Characterization of Single-Cell Cis-regulatory Elements Informs Implications for Cell Differentiation

	Characterization of Single-Cell Cis-regulatory Elements Informs Implications for Cell Differentiation
	Ren, YY; Liu, Z
	2024
发表期刊	GENOME BIOLOGY AND EVOLUTION
ISSN	1759-6653
卷号	16 期号:11
摘要	Cis-regulatory elements govern the specific patterns and dynamics of gene expression in cells during development, which are the fundamental mechanisms behind cell differentiation. However, the genomic characteristics of single-cell cis-regulatory elements closely linked to cell differentiation during development remain unclear. To explore this, we systematically analyzed similar to 250,000 putative single-cell cis-regulatory elements obtained from snATAC-seq analysis of the developing mouse cerebellum. We found that over 80% of these single-cell cis-regulatory elements show pleiotropic effects, being active in 2 or more cell types. The pleiotropic degrees of proximal and distal single-cell cis-regulatory elements are positively correlated with the density and diversity of transcription factor binding motifs and GC content. There is a negative correlation between the pleiotropic degrees of single-cell cis-regulatory elements and their distances to the nearest transcription start sites, and proximal single-cell cis-regulatory elements display higher relevance strengths than distal ones. Furthermore, both proximal and distal single-cell cis-regulatory elements related to cell differentiation exhibit enhanced sequence-level evolutionary conservation, increased density and diversity of transcription factor binding motifs, elevated GC content, and greater distances from their nearest genes. Together, our findings reveal the general genomic characteristics of putative single-cell cis-regulatory elements and provide insights into the genomic and evolutionary mechanisms by which single-cell cis-regulatory elements regulate cell differentiation during development.
收录类别	SCI
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/14478
专题	科研部门_进化发育生物学（刘振）
推荐引用方式 GB/T 7714	Ren, YY,Liu, Z. Characterization of Single-Cell Cis-regulatory Elements Informs Implications for Cell Differentiation[J]. GENOME BIOLOGY AND EVOLUTION,2024,16(11).
APA	Ren, YY,&Liu, Z.(2024).Characterization of Single-Cell Cis-regulatory Elements Informs Implications for Cell Differentiation.GENOME BIOLOGY AND EVOLUTION,16(11).
MLA	Ren, YY,et al."Characterization of Single-Cell Cis-regulatory Elements Informs Implications for Cell Differentiation".GENOME BIOLOGY AND EVOLUTION 16.11(2024).

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