title: An XIST-related small RNA regulates KRAS G-quadruplex formation beyond X-inactivation.
abstract: 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.
authors.affiliation: Graduate Institutes of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.|Division of Cytogenetics, Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
authors.forename: Yuli C
authors.initials: YC
authors.lastname: Chang
authors.affiliation: Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan.
authors.forename: Chien-Chih
authors.initials: CC
authors.lastname: Chiu
authors.affiliation: Graduate Institutes of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.|Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan.
authors.forename: Chung-Yee
authors.initials: CY
authors.lastname: Yuo
authors.affiliation: Epigenome Research Center, China Medical University and Hospital, Taichung, Taiwan.|Department of Bioinformatics and Medical Enginerring, Asia University, Taichung, Taiwan.
authors.forename: Wen-Ling
authors.initials: WL
authors.lastname: Chan
authors.affiliation: Epigenome Research Center, China Medical University and Hospital, Taichung, Taiwan.|Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.|School of Medicine, China Medical University, Taichung, Taiwan.
authors.forename: Ya-Sian
authors.initials: YS
authors.lastname: Chang
authors.affiliation: Graduate Institutes of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.|Division of Hematology/Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
authors.forename: Wen-Hsin
authors.initials: WH
authors.lastname: Chang
authors.affiliation: School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan.
authors.forename: Shou-Mei
authors.initials: SM
authors.lastname: Wu
authors.affiliation: Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan.
authors.forename: Han-Lin
authors.initials: HL
authors.lastname: Chou
authors.affiliation: Graduate Institutes of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.|Division of Cytogenetics, Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.|Division of Hematology/Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
authors.forename: Ta-Chih
authors.initials: TC
authors.lastname: Liu
authors.affiliation: Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Taiwan.
authors.forename: Chi-Yu
authors.initials: CY
authors.lastname: Lu
authors.affiliation: Cell/Gene Therapy Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan.
authors.forename: Wen-Kuang
authors.initials: WK
authors.lastname: Yang
authors.affiliation: Epigenome Research Center, China Medical University and Hospital, Taichung, Taiwan.|Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.|School of Medicine, China Medical University, Taichung, Taiwan.
authors.forename: Jan-Gowth
authors.initials: JG
authors.lastname: Chang
mesh_terms: D045744:Cell Line, Tumor; D005260:Female; D054856:G-Quadruplexes; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D000076245:Heterogeneous Nuclear Ribonucleoprotein A1 / Q000235:genetics / Q000378:metabolism; D006801:Humans; D061986:MCF-7 Cells; D008297:Male; D010750:Phosphoproteins / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D016283:Proto-Oncogene Proteins p21(ras) / Q000235:genetics*; D034622:RNA Interference; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000235:genetics* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics; D049951:X Chromosome Inactivation / Q000235:genetics*; D000097796:Nucleolin
chemical_list: D000076245:Heterogeneous Nuclear Ribonucleoprotein A1; D010750:Phosphoproteins; D016283:Proto-Oncogene Proteins p21(ras); D062085:RNA, Long Noncoding; D058727:RNA, Small Untranslated; D016601:RNA-Binding Proteins; D000097796:Nucleolin; C117307:KRAS protein, human; C077885:XIST non-coding RNA
keywords: G-quadruplexes; XIST; XPi2; non-coding RNA