and an Ultra-Conserved Element Isolated in the Genome ofLife (Basel, Switzerland) · 2023Article
- A map of cis-regulatory modules and constituent transcription factor binding sites in 80% of the mouse genome.BMC genomics · 2022Article
- Using a Machine Learning Approach to Identify Low-Frequency and RareJID innovations : skin science from molecules to population health · 2021Article
- Structural and functional analysis of somatic coding and UTR indels in breast and lung cancer genomes.Scientific reports · 2021Article
- Mechanisms of enhancer action: the known and the unknown.Genome biology · 2021Review
- Fish-Ing for Enhancers in the Heart.International journal of molecular sciences · 2021Review
- Ancient duons may underpin spatial patterning of gene expression in CProceedings of the National Academy of Sciences of the United States of America · 2018Article
- Conserved non-coding elements: developmental gene regulation meets genome organization.Nucleic acids research · 2017Review
- Exonic enhancers: proceed with caution in exome and genome sequencing studies.Genome medicine · 2016Article
- Association of HOMER1 rs2290639 with suicide attempts in Hong Kong Chinese and the potentially functional role of this polymorphism.SpringerPlus · 2016Article
- Systematic dissection of coding exons at single nucleotide resolution supports an additional role in cell-specific transcriptional regulation.PLoS genetics · 2014Article
- Computational characterization of modes of transcriptional regulation of nuclear receptor genes.PloS one · 2014Article
- The mystery of extreme non-coding conservation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Review
- Chromatin and epigenetic features of long-range gene regulation.Nucleic acids research · 2013Review
- Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development.Nucleic acids research · 2013Article
- Article
- Hundreds of conserved non-coding genomic regions are independently lost in mammals.Nucleic acids research · 2012Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Using a comparative genomics approach to reconstruct the fate of genomic regulatory blocks (GRBs) and identify exonic remnants that have survived the disappearance of their host genes after whole-genome duplication (WGD) in teleosts, we discover a set of 38 candidate cis-regulatory coding exons (RCEs) with predicted target genes. These elements demonstrate evolutionary separation of overlapping protein-coding and regulatory information after WGD in teleosts. We present evidence that the corresponding mammalian exons are still under both coding and non-coding selection pressure, are more conserved than other protein coding exons in the host gene and several control sets, and share key characteristics with highly conserved non-coding elements in the same regions. Their dual function is corroborated by existing experimental data. Additionally, we show examples of human exon remnants stemming from the vertebrate 2R WGD. Our findings suggest that long-range cis-regulatory inputs for developmental genes are not limited to non-coding regions, but can also overlap the coding sequence of unrelated genes. Thus, exonic regulatory elements in GRBs might be functionally equivalent to those in non-coding regions, calling for a re-evaluation of the sequence space in which to look for long-range regulatory elements and experimentally test their activity.
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