Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens.
Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens.
复制标题
DOI：
10.1038/s41587-021-00902-x
复制
发表时间：
2021-10
影响因子：
46.9
通讯作者：
Sanjana NE
中科院分区：
文献类型：
--
作者：
Liscovitch-Brauer N;Montalbano A;Deng J;Méndez-Mancilla A;Wessels HH;Moss NG;Kung CY;Sookdeo A;Guo X;Geller E;Jaini S;Smibert P;Sanjana NE
合并的CRISPR筛选已被用于将遗传扰动与基因表达和表型的变化联系起来。在这里，我们描述了一种基于CRISPR的单细胞转座酶可及染色质组合索引测定（CRISPR-sciATAC），以将遗传扰动与大量细胞中的全基因组染色质可及性联系起来。在人类骨髓性白血病细胞中，我们应用CRISPR-sciATAC靶向105个染色质相关基因，生成了约30，000个单细胞的染色质可及性数据。我们将特定染色质重塑的丢失与全球可及性和单个转录因子结合位点的变化相关联。例如，我们发现H3 K27甲基转移酶EZH 2的缺失增加了参与胚胎发育的异染色质区域的可及性，并触发了HOXA和HOXD簇中基因的表达。在一个子集的监管网站，我们还分析了核小体间距的变化后，染色质重塑的损失。CRISPR-sciATAC是一种高通量单细胞方法，用于研究正常和疾病状态下遗传扰动对染色质的作用。基因敲除对染色质可及性的影响用单细胞CRISPR筛选来测量。
Pooled CRISPR screens have been used to connect genetic perturbations with changes in gene expression and phenotypes. Here, we describe a CRISPR-based single-cell combinatorial indexing assay for transposase-accessible chromatin (CRISPR-sciATAC) to link genetic perturbations to genome-wide chromatin accessibility in a large number of cells. In human myelogenous leukemia cells, we apply CRISPR-sciATAC to target 105 chromatin-related genes, generating chromatin accessibility data for ~30,000 single cells. We correlate loss of specific chromatin remodelers with changes in accessibility globally and at the binding sites of individual transcription factors. For example, we show that loss of the H3K27 methyltransferase EZH2 increases accessibility at heterochromatic regions involved in embryonic development and triggers expression of genes in the HOXA and HOXD clusters. At a subset of regulatory sites, we also analyze changes in nucleosome spacing upon loss of chromatin remodelers. CRISPR-sciATAC is a high-throughput single-cell method for studying the role of genetic perturbations on chromatin in normal and disease states. The effects of gene knockouts on chromatin accessibility are measured with single-cell CRISPR screens.
登录
查看更多内容
影响因子：
64.5
作者：
Jaitin, Diego Adhemar;Weiner, Assaf;Amit, Ido
通讯作者：
Amit, Ido
影响因子：
7
作者：
Duttke, Sascha H.;Chang, Max W.;Benner, Christopher
通讯作者：
Benner, Christopher
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
30.8
作者：
Mathur R;Alver BH;San Roman AK;Wilson BG;Wang X;Agoston AT;Park PJ;Shivdasani RA;Roberts CW
通讯作者：
Roberts CW
影响因子：
64.5
作者：
Dixit, Atray;Pamas, Oren;Li, Biyu;Chen, Jenny;Fulco, Charles P.;Jerby-Amon, Livnat;Marjanovic, Nemanja D.;Dionne, Danielle;Burks, Tyler;Raychowdhury, Raktima;Adamson, Britt;Norman, Thomas M.;Lander, Eric S.;Weissman, Jonathan S.;Friedman, Nir;Regev, Aviv
通讯作者：
Regev, Aviv