ArticleProceedings of the National Academy of Sciences of the United States of America2014
Transcription factor binding predicts histone modifications in human cell lines.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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Who cites it
76 citing papers in PubMed, 135 citations in OpenAlex.
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- Machine and Deep Learning Reveal Sequence Determinants Encoding Bivalent Histone Modifications.Communications biology · 2026Article
- An end-to-end generalizable deep learning framework to comprehensively analyze transcriptional regulation.Nature communications · 2026Article
- Chromatin Accessibility in Cancer: Biological Functions, Mechanisms, Therapeutic Potential, and Future Directions.MedComm · 2026Review
- mwHIT: accelerated and accurate histone modification imputation using multi-scale window attention.Frontiers in genetics · 2026Article
- Deciphering Sequence Determinants of Zygotic Genome Activation Genes: Insights From Machine Learning and the ZGAExplorer Platform.Cell proliferation · 2025Article
- Human herpesvirus 6B U65 binds to histone proteins and suppresses interferon production.Journal of virology · 2025Article
- Modelling transcription with explainable AI uncovers context-specific epigenetic gene regulation at promoters and gene bodies.PLoS genetics · 2025Article
- An automated ATAC-seq method reveals sequence determinants of transcription factor dose response in the open chromatin.bioRxiv : the preprint server for biology · 2025Article
- ABCB1 Gene Polymorphisms and Their Contribution to Cognitive Decline in Mild Cognitive Impairment: A Next-Generation Sequencing Study.The journals of gerontology. Series A, Biological sciences and medical sciences · 2025Article
- Prediction of gene expression using histone modification patterns extracted by Particle Swarm Optimization.Bioinformatics (Oxford, England) · 2025Article
- The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models.PLoS computational biology · 2025Article
- Virome-wide analysis of histone modification mimicry motifs carried by viral proteins.Virologica Sinica · 2024Article
- Hidden secrets of the cancer genome: unlocking the impact of non-coding mutations in gene regulatory elements.Cellular and molecular life sciences : CMLS · 2024Review
- Chromatin profiling reveals TFAP4 as a critical transcriptional regulator of bovine satellite cell differentiation.BMC genomics · 2024Article
- Bottom-up data integration in polymer models of chromatin organization.Biophysical journal · 2024Article
- PlantPAN 4.0: updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters.Nucleic acids research · 2024Article
- RNF40 epigenetically modulates glycolysis to support the aggressiveness of basal-like breast cancer.Cell death & disease · 2023Article
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16 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Gene expression in higher organisms is thought to be regulated by a complex network of transcription factor binding and chromatin modifications, yet the relative importance of these two factors remains a matter of debate. Here, we show that a computational approach allows surprisingly accurate prediction of histone modifications solely from knowledge of transcription factor binding both at promoters and at potential distal regulatory elements. This accuracy significantly and substantially exceeds what could be achieved by using DNA sequence as an input feature. Remarkably, we show that transcription factor binding enables strikingly accurate predictions across different cell lines. Analysis of the relative importance of specific transcription factors as predictors of specific histone marks recapitulated known interactions between transcription factors and histone modifiers. Our results demonstrate that reported associations between histone marks and gene expression may be indirect effects caused by interactions between transcription factors and histone-modifying complexes.
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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.