生物
染色质
清脆的
表观遗传学
计算生物学
CRISPR干扰
遗传学
反式激活crRNA
基因表达调控
转录因子
基因
基因组编辑
基因表达
DNA甲基化
作者
Adam J. Rubin,Kevin R. Parker,Ansuman T. Satpathy,Yanyan Qi,Beijing Wu,Alvin J. Ong,Maxwell R. Mumbach,Andrew L. Ji,Daniel Sunwook Kim,Seung Woo Cho,Brian Zarnegar,William J. Greenleaf,Howard Y. Chang,Paul A. Khavari
出处
期刊:Cell
[Elsevier]
日期:2019-01-01
卷期号:176 (1-2): 361-376.e17
被引量:204
标识
DOI:10.1016/j.cell.2018.11.022
摘要
Here, we present Perturb-ATAC, a method that combines multiplexed CRISPR interference or knockout with genome-wide chromatin accessibility profiling in single cells based on the simultaneous detection of CRISPR guide RNAs and open chromatin sites by assay of transposase-accessible chromatin with sequencing (ATAC-seq). We applied Perturb-ATAC to transcription factors (TFs), chromatin-modifying factors, and noncoding RNAs (ncRNAs) in ∼4,300 single cells, encompassing more than 63 genotype-phenotype relationships. Perturb-ATAC in human B lymphocytes uncovered regulators of chromatin accessibility, TF occupancy, and nucleosome positioning and identified a hierarchy of TFs that govern B cell state, variation, and disease-associated cis-regulatory elements. Perturb-ATAC in primary human epidermal cells revealed three sequential modules of cis-elements that specify keratinocyte fate. Combinatorial deletion of all pairs of these TFs uncovered their epistatic relationships and highlighted genomic co-localization as a basis for synergistic interactions. Thus, Perturb-ATAC is a powerful strategy to dissect gene regulatory networks in development and disease.
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