PT  - JOURNAL ARTICLE
AU  - Zhipeng Lu
AU  - Jimmy K. Guo
AU  - Yuning Wei
AU  - Diana R. Dou
AU  - Brian Zarnegar
AU  - Qing Ma
AU  - Rui Li
AU  - Yang Zhao
AU  - Fan Liu
AU  - Hani Choudhry
AU  - Paul A. Khavari
AU  - Howard Y. Chang
TI  - Structural modularity of the XIST ribonucleoprotein complex
AID  - 10.1101/837229
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 837229
4099  - http://biorxiv.org/content/early/2019/11/24/837229.short
4100  - http://biorxiv.org/content/early/2019/11/24/837229.full
AB  - 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.