ArticleNucleic acids research2012
Chromatin domain boundary element search tool for Drosophila.
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 16 papers.
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Who cites it
16 citing papers in PubMed.
- Machine and Deep Learning Methods for Predicting 3D Genome Organization.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Article
- Genomic organization of the autonomous regulatory domain of eyeless locus in Drosophila melanogaster.G3 (Bethesda, Md.) · 2021Article
- Review
- MOCCA: a flexible suite for modelling DNA sequence motif occurrence combinatorics.BMC bioinformatics · 2021Article
- Homeotic Genes: Clustering, Modularity, and Diversity.Frontiers in cell and developmental biology · 2021Review
- Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes.Epigenetics & chromatin · 2020Article
- Genomic organization of Polycomb Response Elements and its functional implication inJournal of biosciences · 2020Article
- O-GlcNAcylation of boundary element associated factor (BEAF 32) in Drosophila melanogaster correlates with active histone marks at the promoters of its target genes.Nucleus (Austin, Tex.) · 2018Article
- Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators.PLoS genetics · 2016Article
- The commonly used eye-specific sev-GAL4 and GMR-GAL4 drivers in Drosophila melanogaster are expressed in tissues other than eyes also.Journal of genetics · 2015Article
- Intrinsic Toxicity of Unchecked Heterochromatin Spread Is Suppressed by Redundant Chromatin Boundary Functions in Schizosacchromyces pombe.G3 (Bethesda, Md.) · 2015Article
- Restraining the enhancers from straying.Journal of biosciences · 2014Article
- Genome-wide mapping of matrix attachment regions in Drosophila melanogaster.BMC genomics · 2014Article
- Transposable element 'roo' attaches to nuclear matrix of the Drosophila melanogaster.Journal of insect science (Online) · 2013Article
- Conserved boundary elements from the Hox complex of mosquito, Anopheles gambiae.Nucleic acids research · 2013Article
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2 authors.
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Abstract
Chromatin domain boundary elements prevent inappropriate interaction between distant or closely spaced regulatory elements and restrict enhancers and silencers to correct target promoters. In spite of having such a general role and expected frequent occurrence genome wide, there is no DNA sequence analysis based tool to identify boundary elements. Here, we report chromatin domain Boundary Element Search Tool (cdBEST), to identify boundary elements. cdBEST uses known recognition sequences of boundary interacting proteins and looks for 'motif clusters'. Using cdBEST, we identified boundary sequences across 12 Drosophila species. Of the 4576 boundary sequences identified in Drosophila melanogaster genome, >170 sequences are repetitive in nature and have sequence homology to transposable elements. Analysis of such sequences across 12 Drosophila genomes showed that the occurrence of repetitive sequences in the context of boundaries is a common feature of drosophilids. We use a variety of genome organization criteria and also experimental test on a subset of the cdBEST boundaries in an enhancer-blocking assay and show that 80% of them indeed function as boundaries in vivo. These observations highlight the role of cdBEST in better understanding of chromatin domain boundaries in Drosophila and setting the stage for comparative analysis of boundaries across closely related species.
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