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Decreased Transcription Factor Binding Levels Nearby Primate Pseudogenes Suggest Regulatory Degeneration
- Source :
- Molecular Biology and Evolution
- Publication Year :
- 2016
- Publisher :
- Oxford University Press, 2016.
-
Abstract
- Characteristics of pseudogene degeneration at the coding level are well-known, such as a shift towards neutral rates of nonsynonymous substitutions and gain of frameshift mutations. In contrast, degeneration of pseudogene transcriptional regulation is not well understood. Here, we test two predictions of regulatory degeneration along the pseudogenized lineage: (1) decreased transcription factor binding and (2) accelerated evolution in putative cis-regulatory regions. We find evidence for decreased TF binding levels nearby two primate pseudogenes compared to functional liver genes. We also find evidence for pseudogene-lineage-specific relaxation of sequence constraint on a fragment of the promoter of the primate pseudogene urate oxidase (Uox) and a nearby cis-regulatory module (CRM). However, the majority of TF-bound sequences nearby pseudogenes do not show evidence for lineage-specific accelerated rates of evolution. We conclude that decreases in TF binding level could be a marker for regulatory degeneration, while sequence degeneration in most CRMs may be obscured by background rates of TF binding site turnover.
- Subjects :
- 0301 basic medicine
Nonsynonymous substitution
Primates
Lineage (genetic)
Pseudogene
0206 medical engineering
02 engineering and technology
Degeneration (medical)
Biology
Frameshift mutation
Evolution, Molecular
03 medical and health sciences
0302 clinical medicine
regulatory evolution
histone modifications
Genetics
Transcriptional regulation
Animals
Humans
Regulatory Elements, Transcriptional
neutral evolution
Molecular Biology
Transcription factor
Gene
Ecology, Evolution, Behavior and Systematics
Discoveries
030304 developmental biology
Regulation of gene expression
0303 health sciences
Models, Genetic
Sequence Analysis, DNA
Biological Evolution
ChIP-seq
030104 developmental biology
Gene Expression Regulation
Macaca
Sequence Alignment
020602 bioinformatics
030217 neurology & neurosurgery
pseudoenhancer
Pseudogenes
Protein Binding
Transcription Factors
Subjects
Details
- Language :
- English
- ISSN :
- 15371719 and 07374038
- Volume :
- 33
- Issue :
- 6
- Database :
- OpenAIRE
- Journal :
- Molecular Biology and Evolution
- Accession number :
- edsair.doi.dedup.....300b4db50975d32e989788fc8324efe8