ArticleBMC genomics2017
Short DNA sequence patterns accurately identify broadly active human enhancers.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance.Genome medicine · 2021Pooled it
- Machine and Deep Learning Reveal Sequence Determinants Encoding Bivalent Histone Modifications.Communications biology · 2026Article
- Deciphering Sequence Determinants of Zygotic Genome Activation Genes: Insights From Machine Learning and the ZGAExplorer Platform.Cell proliferation · 2025Article
- Polygraph: a software framework for the systematic assessment of synthetic regulatory DNA elements.Genome biology · 2025Article
- Article
- Crosstalk between paralogs and isoforms influences p63-dependent regulatory element activity.Nucleic acids research · 2024Article
- Context dependent activity of p63-bound gene regulatory elements.bioRxiv : the preprint server for biology · 2024Article
- Computational methods for identifying enhancer-promoter interactions.Quantitative biology (Beijing, China) · 2023Review
- Differentially Active and Conserved Neural Enhancers Define Two Forms of Adaptive Noncoding Evolution in Humans.Genome biology and evolution · 2022Article
- K-mer Content Changes with Node Degree in Promoter-Enhancer Network of Mouse ES Cells.International journal of molecular sciences · 2021Article
- Pervasive and CpG-dependent promoter-like characteristics of transcribed enhancers.Nucleic acids research · 2020Article
- Article
- The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements.Genome biology · 2019Article
- Sequence Characteristics Distinguish Transcribed Enhancers from Promoters and Predict Their Breadth of Activity.Genetics · 2019Article
- Visual Analytics of Genomic and Cancer Data: A Systematic Review.Cancer informatics · 2019Review
- Computational Biology Solutions to Identify Enhancers-target Gene Pairs.Computational and structural biotechnology journal · 2019Review
- TELS: A Novel Computational Framework for Identifying Motif Signatures of Transcribed Enhancers.Genomics, proteomics & bioinformatics · 2018Article
- Next generation pathways into biomedical informatics: lessons from 10 years of the Vanderbilt Biomedical Informatics Summer Internship Program.JAMIA open · 2018Article
- Human Enhancers Harboring Specific Sequence Composition, Activity, and Genome Organization Are Linked to the Immune Response.Genetics · 2018Article
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Authors and funding
3 authors.
Funding
Abstract
backgroundEnhancers are DNA regulatory elements that influence gene expression. There is substantial diversity in enhancers' activity patterns: some enhancers drive expression in a single cellular context, while others are active across many. Sequence characteristics, such as transcription factor (TF) binding motifs, influence the activity patterns of regulatory sequences; however, the regulatory logic through which specific sequences drive enhancer activity patterns is poorly understood. Recent analysis of Drosophila enhancers suggested that short dinucleotide repeat motifs (DRMs) are general enhancer sequence features that drive broad regulatory activity. However, it is not known whether the regulatory role of DRMs is conserved across species.
resultsWe performed a comprehensive analysis of the relationship between short DNA sequence patterns, including DRMs, and human enhancer activity in 38,538 enhancers across 411 different contexts. In a machine-learning framework, the occurrence patterns of short sequence motifs accurately predicted broadly active human enhancers. However, DRMs alone were weakly predictive of broad enhancer activity in humans and showed different enrichment patterns than in Drosophila. In general, GC-rich sequence motifs were significantly associated with broad enhancer activity, and consistent with this enrichment, broadly active human TFs recognize GC-rich motifs.
conclusionsOur results reveal the importance of specific sequence motifs in broadly active human enhancers, demonstrate the lack of evolutionary conservation of the role of DRMs, and provide a computational framework for investigating the logic of enhancer sequences.
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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.