ArticleGenome biology2012
Analysis of variation at transcription factor binding sites in Drosophila and humans.
Article in Genome biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers, 1 of them a synthesis that pooled it.
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Who cites it
59 citing papers in PubMed, 1 synthesis or guideline pooled it, 103 citations in OpenAlex.
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- Structural underpinnings of mutation rate variations in the human genome.Nucleic acids research · 2023Article
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- Evolution of transcription factor binding through sequence variations and turnover of binding sites.Genome research · 2022Article
- proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms.Nucleic acids research · 2022Article
- Genetic polymorphisms ofFrontiers in genetics · 2022Article
- Transcriptional enhancers and their communication with gene promoters.Cellular and molecular life sciences : CMLS · 2021Review
- A signature of Neanderthal introgression on molecular mechanisms of environmental responses.PLoS genetics · 2021Article
- MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function.Bioinformatics (Oxford, England) · 2020Article
- Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters.Nucleic acids research · 2020Article
- Using mechanistic models for the clinical interpretation of complex genomic variation.Scientific reports · 2019Article
- Serpent/dGATAb regulates Laminin B1 and Laminin B2 expression during Drosophila embryogenesis.Scientific reports · 2019Article
- Stable enhancers are active in development, and fragile enhancers are associated with evolutionary adaptation.Genome biology · 2019Article
- A resource of variant effect predictions of single nucleotide variants in model organisms.Molecular systems biology · 2018Article
Corrections and comments
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Authors and funding
10 authors at 4 institutions in 3 countries.
Funding
Abstract
backgroundAdvances in sequencing technology have boosted population genomics and made it possible to map the positions of transcription factor binding sites (TFBSs) with high precision. Here we investigate TFBS variability by combining transcription factor binding maps generated by ENCODE, modENCODE, our previously published data and other sources with genomic variation data for human individuals and Drosophila isogenic lines.
resultsWe introduce a metric of TFBS variability that takes into account changes in motif match associated with mutation and makes it possible to investigate TFBS functional constraints instance-by-instance as well as in sets that share common biological properties. We also take advantage of the emerging per-individual transcription factor binding data to show evidence that TFBS mutations, particularly at evolutionarily conserved sites, can be efficiently buffered to ensure coherent levels of transcription factor binding.
conclusionsOur analyses provide insights into the relationship between individual and interspecies variation and show evidence for the functional buffering of TFBS mutations in both humans and flies. In a broad perspective, these results demonstrate the potential of combining functional genomics and population genetics approaches for understanding gene regulation.
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Registered trials
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.