ArticleGenome biology and evolution2014
Impacts of pretranscriptional DNA methylation, transcriptional transcription factor, and posttranscriptional microRNA regulations on protein evolutionary rate.
Article in Genome biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
19 citing papers in PubMed, 26 citations in OpenAlex.
- Review
- Histone H3K27 Methylation Perturbs Transcriptional Robustness and Underpins Dispensability of Highly Conserved Genes in Fungi.Molecular biology and evolution · 2022Article
- Genome-Wide DNA Methylation Signatures Predict the Early Asymptomatic Doxorubicin-Induced Cardiotoxicity in Breast Cancer.Cancers · 2021Article
- Molecular Profiling of DNA Methylation and Alternative Splicing of Genes in Skeletal Muscle of Obese Rabbits.Current issues in molecular biology · 2021Article
- A FITM1-Related Methylation Signature Predicts the Prognosis of Patients With Non-Viral Hepatocellular Carcinoma.Frontiers in genetics · 2020Article
- A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations.Genome research · 2019Article
- Demethylation and microRNA differential expression regulate plasma-induced improvement of chicken sperm quality.Scientific reports · 2019Article
- Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease.PloS one · 2018Article
- Body-hypomethylated human genes harbor extensive intragenic transcriptional activity and are prone to cancer-associated dysregulation.Nucleic acids research · 2017Article
- Extensive ceRNA-ceRNA interaction networks mediated by miRNAs regulate development in multiple rhesus tissues.Nucleic acids research · 2016Article
- Complex Patterns of Association between Pleiotropy and Transcription Factor Evolution.Genome biology and evolution · 2016Article
- Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns.BMC genomics · 2016Article
- Genome-wide differential expression of genes and small RNAs in testis of two different porcine breeds and at two different ages.Scientific reports · 2016Article
- Effects of DNA Methylation and Chromatin State on Rates of Molecular Evolution in Insects.G3 (Bethesda, Md.) · 2015Article
- DNA Methylation in Basal Metazoans: Insights from Ctenophores.Integrative and comparative biology · 2015Review
- DNA Methylation within Transcribed Regions.Plant physiology · 2015Review
- Determinants of the rate of protein sequence evolution.Nature reviews. Genetics · 2015Review
- Apparent microRNA-Target-specific Histone Modification in Mammalian Spermatogenesis.Evolutionary bioinformatics online · 2015Article
- The evolution of the coding exome of the Arabidopsis species--the influences of DNA methylation, relative exon position, and exon length.BMC evolutionary biology · 2014Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene expression is largely regulated by DNA methylation, transcription factor (TF), and microRNA (miRNA) before, during, and after transcription, respectively. Although the evolutionary effects of TF/miRNA regulations have been widely studied, evolutionary analysis of simultaneously accounting for DNA methylation, TF, and miRNA regulations and whether promoter methylation and gene body (coding regions) methylation have different effects on the rate of gene evolution remain uninvestigated. Here, we compared human-macaque and human-mouse protein evolutionary rates against experimentally determined single base-resolution DNA methylation data, revealing that promoter methylation level is positively correlated with protein evolutionary rates but negatively correlated with TF/miRNA regulations, whereas the opposite was observed for gene body methylation level. Our results showed that the relative importance of these regulatory factors in determining the rate of mammalian protein evolution is as follows: Promoter methylation ≈ miRNA regulation > gene body methylation > TF regulation, and further indicated that promoter methylation and miRNA regulation have a significant dependent effect on protein evolutionary rates. Although the mechanisms underlying cooperation between DNA methylation and TFs/miRNAs in gene regulation remain unclear, our study helps to not only illuminate the impact of these regulatory factors on mammalian protein evolution but also their intricate interaction within gene regulatory networks.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.