DOCSLIB.ORG

Human Nuclear Rnai-Defective 2 (NRDE2) Is an Essential RNA Splicing Factor

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Human Nuclear Rnai-Defective 2 (NRDE2) Is an Essential RNA Splicing Factor Downloaded from rnajournal.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press Human Nuclear RNAi-Defective 2 (NRDE2) is an essential RNA splicing factor Alan L. Jiao,1,2 Roberto Perales,3 Neil T. Umbreit,4 Jeffrey R. Haswell,1,5 Mary E. Piper,6 Brian D. Adams,1,7 David Pellman,4,8,9 Scott Kennedy,3 Frank J. Slack1 * 1: HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA. 2: Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT USA. 3: Department of Genetics, Harvard Medical School, Boston, MA, USA. 4: Department of Cell Biology, Harvard Medical School, Boston, MA, USA. 5: Department of Biological and Biomedical Sciences, Harvard University, Boston, MA, USA. 6: Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA. 7: Current address: Department of Biological Sciences, University at Albany, The State University of New York, Albany, NY, USA. 8: Department of Pediatric Oncology, Dana-Farber Cancer Institute and Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA. 9: Howard Hughes Medical Institute, Chevy Chase, MD, USA. * Correspondence: [email protected] Running title: NRDE2 suppresses intron retention Keywords: Splicing, nuclear RNAi, intron retention, centrosome, mitosis, genome stability Downloaded from rnajournal.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press Jiao et al. 1 Abstract 2 The accurate inheritance of genetic material is a basic necessity in all domains of life and an 3 unexpectedly large number of RNA processing factors are required for mitotic progression and 4 genome stability. NRDE2 (nuclear RNAi defective-2) is an evolutionarily conserved protein 5 originally discovered for its role in nuclear RNA interference (RNAi) and heritable gene silencing 6 in Caenorhabditis elegans (C. elegans). The function of the human NRDE2 gene remains poorly 7 understood. Here we show that human NRDE2 is an essential protein required for suppressing 8 intron retention in a subset of pre-mRNAs containing short, GC-rich introns with relatively weak 9 5’ and 3’ splice sites. NRDE2 preferentially interacts with components of the U5 small nuclear 10 ribonucleoprotein (snRNP), the exon junction complex, and the RNA exosome. Interestingly, 11 NRDE2-depleted cells exhibit greatly increased levels of genomic instability and DNA damage, 12 as well as defects in centrosome maturation and mitotic progression. We identify the essential 13 centriolar satellite protein, CEP131, as a direct NRDE2-regulated target. NRDE2 specifically 14 binds to and promotes the efficient splicing of CEP131 pre-mRNA, and depleting NRDE2 15 dramatically reduces CEP131 protein expression, contributing to impaired recruitment of critical 16 centrosomal proteins (e.g. γ-tubulin and Aurora Kinase A) to the spindle poles during mitosis. 17 Our work establishes a conserved role for human NRDE2 in RNA splicing, characterizes the 18 severe genomic instability phenotypes observed upon loss of NRDE2, and highlights the direct 19 regulation of CEP131 splicing as one of multiple mechanisms through which such phenotypes 20 might be explained. 21 22 23 24 25 26 2 Downloaded from rnajournal.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press Jiao et al. 27 Introduction 28 The NRDE2 gene was initially discovered in C. elegans for its role in nuclear RNAi, i.e. 29 the small RNA-directed silencing of nuclear transcripts (Guang et al. 2010; Burton et al. 2011). 30 Consistent with a co-transcriptional mechanism of nuclear RNAi (Guang et al. 2010), recent 31 studies have implicated intriguing physical and functional links between nuclear RNAi factors 32 and components of the splicing machinery (Dumesic et al. 2013; Aronica et al. 2015; Akay et al. 33 2017). Indeed, the NRDE2 homolog in S. pombe, Nrl1, was found to associate with RNA splicing 34 and decay factors to regulate cryptic intronic sequences (Lee et al. 2013; Zhou et al. 2015; 35 Aronica et al. 2015). Nrl1 has also been linked to genomic instability, possibly through the 36 regulation of R-loop accumulation (Aronica et al. 2015). The function of human NRDE2 remains 37 poorly understood. 38 Results and Discussion 39 Here we report the functional and biochemical characterization of the human NRDE2 40 (C14ORF102) gene. Unlike its homologs in nematodes and fission yeast (Guang et al. 2010; 41 Aronica et al. 2015), we demonstrate that NRDE2 is an essential gene in human cells. Depletion 42 of NRDE2 resulted in a complete arrest in cell growth and proliferation in all cell lines tested 43 (Fig. 1A). si-NRDE2 specificity was confirmed by the efficient knockdown of NRDE2 mRNA 44 and protein, and by the rescue of proliferation in cells carrying a NRDE2 overexpression 45 construct (Supplemental Fig. 1A-C). Following NRDE2 depletion, FACS analysis revealed an 46 accumulation of cells with 4N DNA content, indicative of an increase in the number of cells in 47 G2 or mitosis (Fig. 1B). Cyclin B1 and phosphorylated histone H3(Ser10) – markers upregulated 48 in late G2 and early mitosis – were also increased (Fig. 1C), further indicating defective cell cycle 49 progression. To investigate the nature and extent of the mitotic delay in individual cells, we 50 performed live cell imaging using RPE-1 (retinal pigment epithelial) cells expressing H2B-GFP 51 (for chromatin visualization) and α-tubulin-mCherry (for mitotic spindle visualization); while 52 50/51 NRDE2-depleted cells examined did complete mitosis, we observed a ~3-fold increase in 3 Downloaded from rnajournal.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press Jiao et al. 53 mitotic time, with the majority of the delay occurring during prometaphase (Fig. 1D and 54 Supplemental Movies). 55 Prometaphase delays are often associated with chromosome missegregation, which can 56 result in micronuclei formation. Micronuclei are clinically relevant markers of genomic 57 instability, and have also been implicated as major sources of DNA damage (Zhang et al. 2015). 58 Indeed, NRDE2-depleted HEK293T cells displayed an increased mitotic index, followed by an 59 increase of cells containing micronuclei and γH2AX foci (a marker of double-stranded DNA 60 breaks), as well as activation of p53 (Supplemental Fig. 1D-F). In MDA-MB-231 breast cancer 61 cells, which are mutant for p53, NRDE2 depletion resulted in a similar, gradual accumulation of 62 DNA damage along with a broad range of aberrant nuclear morphologies characteristic of mitotic 63 defects (Fig. 1E-F). Taken together with recent reports identifying NRDE2 as one of ~1,600 core 64 fitness genes in the human genome (Blomen et al. 2015; Hart et al. 2015), we conclude that 65 NRDE2 plays an essential role in ensuring genomic stability and mitotic progression in most, if 66 not all, human cells. 67 NRDE2 features a conserved stretch of ~350 amino acids defined as the NRDE-2 68 domain, a nuclear localization sequence, and five HAT (half-a-TPR) repeats, short helical motifs 69 found in a variety of RNA processing factors (Hammani et al. 2012) (Supplemental Fig. 2A). 70 While multiple studies have found that RNA processing factors are the most enriched functional 71 category of genes required for mitosis and genome stability (Goshima et al. 2007; Paulsen et al. 72 2009; Neumann et al. 2010), to our knowledge NRDE2 has eluded the “hits” list of all such 73 screens, possibly because of the relatively lengthy time to phenotype seen here (Supplemental 74 Fig. 1E). To begin characterizing the molecular function of NRDE2, we examined the NRDE2 75 protein interactome by immunoprecipitation-mass spectrometry (IP-MS) in HEK293T cells stably 76 expressing NRDE2-GFP. Interestingly, NRDE2 interacted almost exclusively with other RNA 77 processing factors (Fig. 2A, Supplemental Fig. 2B,C Supplemental Table 1). Proteins co- 78 purifying with NRDE2 included known components of the RNA exosome (e.g. EXOSC10 and 4 Downloaded from rnajournal.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press Jiao et al. 79 SKIV2L2) (Lubas et al. 2011), the U5 small nuclear ribonucleoprotein (snRNP) (e.g. EFTUD2) 80 (Fabrizio et al. 1997), and the exon junction complex (EJC) (e.g. eIF4A3) (Singh et al. 2012) 81 (Fig. 2A). SKIV2L2, the most abundant NRDE2-interacting protein we detected, is a conserved 82 DExH/D box RNA helicase component of the human nuclear exosome targeting (NEXT) 83 complex (Lubas et al. 2011); notably, previous proteomic analyses of human SKIV2L2, and its 84 homolog in S. pombe, have both revealed specific associations with NRDE2 (Ogami et al. 2017; 85 Lee et al. 2013). 86 NRDE2 interactions with SKIV2L2, EXOSC10, EFTUD2 and EIF4A3 were confirmed 87 by co-immunoprecipitation (Fig. 2B), and further supported by indirect immunofluorescence 88 (Fig. 2C). Like many splicing factors (Spector and Lamond 2011), the subcellular localization of 89 NRDE2 was nucleoplasmic, reminiscent of nuclear speckles, largely excluded from nucleoli, and 90 diffuse throughout mitotic cells (Fig. 2C). Endogenously tagged zsGreen-NRDE2 exhibited a 91 similar expression pattern (Supplemental Fig. 3A), and endogenously tagged 3XFLAG-NRDE2 92 also co-precipitated with SKIV2L2 (Supplemental Fig. 3B). RNA immunoprecipitation (RIP) of 93 NRDE2 followed by qPCR revealed an enrichment of NRDE2-bound spliceosomal RNAs, 94 particularly the U5 small nuclear RNA (snRNA), with no detectable binding of abundant small 95 nucleolar RNAs (snoRNAs) (Fig. 2D). To our knowledge, NRDE2 has not been previously 96 detected in human spliceosome purifications. Our data demonstrating the association of NRDE2 97 with components of the RNA exosome and the U5 snRNP indicate that NRDE2 may play 98 conserved roles in regulating RNA splicing and/or stability in human cells. 99 A number of reports have suggested that the mechanisms linking various splicing factor 100 knockdowns to mitotic defects converged on the inefficient splicing of a single intron in the 101 CDCA5 gene, which regulates sister chromatid cohesion (Oka et al.
Load more

Recommended publications
  • University of Leicester, Msc Medical Statistics, Thesis, Wilmar
    Thesis MSc in Medical Statistics Department of Health Sciences University of Leicester, United Kingdom Application of Bayesian hierarchical generalized linear models using weakly informative prior distributions to identify rare genetic variant effects on blood pressure Wilmar Igl March 2015 Summary Background Currently rare genetic variants are discussed as a source of \missing heritability" of complex traits. Bayesian hierarchical models were proposed as an efficient method for the estimation and aggregation of conditional effects of rare variants. Here, such models are applied to identify rare variant effects on blood pressure. Methods Empirical data provided by the Genetic Analysis Workshop 19 (2014) included 1,851 Mexican-American individuals with diastolic blood pressure (DBP), systolic blood pressure (SBP), hypertension (HTN) and 461,868 variants from whole- exome sequencing of odd-numbered chromosomes. Bayesian hierarchical generalized linear models using weakly informative prior distributions were applied. Results Associations of rare variants chr1:204214013 (estimate = 39.6, Credible In- terval (CrI) 95% = [25.3, 53.9], Bayesian p = 6:8 × 10−8) in the PLEKHA6 gene and chr11:118518698 (estimate = 32.2, CrI95% = [20.6, 43.9], Bayesian p = 7:0 × 10−8) in the PHLEDB1 gene were identified. Joint effects of grouped rare variants on DBP in 23 genes (Bayesian p = [8:8 × 10−14, 9:3 × 10−8]) and on SBP in 21 genes (Bayesian p = [8:6 × 10−12, 7:8 × 10−8]) in pathways related to hemostasis, sodi- um/calcium transport, ciliary activity, and others were found. No association with hypertension was detected. Conclusions Bayesian hierarchical generalized linear models with weakly informa- tive priors can successfully be applied in exome-wide genetic association analyses of rare variants.
    [Show full text]
  • SNX17 Recruits USP9X to Antagonize MIB1-Mediated Ubiquitination and Degradation of PCM1 During Serum-Starvation-Induced Ciliogenesis
    cells Article SNX17 Recruits USP9X to Antagonize MIB1-Mediated Ubiquitination and Degradation of PCM1 during Serum-Starvation-Induced Ciliogenesis Pengtao Wang 1,2,3,4, Jianhong Xia 2,3, Leilei Zhang 2,3, Shaoyang Zhao 2,3, Shengbiao Li 2,3, Haiyun Wang 2,3, Shan Cheng 4, Heying Li 2,3, Wenguang Yin 2,3, Duanqing Pei 2,3,5,* and Xiaodong Shu 2,3,4,5,6,* 1 School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; [email protected] 2 CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; [email protected] (J.X.); [email protected] (L.Z.); [email protected] (S.Z.); [email protected] (S.L.); [email protected] (H.W.); [email protected] (H.L.); [email protected] (W.Y.) 3 Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China 4 Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; [email protected] 5 Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China 6 Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 511436, China * Correspondence: [email protected] (D.P.); [email protected] (X.S.); Tel.: +86-20-3201-5310 (X.S.) Academic Editor: Tomer Avidor-Reiss Received: 13 September 2019; Accepted: 27 October 2019; Published: 29 October 2019 Abstract: Centriolar satellites are non-membrane cytoplasmic granules that deliver proteins to centrosome during centrosome biogenesis and ciliogenesis.
    [Show full text]
  • USP9X Regulates Centrosome Duplication and Promotes Breast Carcinogenesis
    ARTICLE Received 21 Feb 2016 | Accepted 31 Jan 2017 | Published 31 Mar 2017 DOI: 10.1038/ncomms14866 OPEN USP9X regulates centrosome duplication and promotes breast carcinogenesis Xin Li1,*, Nan Song1,*, Ling Liu1, Xinhua Liu1, Xiang Ding2, Xin Song3, Shangda Yang1, Lin Shan1, Xing Zhou1, Dongxue Su1, Yue Wang1, Qi Zhang1, Cheng Cao1, Shuai Ma1,NaYu1, Fuquan Yang2, Yan Wang1, Zhi Yao4, Yongfeng Shang1,5 & Lei Shi1,4 Defective centrosome duplication is implicated in microcephaly and primordial dwarfism as well as various ciliopathies and cancers. Yet, how the centrosome biogenesis is regulated remains poorly understood. Here we report that the X-linked deubiquitinase USP9X is physically associated with centriolar satellite protein CEP131, thereby stabilizing CEP131 through its deubiquitinase activity. We demonstrate that USP9X is an integral component of centrosome and is required for centrosome biogenesis. Loss-of-function of USP9X impairs centrosome duplication and gain-of-function of USP9X promotes centrosome amplification and chromosome instability. Significantly, USP9X is overexpressed in breast carcinomas, and its level of expression is correlated with that of CEP131 and higher histologic grades of breast cancer. Indeed, USP9X, through regulation of CEP131 abundance, promotes breast carcino- genesis. Our experiments identify USP9X as an important regulator of centrosome biogenesis and uncover a critical role for USP9X/CEP131 in breast carcinogenesis, supporting the pursuit of USP9X/CEP131 as potential targets for breast cancer intervention. 1 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China. 2 Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
    [Show full text]
  • Caracterización De Complejos CDK-Ciclina Atípicos Humanos Eva Quandt Herrera
    Caracterización de complejos CDK-Ciclina atípicos humanos Eva Quandt Herrera ADVERTIMENT. La consulta d’aquesta tesi queda condicionada a l’acceptació de les següents condicions d'ús: La difusió d’aquesta tesi per mitjà del servei TDX (www.tesisenxarxa.net) ha estat autoritzada pels titulars dels drets de propietat intel·lectual únicament per a usos privats emmarcats en activitats d’investigació i docència. No s’autoritza la seva reproducció amb finalitats de lucre ni la seva difusió i posada a disposició des d’un lloc aliè al servei TDX. No s’autoritza la presentació del seu contingut en una finestra o marc aliè a TDX (framing). Aquesta reserva de drets afecta tant al resum de presentació de la tesi com als seus continguts. En la utilització o cita de parts de la tesi és obligat indicar el nom de la persona autora. ADVERTENCIA. La consulta de esta tesis queda condicionada a la aceptación de las siguientes condiciones de uso: La difusión de esta tesis por medio del servicio TDR (www.tesisenred.net) ha sido autorizada por los titulares de los derechos de propiedad intelectual únicamente para usos privados enmarcados en actividades de investigación y docencia. No se autoriza su reproducción con finalidades de lucro ni su difusión y puesta a disposición desde un sitio ajeno al servicio TDR. No se autoriza la presentación de su contenido en una ventana o marco ajeno a TDR (framing). Esta reserva de derechos afecta tanto al resumen de presentación de la tesis como a sus contenidos. En la utilización o cita de partes de la tesis es obligado indicar el nombre de la persona autora.
    [Show full text]
  • Characterizing Genomic Duplication in Autism Spectrum Disorder by Edward James Higginbotham a Thesis Submitted in Conformity
    Characterizing Genomic Duplication in Autism Spectrum Disorder by Edward James Higginbotham A thesis submitted in conformity with the requirements for the degree of Master of Science Graduate Department of Molecular Genetics University of Toronto © Copyright by Edward James Higginbotham 2020 i Abstract Characterizing Genomic Duplication in Autism Spectrum Disorder Edward James Higginbotham Master of Science Graduate Department of Molecular Genetics University of Toronto 2020 Duplication, the gain of additional copies of genomic material relative to its ancestral diploid state is yet to achieve full appreciation for its role in human traits and disease. Challenges include accurately genotyping, annotating, and characterizing the properties of duplications, and resolving duplication mechanisms. Whole genome sequencing, in principle, should enable accurate detection of duplications in a single experiment. This thesis makes use of the technology to catalogue disease relevant duplications in the genomes of 2,739 individuals with Autism Spectrum Disorder (ASD) who enrolled in the Autism Speaks MSSNG Project. Fine-mapping the breakpoint junctions of 259 ASD-relevant duplications identified 34 (13.1%) variants with complex genomic structures as well as tandem (193/259, 74.5%) and NAHR- mediated (6/259, 2.3%) duplications. As whole genome sequencing-based studies expand in scale and reach, a continued focus on generating high-quality, standardized duplication data will be prerequisite to addressing their associated biological mechanisms. ii Acknowledgements I thank Dr. Stephen Scherer for his leadership par excellence, his generosity, and for giving me a chance. I am grateful for his investment and the opportunities afforded me, from which I have learned and benefited. I would next thank Drs.
    [Show full text]
  • Rabbit Anti-AZI1/FITC Conjugated Antibody-SL12977R-FITC
    SunLong Biotech Co.,LTD Tel: 0086-571- 56623320 Fax:0086-571- 56623318 E-mail:[email protected] www.sunlongbiotech.com Rabbit Anti-AZI1/FITC Conjugated antibody SL12977R-FITC Product Name: Anti-AZI1/FITC Chinese Name: FITC标记的中心体蛋白AZI1抗体 5 azacytidine induced 1; 5-azacytidine induced 1; 5-azacytidine-induced protein 1; AZ1; Azi; Azi1; AZI1_HUMAN; Centrosomal protein 131 kDa; Centrosomal protein of 131 Alias: kDa; Centrosomal protein of 131 kDa; Cep131; Cep131; KIAA1118; OTTMUSP00000004498; Pre-acrosome localization protein 1; RP23 37J21.1. Organism Species: Rabbit Clonality: Polyclonal React Species: Human,Mouse,Rat,Chicken,Pig,Cow,Horse,Sheep, ICC=1:50-200IF=1:50-200 Applications: not yet tested in other applications. optimal dilutions/concentrations should be determined by the end user. Molecular weight: 122kDa Form: Lyophilized or Liquid Concentration: 1mg/ml immunogen: KLH conjugated synthetic peptide derived from human AZI1 Lsotype: IgG Purification: affinitywww.sunlongbiotech.com purified by Protein A Storage Buffer: 0.01M TBS(pH7.4) with 1% BSA, 0.03% Proclin300 and 50% Glycerol. Store at -20 °C for one year. Avoid repeated freeze/thaw cycles. The lyophilized antibody is stable at room temperature for at least one month and for greater than a year Storage: when kept at -20°C. When reconstituted in sterile pH 7.4 0.01M PBS or diluent of antibody the antibody is stable for at least two weeks at 2-4 °C. background: AZI1 is a 1,083 amino acid protein that may play a role in spermatogenesis. AZI1 is most highly expressed in spinal cord, followed by testis, ovary, amygdala, cerebellum Product Detail: and thalamus.
    [Show full text]
  • The SON RNA Splicing Factor Is Required for Intracellular Trafficking That Promotes Centriole Assembly
    bioRxiv preprint doi: https://doi.org/10.1101/2021.01.29.428802; this version posted January 29, 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. SON is required for centriole assembly. 1 2 The SON RNA splicing factor is required for intracellular trafficking that 3 promotes centriole assembly. 4 5 6 Alexander J. Stemm-Wolf1, Eileen T. O’Toole2, Ryan M. Sheridan3, Jacob T. Morgan1, and Chad 7 G. Pearson1* 8 9 1 Department of Cell and Developmental Biology, University of Colorado – Anschutz Medical 10 Campus, Aurora CO 80045 11 2 MCDB, University of Colorado – Boulder, Boulder, CO 12 3 RNA Biosciences Initiative (RBI), University of Colorado – Anschutz Medical Campus, Aurora 13 CO 80045 14 15 * Correspondence: [email protected] 16 17 18 19 KEYWORDS: Centrosome, centriole, centriolar satellite, alternative splicing 20 ABBREVIATIONS: MTOC – microtubule organizing center, SIM – structured illumination 21 microscopy, EM – electron microscopy 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.01.29.428802; this version posted January 29, 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. SON is required for centriole assembly. 22 Abstract 23 Control of centrosome assembly is critical for cell division, intracellular trafficking and cilia.
    [Show full text]
  • Content Based Search in Gene Expression Databases and a Meta-Analysis of Host Responses to Infection
    Content Based Search in Gene Expression Databases and a Meta-analysis of Host Responses to Infection A Thesis Submitted to the Faculty of Drexel University by Francis X. Bell in partial fulfillment of the requirements for the degree of Doctor of Philosophy November 2015 c Copyright 2015 Francis X. Bell. All Rights Reserved. ii Acknowledgments I would like to acknowledge and thank my advisor, Dr. Ahmet Sacan. Without his advice, support, and patience I would not have been able to accomplish all that I have. I would also like to thank my committee members and the Biomed Faculty that have guided me. I would like to give a special thanks for the members of the bioinformatics lab, in particular the members of the Sacan lab: Rehman Qureshi, Daisy Heng Yang, April Chunyu Zhao, and Yiqian Zhou. Thank you for creating a pleasant and friendly environment in the lab. I give the members of my family my sincerest gratitude for all that they have done for me. I cannot begin to repay my parents for their sacrifices. I am eternally grateful for everything they have done. The support of my sisters and their encouragement gave me the strength to persevere to the end. iii Table of Contents LIST OF TABLES.......................................................................... vii LIST OF FIGURES ........................................................................ xiv ABSTRACT ................................................................................ xvii 1. A BRIEF INTRODUCTION TO GENE EXPRESSION............................. 1 1.1 Central Dogma of Molecular Biology........................................... 1 1.1.1 Basic Transfers .......................................................... 1 1.1.2 Uncommon Transfers ................................................... 3 1.2 Gene Expression ................................................................. 4 1.2.1 Estimating Gene Expression ............................................ 4 1.2.2 DNA Microarrays ......................................................
    [Show full text]
  • Centriolar Satellites Assemble Centrosomal Microcephaly Proteins
    RESEARCH ARTICLE elifesciences.org Centriolar satellites assemble centrosomal microcephaly proteins to recruit CDK2 and promote centriole duplication Andrew Kodani1, Timothy W Yu2†, Jeffrey R Johnson3†, Divya Jayaraman2, Tasha L Johnson3, Lihadh Al-Gazali4,Laszl o´ Sztriha4, Jennifer N Partlow2, Hanjun Kim1, Alexis L Krup1, Alexander Dammermann5, Nevan J Krogan3, Christopher A Walsh2, Jeremy F Reiter1* 1Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States; 2Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, United States; 3Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States; 4Department of Paediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates; 5Max F. Perutz Laboratories, University of Vienna, Vienna, Austria Abstract Primary microcephaly (MCPH) associated proteins CDK5RAP2, CEP152, WDR62 and CEP63 colocalize at the centrosome. We found that they interact to promote centriole duplication and form a hierarchy in which each is required to localize another to the centrosome, with CDK5RAP2 at the apex, and CEP152, WDR62 and CEP63 at sequentially lower positions. MCPH proteins interact with distinct centriolar satellite proteins; CDK5RAP2 interacts with SPAG5 and CEP72, CEP152 with CEP131, WDR62 with MOONRAKER, and CEP63 with CEP90 and CCDC14. These satellite proteins localize their cognate MCPH interactors to centrosomes and also promote centriole duplication. *For correspondence: Jeremy. Consistent with a role for satellites in microcephaly, homozygous mutations in one satellite gene, [email protected] CEP90, may cause MCPH. The satellite proteins, with the exception of CCDC14, and MCPH proteins †These authors contributed promote centriole duplication by recruiting CDK2 to the centrosome.
    [Show full text]
  • Supplementary Table 1 Double Treatment Vs Single Treatment
    Supplementary table 1 Double treatment vs single treatment Probe ID Symbol Gene name P value Fold change TC0500007292.hg.1 NIM1K NIM1 serine/threonine protein kinase 1.05E-04 5.02 HTA2-neg-47424007_st NA NA 3.44E-03 4.11 HTA2-pos-3475282_st NA NA 3.30E-03 3.24 TC0X00007013.hg.1 MPC1L mitochondrial pyruvate carrier 1-like 5.22E-03 3.21 TC0200010447.hg.1 CASP8 caspase 8, apoptosis-related cysteine peptidase 3.54E-03 2.46 TC0400008390.hg.1 LRIT3 leucine-rich repeat, immunoglobulin-like and transmembrane domains 3 1.86E-03 2.41 TC1700011905.hg.1 DNAH17 dynein, axonemal, heavy chain 17 1.81E-04 2.40 TC0600012064.hg.1 GCM1 glial cells missing homolog 1 (Drosophila) 2.81E-03 2.39 TC0100015789.hg.1 POGZ Transcript Identified by AceView, Entrez Gene ID(s) 23126 3.64E-04 2.38 TC1300010039.hg.1 NEK5 NIMA-related kinase 5 3.39E-03 2.36 TC0900008222.hg.1 STX17 syntaxin 17 1.08E-03 2.29 TC1700012355.hg.1 KRBA2 KRAB-A domain containing 2 5.98E-03 2.28 HTA2-neg-47424044_st NA NA 5.94E-03 2.24 HTA2-neg-47424360_st NA NA 2.12E-03 2.22 TC0800010802.hg.1 C8orf89 chromosome 8 open reading frame 89 6.51E-04 2.20 TC1500010745.hg.1 POLR2M polymerase (RNA) II (DNA directed) polypeptide M 5.19E-03 2.20 TC1500007409.hg.1 GCNT3 glucosaminyl (N-acetyl) transferase 3, mucin type 6.48E-03 2.17 TC2200007132.hg.1 RFPL3 ret finger protein-like 3 5.91E-05 2.17 HTA2-neg-47424024_st NA NA 2.45E-03 2.16 TC0200010474.hg.1 KIAA2012 KIAA2012 5.20E-03 2.16 TC1100007216.hg.1 PRRG4 proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane) 7.43E-03 2.15 TC0400012977.hg.1 SH3D19
    [Show full text]
  • Rnaseq Studies Reveal Distinct Transcriptional Response to Vitamin
    bioRxiv preprint doi: https://doi.org/10.1101/798504; this version posted May 19, 2020. 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 RNAseq studies reveal distinct transcriptional response to vitamin 2 A deficiency in small intestine versus colon, uncovering novel 3 vitamin A-regulated genes 4 5 Zhi Chai1,2,*, Yafei Lyu3,8, Qiuyan Chen2, Cheng-Hsin Wei2,9, Lindsay M. Snyder4,10, Veronika 6 Weaver4, Aswathy Sebastian5, István Albert6, Qunhua Li7, Margherita T. Cantorna4, A. Catharine 2* 7 Ross . 8 9 1Intercollege Graduate Degree Program in Physiology, 2Department of Nutritional Sciences, 10 3Intercollege Graduate Degree Program in Bioinformatics and Genomics, 4Department of 11 Veterinary and Biomedical Sciences, 5Huck Institutes of the Life Sciences, 6Department of 12 Biochemistry and Molecular Biology, 7Department of Statistics. The Pennsylvania State 13 University, University Park, PA, USA. 8Present address: Department of Biostatistics, 14 Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, 15 Philadelphia, PA, USA. 9Present address: Frederick National Laboratory for Cancer Research, 16 Frederick, MD, USA. 10Present address: Center for Evolutionary and Theoretical Immunology, 17 The University of New Mexico, Albuquerque, NM, USA. 18 19 *Corresponding authors 20 A. Catharine Ross ([email protected]) and Zhi Chai ([email protected]) 21 110 Chandlee Laboratory 22 University Park, PA, USA. 16802 bioRxiv preprint doi: https://doi.org/10.1101/798504; this version posted May 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.
    [Show full text]
  • The Use of Whole Exome Sequencing in a Cohort of Transgender Individuals to Identify Rare Genetic Variants J
    www.nature.com/scientificreports OPEN The Use of Whole Exome Sequencing in a Cohort of Transgender Individuals to Identify Rare Genetic Variants J. Graham Theisen1*, Viji Sundaram2, Mary S. Filchak1, Lynn P. Chorich1, Megan E. Sullivan1, James Knight3,4, Hyung-Goo Kim1,5 & Lawrence C. Layman1* Approximately 0.5–1.4% of natal males and 0.2–0.3% of natal females meet DSM-5 criteria for gender dysphoria, with many of these individuals self-describing as transgender men or women. Despite recent improvements both in social acceptance of transgender individuals as well as access to gender afrming therapy, progress in both areas has been hampered by poor understanding of the etiology of gender dysphoria. Prior studies have suggested a genetic contribution to gender dysphoria, but previously proposed candidate genes have not yet been verifed in follow-up investigation. In this study, we expand on the topic of gender identity genomics by identifying rare variants in genes associated with sexually dimorphic brain development and exploring how they could contribute to gender dysphoria. To accomplish this, we performed whole exome sequencing on the genomic DNA of 13 transgender males and 17 transgender females. Whole exome sequencing revealed 120,582 genetic variants. After fltering, 441 variants in 421 genes remained for further consideration, including 21 nonsense, 28 frameshift, 13 splice-region, and 225 missense variants. Of these, 21 variants in 19 genes were found to have associations with previously described estrogen receptor activated pathways of sexually dimorphic brain development. These variants were confrmed by Sanger Sequencing. Our fndings suggest a new avenue for investigation of genes involved in estrogen signaling pathways related to sexually dimorphic brain development and their relationship to gender dysphoria.
    [Show full text]