The Reaction Mechanism of Cellular U Snrnp Assembly
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Integrative Analysis of Phenomic, Genomic, and Transcriptomic To
bioRxiv preprint doi: https://doi.org/10.1101/2020.11.29.392167; this version posted November 30, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Integrative Analysis of Phenomic, Genomic, and Transcriptomic to Identify Potential Functional Genes of Yaks in Plain and Plateau Jiabo Wang1,2, §, Jiuqiang Guan3, §, Kangzhu Yixi1,2,Tao Shu1, Zhixin Chai1,2, Jikun Wang1,2, Hui Wang1,2, Zhijuan Wu1,2, Xin Cai1,2, Jincheng Zhong1,2*,Xiaolin Luo3* 1. Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest Minzu University), Ministry of Education,Chengdu, Sichuan, China; 2. Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province, Chengdu, Sichuan, China; 3. Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China; §These authors contributed equally to this work. *Correspondences should be addressed to JZ ([email protected]) and XL ([email protected]) bioRxiv preprint doi: https://doi.org/10.1101/2020.11.29.392167; this version posted November 30, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Abstract Background: The yak is an important source of livelihood for the people living in the Qinghai-Tibet Plateau. Most genetics detection studies have focused on the comparison between different tissues of different breeds, both living in the Plateau and in the plains. The genetic background and complex regulatory relationship have frequently puzzled researchers. In this study, we divided a population of 10 yaks into two subgroups, namely Plateau (living in the Plateau) and Plain (living in the plains). -
Role of DCP1-DCP2 Complex Regulated by Viral and Host Micrornas in DNA Virus Infection T
Fish and Shellfish Immunology 92 (2019) 21–30 Contents lists available at ScienceDirect Fish and Shellfish Immunology journal homepage: www.elsevier.com/locate/fsi Full length article Role of DCP1-DCP2 complex regulated by viral and host microRNAs in DNA virus infection T ∗ Yuechao Sun, Xiaobo Zhang College of Life Sciences and Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, Zhejiang University, Hangzhou, 310058, People's Republic of China ARTICLE INFO ABSTRACT Keywords: The DCP1-DCP2 complex can regulate the antiviral immunity of animals by the decapping of retrovirus RNAs DCP1-DCP2 complex and the suppression of RNAi during RNA virus infection. However, the influence of DCP1-DCP2 complex on DNA miRNA virus infection and the regulation of DCP1-DCP2 complex by microRNAs (miRNAs) remain unclear. In this study, DNA virus infection the role of miRNA-regulated DCP1-DCP2 complex in DNA virus infection was characterized. Our results showed that the DCP1-DCP2 complex played a positive role in the infection of white spot syndrome virus (WSSV), a DNA virus of shrimp. In the DCP1-DCP2 complex, the N-terminal regulatory domain of DCP2 was interacted with the EVH1 domain of DCP1. Furthermore, shrimp miRNA miR-87 inhibited WSSV infection by targeting the host DCP2 gene and viral miRNA WSSV-miR-N46 took a negative effect on WSSV replication by targeting the host DCP1 gene. Therefore, our study provided novel insights into the underlying mechanism of DCP1-DCP2 complex and its regulation by miRNAs in virus-host interactions. Importance: During RNA virus infection, the DCP1-DCP2 complex can play important roles in the animal anti- viral immunity by decapping retrovirus RNAs and suppressing RNAi. -
Atxn2-CAG100-Knockin Mouse Spinal Cord Shows Progressive TDP43
bioRxiv preprint doi: https://doi.org/10.1101/838177; this version posted November 11, 2019. 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-NC-ND 4.0 International license. Atxn2-CAG100-KnockIn mouse spinal cord shows progressive TDP43 pathology associated with cholesterol biosynthesis suppression Júlia Canet-Pons1§, Nesli-Ece Sen1,2§, Aleksandar Arsovic1, Luis-Enrique Almaguer-Mederos1,3, Melanie V. Halbach1, Jana Key1,2, Claudia Döring4, Anja Kerksiek5, Gina Picchiarelli6, Raphaelle Cassel6, Frédérique René6, Stéphane Dieterlé6, Nina Hein-Fuchs7, Renate König7, Luc Dupuis6, Dieter Lütjohann5, Suzana Gispert1, Georg Auburger1# 1 Experimental Neurology, Medical Faculty, Goethe University, 60590 Frankfurt am Main, Germany; 2 Faculty of Biosciences, Goethe University, 60438 Frankfurt am Main, Germany; 3 Center for Investigation and Rehabilitation of Hereditary Ataxias (CIRAH), Holguín, Cuba; 4 Dr. Senckenberg Institute of Pathology, Medical Faculty, Goethe University, 60590 Frankfurt am Main, Germany; 5 Institute for Clinical Chemistry and Clinical Pharmacology, Medical Faculty, University Bonn, 53127 Bonn, Nordrhein-Westfalen, Germany; 6 UMRS-1118 INSERM, Faculty of Medicine, University of Strasbourg, 67000 Strasbourg, France; 7 Host-Pathogen Interactions, Paul-Ehrlich-Institute, 63225 Langen, Germany. § Joint first authorship # Correspondence to: [email protected], Tel: +49-69-6301-7428, FAX: +49-69-6301-7142 Acknowledgements: 1 bioRxiv preprint doi: https://doi.org/10.1101/838177; this version posted November 11, 2019. 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. -
Role of Cajal Bodies and Nucleolus in the Maturation of the U1 Snrnp in Arabidopsis
CORE Metadata, citation and similar papers at core.ac.uk Provided by PubMed Central Role of Cajal Bodies and Nucleolus in the Maturation of the U1 snRNP in Arabidopsis Zdravko J. Lorkovic´*, Andrea Barta Max F. Perutz Laboratories, Department of Medical Biochemistry, Medical University of Vienna, Vienna, Austria Abstract Background: The biogenesis of spliceosomal snRNPs takes place in both the cytoplasm where Sm core proteins are added and snRNAs are modified at the 59 and 39 termini and in the nucleus where snRNP-specific proteins associate. U1 snRNP consists of U1 snRNA, seven Sm proteins and three snRNP-specific proteins, U1-70K, U1A, and U1C. It has been shown previously that after import to the nucleus U2 and U4/U6 snRNP-specific proteins first appear in Cajal bodies (CB) and then in splicing speckles. In addition, in cells grown under normal conditions U2, U4, U5, and U6 snRNAs/snRNPs are abundant in CBs. Therefore, it has been proposed that the final assembly of these spliceosomal snRNPs takes place in this nuclear compartment. In contrast, U1 snRNA in both animal and plant cells has rarely been found in this nuclear compartment. Methodology/Principal Findings: Here, we analysed the subnuclear distribution of Arabidopsis U1 snRNP-specific proteins fused to GFP or mRFP in transiently transformed Arabidopsis protoplasts. Irrespective of the tag used, U1-70K was exclusively found in the nucleus, whereas U1A and U1C were equally distributed between the nucleus and the cytoplasm. In the nucleus all three proteins localised to CBs and nucleoli although to different extent. Interestingly, we also found that the appearance of the three proteins in nuclear speckles differ significantly. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Epigenetic Loss of the RNA Decapping Enzyme NUDT16 Mediates C-MYC Activation in T-Cell Acute Lymphoblastic Leukemia
OPEN Leukemia (2017) 31, 1622–1657 www.nature.com/leu LETTERS TO THE EDITOR Epigenetic loss of the RNA decapping enzyme NUDT16 mediates C-MYC activation in T-cell acute lymphoblastic leukemia Leukemia (2017) 31, 1622–1625; doi:10.1038/leu.2017.99 Having found the aforementioned NUDT16 CpG island methy- lation profiles, we studied in greater detail their association with the possible transcriptional inactivation of the NUDT16 gene at the RNA and protein levels in leukemia cell lines. We first It is possible that the occurrence of intrinsic defects in RNA performed bisulfite genomic sequencing of mutiple clones in the – processing pathways, such as RNA decapping,1 3 contribute to the T-cell Acute Lymphoblastic Leukemia (T-ALL) cell lines CCRF-CEM, distorted RNA landscapes of cancer cells. After transcription by Jurkat, MOLT-4 and MOLT-16 using primers that encompassed the RNA polymerase II, RNA molecules are equipped with a 5´-end transcription start site-associated CpG island and confirmed the N7-methyl guanosine (m7G)-cap. This m7G-cap is essential for hypermethylated status of the 5′-end region of NUDT16 in translation, stabilizing the RNA molecule and protecting it from comparison to normal T lymphocytes (Figure 1b), validating the – exonucleolytic breakdown.1 3 For RNA decay to occur the DNA methylation patterns obtained by the microarray approach m7G-cap first needs to be removed. This process is known as (Supplementary Figure S2). In contrast, normal T lymphocytes, the – decapping.1 3 The decapping mRNA 2 (DCP2) enzyme,4 also T-ALL cell lines KOPN-8, REH and RS4;11 and the leukemia cell known as the nucleoside diphosphate-linked moiety X motif lines HL-60 and K562 derived from myeloid lineage were all found 20 (NUDT20), was originally thought to be the only mammalian to be unmethylated (Figure 1b; Supplementary Figure S2). -
RNA-Protein Interactions of a Kink
Florida State University Libraries Electronic Theses, Treatises and Dissertations The Graduate School 2005 Biophysical and Biochemical Investigation of an Archaeal Box C/D SRNP: RNA- Protein Interactions of a Kink Turn RNA within the Functional Enzyme Terrie Luong Moore Follow this and additional works at the FSU Digital Library. For more information, please contact [email protected] THE FLORIDA STATE UNIVERSITY COLLEGE OF ARTS AND SCIENCES BIOPHYSICAL AND BIOCHEMICAL INVESTIGATION OF AN ARCHAEAL BOX C/D SRNP: RNA-PROTEIN INTERACTIONS OF A KINK TURN RNA WITHIN THE FUNCTIONAL ENZYME By TERRIE LUONG MOORE A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy Degree Awarded: Summer Semester, 2005 The members of the Committee approve the dissertation of Terrie Luong Moore defended on May 3, 2005. ________________________________ Hong Li Professor Directing Dissertation ________________________________ Lloyd M. Epstein Outside Committee Member ________________________________ Timothy M. Logan Committee Member ________________________________ John G. Dorsey Committee Member Approved: ___________________________________________________ Naresh Dalal, Chair, Department of Chemistry and Biochemistry The Office of Graduate Studies has verified and approved the above named committee members. ii I dedicate this work to my husband, Michael, for being there every step of the way and always giving me hope about the future. Without your love and support, this work would not have been possible. iii ACKNOWLEDGEMENTS I would like to thank my mentor, Dr. Hong Li, first and foremost for taking me into her lab and allowing me to grow intellectually. I would like to thank all of my committee members, Dr. -
Snorna Guide Activities – Real and Ambiguous Svetlana Deryusheva, Gaëlle JS Talross
Downloaded from rnajournal.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Deryusheva, Talross and Gall SnoRNA guide activities – real and ambiguous Svetlana Deryusheva, Gaëlle J.S. Talross 1, Joseph G. Gall Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA 1 Present address: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06510, USA Corresponding authors: e-mail [email protected] [email protected] Running title: Testing snoRNA activities Keywords: modification guide RNA activity, 2’-O-methylation, pseudouridylation, Pus7p, snoRNA 1 Downloaded from rnajournal.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Deryusheva, Talross and Gall ABSTRACT In eukaryotes, rRNAs and spliceosomal snRNAs are heavily modified posttranscriptionally. Pseudouridylation and 2’-O-methylation are the most abundant types of RNA modifications. They are mediated by modification guide RNAs, also known as small nucleolar (sno)RNAs and small Cajal body-specific (sca)RNAs. We used yeast and vertebrate cells to test guide activities predicted for a number of snoRNAs, based on their regions of complementarity with rRNAs. We showed that human SNORA24 is a genuine guide RNA for 18S-Ψ609, despite some non- canonical base-pairing with its target. At the same time, we found quite a few snoRNAs that have the ability to base-pair with rRNAs and can induce predicted modifications in artificial substrate RNAs, but do not modify the same target sequence within endogenous rRNA molecules. Furthermore, certain fragments of rRNAs can be modified by the endogenous yeast modification machinery when inserted into an artificial backbone RNA, even though the same sequences are not modified in endogenous yeast rRNAs. -
Guide Rnas with 5 Caps and Novel Box C/D Snorna-Like Domains For
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Current Biology, Vol. 14, 1985–1995, November 23, 2004, 2004 Elsevier Ltd. All rights reserved. DOI 10.1016/j.cub.2004.11.003 Guide RNAs with 5 Caps and Novel Box C/D snoRNA-like Domains for Modification of snRNAs in Metazoa Kazimierz T. Tycowski, Alar Aab, duced by small nucleolar RNP particles (snoRNPs). Box and Joan A. Steitz* C/D snoRNPs direct 2Ј-O-methylation, while box H/ACA Department of Molecular Biophysics particles are involved in pseudouridylation (reviewed in and Biochemistry [4]). The RNA components of the snoRNPs select the Howard Hughes Medical Institute sites for modification by engaging in extensive base Yale University School of Medicine pairing interactions with the substrate RNA, while meth- 295 Congress Avenue ylation and pseudouridylation are believed to be carried New Haven, Connecticut 06536 out by a snoRNP core protein specific to each particle class. Box C/D snoRNPs are composed of a small RNA mole- Summary cule, typically 70–90 nt long in vertebrates, and a set of at least four proteins: fibrillarin, which is the methyltrans- Background: Spliceosomal snRNAs and ribosomal ferase [5, 6], Nop56, Nop58, and 15.5 kDa (reviewed RNAs in metazoans contain numerous modified resi- in [4]). All box C/D snoRNAs contain four conserved Ј dues that are functionally important. The most common sequence elements: boxes C and D close to the 5 and Ј modifications are site-specific 2Ј-O-methylation and 3 termini, respectively, and internal copies of each box Ј Ј pseudouridylation, both directed by small ribonucleo- referred to as C and D . -
RNA Promotes the Formation of Spatial Compartments in the Nucleus
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.25.267435; this version posted August 25, 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. RNA promotes the formation of spatial compartments in the nucleus 1 1,2,5 1,5 1,5 Sofia A. Quinodoz , Prashant Bhat , Noah Ollikainen , Joanna W. Jachowicz , Abhik K. Banerjee1,3, Peter Chovanec1, Mario R. Blanco1, Amy Chow1, Yolanda Markaki4, Kathrin Plath4, and Mitchell Guttman1* (1) Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA (2) David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA (3) Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA (4) Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA (5) These authors contributed equally to this work. * To whom correspondence should be addressed. [email protected] (MG) bioRxiv preprint doi: https://doi.org/10.1101/2020.08.25.267435; this version posted August 25, 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 SUMMARY 2 The nucleus is a highly organized arrangement of RNA, DNA, and protein molecules that are 3 compartmentalized within three-dimensional (3D) structures involved in shared functional and regulatory 4 processes. Although RNA has long been proposed to play a global role in organizing nuclear structure, 5 exploring the role of RNA in shaping nuclear structure has remained a challenge because no existing 6 methods can simultaneously measure RNA-RNA, RNA-DNA, and DNA-DNA contacts within 3D 7 structures. -
A Non-Canonical Role for the EDC4 Decapping Factor in Regulating
RESEARCH ARTICLE A non-canonical role for the EDC4 decapping factor in regulating MARF1- mediated mRNA decay William R Brothers1, Steven Hebert1, Claudia L Kleinman1,2, Marc R Fabian1,3,4* 1Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada; 2Department of Human Genetics, McGill University, Montreal, Canada; 3Department of Biochemistry, McGill University, Montreal, Canada; 4Department of Oncology, McGill University, Montreal, Canada Abstract EDC4 is a core component of processing (P)-bodies that binds the DCP2 decapping enzyme and stimulates mRNA decay. EDC4 also interacts with mammalian MARF1, a recently identified endoribonuclease that promotes oogenesis and contains a number of RNA binding domains, including two RRMs and multiple LOTUS domains. How EDC4 regulates MARF1 action and the identity of MARF1 target mRNAs is not known. Our transcriptome-wide analysis identifies bona fide MARF1 target mRNAs and indicates that MARF1 predominantly binds their 3’ UTRs via its LOTUS domains to promote their decay. We also show that a MARF1 RRM plays an essential role in enhancing its endonuclease activity. Importantly, we establish that EDC4 impairs MARF1 activity by preventing its LOTUS domains from binding target mRNAs. Thus, EDC4 not only serves as an enhancer of mRNA turnover that binds DCP2, but also as a repressor that binds MARF1 to prevent the decay of MARF1 target mRNAs. Introduction *For correspondence: The regulated decay of eukaryotic mRNA populations plays an important role in the post-transcrip- [email protected] tional control (PTC) of gene expression. These PTC programs are, in turn, critical for regulating a number of biological processes, including during early development, cell proliferation and immune Competing interests: The response. -
Host Cell Factors Necessary for Influenza a Infection: Meta-Analysis of Genome Wide Studies
Host Cell Factors Necessary for Influenza A Infection: Meta-Analysis of Genome Wide Studies Juliana S. Capitanio and Richard W. Wozniak Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta Abstract: The Influenza A virus belongs to the Orthomyxoviridae family. Influenza virus infection occurs yearly in all countries of the world. It usually kills between 250,000 and 500,000 people and causes severe illness in millions more. Over the last century alone we have seen 3 global influenza pandemics. The great human and financial cost of this disease has made it the second most studied virus today, behind HIV. Recently, several genome-wide RNA interference studies have focused on identifying host molecules that participate in Influen- za infection. We used nine of these studies for this meta-analysis. Even though the overlap among genes identified in multiple screens was small, network analysis indicates that similar protein complexes and biological functions of the host were present. As a result, several host gene complexes important for the Influenza virus life cycle were identified. The biological function and the relevance of each identified protein complex in the Influenza virus life cycle is further detailed in this paper. Background and PA bound to the viral genome via nucleoprotein (NP). The viral core is enveloped by a lipid membrane derived from Influenza virus the host cell. The viral protein M1 underlies the membrane and anchors NEP/NS2. Hemagglutinin (HA), neuraminidase Viruses are the simplest life form on earth. They parasite host (NA), and M2 proteins are inserted into the envelope, facing organisms and subvert the host cellular machinery for differ- the viral exterior.