Capture of associated targets on chromatin links long-distance chromatin looping to transcriptional coordination
| Autor: | Hari Singhal, Ryan J. Bourgo, Geoffrey L. Greene |
|---|---|
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Chromatin Immunoprecipitation Science General Physics and Astronomy Genomics Computational biology Biology Endoplasmic Reticulum General Biochemistry Genetics and Molecular Biology Article 03 medical and health sciences Humans Enhancer Promoter Regions Genetic Gene ChIA-PET Genetics Regulation of gene expression Multidisciplinary Binding Sites Oligonucleotide General Chemistry DNA Sequence Analysis DNA Chromatin 030104 developmental biology Gene Expression Regulation Eukaryotic Initiation Factor-4A Chromatin immunoprecipitation Protein Binding |
| Zdroj: | Nature Communications Nature Communications, Vol 7, Iss 1, Pp 1-12 (2016) |
| ISSN: | 2041-1723 |
| Popis: | Here we describe a sensitive and novel method of identifying endogenous DNA–DNA interactions. Capture of Associated Targets on CHromatin (CATCH) uses efficient capture and enrichment of specific genomic loci of interest through hybridization and subsequent purification via complementary biotinylated oligonucleotide. The CATCH assay requires no enzymatic digestion or ligation, requires little starting material, provides high-quality data, has excellent reproducibility and is completed in less than 24 h. Efficacy is demonstrated through capture of three disparate loci, which demonstrate unique subsets of long-distance chromatin interactions enriched for both enhancer marks and oestrogen receptor-binding sites. In each experiment, CATCH-seq peaks representing long-distance chromatin interactions were centred near the TSS of genes, and, critically, the genes identified as physically interacting are shown to be transcriptionally coexpressed. These interactions could potentially create transcriptional hubs for the regulation of gene expression programmes. Chromatin architecture is a key regulator of transcriptional processes, however current methods to investigate it have technical limitations. Here, the authors describe a novel chromatin capture technique, CATCH, which can be used to identify and characterize complex genomic interaction networks. |
| Databáze: | OpenAIRE |
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