ArticleNucleic acids research2012
Genome-wide prediction and analysis of human chromatin boundary elements.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 43 citations in OpenAlex.
- Transposable elements contribute to the evolution of host shift-related genes in cactophilicGenome research · 2026Article
- SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells.Nature communications · 2023Article
- Review
- Review
- tRNA Genes Affect Chromosome Structure and Function via Local Effects.Molecular and cellular biology · 2019Article
- Morphometric Analysis of Recognized Genes for Autism Spectrum Disorders and Obesity in Relationship to the Distribution of Protein-Coding Genes on Human Chromosomes.International journal of molecular sciences · 2016Article
- MIR retrotransposon sequences provide insulators to the human genome.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Intrinsic Toxicity of Unchecked Heterochromatin Spread Is Suppressed by Redundant Chromatin Boundary Functions in Schizosacchromyces pombe.G3 (Bethesda, Md.) · 2015Article
- Impacts of Chromatin States and Long-Range Genomic Segments on Aging and DNA Methylation.PloS one · 2015Article
- CTCF induces histone variant incorporation, erases the H3K27me3 histone mark and opens chromatin.Nucleic acids research · 2014Article
- A novel tRNA variable number tandem repeat at human chromosome 1q23.3 is implicated as a boundary element based on conservation of a CTCF motif in mouse.Nucleic acids research · 2014Article
- Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression.Mobile DNA · 2014Article
- Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes.Genome biology · 2013Article
- Compound cis-regulatory elements with both boundary and enhancer sequences in the human genome.Bioinformatics (Oxford, England) · 2013Article
- Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features.Nucleic acids research · 2013Article
- Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs.PLoS genetics · 2013Article
- New insights from existing sequence data: generating breakthroughs without a pipette.Molecular cell · 2013Article
- Article
- Role of CTCF protein in regulating FMR1 locus transcription.PLoS genetics · 2013Article
- A computational model for histone mark propagation reproduces the distribution of heterochromatin in different human cell types.PloS one · 2013Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Boundary elements partition eukaryotic chromatin into active and repressive domains, and can also block regulatory interactions between domains. Boundary elements act via diverse mechanisms making accurate feature-based computational predictions difficult. Therefore, we developed an unbiased algorithm that predicts the locations of human boundary elements based on the genomic distributions of chromatin and transcriptional states, as opposed to any intrinsic characteristics that they may possess. Application of our algorithm to ChIP-seq data for histone modifications and RNA Pol II-binding data in human CD4(+) T cells resulted in the prediction of 2542 putative chromatin boundary elements genome wide. Predicted boundary elements display two distinct features: first, position-specific open chromatin and histone acetylation that is coincident with the recruitment of sequence-specific DNA-binding factors such as CTCF, EVI1 and YYI, and second, a directional and gradual increase in histone lysine methylation across predicted boundaries coincident with a gain of expression of non-coding RNAs, including examples of boundaries encoded by tRNA and other non-coding RNA genes. Accordingly, a number of the predicted human boundaries may function via the synergistic action of sequence-specific recruitment of transcription factors leading to non-coding RNA transcriptional interference and the blocking of facultative heterochromatin propagation by transcription-associated chromatin remodeling complexes.
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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.