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用KAS-ATAC-seqq进行转录中的cis调节元件的定量分析

Ruitu Lyu^1,2,3, Yun Gao^4,5,6, Tong Wu^4,5,6

¹Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA. lvruitu@uchicago.edu.

Nature communications

|August 10, 2024

概括

我们开发了Kethoxal-Assisted Single-stranded DNA Assay for Transposase-Accessible Chromatin with Sequencing (KAS-ATAC-seq),用于精确测量 cis调节元件 (CREs) 的转录活性. 这种方法准确地识别了单链转录增强剂 (SSTEs) 和它们的功能角色.

科学领域:

基因组学就是基因组学.
分子生物学分子生物学
表观遗传学在表观遗传学中,表观遗传学是指表观遗传学.

背景情况:

细胞调节元件 (CREs) 对于控制跨生物系统的基因表达至关重要.
精确识别功能性CREs是理解细胞过程中的基因调节网络的关键.

研究的目的:

开发和验证Kethoxal-Assisted单链DNA测定转化酶可访问的染色体与测序 (KAS-ATAC-seq) 用于对CRE转录活性进行定量分析.
精确测量ATAC-seq峰值内的单链DNA (ssDNA) 水平,以识别转录调节序列,特别是单链转录增强剂 (SSTEs).

主要方法:

开发了KAS-ATAC-seq以通过测量在ATAC-seq峰值内的ssDNA水平来定量分析CREs的转录活性.
该方法精确地识别了转录调节序列,并描述了单链转录增强剂 (SSTEs).

主要成果:

KAS-ATAC-seq精确测量ssDNA水平,使得识别转录调节序列和单链转录增强剂 (SSTEs) 成为可能.
发现SSTEs被丰富了新生的RNA和转录因子结合部位,这些部位对细胞身份至关重要.
该研究证明了KAS-ATAC-seq在对视网膜酸 (RA) 的反应中在小鼠神经分化过程中识别立即早期激活的CREs的能力.

结论:

在转录中,KAS-ATAC-seq提供了更精确的功能CREs注释.
这种方法为SSTE亚型提供了详细的表征和功能洞察.
未来KAS-ATAC-seq的应用将促进对各种生物过程中的基因调节动态的理解.

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