An XIST-related small RNA regulates KRAS G-quadruplex formation beyond X-inactivation
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Yuli C. Chang1,2, Chien-Chih Chiu3, Chung-Yee Yuo1,6, Wen-Ling Chan4,8, Ya-Sian Chang4,11,12, Wen-Hsin Chang1,7, Shou-Mei Wu5, Han-Lin Chou3, Ta-Chih Liu1,2,7, Chi-Yu Lu9, Wen-Kuang Yang10, Jan-Gowth Chang4,11,12
1Graduate Institutes of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
2Division of Cytogenetics, Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
3Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
4Epigenome Research Center, China Medical University and Hospital, Taichung, Taiwan
5School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
6Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
7Division of Hematology/Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
8Department of Bioinformatics and Medical Enginerring, Asia University, Taichung, Taiwan
9Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Taiwan
10Cell/Gene Therapy Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
11Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
12School of Medicine, China Medical University, Taichung, Taiwan
Keywords: XPi2, non-coding RNA, XIST, G-quadruplexes
Received: March 01, 2016 Accepted: October 31, 2016 Published: November 17, 2016
X-inactive-specific transcript (XIST), a long non-coding RNA, is essential for the initiation of X-chromosome inactivation. However, little is known about other roles of XIST in the physiological process in eukaryotic cells. In this study, the bioinformatics approaches revealed XIST could be processed into a small non-coding RNA XPi2. The XPi2 RNA was confirmed by a northern blot assay; its expression was gender-independent, suggesting the role of XPi2 was beyond X-chromosome inactivation. The pull-down assay combined with LC-MS-MS identified two XPi2-associated proteins, nucleolin and hnRNP A1, connected to the formation of G-quadruplex. Moreover, the microarray data showed the knockdown of XPi2 down-regulated the KRAS pathway. Consistently, we tested the expression of ten genes, including KRAS, which was correlated with a G-quadruplex formation and found the knockdown of XPi2 caused a dramatic decrease in the transcription level of KRAS among the ten genes. The results of CD/NMR assay also supported the interaction of XPi2 and the polypurine-polypyrimidine element of KRAS. Accordingly, XPi2 may stimulate the KRAS expression by attenuating G-quadruplex formation. Our present work sheds light on the novel role of small RNA XPi2 in modulating the G-quadruplex formation which may play some essential roles in the KRAS- associated carcinogenesis.
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