ArticleNature communications2021
Chromatin information content landscapes inform transcription factor and DNA interactions.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Using a modular massively parallel reporter assay to discover context-dependent regulatory activity in type 2 diabetes-linked noncoding regions.HGG advances · 2026Article
- Many roads lead to a plant cistrome: mapping and interpreting transcription factor binding in plants.Genome biology · 2026Review
- Deciphering the 3D genome organization across species from Hi-C data.Nucleic acids research · 2026Article
- Cooperation of transposable elements to endow global networks of initiators of hybrid assembly pathways of endogenous multiprotein complexes.Frontiers in cellular and infection microbiology · 2026Article
- p53 regulates the expression of histone modifiers to restrict stemness and maintain differentiated luminal identity in breast cancer.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Genetic integration with cell-specific nucleosome positioning resolves causal relationships underlying chromatin accessibility profiles.bioRxiv : the preprint server for biology · 2025Article
- Massively parallel reporter assay reveals promoter-, position-, and strand-specific effects in transcription start sites.bioRxiv : the preprint server for biology · 2025Article
- Integrative single-cell multi-omics profiling of human pancreatic islets identifies T1D-associated genes and regulatory signals.Cell reports · 2025Article
- Extensive differential gene expression and regulation by sex in human skeletal muscle.Cell genomics · 2025Article
- Chromatin-dependent motif syntax defines differentiation trajectories.Molecular cell · 2025Article
- Stress during puberty and adulthood pregnancy impact histone acetylation regulators in the hypothalamus.Neuroscience · 2025Article
- H3K14la drives endothelial dysfunction in sepsis-induced ARDS by promoting SLC40A1/transferrin-mediated ferroptosis.MedComm · 2025Article
- Article
- ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants.bioRxiv : the preprint server for biology · 2025Article
- Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation.bioRxiv : the preprint server for biology · 2024Article
- Multiscale chromatin dynamics and high entropy in plant iPSC ancestors.Journal of cell science · 2024Article
- The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation.G3 (Bethesda, Md.) · 2024Article
- Regulatory networks driving expression of genes critical for glioblastoma are controlled by the transcription factor c-Jun and the pre-existing epigenetic modifications.Clinical epigenetics · 2023Article
- Nucleome programming is required for the foundation of totipotency in mammalian germline development.The EMBO journal · 2022Article
- Pseudogenes and Liquid Phase Separation in Epigenetic Expression.Frontiers in oncology · 2022Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Interactions between transcription factors and chromatin are fundamental to genome organization and regulation and, ultimately, cell state. Here, we use information theory to measure signatures of organized chromatin resulting from transcription factor-chromatin interactions encoded in the patterns of the accessible genome, which we term chromatin information enrichment (CIE). We calculate CIE for hundreds of transcription factor motifs across human samples and identify two classes: low and high CIE. The 10-20% of common and tissue-specific high CIE transcription factor motifs, associate with higher protein-DNA residence time, including different binding site subclasses of the same transcription factor, increased nucleosome phasing, specific protein domains, and the genetic control of both chromatin accessibility and gene expression. These results show that variations in the information encoded in chromatin architecture reflect functional biological variation, with implications for cell state dynamics and memory.
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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 Socratic graph.