ArticleNature communications2016
Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Formation of topologically associated chromatin domains using quantum annealing.Scientific reports · 2026Article
- Review
- Continuous chromatin state feature annotation of the human epigenome.Bioinformatics (Oxford, England) · 2022Article
- Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns.PLoS computational biology · 2021Review
- Annotating the Insect Regulatory Genome.Insects · 2021Review
- Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function.BMC genomics · 2019Article
- Learning the Formation Mechanism of Domain-Level Chromatin States with Epigenomics Data.Biophysical journal · 2019Article
- REDfly: the transcriptional regulatory element database for Drosophila.Nucleic acids research · 2019Article
- Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities.Nucleic acids research · 2018Article
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Authors and funding
2 authors.
Funding
Abstract
Interpreting the functional state of chromatin from the combinatorial binding patterns of chromatin factors, that is, the chromatin codes, is crucial for decoding the epigenetic state of the cell. Here we present a systematic map of Drosophila chromatin states derived from data-driven probabilistic modelling of dependencies between chromatin factors. Our model not only recapitulates enhancer-like chromatin states as indicated by widely used enhancer marks but also divides these states into three functionally distinct groups, of which only one specific group possesses active enhancer activity. Moreover, we discover a strong association between one specific enhancer state and RNA Polymerase II pausing, linking transcription regulatory potential and chromatin organization. We also observe that with the exception of long-intron genes, chromatin state transition positions in transcriptionally active genes align with an absolute distance to their corresponding transcription start site, regardless of gene length. Using our method, we provide a resource that helps elucidate the functional and spatial organization of the chromatin code landscape.
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