ArticleGenome research2014
Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
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Who cites it
89 citing papers in PubMed, 154 citations in OpenAlex.
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- Discovering the complete enhancer map of human herpesviruses using a natural language processing model.Nature communications · 2025Article
- Regulatory logic of neuronal identity specification inbioRxiv : the preprint server for biology · 2025Article
- 3D chromatin structures precede genome activation in Drosophila embryogenesis.Cell genomics · 2025Article
- Ultrastable and versatile multimeric ensembles of FoxP3 on microsatellites.Molecular cell · 2025Article
- Copy Number Variations in Short Tandem Repeats Modulate Growth Traits in Penaeid Shrimp Through Neighboring Gene Regulation.Animals : an open access journal from MDPI · 2025Article
- Cotton under heat stress: a comprehensive review of molecular breeding, genomics, and multi-omics strategies.Frontiers in genetics · 2025Review
- A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity.Nucleic acids research · 2024Article
- Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila.Nature communications · 2024Article
- Su(Hw) interacts with Combgap to establish long-range chromatin contacts.Epigenetics & chromatin · 2024Article
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- Cis-Regulatory Elements in Mammals.International journal of molecular sciences · 2023Review
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- Interplay Between Polymorphic Short Tandem Repeats and Gene Expression Variation in Caenorhabditis elegans.Molecular biology and evolution · 2023Article
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- Prediction accuracy of regulatory elements from sequence varies by functional sequencing technique.Frontiers in cellular and infection microbiology · 2023Article
- Spatial and temporal control of expression with light-gated LOV-LexA.G3 (Bethesda, Md.) · 2022Article
- High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation.Genome biology · 2022Review
29 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene expression is determined by genomic elements called enhancers, which contain short motifs bound by different transcription factors (TFs). However, how enhancer sequences and TF motifs relate to enhancer activity is unknown, and general sequence requirements for enhancers or comprehensive sets of important enhancer sequence elements have remained elusive. Here, we computationally dissect thousands of functional enhancer sequences from three different Drosophila cell lines. We find that the enhancers display distinct cis-regulatory sequence signatures, which are predictive of the enhancers' cell type-specific or broad activities. These signatures contain transcription factor motifs and a novel class of enhancer sequence elements, dinucleotide repeat motifs (DRMs). DRMs are highly enriched in enhancers, particularly in enhancers that are broadly active across different cell types. We experimentally validate the importance of the identified TF motifs and DRMs for enhancer function and show that they can be sufficient to create an active enhancer de novo from a nonfunctional sequence. The function of DRMs as a novel class of general enhancer features that are also enriched in human regulatory regions might explain their implication in several diseases and provides important insights into gene regulation.
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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.