Xinshu Grace Xiao

Laboratory Address:
Terasaki Life Sciences Building, 2045

Office Address:
Terasaki Life Sciences Building, 2000E
Los Angeles,

Affiliations
Affiliations
Professor, Integrative Biology and Physiology
Member, Bioinformatics GPB Home Area, Gene Regulation GPB Home Area, JCCC Gene Regulation Program Area, Molecular, Cellular & Integrative Physiology GPB Home Area
Research Interests
With similar number of genes as in simpler organisms, mammals demonstrate an amazing degree of phenotypic diversity. Mammalian gene expression is under tight regulation temporally and spatially, which contributes to the formation of different cell types, tissues, and organs. Gene regulation involves a complex network of players, including multiple DNA, RNA sequence elements and RNA and protein factors. These regulators interact with each other and carry out combinatorial regulatory functions. Our lab uses both computational and experimental approaches to study the biology of gene regulation from a systems point of view. Our current focus pertains to the regulation of gene expression at the RNA level via the process of pre-mRNA splicing and other post-transcriptional (or co-transcriptional) mechanisms. Splicing is a critical step enabling diversity in gene expression programs. At least half of all human genes undergo alternative splicing which allows multiple gene products with potentially different functions to be produced from a single gene locus. We are currently investigating splicing regulatory mechanisms using comparative genomics, high-throughput technologies, such as deep sequencing and microarrays, and systems level computational analysis, such as system identification and modeling approaches. A long-term goal of our research is to better understand the involvement of splicing in gene expression programs of different disease models.
Publications
Hsiao Yun-Hua Esther, Bahn Jae Hoon, Lin Xianzhi, Chan Tak-Ming, Wang Rena, Xiao Xinshu Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins. Genome research. 2016; 26(4): 440-50.
Cass Ashley A, Bahn Jae Hoon, Lee Jae-Hyung, Greer Christopher, Lin Xianzhi, Kim Yong, Hsiao Yun-Hua Esther, Xiao Xinshu Global analyses of endonucleolytic cleavage in mammals reveal expanded repertoires of cleavage-inducing small RNAs and their targets. Nucleic acids research. 2016; 44(7): 3253-63.
Fuxjager Matthew J, Lee Jae-Hyung, Chan Tak-Ming, Bahn Jae Hoon, Chew Jenifer G, Xiao Xinshu, Schlinger Barney A Research Resource: Hormones, Genes, and Athleticism: Effect of Androgens on the Avian Muscular Transcriptome. Molecular endocrinology (Baltimore, Md.). 2016; 30(2): 254-71.
Gao Chen, Ren Shuxun, Lee Jae-Hyung, Qiu Jinsong, Chapski Douglas J, Rau Christoph D, Zhou Yu, Abdellatif Maha, Nakano Astushi, Vondriska Thomas M, Xiao Xinshu, Fu Xiang-Dong, Chen Jau-Nian, Wang Yibin RBFox1-mediated RNA splicing regulates cardiac hypertrophy and heart failure. The Journal of clinical investigation. 2016; 126(1): 195-206.
Bhate Amruta, Parker Darren J, Bebee Thomas W, Ahn Jaegyoon, Arif Waqar, Rashan Edrees H, Chorghade Sandip, Chau Anthony, Lee Jae-Hyung, Anakk Sayeepriyadarshini, Carstens Russ P, Xiao Xinshu, Kalsotra Auinash ESRP2 controls an adult splicing programme in hepatocytes to support postnatal liver maturation. Nature communications. 2015; 6(24): 8768.
Ahn Jaegyoon, Xiao Xinshu RASER: reads aligner for SNPs and editing sites of RNA. Bioinformatics (Oxford, England). 2015; 31(24): 3906-13.
Zhang Qing, Xiao Xinshu Genome sequence-independent identification of RNA editing sites. Nature methods. 2015; 12(4): 347-50.
Bahn Jae Hoon, Ahn Jaegyoon, Lin Xianzhi, Zhang Qing, Lee Jae-Hyung, Civelek Mete, Xiao Xinshu Genomic analysis of ADAR1 binding and its involvement in multiple RNA processing pathways. Nature communications. 2015; 6(6): 6355.
Li Ziwei, Yu Juehua, Hosohama Linzi, Nee Kevin, Gkountela Sofia, Chaudhari Sonal, Cass Ashley A, Xiao Xinshu, Clark Amander T The Sm protein methyltransferase PRMT5 is not required for primordial germ cell specification in mice. The EMBO journal. 2015; 34(6): 748-58.
Lin Xianzhi, Lo Hsien-Chun, Wong David T W, Xiao Xinshu Noncoding RNAs in human saliva as potential disease biomarkers. Frontiers in genetics. 2015; 6(1): 175.
Romay Milagros C, Che Nam, Becker Scott N, Pouldar Delila, Hagopian Raffi, Xiao Xinshu, Lusis Aldons J, Berliner Judith A, Civelek Mete Regulation of NF-κB signaling by oxidized glycerophospholipid and IL-1β induced miRs-21-3p and -27a-5p in human aortic endothelial cells. Journal of lipid research. 2015; 56(1): 38-50.
Bahn Jae Hoon, Zhang Qing, Li Feng, Chan Tak-Ming, Lin Xianzhi, Kim Yong, Wong David T W, Xiao Xinshu The landscape of microRNA, Piwi-interacting RNA, and circular RNA in human saliva. Clinical chemistry. 2015; 61(1): 221-30.
Xu Yilin, Gao Xin D, Lee Jae-Hyung, Huang Huilin, Tan Haiyan, Ahn Jaegyoon, Reinke Lauren M, Peter Marcus E, Feng Yue, Gius David, Siziopikou Kalliopi P, Peng Junmin, Xiao Xinshu, Cheng Chonghui Cell type-restricted activity of hnRNPM promotes breast cancer metastasis via regulating alternative splicing. Genes & development. 2014; 28(11): 1191-203.
Xiao Xinshu Grace, Touma Marlin, Wang Yibin Decoding the noncoding transcripts in human heart failure. Circulation. 2014; 129(9): 958-60.
Lee Jae-Hyung, Ang Jason K, Xiao Xinshu Analysis and design of RNA sequencing experiments for identifying RNA editing and other single-nucleotide variants. RNA (New York, N.Y.). 2013; 19(6): 725-32.
Chan Tak-Ming, Lo Leung-Yau, Sze-To Ho-Yin, Leung Kwong-Sak, Xiao Xinshu, Wong Man-Hon Modeling associated protein-DNA pattern discovery with unified scores. IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM. 2013; 10(3): 696-707.
Wang Yang, Xiao Xinshu, Zhang Jianming, Choudhury Rajarshi, Robertson Alex, Li Kai, Ma Meng, Burge Christopher B, Wang Zefeng A complex network of factors with overlapping affinities represses splicing through intronic elements. Nature structural & molecular biology. 2013; 20(1): 36-45.
Bass Brenda, Hundley Heather, Li Jin Billy, Peng Zhiyu, Pickrell Joe, Xiao Xinshu Grace, Yang Li The difficult calls in RNA editing. Interviewed by H Craig Mak. Nature biotechnology. 2012; 30(12): 1207-9.
Wang Yang, Ma Meng, Xiao Xinshu, Wang Zefeng Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules. Nature structural & molecular biology. 2012; 19(10): 1044-52.
Anderson Erik S, Lin Chia-Ho, Xiao Xinshu, Stoilov Peter, Burge Christopher B, Black Douglas L The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B. RNA (New York, N.Y.). 2012; 18(5): 1041-9.
Li Gang, Bahn Jae Hoon, Lee Jae-Hyung, Peng Guangdun, Chen Zugen, Nelson Stanley F, Xiao Xinshu Identification of allele-specific alternative mRNA processing via transcriptome sequencing. Nucleic acids research. 2012; 18(5): .
Bahn Jae Hoon, Lee Jae-Hyung, Li Gang, Greer Christopher, Peng Guangdun, Xiao Xinshu Accurate identification of A-to-I RNA editing in human by transcriptome sequencing. Genome research. 2012; 22(1): 142-50.
Gomez Gustavo, Lee Jae-Hyung, Veldman Matthew B, Lu Jing, Xiao Xinshu, Lin Shuo Identification of vascular and hematopoietic genes downstream of etsrp by deep sequencing in zebrafish. PloS one. 2012; 7(3): e31658.
Lee Jae-Hyung, Gao Chen, Peng Guangdun, Greer Christopher, Ren Shuxun, Wang Yibin, Xiao Xinshu Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts. Circulation research. 2011; 109(12): 1332-41.
Xiao Xinshu, Lee Jae-Hyung Systems analysis of alternative splicing and its regulation. Wiley interdisciplinary reviews. Systems biology and medicine. 2011; 2(5): 550-65.
Puppione Donald L, Ryan Christopher M, Bassilian Sara, Souda Puneet, Xiao Xinshu, Ryder Oliver A, Whitelegge Julian P Detection of two distinct forms of apoC-I in great apes. Comparative biochemistry and physiology. Part D, Genomics & proteomics. 2010; 5(1): 73-9.
Xiao X, Wang Z, Jang M, Nutiu R, Wang ET, Burge CB Splice site strength-dependent activity and genetic buffering by poly-G runs. Nature Structural & Molecular Biology 2009; 16(10): 1094-1100.
Kalsotra Auinash, Xiao Xinshu, Ward Amanda J, Castle John C, Johnson Jason M, Burge Christopher B, Cooper Thomas A A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart. Proceedings of the National Academy of Sciences of the United States of America. 2008; 105(51): 20333-8.
Xiao Xinshu, Wang Zefeng, Jang Minyoung, Burge Christopher B Coevolutionary networks of splicing cis-regulatory elements. Proceedings of the National Academy of Sciences of the United States of America. 2007; 104(47): 18583-8.
Calarco John A, Xing Yi, Cáceres Mario, Calarco Joseph P, Xiao Xinshu, Pan Qun, Lee Christopher, Preuss Todd M, Blencowe Benjamin J Global analysis of alternative splicing differences between humans and chimpanzees. Genes & development. 2007; 21(22): 2963-75.
Stadler Michael B, Shomron Noam, Yeo Gene W, Schneider Aniket, Xiao Xinshu, Burge Christopher B Inference of splicing regulatory activities by sequence neighborhood analysis. PLoS genetics. 2006; 2(11): e191.
Xiao Xinshu, Mukkamala Ramakrishna, Cohen Richard J A weighted-principal component regression method for the identification of physiologic systems. IEEE transactions on bio-medical engineering. 2006; 53(8): 1521-30.
Wang Zefeng, Xiao Xinshu, Van Nostrand Eric, Burge Christopher B General and specific functions of exonic splicing silencers in splicing control. Molecular cell. 2006; 23(1): 61-70.
Xiao Xinshu, Mullen Thomas J, Mukkamala Ramakrishna System identification: a multi-signal approach for probing neural cardiovascular regulation. Physiological measurement. 2005; 26(3): R41-71.
Xiao Xinshu, Li Ying, Mukkamala Ramakrishna A model order selection criterion with applications to cardio-respiratory-renal systems. IEEE transactions on bio-medical engineering. 2005; 52(3): 445-53.