ArticleGenome research2006
Evolutionary turnover of mammalian transcription start sites.
Article in Genome research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- The emerging roles of long non-coding RNAs in the nervous system.Nature reviews. Neuroscience · 2025Review
- Roles of transposable elements and DNA methylation in the formation of CpG islands and CpG-depleted regulatory elements.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Article
- Quantification and modeling of turnover dynamics of de novo transcripts in Drosophila melanogaster.Nucleic acids research · 2024Article
- Evolution of tissue and developmental specificity of transcription start sites in Bos taurus indicus.Communications biology · 2021Article
- Locally acting transcription factors regulate p53-dependent cis-regulatory element activity.Nucleic acids research · 2020Article
- Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome.Genome research · 2018Article
- Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum.RNA biology · 2018Article
- Lineage-specific genomics: Frequent birth and death in the human genome: The human genome contains many lineage-specific elements created by both sequence and functional turnover.BioEssays : news and reviews in molecular, cellular and developmental biology · 2016Review
- Evolution of Epigenetic Regulation in Vertebrate Genomes.Trends in genetics : TIG · 2016Review
- Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites.The Plant cell · 2015Article
- The frequent evolutionary birth and death of functional promoters in mouse and human.Genome research · 2015Article
- Article
- Evidence for evolutionary and nonevolutionary forces shaping the distribution of human genetic variants near transcription start sites.PloS one · 2014Article
- Nucleosome positioning and kinetics near transcription-start-site barriers are controlled by interplay between active remodeling and DNA sequence.Nucleic acids research · 2014Article
- The transcription start site landscape of C. elegans.Genome research · 2013Article
- Transcription start site evolution in Drosophila.Molecular biology and evolution · 2013Article
- 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing.Nature protocols · 2012Article
- Aberrant transcription and post-transcriptional processing of hepatitis C virus non-structural genes in transgenic mice.Transgenic research · 2011Article
- Article
Corrections and comments
- Erratum issuedHayshizaki, Yoshihide [corrected to Hayashizaki, Yoshihide]
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alignments of homologous genomic sequences are widely used to identify functional genetic elements and study their evolution. Most studies tacitly equate homology of functional elements with sequence homology. This assumption is violated by the phenomenon of turnover, in which functionally equivalent elements reside at locations that are nonorthologous at the sequence level. Turnover has been demonstrated previously for transcription-factor-binding sites. Here, we show that transcription start sites of equivalent genes do not always reside at equivalent locations in the human and mouse genomes. We also identify two types of partial turnover, illustrating evolutionary pathways that could lead to complete turnover. These findings suggest that the signals encoding transcription start sites are highly flexible and evolvable, and have cautionary implications for the use of sequence-level conservation to detect gene regulatory elements.
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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.