Identification of physical interactions between genomic regions by enChIP‐Seq. (5th May 2017)

• Record Type: Journal Article
• Authors: Fujita, Toshitsugu; Yuno, Miyuki; Suzuki, Yutaka; Sugano, Sumio; Fujii, Hodaka
• Is Part Of: Genes to cells. Volume 22:Number 6(2017)
• Page Start: 506
• Page End: 520
• Publication Date: 2017-05-05
• Subjects: Cytogenetics -- Periodicals; Cells -- Mechanical properties -- Periodicals; Molecular genetics -- Periodicals; Genes -- Periodicals; Molecular biology -- Periodicals; Cytology -- Periodicals; Biomechanics -- Periodicals; 571.6
• DOI: 10.1111/gtc.12492
• Languages: English
• ISSNs: 1356-9597

Abstract

Abstract : Physical interactions between genomic regions play critical roles in the regulation of genome functions, including gene expression. Here, we show the feasibility of using engineered DNA‐binding molecule‐mediated chromatin immunoprecipitation (enChIP) in combination with next‐generation sequencing (NGS) (enChIP‐Seq) to detect such interactions. In enChIP‐Seq, the target genomic region is captured by an engineered DNA‐binding complex, such as a clustered regularly interspaced short palindromic repeats (CRISPR) system consisting of a catalytically inactive form of Cas9 and a single guide RNA. Subsequently, the genomic regions that physically interact with the target genomic region in the captured complex are sequenced by NGS. Using enChIP‐Seq, we found that the 5′HS5 locus, which is involved in the regulation of globin genes expression at the β ‐globin locus, interacts with multiple genomic regions upon erythroid differentiation in the human erythroleukemia cell line K562. Genes near the genomic regions inducibly associated with the 5′HS5 locus were transcriptionally up‐regulated in the differentiated state, suggesting the existence of a coordinated transcription mechanism mediated by physical interactions between these loci. Thus, enChIP‐Seq might be a potentially useful tool for detecting physical interactions between genomic regions in a nonbiased manner, which would facilitate elucidation of the molecular mechanisms underlying regulation of genome functions. Abstract : In this study, we combined enChIP with NGS (enChIP‐Seq) to detect chromosomal interactions. Using enChIP‐Seq, we showed that the 5′HS5 locus physically interacts with multiple genomic regions upon erythroid differentiation in K562. Thus, enChIP‐Seq represents a potentially useful tool for analysis of genome functions.