Structural modularity of the XIST ribonucleoprotein complex

• Published in: Nature communications Vol. 11; no. 1; pp. 6163 - 14
• Main Authors: Lu, Zhipeng, Guo, Jimmy K., Wei, Yuning, Dou, Diana R., Zarnegar, Brian, Ma, Qing, Li, Rui, Zhao, Yang, Liu, Fan, Choudhry, Hani, Khavari, Paul A., Chang, Howard Y.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 02-12-2020; Nature Publishing Group; Nature Portfolio
• Subjects: 42/100; 42/41; 45/90; 45/91; 631/114/2401; 631/45/500; Adenine - analogs & derivatives; Adenine - metabolism; Animals; Base Sequence; Binding; Cell Line; Chromosomes; Conserved Sequence; CRISPR; CRISPR-Cas Systems; Cross-Linking Reagents; Domains; Female; Ficusin - chemistry; Formaldehyde - chemistry; Gene expression; Gene Knock-In Techniques; Humanities and Social Sciences; Humans; Inactivation; K562 Cells; Male; Mice; Modular structures; Modularity; Mouse Embryonic Stem Cells - cytology; Mouse Embryonic Stem Cells - metabolism; multidisciplinary; N6-methyladenosine; Nucleation; Nucleic Acid Conformation; Permutations; Pregnancy; Protein structure; Proteins; Ribonucleic acid; Ribonucleoproteins - chemistry; Ribonucleoproteins - genetics; Ribonucleoproteins - metabolism; RNA; RNA, Long Noncoding - chemistry; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; Science; Science (multidisciplinary); Secondary structure; Sequence Analysis, RNA; Structure-function relationships; X chromosomes
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-20040-3

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 m
6
A modification. Thus modular architecture plays an essential role, in addition to sequence motifs, in determining the specificity of RBP binding and m
6
A 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.
The long noncoding RNA XIST plays a central role in sex-specific gene expression in humans by silencing one of two X chromosomes in female cells. Here the authors show that higher order secondary structure creates the modular domain structure of XIST ribonucleoprotein complex and spatial separation of functions.