ArticleGenome research2017
Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 50 citations in OpenAlex.
- Understanding super enhancers in genome architecture and their roles in livestock breeding.BMC genomics · 2026Review
- Super-silencers are crucial for development and carcinogenesis in B cells.Nature communications · 2025Article
- Super-enhancer-driven EFNA1 fuels tumor progression in cervical cancer via the FOSL2-Src/AKT/STAT3 axis.The Journal of clinical investigation · 2025Article
- Mir-483-5p-mediated activating of IGF2/H19 enhancer up-regulates IGF2/H19 expression via chromatin loops to promote the malignant progression of hepatocellular carcinoma.Molecular cancer · 2025Article
- Metabolic stress in space: ROS-induced mutations in mice hint at a new path to cancer.Redox biology · 2024Article
- Evolutionary conservation of VSX2 super-enhancer modules in retinal development.Development (Cambridge, England) · 2024Article
- Haplotype-resolved 3D chromatin architecture of the hybrid pig.Genome research · 2024Article
- Super-Enhancers and Their Parts: From Prediction Efforts to Pathognomonic Status.International journal of molecular sciences · 2024Review
- Functional annotation of regulatory elements in rainbow trout uncovers roles of the epigenome in genetic selection and genome evolution.GigaScience · 2024Article
- Zebrafish regulatory genomic resources for disease modelling and regeneration.Disease models & mechanisms · 2023Article
- Review
- Polyglutamine-expanded ATXN7 alters a specific epigenetic signature underlying photoreceptor identity gene expression in SCA7 mouse retinopathy.Journal of biomedical science · 2022Article
- Regeneration and developmental enhancers are differentially compatible with minimal promoters.Developmental biology · 2022Article
- Identification and functional validation of super-enhancers inProceedings of the National Academy of Sciences of the United States of America · 2022Article
- Super-enhancers conserved within placental mammals maintain stem cell pluripotency.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Senescent cells limit p53 activity via multiple mechanisms to remain viable.Nature communications · 2022Article
- Dynamic 3D genome reorganization during development and metabolic stress of the porcine liver.Cell discovery · 2022Article
- Multidimensional chromatin profiling of zebrafish pancreas to uncover and investigate disease-relevant enhancers.Nature communications · 2022Article
- Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis.Nature communications · 2022Article
- Role of CNSs Conserved Distal Cis-Regulatory Elements in CD4 + T Cell Development and Differentiation.Frontiers in immunology · 2022Review
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Super-enhancers (SEs) are key transcriptional drivers of cellular, developmental, and disease states in mammals, yet the conservational and regulatory features of these enhancer elements in nonmammalian vertebrates are unknown. To define SEs in zebrafish and enable sequence and functional comparisons to mouse and human SEs, we used genome-wide histone H3 lysine 27 acetylation (H3K27ac) occupancy as a primary SE delineator. Our study determined the set of SEs in pluripotent state cells and adult zebrafish tissues and revealed both similarities and differences between zebrafish and mammalian SEs. Although the total number of SEs was proportional to the genome size, the genomic distribution of zebrafish SEs differed from that of the mammalian SEs. Despite the evolutionary distance separating zebrafish and mammals and the low overall SE sequence conservation, ∼42% of zebrafish SEs were located in close proximity to orthologs that also were associated with SEs in mouse and human. Compared to their nonassociated counterparts, higher sequence conservation was revealed for those SEs that have maintained orthologous gene associations. Functional dissection of two of these SEs identified conserved sequence elements and tissue-specific expression patterns, while chromatin accessibility analyses predicted transcription factors governing the function of pluripotent state zebrafish SEs. Our zebrafish annotations and comparative studies show the extent of SE usage and their conservation across vertebrates, permitting future gene regulatory studies in several tissues.
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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.