ArticlePloS one2017
Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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51 citing papers in PubMed.
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- FACT depletion demonstrates a role for nucleosome organization in TAD formation.Molecular systems biology · 2026Article
- Antisense transcription can induce expression memory via stable promoter repression.Genome biology · 2025Article
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- Integration of chromosome locations and functional aspects of enhancers and topologically associating domains in knowledge graphs enables versatile queries about gene regulation.Nucleic acids research · 2024Article
- Functional identification of cis-regulatory long noncoding RNAs at controlled false discovery rates.Nucleic acids research · 2024Article
- Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation.Molecular cell · 2023Article
- Reliable genotyping of recombinant genomes using a robust hidden Markov model.Plant physiology · 2023Article
- Optimized high-throughput screening of non-coding variants identified from genome-wide association studies.Nucleic acids research · 2023Article
- A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers.Nature biotechnology · 2022Article
- 3DFAACTS-SNP: using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of type 1 diabetes (T1D) risk.Epigenetics & chromatin · 2022Article
- Defining pervasive transcription units using chromatin RNA-sequencing data.STAR protocols · 2022Article
- The chromatin remodeller ATRX facilitates diverse nuclear processes, in a stochastic manner, in both heterochromatin and euchromatin.Nature communications · 2022Article
- Oct4 differentially regulates chromatin opening and enhancer transcription in pluripotent stem cells.eLife · 2022Article
- RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history.G3 (Bethesda, Md.) · 2022Article
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6 authors.
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Abstract
Accurate maps of promoters and enhancers are required for understanding transcriptional regulation. Promoters and enhancers are usually mapped by integration of chromatin assays charting histone modifications, DNA accessibility, and transcription factor binding. However, current algorithms are limited by unrealistic data distribution assumptions. Here we propose GenoSTAN (Genomic STate ANnotation), a hidden Markov model overcoming these limitations. We map promoters and enhancers for 127 cell types and tissues from the ENCODE and Roadmap Epigenomics projects, today's largest compendium of chromatin assays. Extensive benchmarks demonstrate that GenoSTAN generally identifies promoters and enhancers with significantly higher accuracy than previous methods. Moreover, GenoSTAN-derived promoters and enhancers showed significantly higher enrichment of complex trait-associated genetic variants than current annotations. Altogether, GenoSTAN provides an easy-to-use tool to define promoters and enhancers in any system, and our annotation of human transcriptional cis-regulatory elements constitutes a rich resource for future research in biology and medicine.
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