Structural insights reveal the specific recognition of roX RNA by the dsRNA-binding domains of the RNA helicase MLE and its indispensable role in dosage compensation in Drosophila

• Published in: Nucleic acids research Vol. 47; no. 6; pp. 3142 - 3157
• Main Authors: Lv, Mengqi, Yao, Yixiang, Li, Fudong, Xu, Ling, Yang, Lingna, Gong, Qingguo, Xu, Yong-Zhen, Shi, Yunyu, Fan, Yu-Jie, Tang, Yajun
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 08.04.2019
• Subjects: Animals; Chromosomal Proteins, Non-Histone - chemistry; Chromosomal Proteins, Non-Histone - genetics; DNA Helicases - chemistry; DNA Helicases - genetics; Dosage Compensation, Genetic; Drosophila melanogaster - genetics; Drosophila Proteins - chemistry; Drosophila Proteins - genetics; RNA and RNA-protein complexes; RNA, Double-Stranded - chemistry; RNA, Double-Stranded - genetics; Transcription Factors - chemistry; Transcription Factors - genetics; X Chromosome - genetics
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gky1308

Abstract In Drosophila, dosage compensation globally upregulates the expression of genes located on male single X-chromosome. Maleless (MLE) helicase plays an essential role to incorporate the roX lncRNA into the dosage compensation complex (MSL-DCC), and such function is essentially dependent on its dsRNA-binding domains (dsRBDs). Here, we report a 2.90Å crystal structure of tandem dsRBDs of MLE in complex with a 55mer stem-loop of roX2 (R2H1). MLE dsRBDs bind to R2H1 cooperatively and interact with two successive minor grooves and a major groove of R2H1, respectively. The recognition of R2H1 by MLE dsRBDs involves both shape- and sequence-specificity. Moreover, dsRBD2 displays a stronger RNA affinity than dsRBD1, and mutations of key residues in either MLE dsRBD remarkably reduce their affinities for roX2 both in vitro and in vivo. In Drosophila, the structure-based mle mutations generated using the CRISPR/Cas9 system, are partially male-lethal and indicate the inter-regulation among the components of the MSL-DCC at multiple levels. Hence, our research provides structural insights into the interactions between MLE dsRBDs and R2H1 and facilitates a deeper understanding of the mechanism by which MLE tandem dsRBDs play an indispensable role in specific recognition of roX and the assembly of the MSL-DCC in Drosophila dosage compensation.