ArticleNature biotechnology2016
Co-ChIP enables genome-wide mapping of histone mark co-occurrence at single-molecule resolution.
Article in Nature biotechnology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
50 citing papers in PubMed, 94 citations in OpenAlex.
- Epigenetic de-repression of basal cell metaplasia in aging AT2 cells is a risk factor for idiopathic pulmonary fibrosis (IPF).bioRxiv : the preprint server for biology · 2026Article
- Histone modification cross-talk: analytical tools and molecular mechanisms.The Biochemical journal · 2026Review
- CoCUT&Tag maps linked chromatin states at single-molecule, single-cell resolution.bioRxiv : the preprint server for biology · 2026Article
- Chromatin profiling identifies putative dual roles for H3K27me3 in regulating cell type-specific genes and transposable elements in choanoflagellates.Nature communications · 2025Article
- Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIP.Nature communications · 2025Article
- Polycomb repressive complex 2 (PRC2) pathway's role in cancer cell plasticity and drug resistance.Functional & integrative genomics · 2025Review
- Visualizing epigenetic modifications and their spatial proximities in single cells using three DNA-encoded amplifying FISH imaging strategies: BEA-FISH, PPDA-FISH and Cell-TALKING.Nature protocols · 2025Article
- Emerging toolkits for decoding the co-occurrence of modified histones and chromatin proteins.EMBO reports · 2024Review
- Nucleosomal asymmetry: a novel mechanism to regulate nucleosome function.Biochemical Society transactions · 2024Review
- A low-input high resolution sequential chromatin immunoprecipitation method captures genome-wide dynamics of bivalent chromatin.Epigenetics & chromatin · 2024Article
- Epigenetic regulation of chemokine (CC-motif) ligand 2 in inflammatory diseases.Cell proliferation · 2023Review
- Short tandem repeats are important contributors to silencer elements in T cells.Nucleic acids research · 2023Article
- Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag.Nature biotechnology · 2023Article
- Cocaine regulation of Nr4a1 chromatin bivalency and mRNA in male and female mice.Scientific reports · 2022Article
- Polycomb Directed Cell Fate Decisions in Development and Cancer.Epigenomes · 2022Review
- Article
- High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq).The Journal of cell biology · 2021Article
- Simultaneous profiling of multiple chromatin proteins in the same cells.Molecular cell · 2021Article
- Mathematical modeling of histone modifications reveals the formation mechanism and function of bivalent chromatin.iScience · 2021Article
- A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation.Genome research · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Histone modifications play an important role in chromatin organization and transcriptional regulation, but despite the large amount of genome-wide histone modification data collected in different cells and tissues, little is known about co-occurrence of modifications on the same nucleosome. Here we present a genome-wide quantitative method for combinatorial indexed chromatin immunoprecipitation (co-ChIP) to characterize co-occurrence of histone modifications on nucleosomes. Using co-ChIP, we study the genome-wide co-occurrence of 14 chromatin marks (70 pairwise combinations), and find previously undescribed co-occurrence patterns, including the co-occurrence of H3K9me1 and H3K27ac in super-enhancers. Finally, we apply co-ChIP to measure the distribution of the bivalent H3K4me3-H3K27me3 domains in two distinct mouse embryonic stem cell (mESC) states and in four adult tissues. We observe dynamic changes in 5,786 regions and discover both loss and de novo gain of bivalency in key tissue-specific regulatory genes, suggesting a functional role for bivalent domains during different stages of development. These results show that co-ChIP can reveal the complex interactions between histone modifications.
Indexed as
Identifiers
What OpenQuestion holds
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.