Structural modularity of the XIST ribonucleoprotein complex

Nat Commun. 2020 Dec 2;11(1):6163. doi: 10.1038/s41467-020-20040-3.

Zhipeng Lu ¹ ², Jimmy K Guo ³, Yuning Wei ³, Diana R Dou ³, Brian Zarnegar ⁴, Qing Ma ³ ⁵, Rui Li ³, Yang Zhao ³, Fan Liu ³, Hani Choudhry ³ ⁶, Paul A Khavari ⁴, Howard Y Chang ⁷ ⁸ ⁹

Affiliations

1 Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA. zhipengl@usc.edu.
2 Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, 90089, USA. zhipengl@usc.edu.
3 Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA.
4 Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
5 Synthetic Biology Department, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, PR China.
6 Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, 22252, Saudi Arabia.
7 Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA. howchang@stanford.edu.
8 Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA. howchang@stanford.edu.
9 Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305, USA. howchang@stanford.edu.

PMID: 33268787 DOI: 10.1038/s41467-020-20040-3

Abstract

Long noncoding RNAs are thought to regulate gene expression by organizing protein complexes through unclear mechanisms. XIST controls the inactivation of an entire X chromosome in female placental mammals. Here we develop and integrate several orthogonal structure-interaction methods to demonstrate that XIST RNA-protein complex folds into an evolutionarily conserved modular architecture. Chimeric RNAs and clustered protein binding in fRIP and eCLIP experiments align with long-range RNA secondary structure, revealing discrete XIST domains that interact with distinct sets of effector proteins. CRISPR-Cas9-mediated permutation of the Xist A-repeat location shows that A-repeat serves as a nucleation center for multiple Xist-associated proteins and m⁶A modification. Thus modular architecture plays an essential role, in addition to sequence motifs, in determining the specificity of RBP binding and m⁶A modification. Together, this work builds a comprehensive structure-function model for the XIST RNA-protein complex, and suggests a general strategy for mechanistic studies of large ribonucleoprotein assemblies.

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