ArticleNucleic acids research2016
Maps of context-dependent putative regulatory regions and genomic signal interactions.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 12 citations in OpenAlex.
- Identification of mammalian transcription factors that bind to inaccessible chromatin.Nucleic acids research · 2023Article
- The ThioesteraseOmics : a journal of integrative biology · 2021Article
- Functional annotation of noncoding mutations in cancer.Life science alliance · 2021Article
- Multifaceted regulation of hepatic lipid metabolism by YY1.Life science alliance · 2021Article
- Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases.Scientific reports · 2019Article
- On the problem of confounders in modeling gene expression.Bioinformatics (Oxford, England) · 2019Review
- HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications.Bioinformatics (Oxford, England) · 2018Article
- Probing instructions for expression regulation in gene nucleotide compositions.PLoS computational biology · 2018Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene transcription is regulated mainly by transcription factors (TFs). ENCODE and Roadmap Epigenomics provide global binding profiles of TFs, which can be used to identify regulatory regions. To this end we implemented a method to systematically construct cell-type and species-specific maps of regulatory regions and TF-TF interactions. We illustrated the approach by developing maps for five human cell-lines and two other species. We detected ∼144k putative regulatory regions among the human cell-lines, with the majority of them being ∼300 bp. We found ∼20k putative regulatory elements in the ENCODE heterochromatic domains suggesting a large regulatory potential in the regions presumed transcriptionally silent. Among the most significant TF interactions identified in the heterochromatic regions were CTCF and the cohesin complex, which is in agreement with previous reports. Finally, we investigated the enrichment of the obtained putative regulatory regions in the 3D chromatin domains. More than 90% of the regions were discovered in the 3D contacting domains. We found a significant enrichment of GWAS SNPs in the putative regulatory regions. These significant enrichments provide evidence that the regulatory regions play a crucial role in the genomic structural stability. Additionally, we generated maps of putative regulatory regions for prostate and colorectal cancer human cell-lines.
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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 Socratic graph.