Proteome-wide profiling of transcriptional machinery on accessible chromatin with biotinylated transposons

被引：8

作者：

Zhang, Haizhu ^{[1
]}

Qin, Zhaoyu ^{[1
]}

Yue, Xuetong ^{[1
]}

Liu, Yang ^{[1
]}

Sun, Xiaogang ^{[2
]}

Feng, Jinwen ^{[1
]}

Xu, Ziyan ^{[1
]}

Zhao, Jiangyan ^{[1
]}

Li, Kai ^{[1
]}

Qiu, Jiange ^{[3
]}

Yang, Wenjun ^{[4
]}

He, Fuchu ^{[1
,5
]}

Ding, Chen ^{[1
,2
,3
]}

机构：

[1] Fudan Univ, Zhongshan Hosp, Sch Life Sci,Human Phenome Inst, Inst Biomed Sci,State Key Lab Genet Engn, Shanghai 200433, Peoples R China

[2] Henan Normal Univ, Coll Life Sci, Overseas Expertise Intro Ctr Discipline Innovat P, State Key Lab Cell Differentiat & Regulat, Xinxiang 453007, Henan, Peoples R China

[3] Zhengzhou Univ, Acad Med Sci, Cell Signaling & Prote Res Ctr, Zhengzhou 450000, Peoples R China

[4] Shanghai Jiao Tong Univ, Dept Pediat Orthoped, Xin Hua Hosp, Sch Med, Shanghai 200092, Peoples R China

[5] Natl Ctr Prot Sci, Beijing Proteome Res Ctr, State Key Lab Prote, Beijing 102206, Peoples R China

来源：

SCIENCE ADVANCES | 2021年 / 7卷 / 43期

基金：

中国博士后科学基金; 国家重点研发计划; 中国国家自然科学基金;

关键词：

NF-KAPPA-B; STEM-CELL FATE; ESTROGEN-RECEPTOR; DNA-BINDING; C-JUN; PROTEINS; ELEMENTS; REVEALS; GENOME; PHOSPHORYLATION;

D O I：

10.1126/sciadv.abh1022

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

To directly and quantitatively identify the transcriptional protein complexes assembled on accessible chromatin, we develop an assay for transposase-accessible chromatin using mass spectrum (ATAC-MS) based on direct transposition of biotinylated adaptors into open chromatin. Coupling with activated gene sequence information by ATAC-seq, ATAC-MS can profile the accessible chromatin-protein machinery. ATAC-MS, combined with fractionation strategies (fATAC-MS), can provide a high-resolution chromatin-transcriptional machinery atlas. ATAC-MS with a novel Tn5-dCas9 fusion protein [dCas9-targeted ATAC-MS (ctATAC-MS)] further facilitates systematic pinpointing of the transcriptional machinery at specific open chromatin regions. We used ATAC-MS and ATAC-seq to investigate transcriptional regulation during C2C12 cell differentiation and demonstrated the role of RFX1 in regulating the proliferation and differentiation of C2C12 cells. Our strategy provides a universal toolbox including ATAC-MS, fATAC-MS, and ctATAC-MS, which enables us to portray the transcriptional regulation machinery atlas in genome scale and investigate the protein-DNA complex at a specific genomic locus.

引用

页数：22

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