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University of California, San Diego
UNIVERSITY OF CALIFORNIA, SAN DIEGO The post-terminal differentiation fate of RNAs revealed by next-generation sequencing A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Biomedical Sciences by Gloria Kuo Lefkowitz Committee in Charge: Professor Benjamin D. Yu, Chair Professor Richard Gallo Professor Bruce A. Hamilton Professor Miles F. Wilkinson Professor Eugene Yeo 2012 Copyright Gloria Kuo Lefkowitz, 2012 All rights reserved. The Dissertation of Gloria Kuo Lefkowitz is approved, and it is acceptable in quality and form for publication on microfilm and electronically: __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ Chair University of California, San Diego 2012 iii DEDICATION Ma and Ba, for your early indulgence and support. Matt and James, for choosing more practical callings. Roy, my love, for patiently sharing the ups and downs of this journey. iv EPIGRAPH It is foolish to tear one's hair in grief, as though sorrow would be made less by baldness. ~Cicero v TABLE OF CONTENTS Signature Page .............................................................................................................. iii Dedication .................................................................................................................... -
Transcription-Factor Polymorphism Associated with Tissue-Specific Gene
bioRxiv preprint doi: https://doi.org/10.1101/405936; this version posted August 31, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. TF-TWAS: Transcription-factor polymorphism associated with tissue-specific gene expression Yi-Ching Tang 1, Assaf Gottlieb 1* 1 Center for precision health, School of Biomedical informatics, University of Texas Health Science Center at Houston, Houston, TX, 77030 * Corresponding author: Assaf Gottlieb, Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center in Houston, 7000 Fannin st, Houston, TX, 77030 Email: [email protected] Tel: +1-(713) 5003698 Running Title: TF-TWAS: TF polymorphism affecting gene expression Keywords: “transcriptome-wide association studies”, “TWAS”, “Transcription Factor polymorphism” bioRxiv preprint doi: https://doi.org/10.1101/405936; this version posted August 31, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract Transcriptional regulation is associated with a broad range of diseases. Methods associating genetic polymorphism with gene transcription levels offer key insights for understanding the transcriptional regulation plan. The majority of gene imputation methods focus on modeling polymorphism in the cis regions of the gene, partially owing to the large genetic search space. We hypothesize that polymorphism within transcription factors (TFs) may help explain transcription levels of their transcribed genes. -
Functional Annotations of Single-Nucleotide Polymorphism
CLINICAL RESEARCH e-ISSN 1643-3750 © Med Sci Monit, 2020; 26: e922710 DOI: 10.12659/MSM.922710 Received: 2020.01.08 Accepted: 2020.02.20 Functional Annotations of Single-Nucleotide Available online: 2020.03.30 Published: 2020.05.25 Polymorphism (SNP)-Based and Gene-Based Genome-Wide Association Studies Show Genes Affecting Keratitis Susceptibility Authors’ Contribution: BCDEF 1 Yue Xu* 1 Department of Ophthalmology, First Affiliated Hospital of Soochow University, Study Design A BCDEF 2 Xiao-Lin Yang* Suzhou, Jiangsu, P.R. China Data Collection B 2 Center for Genetic Epidemiology and Genomics, School of Public Health, Medical Statistical Analysis C BCD 1 Xiao-Long Yang College of Soochow University, Suzhou, Jiangsu, P.R. China Data Interpretation D BC 1 Ya-Ru Ren Manuscript Preparation E BC 1 Xin-Yu Zhuang Literature Search F Funds Collection G ADE 2 Lei Zhang ADE 1 Xiao-Feng Zhang * Yue Xu and Xiao-Lin Yang contributed equally Corresponding Authors: Xiao-Feng Zhang, e-mail: [email protected], Lei Zhang, e-mail: [email protected] Source of support: Departmental sources Background: Keratitis is a complex condition in humans and is the second most common cause of legal blindness worldwide. Material/Methods: To reveal the genomic loci underlying keratitis, we performed functional annotations of SNP-based and gene- based genome-wide association studies of keratitis in the UK Biobank (UKB) cohort with 337 199 subjects of European ancestry. Results: The publicly available SNP-based association results showed a total of 34 SNPs, from 14 distinct loci, associated with keratitis in the UKB. Gene-based association analysis identified 2 significant genes:IQCF3 (p=2.0×10–6) and SOD3 (p=2.0×10–6). -
Functionally Diverse Dendritic Mrnas Rapidly Associate with Ribosomes Following a Novel Experience
ARTICLE Received 19 Feb 2014 | Accepted 24 Jun 2014 | Published 29 Jul 2014 DOI: 10.1038/ncomms5510 Functionally diverse dendritic mRNAs rapidly associate with ribosomes following a novel experience Joshua A. Ainsley1, Laurel Drane1, Jonathan Jacobs1, Kara A. Kittelberger1,w & Leon G. Reijmers1 The subcellular localization and translation of messenger RNA (mRNA) supports functional differentiation between cellular compartments. In neuronal dendrites, local translation of mRNA provides a rapid and specific mechanism for synaptic plasticity and memory forma- tion, and might be involved in the pathophysiology of certain brain disorders. Despite the importance of dendritic mRNA translation, little is known about which mRNAs can be translated in dendrites in vivo and when their translation occurs. Here we collect ribosome- bound mRNA from the dendrites of CA1 pyramidal neurons in the adult mouse hippocampus. We find that dendritic mRNA rapidly associates with ribosomes following a novel experience consisting of a contextual fear conditioning trial. High throughput RNA sequencing followed by machine learning classification reveals an unexpected breadth of ribosome-bound den- dritic mRNAs, including mRNAs expected to be entirely somatic. Our findings are in agree- ment with a mechanism of synaptic plasticity that engages the acute local translation of functionally diverse dendritic mRNAs. 1 Department of Neuroscience, Tufts University, Boston, Massachusetts 02111, USA. w Present address: Center for Translational Social Neuroscience, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30322, USA. Correspondence and requests for materials should be addressed to L.R. (email: [email protected]). NATURE COMMUNICATIONS | 5:4510 | DOI: 10.1038/ncomms5510 | www.nature.com/naturecommunications 1 & 2014 Macmillan Publishers Limited. -
Histone-Related Genes Are Hypermethylated in Lung Cancer
Published OnlineFirst October 1, 2019; DOI: 10.1158/0008-5472.CAN-19-1019 Cancer Genome and Epigenome Research Histone-Related Genes Are Hypermethylated in Lung Cancer and Hypermethylated HIST1H4F Could Serve as a Pan-Cancer Biomarker Shihua Dong1,Wei Li1, Lin Wang2, Jie Hu3,Yuanlin Song3, Baolong Zhang1, Xiaoguang Ren1, Shimeng Ji3, Jin Li1, Peng Xu1, Ying Liang1, Gang Chen4, Jia-Tao Lou2, and Wenqiang Yu1 Abstract Lung cancer is the leading cause of cancer-related deaths lated in all 17 tumor types from TCGA datasets (n ¼ 7,344), worldwide. Cytologic examination is the current "gold stan- which was further validated in nine different types of cancer dard" for lung cancer diagnosis, however, this has low sensi- (n ¼ 243). These results demonstrate that HIST1H4F can tivity. Here, we identified a typical methylation signature of function as a universal-cancer-only methylation (UCOM) histone genes in lung cancer by whole-genome DNA methyl- marker, which may aid in understanding general tumorigen- ation analysis, which was validated by The Cancer Genome esis and improve screening for early cancer diagnosis. Atlas (TCGA) lung cancer cohort (n ¼ 907) and was further confirmed in 265 bronchoalveolar lavage fluid samples with Significance: These findings identify a new biomarker for specificity and sensitivity of 96.7% and 87.0%, respectively. cancer detection and show that hypermethylation of histone- More importantly, HIST1H4F was universally hypermethy- related genes seems to persist across cancers. Introduction to its low specificity, LDCT is far from satisfactory as a screening tool for clinical application, similar to other currently used cancer Lung cancer is one of the most common malignant tumors and biomarkers, such as carcinoembryonic antigen (CEA), neuron- the leading cause of cancer-related deaths worldwide (1, 2). -
A Yeast Phenomic Model for the Influence of Warburg Metabolism on Genetic Buffering of Doxorubicin Sean M
Santos and Hartman Cancer & Metabolism (2019) 7:9 https://doi.org/10.1186/s40170-019-0201-3 RESEARCH Open Access A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin Sean M. Santos and John L. Hartman IV* Abstract Background: The influence of the Warburg phenomenon on chemotherapy response is unknown. Saccharomyces cerevisiae mimics the Warburg effect, repressing respiration in the presence of adequate glucose. Yeast phenomic experiments were conducted to assess potential influences of Warburg metabolism on gene-drug interaction underlying the cellular response to doxorubicin. Homologous genes from yeast phenomic and cancer pharmacogenomics data were analyzed to infer evolutionary conservation of gene-drug interaction and predict therapeutic relevance. Methods: Cell proliferation phenotypes (CPPs) of the yeast gene knockout/knockdown library were measured by quantitative high-throughput cell array phenotyping (Q-HTCP), treating with escalating doxorubicin concentrations under conditions of respiratory or glycolytic metabolism. Doxorubicin-gene interaction was quantified by departure of CPPs observed for the doxorubicin-treated mutant strain from that expected based on an interaction model. Recursive expectation-maximization clustering (REMc) and Gene Ontology (GO)-based analyses of interactions identified functional biological modules that differentially buffer or promote doxorubicin cytotoxicity with respect to Warburg metabolism. Yeast phenomic and cancer pharmacogenomics data were integrated to predict differential gene expression causally influencing doxorubicin anti-tumor efficacy. Results: Yeast compromised for genes functioning in chromatin organization, and several other cellular processes are more resistant to doxorubicin under glycolytic conditions. Thus, the Warburg transition appears to alleviate requirements for cellular functions that buffer doxorubicin cytotoxicity in a respiratory context. -
Functional Annotation of Human Long Noncoding Rnas Using Chromatin
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.13.426305; this version posted January 14, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Funconal annotaon of human long noncoding RNAs using chroman conformaon data Saumya Agrawal1, Tanvir Alam2, Masaru Koido1,3, Ivan V. Kulakovskiy4,5, Jessica Severin1, Imad ABugessaisa1, Andrey Buyan5,6, Josee Dos&e7, Masayoshi Itoh1,8, Naoto Kondo9, Yunjing Li10, Mickaël Mendez11, Jordan A. Ramilowski1,12, Ken Yagi1, Kayoko Yasuzawa1, CHi Wai Yip1, Yasushi Okazaki1, MicHael M. Ho9man11,13,14,15, Lisa Strug10, CHung CHau Hon1, CHikashi Terao1, Takeya Kasukawa1, Vsevolod J. Makeev4,16, Jay W. SHin1, Piero Carninci1, MicHiel JL de Hoon1 1RIKEN Center for Integra&ve Medical Sciences, YokoHama, Japan. 2College of Science and Engineering, Hamad Bin KHalifa University, DoHa, Qatar. 3Ins&tute of Medical Science, THe University of Tokyo, Tokyo, Japan. 4Vavilov Ins&tute of General Gene&cs, Russian Academy of Sciences, Moscow, Russia. 5Ins&tute of Protein ResearcH, Russian Academy of Sciences, PusHcHino, Russia. 6Faculty of Bioengineering and Bioinforma&cs, Lomonosov Moscow State University, Moscow, Russia. 7Department of BiocHemistry, Rosalind and Morris Goodman Cancer ResearcH Center, McGill University, Montréal, QuéBec, Canada. 8RIKEN Preven&ve Medicine and Diagnosis Innova&on Program, Wako, Japan. 9RIKEN Center for Life Science TecHnologies, YokoHama, Japan. 10Division of Biosta&s&cs, Dalla Lana ScHool of PuBlic HealtH, University of Toronto, Toronto, Ontario, Canada. 11Department of Computer Science, University of Toronto, Toronto, Ontario, Canada. 12Advanced Medical ResearcH Center, YokoHama City University, YokoHama, Japan. -
2020 UTGCP Research Newsletter
O C T O B E R 2 0 2 0 | I S S U E N O . 2 UTGCP ANNUAL RESEARCH NEWSLETTER Celebrating Excellence in Genetic Counseling Research shout-out to our students completing their M.S. research during a pandemic what's inside: Hyperlinks to the complete abstracts and conferences are Research from our students included when available. (classes of 2020 & 2021) Please consider supporting our Research submitted by alumni students' research efforts & faculty (Jan-Dec 2019) through the UTGCP Research & Education Fund at launch.uth.edu/utgcp O C T O B E R 2 0 2 0 | I S S U E N O . 2 CONGRATS CLASS OF 2020! Thesis defense looked a little different this year... Sarah Burke - “Understanding genetic counselors' approaches to direct-to- consumer testing for hereditary Emily Stiglich - “Genetic counselors' experiences with breast cancer" and approaches to discordant genotypic and phenotypic Advisor: Maureen sex" Mork, MS, CGC Advisor: Victoria Wagner, MS, CGC Wendi Betting - “Factors that impact uptake of carrier screening by male Autumn Vara - reproductive partners of female “Frequency of prenatal patients" copy number variants involving Advisor: Meagan Choates, MS, CGC the sex chromosomes in a clinical setting" Advisor: David F. Rodriguez- Buritica, MD Addison Johnson - “Assessing patient attitudes toward genetic testing for hereditary hematologic malignancies" Advisor: Sarah Bannon, MS, CGC Aranza Gonzalez- Caroline Bertsch - “The course Cendejas - of acute stress disorder and “Implementation of post traumatic stress disorder genetic carrier in patients and infants in the screening in the OB population: healthcare neonatal intensive care unit cost impact and Bradley Power - “Investigating medical with or without genetic recommendation examiner's practices: genetic evaluation for anomalies" adherence" fatal acute aortic dissection" Advisor: Jennifer Czerwinski, Advisor: Rebecca Carter, MS, CGC Advisor: Krista Qualmann, MS, CGC MS, CGC O C T O B E R 2 0 2 0 | I S S U E N O . -
A Master Autoantigen-Ome Links Alternative Splicing, Female Predilection, and COVID-19 to Autoimmune Diseases
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.30.454526; this version posted August 4, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. A Master Autoantigen-ome Links Alternative Splicing, Female Predilection, and COVID-19 to Autoimmune Diseases Julia Y. Wang1*, Michael W. Roehrl1, Victor B. Roehrl1, and Michael H. Roehrl2* 1 Curandis, New York, USA 2 Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA * Correspondence: [email protected] or [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.07.30.454526; this version posted August 4, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract Chronic and debilitating autoimmune sequelae pose a grave concern for the post-COVID-19 pandemic era. Based on our discovery that the glycosaminoglycan dermatan sulfate (DS) displays peculiar affinity to apoptotic cells and autoantigens (autoAgs) and that DS-autoAg complexes cooperatively stimulate autoreactive B1 cell responses, we compiled a database of 751 candidate autoAgs from six human cell types. At least 657 of these have been found to be affected by SARS-CoV-2 infection based on currently available multi-omic COVID data, and at least 400 are confirmed targets of autoantibodies in a wide array of autoimmune diseases and cancer. -
Rap1-Mediated Chromatin and Gene Expression Changes at Senescence
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2019 Rap1-Mediated Chromatin And Gene Expression Changes At Senescence Shufei Song University of Pennsylvania Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Biochemistry Commons, and the Cell Biology Commons Recommended Citation Song, Shufei, "Rap1-Mediated Chromatin And Gene Expression Changes At Senescence" (2019). Publicly Accessible Penn Dissertations. 3557. https://repository.upenn.edu/edissertations/3557 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/3557 For more information, please contact [email protected]. Rap1-Mediated Chromatin And Gene Expression Changes At Senescence Abstract ABSTRACT RAP1-MEDIATED CHROMATIN AND GENE EXPRESSION CHANGES AT SENESCENCE The telomeric protein Rap1 has been extensively studied for its roles as a transcriptional activator and repressor. Indeed, in both yeast and mammals, Rap1 is known to bind throughout the genome to reorganize chromatin and regulate gene transcription. Previously, our lab published evidence that Rap1 plays important roles in cellular senescence. In telomerase-deficient S. cerevisiae, Rap1 relocalizes from telomeres and subtelomeres to new Rap1 target at senescence (NRTS). This leads to two types of histone loss: Rap1 lowers global histone levels by repressing histone gene transcription and it also results in local nucleosome displacement at the promoters of the activated NRTS. Here, I examine mechanisms of site-specific histone loss by presenting evidence that Rap1 can directly interact with histone tetramers H3/H4, and map this interaction to a three-amino-acid-patch within the DNA binding domain. Functional studies are performed in vivo using a mutant form of Rap1 with weakened histone interactions, and deficient promoter clearance as well as blunted gene activation is observed, indicating that direct Rap1-H3/H4 interactions are involved in nucleosome displacement. -
Multi-Trait Analysis for Genome-Wide Association Study of Five Psychiatric
Wu et al. Translational Psychiatry (2020) 10:209 https://doi.org/10.1038/s41398-020-00902-6 Translational Psychiatry ARTICLE Open Access Multi-trait analysis for genome-wide association study of five psychiatric disorders Yulu Wu1,2, Hongbao Cao3, Ancha Baranova4,5, Hailiang Huang6,7,ShengLi8,LeiCai8,ShuquanRao9, Minhan Dai1,2, Min Xie1,2,YikaiDou1,2, Qinjian Hao 10,LingZhu1,2, Xiangrong Zhang11,YinYao12, Fuquan Zhang 13, Mingqing Xu8,14 and Qiang Wang 1,2 Abstract We conducted a cross-trait meta-analysis of genome-wide association study on schizophrenia (SCZ) (n = 65,967), bipolar disorder (BD) (n = 41,653), autism spectrum disorder (ASD) (n = 46,350), attention deficit hyperactivity disorder (ADHD) (n = 55,374), and depression (DEP) (n = 688,809). After the meta-analysis, the number of genomic loci increased from 14 to 19 in ADHD, from 3 to 10 in ASD, from 45 to 57 in DEP, from 8 to 54 in BD, and from 64 to 87 in SCZ. We observed significant enrichment of overlapping genes among different disorders and identified a panel of cross-disorder genes. A total of seven genes were found being commonly associated with four out of five psychiatric conditions, namely GABBR1, GLT8D1, HIST1H1B, HIST1H2BN, HIST1H4L, KCNB1, and DCC. The SORCS3 gene was highlighted due to the fact that it was involved in all the five conditions of study. Analysis of correlations unveiled the existence of two clusters of related psychiatric conditions, SCZ and BD that were separate from the other three traits, and formed another group. Our results may provide a new insight for genetic basis of the five psychiatric disorders. -
A Mutation in Histone H2B Represents a New Class of Oncogenic Driver
Published OnlineFirst July 23, 2019; DOI: 10.1158/2159-8290.CD-19-0393 RESEARCH ARTICLE A Mutation in Histone H2B Represents a New Class of Oncogenic Driver Richard L. Bennett1, Aditya Bele1, Eliza C. Small2, Christine M. Will2, Behnam Nabet3, Jon A. Oyer2, Xiaoxiao Huang1,4, Rajarshi P. Ghosh5, Adrian T. Grzybowski6, Tao Yu7, Qiao Zhang8, Alberto Riva9, Tanmay P. Lele8, George C. Schatz4, Neil L. Kelleher4, Alexander J. Ruthenburg6, Jan Liphardt5, and Jonathan D. Licht1 Downloaded from cancerdiscovery.aacrjournals.org on September 30, 2021. © 2019 American Association for Cancer Research. Published OnlineFirst July 23, 2019; DOI: 10.1158/2159-8290.CD-19-0393 ABSTRACT By examination of the cancer genomics database, we identified a new set of mutations in core histones that frequently recur in cancer patient samples and are predicted to disrupt nucleosome stability. In support of this idea, we characterized a glutamate to lysine mutation of histone H2B at amino acid 76 (H2B-E76K), found particularly in bladder and head and neck cancers, that disrupts the interaction between H2B and H4. Although H2B-E76K forms dimers with H2A, it does not form stable histone octamers with H3 and H4 in vitro, and when recon- stituted with DNA forms unstable nucleosomes with increased sensitivity to nuclease. Expression of the equivalent H2B mutant in yeast restricted growth at high temperature and led to defective nucleosome-mediated gene repression. Significantly, H2B-E76K expression in the normal mammary epithelial cell line MCF10A increased cellular proliferation, cooperated with mutant PIK3CA to pro- mote colony formation, and caused a significant drift in gene expression and fundamental changes in chromatin accessibility, particularly at gene regulatory elements.