ArticleNucleic acids research2016
Modeling co-occupancy of transcription factors using chromatin features.
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 15 papers.
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Who cites it
15 citing papers in PubMed, 27 citations in OpenAlex.
- The combinatorial binding syntax of transcription factors in forebrain-specific enhancers.Biology open · 2025Article
- Role of primary aging hallmarks in Alzheimer´s disease.Theranostics · 2023Review
- Asymmetric Predictive Relationships Across Histone Modifications.Nature machine intelligence · 2022Article
- Co-occupancy identifies transcription factor co-operation for axon growth.Nature communications · 2021Article
- Evidence of widespread, independent sequence signature for transcription factor cobinding.Genome research · 2021Article
- Learning and interpreting the gene regulatory grammar in a deep learning framework.PLoS computational biology · 2020Article
- FOXA2 Is Required for Enhancer Priming during Pancreatic Differentiation.Cell reports · 2019Article
- KLF6 and STAT3 co-occupy regulatory DNA and functionally synergize to promote axon growth in CNS neurons.Scientific reports · 2018Article
- Integrating ChIP-seq with other functional genomics data.Briefings in functional genomics · 2018Review
- Identifying Transcriptional Regulatory Modules Among Different Chromatin States in Mouse Neural Stem Cells.Frontiers in genetics · 2018Article
- WHIRLY1 Occupancy Affects Histone Lysine Modification andFrontiers in plant science · 2018Article
- RPI-Bind: a structure-based method for accurate identification of RNA-protein binding sites.Scientific reports · 2017Article
- Heterogeneity of transcription factor binding specificity models within and across cell lines.Genome research · 2016Article
- Classification of Promoters Based on the Combination of Core Promoter Elements Exhibits Different Histone Modification Patterns.PloS one · 2016Article
- Epigenetics and Cellular Metabolism.Genetics & epigenetics · 2016Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Regulation of gene expression requires both transcription factor (TFs) and epigenetic modifications, and interplays between the two types of factors have been discovered. However study of relationships between chromatin features and TF-TF co-occupancy remains limited. Here, we revealed the relationship by first illustrating distinct profile patterns of chromatin features related to different binding events, including single TF binding and TF-TF co-occupancy of 71 TFs from five human cell lines. We further implemented statistical analyses to demonstrate the relationship by accurately predicting co-occupancy genome-widely using chromatin features including DNase I hypersensitivity, 11 histone modifications (HMs) and GC content. Remarkably, our results showed that the combination of chromatin features enables accurate predictions across the five cells. For individual chromatin features, DNase I enables high and consistent predictions. H3K27ac, H3K4me 2, H3K4me3 and H3K9ac are more reliable predictors than other HMs. Although the combination of 11 HMs achieves accurate predictions, their predictive ability varies considerably when a model obtained from one cell is applied to others, indicating relationship between HMs and TF-TF co-occupancy is cell type dependent. GC content is not a reliable predictor, but the addition of GC content to any other features enhances their predictive ability. Together, our results elucidate a strong relationship between TF-TF co-occupancy and chromatin features.
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