DOCSLIB.ORG

Unraveling the Beta Cell Translatome: Elucidation of an Erk/Hnrnpk/Jund Axis Austin Lewis Good University of Pennsylvania, [email protected]

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Unraveling the Beta Cell Translatome: Elucidation of an Erk/Hnrnpk/Jund Axis Austin Lewis Good University of Pennsylvania, Algood6@Gmail.Com University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2019 Unraveling The Beta Cell Translatome: Elucidation Of An Erk/hnrnpk/jund Axis Austin Lewis Good University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Cell Biology Commons, Genetics Commons, and the Molecular Biology Commons Recommended Citation Good, Austin Lewis, "Unraveling The Beta Cell Translatome: Elucidation Of An Erk/hnrnpk/jund Axis" (2019). Publicly Accessible Penn Dissertations. 3327. https://repository.upenn.edu/edissertations/3327 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/3327 For more information, please contact [email protected]. Unraveling The Beta Cell Translatome: Elucidation Of An Erk/hnrnpk/ jund Axis Abstract In type 2 diabetes, oxidative stress contributes to the dysfunction and loss of pancreatic β cells. A highly conserved feature of the cellular response to stress is the regulation of mRNA translation, however, the mechanisms underlying this process in β cells are not fully understood. Here we use TRAP-seq to examine changes in the ribosome occupancy of mRNAs during conditions associated with β cell dysfunction, leading us to identify a cohort of translationally regulated genes with 3’UTR enrichment of a cytosine-rich motif. Of particular interest was the gene encoding JUND, a transcription factor with anti-oxidant functions in other cell types but whose role in cells is unknown. Interestingly, JUND is translationally upregulated in islets exposed to high glucose and free fatty acid levels, and depletion of JUND in β cells reduces oxidative stress and apoptosis caused by these conditions. Transcriptome assessment demonstrates that JUND regulates a cohort of genes that are commonly dysregulated during β cell dysfunction, including pro-oxidant and pro- inflammatory genes, consistent with this factor enhancing, rather than reducing, oxidative stress levels in cells. Further, hnRNPK, an RNA binding protein with specificity for cytosine-rich stretches, binds to the mRNA encoding JUND and is required for its post-transcriptional upregulation during metabolic stress. Although the absolute levels of hnRNPK do not change, there is a significant increase in hnRNPK phosphorylation during glucolipotoxicity. Importantly, this hnRNPK/JUND axis is activated in islets from diabetic db/db mice and in human islets exposed to metabolic stress. Finally, a series of mechanistic studies indicate that hnRNPK post- transcriptionally regulates JUND in a MEK/ERK- and DDX3X-dependent manner. Thus, a translation- centric approach uncovered hnRNPK and JUND as stress-responsive factors in β cells that contribute to redox imbalance and apoptosis during pathophysiologically relevant stress. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Doris A. Stoffers Keywords Beta cells, Diabetes, Oxidative stress, RNA binding proteins, Transcriptional regulation, Translation Subject Categories Cell Biology | Genetics | Molecular Biology This dissertation is available at ScholarlyCommons: https://repository.upenn.edu/edissertations/3327 UNRAVELING THE β CELL TRANSLATOME: ELUCIDATION OF AN ERK/HNRNPK/JUND AXIS Austin L. Good A DISSERTATION in Cell and Molecular Biology Presented to the Faculties of the University of Pennsylvania in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy 2019 Supervisor of Dissertation _________________ Doris A. Stoffers, M.D., Ph.D. Sylvan H. Eisman Professor of Medicine Graduate Group Chairperson _________________ Daniel S. Kessler, Ph.D. Associate Professor of Cell and Developmental Biology Dissertation Committee Klaus H. Kaestner, Ph.D. Thomas and Evelyn Suor Butterworth Professor in Genetics Patrick Seale, Ph.D. Associate Professor of Cell and Developmental Biology Stephen A. Liebhaber, M.D. Professor of Genetics Zissimos Mourelatos, M.D. Professor of Pathology and Laboratory Medicine ACKNOWLEDGMENTS I would like to thank the many people that have contributed to my scientific development and research endeavors during my graduate work. I am very grateful to my thesis advisor, Dr. Doris Stoffers, for her mentorship and support throughout this process. Her curiosity and excitement to more deeply understand scientific questions provide a wonderful model for her trainees. Throughout my training, Doris encouraged me to develop my own ideas and hypotheses while also serving as the guard rails to keep me on track when necessary. Her mentorship allowed me to grow as an investigator and gave me confidence to tackle complex problems. I am also very grateful for the opportunity to work alongside and interact with many bright and enthusiastic members of the Stoffers lab during my graduate work who have all contributed to my training. I especially want to thank Dr. Corey Cannon who served as a wonderful mentor for me when I joined the lab and who laid the foundation for all of the work presented here. I also want to thank Dave Groff and Dr. Andrea Rozo for putting up with all of my urgent order requests over the years. I also thank Drs. Christine Juliana, Diana Stanescu, Andrea Rozo, Jeff Raum, Ben Ediger, and Juxiang Yang for their many suggestions and advice on my project. I want to thank Matt Haemmerle and Alexis Oguh for their grad student camaraderie, and I wish them the best of luck in their thesis work and future endeavors. I would also like to thank Dr. Skip Brass for sharing his wisdom throughout the many stages of the MD-PhD program, and Maggie Krall for being a listening ear and giving perceptive advice. I am very lucky to have a family that provides me with unwavering support and encouragement. Amanda, Matt, Julian, and Camille, spending time together always provides a necessary escape from the world of science and gives me perspective to keep moving forward with a clear head. Mom and Dad, I can’t thank you enough for the love and support you have always given me. I can’t imagine better role models. And finally, I thank my wife Charly Ann for always making me smile at the end of a long day. You are my rock and I can’t wait for the many adventures ahead. ii ABSTRACT UNRAVELING THE β CELL TRANSLATOME: ELUCIDATION OF AN ERK/HNRNPK/JUND AXIS AUSTIN L. GOOD DORIS A. STOFFERS, M.D., Ph.D. In type 2 diabetes, oxidative stress contributes to the dysfunction and loss of pancreatic β cells. A highly conserved feature of the cellular response to stress is the regulation of mRNA translation, however, the mechanisms underlying this process in β cells are not fully understood. Here we use TRAP-seq to examine changes in the ribosome occupancy of mRNAs during conditions associated with β cell dysfunction, leading us to identify a cohort of translationally regulated genes with 3’UTR enrichment of a cytosine-rich motif. Of particular interest was the gene encoding JUND, a transcription factor with anti-oxidant functions in other cell types but whose role in β cells is unknown. Interestingly, JUND is translationally upregulated in islets exposed to high glucose and free fatty acid levels, and depletion of JUND in β cells reduces oxidative stress and apoptosis caused by these conditions. Transcriptome assessment demonstrates that JUND regulates a cohort of genes that are commonly dysregulated during β cell dysfunction, including pro-oxidant and pro-inflammatory genes, consistent with this factor enhancing, rather than reducing, oxidative stress levels in β cells. Further, hnRNPK, an RNA binding protein with specificity for cytosine-rich stretches, binds to the mRNA encoding JUND and is required for its post-transcriptional upregulation during metabolic stress. Although the absolute levels of hnRNPK do not change, there is a significant increase in hnRNPK phosphorylation during glucolipotoxicity. Importantly, this hnRNPK/JUND axis is activated in islets from diabetic db/db mice and in human islets exposed to metabolic stress. Finally, a series of mechanistic studies indicate that hnRNPK post-transcriptionally regulates JUND in a MEK/ERK- and DDX3X-dependent manner. Thus, a translation-centric approach uncovered hnRNPK and JUND as stress-responsive factors in β cells that contribute to redox imbalance and apoptosis during pathophysiologically relevant stress. iii TABLE OF CONTENTS ACKNOWLEDGMENTS ......................................................................................................... II ABSTRACT .............................................................................................................................. III LIST OF TABLES .................................................................................................................. VII LIST OF ILLUSTRATIONS .............................................................................................. VIII CHAPTER 1: INTRODUCTION ........................................................................................... 1 1.1 Paradigms of β cell demise in type 2 diabetes ....................................................................... 1 1.1.1 Impaired insulin secretion ........................................................................................................... 2 1.1.2 β cell apoptosis ............................................................................................................................. 4 1.1.3 Loss of β cell identify ..................................................................................................................
Load more

Recommended publications
  • SRC Antibody - N-Terminal Region (ARP32476 P050) Data Sheet
    SRC antibody - N-terminal region (ARP32476_P050) Data Sheet Product Number ARP32476_P050 Product Name SRC antibody - N-terminal region (ARP32476_P050) Size 50ug Gene Symbol SRC Alias Symbols ASV; SRC1; c-SRC; p60-Src Nucleotide Accession# NM_005417 Protein Size (# AA) 536 amino acids Molecular Weight 60kDa Product Format Lyophilized powder NCBI Gene Id 6714 Host Rabbit Clonality Polyclonal Official Gene Full Name V-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian) Gene Family SH2D This is a rabbit polyclonal antibody against SRC. It was validated on Western Blot by Aviva Systems Biology. At Aviva Systems Biology we manufacture rabbit polyclonal antibodies on a large scale (200-1000 Description products/month) of high throughput manner. Our antibodies are peptide based and protein family oriented. We usually provide antibodies covering each member of a whole protein family of your interest. We also use our best efforts to provide you antibodies recognize various epitopes of a target protein. For availability of antibody needed for your experiment, please inquire (). Peptide Sequence Synthetic peptide located within the following region: QTPSKPASADGHRGPSAAFAPAAAEPKLFGGFNSSDTVTSPQRAGPLAGG This gene is highly similar to the v-src gene of Rous sarcoma virus. This proto-oncogene may play a role in the Description of Target regulation of embryonic development and cell growth. SRC protein is a tyrosine-protein kinase whose activity can be inhibited by phosphorylation by c-SRC kinase. Mutations in this gene could be involved in the
    [Show full text]
  • Interplay Between Coding and Exonic Splicing Regulatory Sequences
    Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Research Interplay between coding and exonic splicing regulatory sequences Nicolas Fontrodona,1,4 Fabien Aubé,1,4 Jean-Baptiste Claude,1 Hélène Polvèche,1,5 Sébastien Lemaire,1 Léon-Charles Tranchevent,2 Laurent Modolo,3 Franck Mortreux,1 Cyril F. Bourgeois,1 and Didier Auboeuf1 1Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France; 2Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health (LIH), L-1445 Strassen, Luxembourg; 3LBMC Biocomputing Center, CNRS UMR 5239, INSERM U1210, F-69007, Lyon, France The inclusion of exons during the splicing process depends on the binding of splicing factors to short low-complexity reg- ulatory sequences. The relationship between exonic splicing regulatory sequences and coding sequences is still poorly un- derstood. We demonstrate that exons that are coregulated by any given splicing factor share a similar nucleotide composition bias and preferentially code for amino acids with similar physicochemical properties because of the nonran- domness of the genetic code. Indeed, amino acids sharing similar physicochemical properties correspond to codons that have the same nucleotide composition bias. In particular, we uncover that the TRA2A and TRA2B splicing factors that bind to adenine-rich motifs promote the inclusion of adenine-rich exons coding preferentially for hydrophilic amino acids that correspond to adenine-rich codons. SRSF2 that binds guanine/cytosine-rich motifs promotes the inclusion of GC-rich exons coding preferentially for small amino acids, whereas SRSF3 that binds cytosine-rich motifs promotes the inclusion of exons coding preferentially for uncharged amino acids, like serine and threonine that can be phosphorylated.
    [Show full text]
  • Stefano Sellitto 19-05-2020.Pdf
    RNA Binding Proteins: from physiology to pathology An update Stefano Sellitto RBPs regulate the RNA metabolism A ‘conventional’ RNA-Binding Protein (RBP) participates in the formation of ribonucleoprotein (RNP) complexes that are principally involved in gene expression. Keene, 2007 High-Throughuput sequencing to study the RBPs world RIP-Seq (i)CLIP PAR-CLIP Hentze et al., 2018 The concept of RNA operon The RBPs profile is highly dynamic The combinatorial association of many RBPs acting in trans on RNA molecules results in the metabolic regulation of a distinct RNA subpopulations. Keene, 2007 The molecular features of protein-RNA interactions "Classical" RNA-Binding Domains Lunde et al., 2007 "Classical" RNA-Binding Domains RNA-recognition motif (RRM) double-stranded RNA-binding motif (dsRBM) Zinc-finger motif Stefl et al., 2005 Modularity of RBPs RBPs are usually composed by several repeated domains Lunde et al., 2007 Expanding the concept of the RNA Binding Hentze et al., 2018 Novel types of RNA binding Hentze et al., 2018 Lunde et al., 2007 RNA metabolism and neurological diseases RNA binding proteins preserves neuronal integrity De Conti et al., 2017 Alterations of RBPs in neurological disorders Nussbacher et al., 2019 Microsatellite expansion in FXS: reduced FMR1 transcription The reduction of FMRP levels induces an overexpressed LTD activity Bassell & Warren, 2008 Huber et al., 2002 Microsatellite expansion in FXTAS: FMR1 RNA-meidated toxicity FMR1 expanded RNA impairs the miRNA processing Sellier et al., 2013 Loss-of-function VS Gain-of-function Park et al., 2015 TDP-43 and FUS/TLS Ling et al., 2013 TDP-43 and FUS/TLS in ALS and FTD Ling et al., 2013 Cookson, 2017 Loss-of-function VS Gain-of-function Nucelar clearance (LOF) TDP-43 Nuclear TDP-43 (LOF) Loss of TDP-43 negative autoregulation Nucleus Abolishing RNA binding ability Cytoplasmatic stress (GOF) mitigates mutant TDP-43 toxicity Prevent mutant TDP-43 toxic activity on RNAs (GOF) Ihara et al., 2013 .
    [Show full text]
  • Save Pdf (0.04
    58 cambridge.org/jcts 2172 with these clinical observations, we observed altered myelopoiesis in HnrnpkTg mice. These mice demonstrate increased CD11b + Gr1 + populations in the Association between CYP450 polymorphisms and the bone marrow and peripheral blood. Indeed, these mice develop myeloid use of complementary medicine among patients with leukemia, indicated by >20% of circulating white blood cells harboring markers drug-resistant epilepsy in Puerto Rico of immature stem cells in conjunction with positive myeloperoxidase staining Bianca A. Torres-Hernández, Miriam E. Ríos Motta, Adrián Llerenaes and blast-appearing morphology. RPPA revealed expression of c-Myc positively correlated with increased hnRNP K levels. In HnrnpkTg mice, c-Myc protein and Jorge Duconge was increased, yet MYC RNA was invariably decreased compared to wildtype. University of Puerto Rico-Medical Sciences Campus, San Juan, Puerto To decipher a mechanism by which this may occur, we demonstrated a post- Rico transcriptional interaction between hnRNP K and c-Myc in vivo. JQ1, a BRD4 inhibitor, that epigenetically decreases c-Myc expression showed preferential activity against myeloid cells expressing high levels of hnRNP K both in vitro and OBJECTIVES/SPECIFIC AIMS: Patients with epilepsy often combine their in vivo. DISCUSSION/SIGNIFICANCE OF IMPACT: These preliminary studies antiepileptic drugs (AEDs) with complementary medicine (CM). They use CM demonstrate that hnRNP K overexpression causes myeloid malignancies in to treat their symptoms of comorbidities disorder, to reduce the side effect of both mouse and man. We have determined that c-Myc contributes in part to the AEDs or trying to achieve better control of their seizures. However, the hnRNP K-mediated leukemogenesis, and that targeting c-Myc may be an inconsistent patters of the use of CM among countries have been attributed to effective strategy for hnRNP K-overexpressing AML.
    [Show full text]
  • KH Domain Containing RNA-Binding Proteins Coordinate with Micrornas to Regulate
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.03.235127; this version posted August 4, 2020. 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. 1 KH domain containing RNA-binding proteins coordinate with microRNAs to regulate 2 Caenorhabditis elegans development. 3 4 Haskell D 1, Zinovyeva A1*. 5 6 7 (1) Division of Biology. Kansas State University. Manhattan, KS, 66506 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.03.235127; this version posted August 4, 2020. 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. 24 Running title: KH domain proteins coordinate with microRNAs, C. elegans 25 26 27 28 29 30 Keywords: microRNA, RNA binding protein, KH domain, hnRNPK 31 32 33 34 35 * Corresponding author: Anna Zinovyeva, PhD, 28 Ackert Hall, 1717 Claflin Road, Manhattan, 36 KS 66506, phone: 1-785-532-7727, email: [email protected] 37 38 39 40 41 42 43 44 45 46 2 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.03.235127; this version posted August 4, 2020. 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.
    [Show full text]
  • Genetic and Pharmacological Approaches to Preventing Neurodegeneration
    University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2012 Genetic and Pharmacological Approaches to Preventing Neurodegeneration Marco Boccitto University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Neuroscience and Neurobiology Commons Recommended Citation Boccitto, Marco, "Genetic and Pharmacological Approaches to Preventing Neurodegeneration" (2012). Publicly Accessible Penn Dissertations. 494. https://repository.upenn.edu/edissertations/494 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/494 For more information, please contact [email protected]. Genetic and Pharmacological Approaches to Preventing Neurodegeneration Abstract The Insulin/Insulin-like Growth Factor 1 Signaling (IIS) pathway was first identified as a major modifier of aging in C.elegans. It has since become clear that the ability of this pathway to modify aging is phylogenetically conserved. Aging is a major risk factor for a variety of neurodegenerative diseases including the motor neuron disease, Amyotrophic Lateral Sclerosis (ALS). This raises the possibility that the IIS pathway might have therapeutic potential to modify the disease progression of ALS. In a C. elegans model of ALS we found that decreased IIS had a beneficial effect on ALS pathology in this model. This beneficial effect was dependent on activation of the transcription factor daf-16. To further validate IIS as a potential therapeutic target for treatment of ALS, manipulations of IIS in mammalian cells were investigated for neuroprotective activity. Genetic manipulations that increase the activity of the mammalian ortholog of daf-16, FOXO3, were found to be neuroprotective in a series of in vitro models of ALS toxicity.
    [Show full text]
  • Integrated Analyses of Translatome and Proteome Identify the Rules of Translation Selectivity in RPS14-Deficient Cells
    ARTICLE Red Cell Biology and its Disorders Integrated analyses of translatome and Ferrata Storti Foundation proteome identify the rules of translation selectivity in RPS14-deficient cells Ismael Boussaid,1 Salomé Le Goff,1,2,* Célia Floquet,1,* Emilie-Fleur Gautier,1,3 Anna Raimbault,1 Pierre-Julien Viailly,4 Dina Al Dulaimi,1 Barbara Burroni,5 Isabelle Dusanter-Fourt,1 Isabelle Hatin,6 Patrick Mayeux,1,2,3,# Bertrand Cosson7,# and Michaela Fontenay1,2,3,4,8 Haematologica 2021 1 Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris; Volume 106(3):746-758 2Laboratoire d’Excellence du Globule Rouge GR-Ex, Université de Paris, Paris; 3Proteomic Platform 3P5, Université de Paris, Paris; 4Centre Henri-Becquerel, Institut de Recherche et d’Innovation Biomedicale de Haute Normandie, INSERM U1245, Rouen; 5Assistance Publique-Hôpitaux de Paris, Centre-Université de Paris - Cochin, Service de Pathologie, Paris; 6Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université de Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex; 7Université de Paris, Epigenetics and Cell Fate, CNRS UMR 7216, Paris and 8Assistance Publique- Hôpitaux de Paris, Centre-Université de Paris - Hôpital Cochin, Service d’Hématologie Biologique, Paris, France *SLG and CF contributed equally to this work. #PM and BC contributed equally as co-senior authors. ABSTRACT n ribosomopathies, the Diamond-Blackfan anemia (DBA) or 5q- syn- drome, ribosomal protein (RP) genes are affected by mutation or deletion, Iresulting in bone marrow erythroid hypoplasia. Unbalanced production of ribosomal subunits leading to a limited ribosome cellular content regu- lates translation at the expense of the master erythroid transcription factor GATA1.
    [Show full text]
  • Molecular Basis of Sequence-Specific Single-Stranded DNA Recognition By
    The EMBO Journal Vol. 21 No. 13 pp. 3476±3485, 2002 Molecular basis of sequence-speci®c single-stranded DNA recognition by KH domains: solution structure of a complex between hnRNP K KH3 and single-stranded DNA Demetrios T.Braddock1,2, James L.Baber1, mitosis (Michelotti et al., 1997) and the tight control of David Levens2 and G.Marius Clore1,3 oncogenes (He et al., 2000; Liu et al., 2001). Recently, we solved the structure of a complex between 1Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of the KH3 and KH4 domains of FBP (FBP3/4) and a Health, Bethesda, MD 20892-0510 and 2Laboratory of Pathology, ssDNA 29mer from FUSE (Braddock et al., 2002). In the Building 10, National Cancer Institute, National Institutes of Health, FBP3/4±FUSE complex, KH3 and KH4 bind in a speci®c Bethesda, MD 20892, USA orientation and register to the ssDNA 29mer, which is 3Corresponding author preserved in complexes of the individual KH domains e-mail: [email protected] bound to shorter oligonucleotides, 9±10 bp in length, encompassing their respective target sites in the larger To elucidate the basis of sequence-speci®c single- complex. Although the ssDNA binding site is located stranded (ss) DNA recognition by K homology (KH) within a relatively narrow groove that generally favors domains, we have solved the solution structure of a pyrimidines over purines, the origin of further sequence- complex between the KH3 domain of the transcrip- speci®c base recognition appears to be subtle.
    [Show full text]
  • Comparative Transcriptome and Translatome Analysis in Contrasting
    Li et al. BMC Genomics 2018, 19(Suppl 10):935 https://doi.org/10.1186/s12864-018-5279-4 RESEARCH Open Access Comparative transcriptome and translatome analysis in contrasting rice genotypes reveals differential mRNA translation in salt-tolerant Pokkali under salt stress Yong-Fang Li1,2*†, Yun Zheng3†, Lakshminarayana R. Vemireddy2, Sanjib Kumar Panda2, Smitha Jose2, Alok Ranjan2, Piyalee Panda2, Ganesan Govindan2, Junxia Cui1,KangningWei1, Mahmoud W. Yaish4, Gnanambal Charmaine Naidoo5 and Ramanjulu Sunkar2* From 29th International Conference on Genome Informatics Yunnan, China. 3-5 December 2018 Abstract Background: Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is a highly salt-tolerant landrace, whereas IR29 is a salt-sensitive but widely cultivated genotype. Comparative analysis of these genotypes may offer a better understanding of the salinity tolerance mechanisms in rice. Although most stress-responsive genes are regulated at the transcriptional level, in many cases, changes at the transcriptional level are not always accompanied with the changes in protein abundance, which suggests that the transcriptome needstobestudiedinconjunctionwiththeproteometolink the phenotype of stress tolerance or sensitivity. Published reports have largely underscored the importance of transcriptional regulation during salt stress in these genotypes, but the regulation at the translational level has been rarely studied. Using RNA-Seq, we simultaneously analyzed the transcriptome and translatome from control and salt-exposed
    [Show full text]
  • The Global View of Translation
    International Journal of Molecular Sciences Review Translatomics: The Global View of Translation Jing Zhao 1, Bo Qin 2, Rainer Nikolay 2 , Christian M. T. Spahn 2 and Gong Zhang 1,* 1 Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China; [email protected] 2 Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; [email protected] (B.Q.); [email protected] (R.N.); [email protected] (C.M.T.S.) * Correspondence: [email protected]; Tel.: +86-20-8522-1790 Received: 6 November 2018; Accepted: 2 January 2019; Published: 8 January 2019 Abstract: In all kingdoms of life, proteins are synthesized by ribosomes in a process referred to as translation. The amplitude of translational regulation exceeds the sum of transcription, mRNA degradation and protein degradation. Therefore, it is essential to investigate translation in a global scale. Like the other “omics”-methods, translatomics investigates the totality of the components in the translation process, including but not limited to translating mRNAs, ribosomes, tRNAs, regulatory RNAs and nascent polypeptide chains. Technical advances in recent years have brought breakthroughs in the investigation of these components at global scale, both for their composition and dynamics. These methods have been applied in a rapidly increasing number of studies to reveal multifaceted aspects of translation control. The process of translation is not restricted to the conversion of mRNA coding sequences into polypeptide chains, it also controls the composition of the proteome in a delicate and responsive way.
    [Show full text]
  • RNA Regulons and the RNA-Protein Interaction Network
    BioMol Concepts, Vol. 3 (2012), pp. 403–414 • Copyright © by Walter de Gruyter • Berlin • Boston. DOI 10.1515/bmc-2012-0016 Review RNA regulons and the RNA-protein interaction network Jochen Imig 1, a , Alexander Kanitz 1, a and Introduction Andr é P. Gerber 1,2, * In 1961, Fran ç ois Jacob and Jacques Monod described 1 Institute of Pharmaceutical Sciences , Department of the fi rst gene regulatory system in E. coli – the bacterial Chemistry and Applied Biosciences, ETH Zurich, lac operon (1) . An operon refers to a single, polycistronic CH-8093 Zurich , Switzerland transcriptional unit composed of a cluster of functionally 2 Department of Microbial and Cellular Sciences , Faculty and/or structurally related genes that are under the control of Health and Medical Sciences, University of Surrey, of a single regulatory unit that can be activated or repressed Guildford GU2 7XH , UK by a trans -acting factor. The operon concept was revolution- * Corresponding author ary as it implied that transcriptional units might bear infor- e-mail: [email protected] mation for the coordinate expression of functionally related proteins. Such an integrative architecture enables prokaryotes to quickly coordinate gene expression in response to environ- Abstract mental stimuli. However, DNA operons limit the fl exibility to regulate the expression of genes individually and would The development of genome-wide analysis tools has prompted therefore be detrimental to the regulation of genes that have global investigation of the gene expression program, reveal- multiple functions. ing highly coordinated control mechanisms that ensure proper DNA operons, which lead to the production of polycis- spatiotemporal activity of a cell ’ s macromolecular compo- tronic transcripts, predominantly occur in prokaryotes (2) .
    [Show full text]
  • Human Proteins That Interact with RNA/DNA Hybrids
    Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Resource Human proteins that interact with RNA/DNA hybrids Isabel X. Wang,1,2 Christopher Grunseich,3 Jennifer Fox,1,2 Joshua Burdick,1,2 Zhengwei Zhu,2,4 Niema Ravazian,1 Markus Hafner,5 and Vivian G. Cheung1,2,4 1Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA; 2Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA; 3Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland 20892, USA; 4Department of Pediatrics, University of Michigan, Ann Arbor, Michigan 48109, USA; 5Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland 20892, USA RNA/DNA hybrids form when RNA hybridizes with its template DNA generating a three-stranded structure known as the R-loop. Knowledge of how they form and resolve, as well as their functional roles, is limited. Here, by pull-down assays followed by mass spectrometry, we identified 803 proteins that bind to RNA/DNA hybrids. Because these proteins were identified using in vitro assays, we confirmed that they bind to R-loops in vivo. They include proteins that are involved in a variety of functions, including most steps of RNA processing. The proteins are enriched for K homology (KH) and helicase domains. Among them, more than 300 proteins preferred binding to hybrids than double-stranded DNA. These proteins serve as starting points for mechanistic studies to elucidate what RNA/DNA hybrids regulate and how they are regulated.
    [Show full text]