ArticleBMC genomics2013
Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 44 citations in OpenAlex.
- Article
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- Heat shock transcription factors demonstrate a distinct mode of interaction with mitotic chromosomes.Nucleic acids research · 2023Article
- RGMQL: scalable and interoperable computing of heterogeneous omics big data and metadata in R/Bioconductor.BMC bioinformatics · 2022Article
- Master lineage transcription factors anchor trans mega transcriptional complexes at highly accessible enhancer sites to promote long-range chromatin clustering and transcription of distal target genes.Nucleic acids research · 2021Article
- PRG2 and AQPEP are misexpressed in fetal membranes in placenta previa and percreta†.Biology of reproduction · 2021Article
- The latency-associated transcript locus of herpes simplex virus 1 is a virulence determinant in human skin.PLoS pathogens · 2020Article
- Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations.Genome research · 2020Article
- Functional dissection of the DORNRÖSCHEN-LIKE enhancer 2 during embryonic and phyllotactic patterning.Planta · 2020Article
- IGAP-integrative genome analysis pipeline reveals new gene regulatory model associated with nonspecific TF-DNA binding affinity.Computational and structural biotechnology journal · 2020Article
- Transcription factor Sp2 potentiates binding of the TALE homeoproteins Pbx1:Prep1 and the histone-fold domain protein Nf-y to composite genomic sites.The Journal of biological chemistry · 2018Article
- KLF6 and STAT3 co-occupy regulatory DNA and functionally synergize to promote axon growth in CNS neurons.Scientific reports · 2018Article
- Theoretical principles of transcription factor traffic on folded chromatin.Nature communications · 2018Article
- Article
- RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.Nucleic acids research · 2017Article
- Genome-wide identification and characterisation of HOT regions in the human genome.BMC genomics · 2016Article
- From milliseconds to lifetimes: tracking the dynamic behavior of transcription factors in gene networks.Trends in genetics : TIG · 2015Review
- Functional annotation of HOT regions in the human genome: implications for human disease and cancer.Scientific reports · 2015Article
- Dynamic switching of active promoter and enhancer domains regulates Tet1 and Tet2 expression during cell state transitions between pluripotency and differentiation.Molecular and cellular biology · 2015Article
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundHigh-occupancy target (HOT) regions are compact genome loci occupied by many different transcription factors (TFs). HOT regions were initially defined in invertebrate model organisms, and we here show that they are a ubiquitous feature of the human gene-regulation landscape.
resultsWe identified HOT regions by a comprehensive analysis of ChIP-seq data from 96 DNA-associated proteins in 5 human cell lines. Most HOT regions co-localize with RNA polymerase II binding sites, but many are not near the promoters of annotated genes. At HOT promoters, TF occupancy is strongly predictive of transcription preinitiation complex recruitment and moderately predictive of initiating Pol II recruitment, but only weakly predictive of elongating Pol II and RNA transcript abundance. TF occupancy varies quantitatively within human HOT regions; we used this variation to discover novel associations between TFs. The sequence motif associated with any given TF's direct DNA binding is somewhat predictive of its empirical occupancy, but a great deal of occupancy occurs at sites without the TF's motif, implying indirect recruitment by another TF whose motif is present.
conclusionsMammalian HOT regions are regulatory hubs that integrate the signals from diverse regulatory pathways to quantitatively tune the promoter for RNA polymerase II recruitment.
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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.