ArticleNucleic acids research2018
Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
27 citing papers in PubMed, 47 citations in OpenAlex.
- A function of Spalt proteins in heterochromatin organization and maintenance of genomic DNA integrity.Development (Cambridge, England) · 2025Article
- Entangled and non-modular enhancer sequences producing independent spatial activities.Science advances · 2024Article
- Inter3D: Capture of TAD Reorganization Endows Variant Patterns of Gene Transcription.Genomics, proteomics & bioinformatics · 2024Article
- Atypical Modes of CTCF Binding Facilitate Tissue-Specific and Neuronal Activity-Dependent Gene Expression States.Molecular neurobiology · 2024Article
- The genetic regulatory architecture and epigenomic basis for age-related changes in rattlesnake venom.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Identification of somatic mutation-driven enhancers and their clinical utility in breast cancer.iScience · 2024Article
- ASH2L regulates postnatal neurogenesis through Onecut2-mediated inhibition of TGF-β signaling pathway.Cell death and differentiation · 2023Article
- Toward a comprehensive catalog of regulatory elements.Human genetics · 2023Review
- Relating enhancer genetic variation across mammals to complex phenotypes using machine learning.Science (New York, N.Y.) · 2023Article
- Matching queried single-cell open-chromatin profiles to large pools of single-cell transcriptomes and epigenomes for reference supported analysis.Genome research · 2023Article
- Acetate supplementation restores cognitive deficits caused by ARID1A haploinsufficiency in excitatory neurons.EMBO molecular medicine · 2022Article
- Hnf1b renal expression directed by a distal enhancer responsive to Pax8.Scientific reports · 2022Article
- Differential enrichment of H3K9me3 in intrahepatic cholangiocarcinoma.BMC medical genomics · 2022Article
- Ranking reprogramming factors for cell differentiation.Nature methods · 2022Article
- Investigating chromatin accessibility during development and differentiation by ATAC-sequencing to guide the identification of cis-regulatory elements.Biochemical Society transactions · 2022Article
- Article
- Coordinated Gene Expression and Chromatin Regulation during Hydra Head Regeneration.Genome biology and evolution · 2021Article
- Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows.International journal of molecular sciences · 2021Article
- Mitochondrial dysfunction-induced H3K27 hyperacetylation perturbs enhancers in Parkinson's disease.JCI insight · 2021Article
- PPARγ-Induced Global H3K27 Acetylation Maintains Osteo/Cementogenic Abilities of Periodontal Ligament Fibroblasts.International journal of molecular sciences · 2021Article
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 2 countries.
Funding
Abstract
Enhancers are distal cis-regulatory elements that modulate gene expression. They are depleted of nucleosomes and enriched in specific histone modifications; thus, calling DNase-seq and histone mark ChIP-seq peaks can predict enhancers. We evaluated nine peak-calling algorithms for predicting enhancers validated by transgenic mouse assays. DNase and H3K27ac peaks were consistently more predictive than H3K4me1/2/3 and H3K9ac peaks. DFilter and Hotspot2 were the best DNase peak callers, while HOMER, MUSIC, MACS2, DFilter and F-seq were the best H3K27ac peak callers. We observed that the differential DNase or H3K27ac signals between two distant tissues increased the area under the precision-recall curve (PR-AUC) of DNase peaks by 17.5-166.7% and that of H3K27ac peaks by 7.1-22.2%. We further improved this differential signal method using multiple contrast tissues. Evaluated using a blind test, the differential H3K27ac signal method substantially improved PR-AUC from 0.48 to 0.75 for predicting heart enhancers. We further validated our approach using postnatal retina and cerebral cortex enhancers identified by massively parallel reporter assays, and observed improvements for both tissues. In summary, we compared nine peak callers and devised a superior method for predicting tissue-specific mouse developmental enhancers by reranking the called peaks.
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Registered trials
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.