Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons

被引：40

作者：

Dong, Xianjun ^{[1
,2
]}

Navratilova, Pavla ^{[2
]}

Fredman, David ^{[2
]}

Drivenes, Oyvind ^{[2
]}

Becker, Thomas S. ^{[2
]}

Lenhard, Boris ^{[1
,2
]}

机构：

[1] Univ Bergen, Computat Biol Unit, Bergen Ctr Computat Sci, N-5008 Bergen, Norway

[2] Univ Bergen, Sars Ctr Marine Mol Biol, N-5008 Bergen, Norway

来源：

NUCLEIC ACIDS RESEARCH | 2010年 / 38卷 / 04期

关键词：

CONSERVED NONCODING ELEMENTS; RNA SELECTION PRESSURE; ULTRACONSERVED ELEMENTS; MESSENGER-RNA; KA/KS RATIO; REGION; GENE; TRANSCRIPTION; ENHANCER; EXPRESSION;

D O I：

10.1093/nar/gkp1124

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：1071 / 1085

页数：15

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