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Dissecting Tissue-Specific Super-Enhancers by Integrating Genome-Wide Analyses and CRISPR/Cas9 Genome Editing

Authors
Yoo, Kyung HyunHennighausen, LotharShin, Ha Youn
Issue Date
Mar-2019
Publisher
SPRINGER/PLENUM PUBLISHERS
Keywords
Super-enhancer; Genome-wide analysis; CRISPR; Cas9; Cell type-specific gene regulation; Mammary gland development
Citation
JOURNAL OF MAMMARY GLAND BIOLOGY AND NEOPLASIA, v.24, no.1, pp 47 - 59
Pages
13
Journal Title
JOURNAL OF MAMMARY GLAND BIOLOGY AND NEOPLASIA
Volume
24
Number
1
Start Page
47
End Page
59
URI
https://scholarworks.sookmyung.ac.kr/handle/2020.sw.sookmyung/3757
DOI
10.1007/s10911-018-9417-z
ISSN
1083-3021
1573-7039
Abstract
Recent advances in genome-wide sequencing technologies have provided researchers with unprecedented opportunities to discover the genomic structures of gene regulatory units in living organisms. In particular, the integration of ChIP-seq, RNA-seq, and DNase-seq techniques has facilitated the mapping of a new class of regulatory elements. These elements, called super-enhancers, can regulate cell-type-specific gene sets and even fine-tune gene expression regulation in response to external stimuli, and have become a hot topic in genome biology. However, there is scant genetic evidence demonstrating their unique biological relevance and the mechanisms underlying these biological functions. In this review, we describe a robust genome-wide strategy for mapping cell-type-specific enhancers or super-enhancers in the mammary genome. In this strategy, genome-wide screening of active enhancer clusters that are co-occupied by mammary-enriched transcription factors, co-factors, and active enhancer marks is used to identify bona fide mammary tissue-specific super-enhancers. The in vivo function of these super-enhancers and their associated regulatory elements may then be investigated in various ways using the advanced CRISPR/Cas9 genome-editing technology. Based on our experience targeting various mammary genomic sites using CRISPR/Cas9 in mice, we comprehensively discuss the molecular consequences of the different targeting methods, such as the number of gRNAs and the dependence on their simultaneous or sequential injections. We also mention the considerations that are essential for obtaining accurate results and shed light on recent progress that has been made in developing modified CRISPR/Cas9 genome-editing techniques. In the future, the coupling of advanced genome-wide sequencing and genome-editing technologies could provide new insights into the complex genetic regulatory networks involved in mammary-gland development.
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