ArticleGenome research2012
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 554 papers, 1 of them a synthesis that pooled it.
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Who cites it
554 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Identification of a novel genetic locus associated with immune-mediated thrombotic thrombocytopenic purpura.Haematologica · 2022Pooled it
- A transcription factor by any other name - function beyond DNA binding and transactivation.EMBO reports · 2026Review
- Functional Annotation of GWAS Loci Using Public Transcriptome and Epigenome Datasets Reveals Non-Coding Genes and Regulatory Elements Which May Contribute to BMI.International journal of molecular sciences · 2026Article
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- The Encyclopedia of DNA Elements.bioRxiv : the preprint server for biology · 2026Article
- Emergence and evolution of protein-coding de novo genes.Nature reviews. Genetics · 2026Review
- Intrinsic DNA codes govern distinct modes of nucleosome-transcription factor interactions.Nature communications · 2026Article
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- ChromBERT: A foundation model for learning interpretable representations for context-specific transcriptional regulatory networks.Cell genomics · 2026Article
- Evaluating the reliability of tools for mRNA annotation and IRES studies.bioRxiv : the preprint server for biology · 2026Article
- Endogenous retroviral elements LTR8B and MER65 rewire PSG9 regulation to control trophoblast syncytialization and pre-eclampsia risk.Genome biology · 2026Article
- Sequence-based modeling of low-affinity transcription factor-DNA binding through deep learning.NAR genomics and bioinformatics · 2026Article
- BARTsc identifies key transcriptional regulators from single-cell omics data.bioRxiv : the preprint server for biology · 2026Article
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- High-resolution map of chromatin accessibility - insights into the focused binding of a large number of transcription factors.Epigenetics & chromatin · 2026Article
- MiniPromoters Ple384 (TH) and Ple388 (PITX3) for targeting midbrain dopaminergic neurons in mice and monkeys.Scientific reports · 2026Article
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- MotifPeeker: benchmarking epigenomic profiling methods using motifs.Bioinformatics advances · 2026Article
- Insights from GWAS, TWAS, and DEG analysis: CDKN2B-AS1, MAP3K4, and P2RX2-encoded P2X2 receptor identified as potential therapeutic targets for ischemic heart disease in Russian adults and long-living individuals.Frontiers in cardiovascular medicine · 2026Article
- Article
494 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors.
Funding
Abstract
Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) has become the dominant technique for mapping transcription factor (TF) binding regions genome-wide. We performed an integrative analysis centered around 457 ChIP-seq data sets on 119 human TFs generated by the ENCODE Consortium. We identified highly enriched sequence motifs in most data sets, revealing new motifs and validating known ones. The motif sites (TF binding sites) are highly conserved evolutionarily and show distinct footprints upon DNase I digestion. We frequently detected secondary motifs in addition to the canonical motifs of the TFs, indicating tethered binding and cobinding between multiple TFs. We observed significant position and orientation preferences between many cobinding TFs. Genes specifically expressed in a cell line are often associated with a greater occurrence of nearby TF binding in that cell line. We observed cell-line-specific secondary motifs that mediate the binding of the histone deacetylase HDAC2 and the enhancer-binding protein EP300. TF binding sites are located in GC-rich, nucleosome-depleted, and DNase I sensitive regions, flanked by well-positioned nucleosomes, and many of these features show cell type specificity. The GC-richness may be beneficial for regulating TF binding because, when unoccupied by a TF, these regions are occupied by nucleosomes in vivo. We present the results of our analysis in a TF-centric web repository Factorbook (http://factorbook.org) and will continually update this repository as more ENCODE data are generated.
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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.