ArticleNucleic acids research2016
Peak-valley-peak pattern of histone modifications delineates active regulatory elements and their directionality.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 35 citations in OpenAlex.
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- BMI1 represses G-quadruplex DNA formation to maintain genomic stability during replication.The Journal of biological chemistry · 2026Article
- Data-driven projections of candidate enhancer-activating SNPs in immune regulation.BMC genomics · 2025Article
- Regulation of transcription patterns, poly(ADP-ribose), and RNA-DNA hybrids by the ATM protein kinase.Cell reports · 2024Article
- Regulation of transcription patterns, poly-ADP-ribose, and RNA-DNA hybrids by the ATM protein kinase.bioRxiv : the preprint server for biology · 2023Article
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- Methyl-CpG binding domain 2 (Mbd2) is an epigenetic regulator of autism-risk genes and cognition.Translational psychiatry · 2023Article
- TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors.GigaScience · 2022Article
- Differential regulation of alternate promoter regions iniScience · 2022Article
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- Myod1 and GR coordinate myofiber-specific transcriptional enhancers.Nucleic acids research · 2021Article
- Ancestrally Duplicated Conserved Noncoding Element Suggests Dual Regulatory Roles of HOTAIR in cis and trans.iScience · 2020Article
- Specific subfamilies of transposable elements contribute to different domains of T lymphocyte enhancers.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- EpiSAFARI: sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements.Bioinformatics (Oxford, England) · 2020Article
- Characterization of histone modification patterns and prediction of novel promoters using functional principal component analysis.PloS one · 2020Article
- Class 3 semaphorins are transcriptionally regulated by 1,25(OH)The Journal of steroid biochemistry and molecular biology · 2017Article
- CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction.BMC bioinformatics · 2017Article
- Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters.Epigenetics & chromatin · 2017Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Formation of nucleosome free region (NFR) accompanied by specific histone modifications at flanking nucleosomes is an important prerequisite for enhancer and promoter activity. Due to this process, active regulatory elements often exhibit a distinct shape of histone signal in the form of a peak-valley-peak (PVP) pattern. However, different features of PVP patterns and their robustness in predicting active regulatory elements have never been systematically analyzed. Here, we present PARE, a novel computational method that systematically analyzes the H3K4me1 or H3K4me3 PVP patterns to predict NFRs. We show that NFRs predicted by H3K4me1 and me3 patterns are associated with active enhancers and promoters, respectively. Furthermore, asymmetry in the height of peaks flanking the central valley can predict the directionality of stable transcription at promoters. Using PARE on ChIP-seq histone modifications from four ENCODE cell lines and four hematopoietic differentiation stages, we identified several enhancers whose regulatory activity is stage specific and correlates positively with the expression of proximal genes in a particular stage. In conclusion, our results demonstrate that PVP patterns delineate both the histone modification landscape and the transcriptional activities governed by active enhancers and promoters, and therefore can be used for their prediction. PARE is freely available at http://servers.binf.ku.dk/pare.
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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.