ArticleNucleic acids research2019
HOT or not: examining the basis of high-occupancy target regions.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 75 citations in OpenAlex.
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- Mixing features of transcription factors and genes enable accurate prediction of gene regulation relationships for unknown transcription factors.NAR genomics and bioinformatics · 2026Article
- Beyond blacklists: a critical assessment of exclusion set generation strategies and alternative approaches.Bioinformatics (Oxford, England) · 2026Article
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- Functional characteristics and computational model of abundant hyperactive loci in the human genome.eLife · 2024Article
- A Compendium of G-Flipon Biological Functions That Have Experimental Validation.International journal of molecular sciences · 2024Review
- Overlooked poor-quality patient samples in sequencing data impair reproducibility of published clinically relevant datasets.Genome biology · 2024Article
- Functional characteristics and computational model of abundant hyperactive loci in the human genome.bioRxiv : the preprint server for biology · 2024Article
- Multiomic profiling of transcription factor binding and function in human brain.Nature neuroscience · 2024Article
- Modeling 0.6 million genes for the rational design of functionalProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Analysis of REST binding sites with canonical and non-canonical motifs in human cell lines.BMC medical genomics · 2024Article
- Less-is-more: selecting transcription factor binding regions informative for motif inference.Nucleic acids research · 2024Article
- Binding profiles for 954 Drosophila andbioRxiv : the preprint server for biology · 2024Article
- Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells.Genome research · 2023Article
- Identification of transcription factor high accumulation DNA zones.BMC bioinformatics · 2023Article
- Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes.Genome research · 2023Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-occupancy target (HOT) regions are segments of the genome with unusually high number of transcription factor binding sites. These regions are observed in multiple species and thought to have biological importance due to high transcription factor occupancy. Furthermore, they coincide with house-keeping gene promoters and consequently associated genes are stably expressed across multiple cell types. Despite these features, HOT regions are solely defined using ChIP-seq experiments and shown to lack canonical motifs for transcription factors that are thought to be bound there. Although, ChIP-seq experiments are the golden standard for finding genome-wide binding sites of a protein, they are not noise free. Here, we show that HOT regions are likely to be ChIP-seq artifacts and they are similar to previously proposed 'hyper-ChIPable' regions. Using ChIP-seq data sets for knocked-out transcription factors, we demonstrate presence of false positive signals on HOT regions. We observe sequence characteristics and genomic features that are discriminatory of HOT regions, such as GC/CpG-rich k-mers, enrichment of RNA-DNA hybrids (R-loops) and DNA tertiary structures (G-quadruplex DNA). The artificial ChIP-seq enrichment on HOT regions could be associated to these discriminatory features. Furthermore, we propose strategies to deal with such artifacts for the future ChIP-seq studies.
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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.