DOCSLIB.ORG

Mrna Structure Dynamics Identifies the Embryonic RNA Regulome

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mrna Structure Dynamics Identifies the Embryonic RNA Regulome bioRxiv preprint doi: https://doi.org/10.1101/274290; this version posted March 1, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. mRNA structure dynamics identifies the embryonic RNA regulome Jean-Denis Beaudoin1,*,‡, Eva Maria Novoa2,3,4,5,*, Charles E Vejnar1, Valeria Yartseva1, Carter Takacs1, Manolis Kellis2,3 and Antonio J Giraldez1,6,‡ RNA folding plays a crucial role in RNA function. However, our knowledge of the global structure of the transcriptome is limited to steady-state conditions, hindering our understanding of how RNA structure dynamics influences gene function. Here, we have characterized mRNA structure dynamics during zebrafish development. We observe that on a global level, translation guides structure rather than structure guiding translation. We detect a decrease in structure in translated regions, and we identify the ribosome as a major remodeler of RNA structure in vivo. In contrast, we find that 3’-UTRs form highly folded structures in vivo, which can affect gene expression by modulating miRNA activity. Furthermore, we find that dynamic 3’-UTR structures encode RNA decay elements, including regulatory elements in nanog and cyclin A1, key maternal factors orchestrating the maternal-to-zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs. Introduction Previous studies have focused on the global analysis of RNA structures in cells at RNA carries out a broad range of functions,1 and steady-state. However, in an organism, critical RNA structure has emerged as a fundamental developmental and metabolic decisions are often regulatory mechanism, modulating various post- made when cells transition between cellular transcriptional events such as splicing2, states. Consequently, to understand the subcellular localization3, translation4,5 and decay6. relationship between RNA structure, regulation, RNA probing reagents combined with high- and function in vivo, it is paramount to determine throughput sequencing7 allow the interrogation of how RNA structures change in dynamic cellular RNA structure in a transcriptome-wide manner in environments. During the maternal-to-zygotic vitro and in vivo8,9. These approaches have transition (MZT) in animals, the embryo is initially identified common features in RNA structures and transcriptionally silent, and gene expression is their regulation at steady-state10-14, suggesting primarily orchestrated by post-transcriptional that RNAs tend to be unfolded in vivo13,15. regulation of maternally-deposited mRNA However, the cellular factors that remodel RNA translation and decay25,26. These regulatory folding in vivo remain unknown. pathways are central to embryogenesis, controlling mRNA translation, the cell cycle, and While the ribosome possesses a the activation of the zygotic genome25,27. Among 16 constitutive mRNA helicase activity , stable RNA the set of maternally-deposited mRNAs, the structures found within coding regions can reduce transcription factors nanog, oct4, and sox19b are 17,18 the rate of translation in vitro . Similarly, the highly translated. Their combined function is intrinsic structure adopted by coding regions required to activate a large fraction of the zygotic instruct the rate of translation in bacteria, where program28,29. One of the first zygotically sequences forming stable structures show transcribed RNAs is the microRNA miR-43028,30, 19 reduced translation in vivo . In addition, stable which causes translation repression, structures located in 5’UTR or surrounding the deadenylation and clearance of hundreds of AUG initiation codon repress translation and maternal mRNAs during the MZT31-33. Thus, the modulate protein output in bacteria and MZT provides an ideal system to understand how 20-23 eukaryotes . However, in plant and yeast, the entire cellular population of RNA structures is highly structured mRNA in vitro correlated with remodeled across changing cellular states, and 9,24 higher ribosome density and protein output , how these changes may impact gene regulation. yet, other studies found that RNA structure in Here, we analyze mRNA structural dynamics yeast were not correlated with translation during zebrafish embryogenesis to investigate the 13 efficiency . 1Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA 2Computer Science and Electrical Engineering Department, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA 3The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139; USA 4Department of Neuroscience; Garvan Institute of Medical Research Darlinghurst NSW 2010; Australia 5School of Medicine, University of New South Wales, Sydney NSW 2052; Australia 6Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut 06520; USA *Co-first authors ‡To whom correspondence should be addressed e-mail: [email protected] or [email protected] phone: +1 203-785-5423; fax: +1 203-785-4415 1 bioRxiv preprint doi: https://doi.org/10.1101/274290; this version posted March 1, 2018. 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. relationship between RNA structure and gene analysis revealed global changes in mRNA regulation in vivo. structure during the MZT (Extended Data Fig. 1i- k). Changes in translation, analyzed by ribosome Results footprinting34, were correlated with global mRNA accessibility changes in coding sequences (CDS) Dynamic structure reflects translation and 5’-UTRs, but not in 3’-UTRs (Fig. 1b and changes Extended Data Fig. 1l). We analyzed differentially structured regions over development as 100-nt We analyzed the structure of the zebrafish sliding windows (Fig. 1c) and observed that transcriptome during the MZT using DMS-seq (Fig mRNAs with decreasing rates of translation 1a), which we validated as an accurate readout of between 2 and 6 hours post-fertilization (hpf) in vivo RNA structure (Extended Data Fig. 1). Our increase in structure (orange), and those whose Figure 1. Relationship between mRNA structure and translation during the MZT. a, Schematic view of the profound transcriptomic remodeling that occurs during the maternal-to-zygotic transition. After a transcriptionally silent period (gray), the maternal program (pink) transitions to a zygotic program (blue). b, Correlation between the per-transcript changes in translation efficiency (6-2 hpf) and CDS accessibility (6/2 hpf). c, Methodology used to identify local RNA structure changes between conditions. Differentially structured (DS) sliding windows are defined as those that are significantly changing (P<0.05) based on the Kolmogorov- Smirnov test, and show an increase (>1.1) or decrease (<0.9) in their Gini index ratio. d, In the left panel, structure changes of each 100-nt window (Gini ratio 6/2 hpf) along each transcript (total of 1,273) are shown. Transcripts are ranked by their changes in translation efficiency during the MZT (6-2 hpf). Each transcript region (5’-UTR, CDS, 3’-UTR) has been normalized by its length. In the right panel, cumulative distributions of differentially structured windows for transcripts that increase (top 20%, upper panel) and decrease (bottom 20%, lower panel) translation are shown. e, Cumulative distribution of global CDS accessibilities in vivo, showing that highly translated mRNAs exhibit increased CDS accessibility in vivo at 2 hpf, a stage at which the rate of translation spans ~10,000-fold between highly and poorly translated mRNAs. Transcripts have been binned into quintiles according to their translation efficiency. P-value was computed using a one-sided Mann-Whitney U test. 2 bioRxiv preprint doi: https://doi.org/10.1101/274290; this version posted March 1, 2018. 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. translation increases become less structured 2a, lower panel). To distinguish between these (turquoise) (Fig. 1d). These results indicate that scenarios, we compared the accessibility of translation and mRNA structure are anti- transcripts analyzed in vitro, binned by their correlated in vivo, in contrast to previous translation efficiency in vivo (see Methods) (Fig. reports9,13,24,35. Moreover, we compared the 2b and Extended Data Fig. 2a). We found that accessibilities of the different mRNA regions (5’- lowly and highly translated mRNAs show similar UTR, CDS and 3’-UTR) and found that highly CDS accessibility in vitro, distinct from in vivo translated mRNAs display a greater accessibility (Fig. 2b, c and Extended Data Fig. 2a-c), in their CDS (P=2.3e-118) and, to a lesser extent, suggesting that the differences in mRNA in their 5’-UTRs (P=1.9e-11) (Fig. 1e and accessibility between highly and lowly translated Extended Data Fig. 2a). mRNAs are not intrinsic to the nucleotide sequence. While very stable structures in the 5’- Pre-existing RNA structure differences UTR clearly disrupt translation20,22,23, we observed might determine mRNA translation, where less no correlation between translation and structure of structured mRNAs would be more accessible and, 5’-UTRs or the AUG initiation codons in vitro (Fig. consequently, translated more effectively (Fig. 2a, 2d, e and Extended Data Fig. 2d-g). Thus, on a upper panel). Alternatively,
Load more

Recommended publications
  • Transcriptional Targets of Hepatocyte Growth Factor Signaling and Ki-Ras Oncogene Activation in Colorectal Cancer
    Oncogene (2006) 25, 91–102 & 2006 Nature Publishing Group All rights reserved 0950-9232/06 $30.00 www.nature.com/onc ORIGINAL ARTICLE Transcriptional targets of hepatocyte growth factor signaling and Ki-ras oncogene activation in colorectal cancer IM Seiden-Long1,2, KR Brown1,2, W Shih1, DA Wigle3, N Radulovich1, I Jurisica1,2,4 and M-S Tsao1,2,5 1Ontario Cancer Institute/Princess Margaret Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada; 2Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; 3Department of Surgery, University of Toronto, Toronto, Ontario, Canada; 4Department of Computer Science, University of Toronto, Toronto, Ontario, Canada and 5Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada Both Ki-ras mutation and hepatocyte growth factor Introduction (HGF) receptor Met overexpression occur at high frequency in colon cancer. This study investigates the Colorectal carcinogenesis is characterized by a well- transcriptional changes induced by Ki-ras oncogene and delineated series of genetic mutations and aberrant gene HGF/Met signaling activation in colon cancer cell lines in expression events (Fearon and Vogelstein, 1990). Ki-ras vitro and in vivo. The model system used in these studies oncogene activation and the overexpression of growth included the DLD-1 colon cancer cell line with a mutated factor receptors on the cell surface have been shown to Ki-ras allele, and the DKO-4 cell line generated from play important rolesin colon cancer progression DLD-1, with its mutant Ki-ras allele inactivated by (Shirasawa et al., 1993; Fazekas et al., 2000). Ki-ras is targeted disruption.
    [Show full text]
  • Systems Biology Lecture Outline (Systems Biology) Michael K
    Spring 2019 – Epigenetics and Systems Biology Lecture Outline (Systems Biology) Michael K. Skinner – Biol 476/576 CUE 418, 10:35-11:50 am, Tuesdays & Thursdays January 22 & 29, 2019 Weeks 3 and 4 Systems Biology (Components & Technology) Components (DNA, Expression, Cellular, Organ, Physiology, Organism, Differentiation, Development, Phenotype, Evolution) Technology (Genomics, Transcriptomes, Proteomics) (Interaction, Signaling, Metabolism) Omics (Data Processing and Resources) Required Reading ENCODE (2012) ENCODE Explained. Nature 489:52-55. Tavassoly I, Goldfarb J, Iyengar R. (2018) Essays Biochem. 62(4):487-500. Literature Sundaram V, Wang T. Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re-Visiting the "Gene-Battery" Model. Bioessays. 2018 40(1). doi: 10.1002/bies.201700155. Abil Z, Ellefson JW, Gollihar JD, Watkins E, Ellington AD. Compartmentalized partnered replication for the directed evolution of genetic parts and circuits. Nat Protoc. 2017 Dec;12(12):2493- 2512. Filipp FV. Crosstalk between epigenetics and metabolism-Yin and Yang of histone demethylases and methyltransferases in cancer. Brief Funct Genomics. 2017 Nov 1;16(6):320-325. Chen Z, Li S, Subramaniam S, Shyy JY, Chien S. Epigenetic Regulation: A New Frontier for Biomedical Engineers. Annu Rev Biomed Eng. 2017 Jun 21;19:195-219. Hollick JB. Paramutation and related phenomena in diverse species. Nat Rev Genet. 2017 Jan;18(1):5-23. Macovei A, Pagano A, Leonetti P, Carbonera D, Balestrazzi A, Araújo SS. Systems biology and genome-wide approaches to unveil the molecular players involved in the pre-germinative metabolism: implications on seed technology traits. Plant Cell Rep. 2017 May;36(5):669-688. Bagchi DN, Iyer VR.
    [Show full text]
  • The Human Proteome Co-Regulation Map Reveals Functional Relationships Between Proteins
    bioRxiv preprint doi: https://doi.org/10.1101/582247; this version posted March 19, 2019. The copyright holder for this preprint (which was 19/03/2019not certified by peer review) is the author/funder, who hasNBT_manuscript_revised granted bioRxiv a license - toGoogle display Docs the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 1 The human proteome co-regulation map reveals functional relationships 2 between proteins 3 Georg Kustatscher1 *, Piotr Grabowski2 *, Tina A. Schrader3 , Josiah B. Passmore3 , Michael 4 Schrader3 , Juri Rappsilber1,2# 5 1 Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK 6 2 Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, 7 Germany 8 3 Biosciences, University of Exeter, Exeter EX4 4QD, UK 9 * Equal contribution 10 # Communicating author: [email protected] 11 Submission as Resource article. 12 The annotation of protein function is a longstanding challenge of cell biology that 13 suffers from the sheer magnitude of the task. Here we present ProteomeHD, which 14 documents the response of 10,323 human proteins to 294 biological perturbations, 15 measured by isotope-labelling mass spectrometry. Using this data matrix and robust 16 machine learning we create a co-regulation map of the cell that reflects functional 17 associations between human proteins. The map identifies a functional context for 18 many uncharacterized proteins, including microproteins that are difficult to study with 19 traditional methods. Co-regulation also captures relationships between proteins 20 which do not physically interact or co-localize. For example, co-regulation of the 21 peroxisomal membrane protein PEX11β with mitochondrial respiration factors led us 22 to discover a novel organelle interface between peroxisomes and mitochondria in 23 mammalian cells.
    [Show full text]
  • The Complexity of Mirna-Mediated Repression
    Cell Death and Differentiation (2015) 22, 22–33 & 2015 Macmillan Publishers Limited All rights reserved 1350-9047/15 www.nature.com/cdd Review The complexity of miRNA-mediated repression A Wilczynska*,1 and M Bushell*,1 Since their discovery 20 years ago, miRNAs have attracted much attention from all areas of biology. These short (B22 nt) non-coding RNA molecules are highly conserved in evolution and are present in nearly all eukaryotes. They have critical roles in virtually every cellular process, particularly determination of cell fate in development and regulation of the cell cycle. Although it has long been known that miRNAs bind to mRNAs to trigger translational repression and degradation, there had been much debate regarding their precise mode of action. It is now believed that translational control is the primary event, only later followed by mRNA destabilisation. This review will discuss the most recent advances in our understanding of the molecular underpinnings of miRNA-mediated repression. Moreover, we highlight the multitude of regulatory mechanisms that modulate miRNA function. Cell Death and Differentiation (2015) 22, 22–33; doi:10.1038/cdd.2014.112; published online 5 September 2014 Facts impact their protein output. The dysregulation of miRNA expression in many disease conditions has been thoroughly miRNA-mediated translational repression is a pre-requisite documented (for details see Croce1). In addition, extensive for target mRNA degradation. shortening of mRNA 30UTRs, which causes loss of miRNA RNA helicases are critical to the inhibition of translation target sites resulting in the post-transcriptional upregulation initiation by miRNA. of critical oncogenes, has been observed in cancer cells Modifications of RISC components have critical roles in (Figure 2d).2,3 Conversely, lengthening of 30UTRs and thus an controlling the miRNA pathway.
    [Show full text]
  • Back-Of-The-Envelope Guide (A Tutorial) to 10 Intracellular Landscapes
    MOJ Proteomics & Bioinformatics Review Article Open Access Back-of-the-envelope guide (a tutorial) to 10 intracellular landscapes Abstract Volume 7 Issue 1 - 2018 Landscape is a metaphor for conceptualizing and visualizing a score across one or Maurice HT Ling1,2 more biological entities or concepts. This review provides a cursory overview of 1Colossus Technologies LLP, Republic of Singapore 10 landscapes (in alphabetical order, copy number, fluxome, genome, molecular, 2HOHY Pte. Ltd., Republic of Singapore metabolome, mutation, phenome, proteome, regulome, and transcriptome) in intracellular biology without going into extensive depth; hence, this article can act as Correspondence: Maurice HT Ling, Colossus Technologies a first tutorial into intracellular landscapes. The value ahead is to be able to compare LLP, 8 Burns Road, Trivex, Singapore 369977, Republic of and interrogate across multiple landscapes at different resolutions. Singapore, Tel +6596669233, Email [email protected] Received: January 29, 2018 | Published: February 06, 2018 Definition of a “landscape” Since Wright,1 the concept of landscape had been used to reference a metaphoric representation of an overview of one or more biological 1 The concept of landscape was first introduced by Sewell Wright, entities. This article reviews 10 landscapes (in alphabetical order, as a metaphor to visual a scale or score across a biological entity, copy number, fluxome, genome, molecular, metabolome, mutation, such as a chromosome (Figure 1). In a linear biological entity, such as phenome, proteome, regulome, and transcriptome) in intracellular a chromosome; the biological entity is represented on the horizontal biology with the aim of presenting a cursory, back of the envelope axis and the score, such as GC content, is represented on the vertical overview without going into extensive depth into each landscape.
    [Show full text]
  • Bioinformatics Strategies for Identification of Cancer Biomarkers and Targets in Pathogens Associated with Cancer
    FEDERAL UNIVERSITY OF MINAS GERAIS INSTITUTE OF BIOLOGICAL SCIENCE DEPARTMENT OF GENERAL BIOLOGY GRADUATE PROGRAM OF BIOINFORMATICS BIOINFORMATICS STRATEGIES FOR IDENTIFICATION OF CANCER BIOMARKERS AND TARGETS IN PATHOGENS ASSOCIATED WITH CANCER PhD STUDENT: Debmalya Barh SUPERVISOR: Prof. Dr. Vasco Ariston de Carvalho Azevedo Page 1 of 237 DEBMALYA BARH Bioinformatics strategies for identification of cancer biomarkers and targets in pathogens associated with cancer PhD STUDENT: Debmalya Barh SUPERVISOR: Prof. Dr. Vasco Ariston de Carvalho Azevedo FEDERAL UNIVERSITY OF MINAS GERAIS INSTITUTE OF BIOLOGICAL SCIENCES BELO HORIZONTE - MG February – 2017 Page 2 of 237 043 Barh, Debmalya. Bioinformatics strategies for identification of cancer biomarkers and targets in pathogens associated with cancer [manuscrito] / Debmalya Barh. – 2017. 237 f. : il. ; 29,5 cm. Supervisor: Vasco Ariston de Carvalho Azevedo. Tese (doutorado) – Federal University of Minas Gerais, Institute of Biological Sciences. 1. Bioinformática - Teses. 2. Marcadores biológicos. 3. Doenças transmissíveis - Teses. 4. Transcriptômica - Teses. 5. MicroRNAs - Teses. I. Azevedo , Vasco Ariston de Carvalho. II. Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. III. Título. CDU: 573:004 TABLE OF CONTENTS TABLE OF CONTENTS……………………………………………………………………………………i DEDICATION………………………………………………………………………………………..……iii ACKNOWLEDGEMENTS…………………………………………………………………………..……iv LIST OF ABBREVIATIONS…………………………………………………………………….……….. v ABSTRACT………………………………………………………………………………………...……..vii
    [Show full text]
  • Mechanism of Translation Regulation of BTG1 by Eif3 Master's Thesis
    Mechanism of Translation Regulation of BTG1 by eIF3 Master’s Thesis Presented to The Faculty of the Graduate School of Arts and Sciences Brandeis University Department of Biology Amy S.Y. Lee, Advisor In Partial Fulfillment of the Requirements for the Degree Master of Science in Biology by Shih-Ming (Annie) Huang May 2019 Copyright by Shih-Ming (Annie) Huang © 2019 ACKNOWLEDGEMENT I would like to express my deepest gratitude to Dr. Amy S.Y. Lee for her continuous patience, support, encouragement, and guidance throughout this journey. I am very thankful for all the members of the Lee Lab for providing me with this caring and warm environment to complete my work. I would also like to thank Dr. James NuñeZ for collaborating with us on this project and helping us in any shape or form. iii ABSTRACT Mechanism of Translation Regulation of BTG1 by eIF3 A thesis presented to the Department of Biology Graduate School of Arts and Sciences Brandeis University Waltham, Massachusetts By Shih-Ming (Annie) Huang REDACTED iv TABLE OF CONTENTS REDACTED v LIST OF FIGURES REDACTED vi INTRODUCTION I. Gene Regulation All cells in our bodies contain the same genome, but distinct cell types express very different sets of genes. The sets of gene expressed under specific conditions determine what the cell can do, by controlling the proteins and functional RNAs the cell contains. The process of controlling which genes are expressed is known as gene regulation. Any step along the gene expression pathway can be controlled, from DNA transcription, translation of mRNAs into proteins, to post-translational modifications.
    [Show full text]
  • Organizational Properties of a Functional Mammalian Cis-Regulome
    bioRxiv preprint doi: https://doi.org/10.1101/550897; this version posted February 15, 2019. 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. Organizational properties of a functional mammalian cis-regulome Virendra K. Chaudhri, Krista Dienger-Stambaugh, Zhiguo Wu, Mahesh Shrestha and Harinder Singh*# Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, 45220, USA #Current address: Center for Systems Immunology, Departments of Immunology and Computational and Systems Biology, The University of Pittsburgh, Pittsburgh, PA 15213 *Corresponding author Email: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/550897; this version posted February 15, 2019. 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 Mammalian genomic states are distinguished by their chromatin and transcription profiles. Most genomic analyses rely on chromatin profiling to infer cis-regulomes controlling distinctive cellular states. By coupling FAIRE-seq with STARR-seq and integrating Hi-C we assemble a functional cis-regulome for activated murine B- cells. Within 55,130 accessible chromatin regions we delineate 9,989 active enhancers communicating with 7,530 promoters. The cis-regulome is dominated by long range enhancer-promoter interactions (>100kb) and complex combinatorics, implying rapid evolvability. Genes with multiple enhancers display higher rates of transcription and multi-genic enhancers manifest graded levels of H3K4me1 and H3K27ac in poised and activated states, respectively. Motif analysis of pathway-specific enhancers reveals diverse transcription factor (TF) codes controlling discrete processes.
    [Show full text]
  • Importance of CNOT8 Deadenylase Subunit in DNA Damage Responses Following Ionizing Radiation (IR)
    Reports of Biochemistry & Molecular Biology Vol.9, No.1, July 2020 Original article www.RBMB.net Importance of CNOT8 Deadenylase Subunit in DNA Damage Responses Following Ionizing Radiation (IR) Samira Eskandarian1,2, Roger Grand2, Shiva Irani*1, Mohsen Saeedi3, Reza Mirfakhraie4 Abstract Background: The Ccr4-Not protein complex (CNOT complex) is a key regulator of gene expression in eukaryotic cells. Ccr4-Not Complex is composed of at least nine conserved subunits in mammalian cells with two main enzymatic activities. CNOT8 is a subunit of the complex with deadenylase activity that interacts transiently with the CNOT6 or CNOT6L subunits. Here, we focused on the role of the human CNOT8 subunit in the DNA damage response (DDR). Methods: Cell viability was assessed to measure ATP level using a Cell Titer-Glo Luminescence reagent up to 4 days’ post CNOT8 siRNA transfection. In addition, expression level of phosphorylated proteins in signalling pathways were detected by western blotting and immunofluorescence microscopy. CNOT8- depleted Hela cells post- 3 Gy ionizing radiation (IR) treatment were considered as a control. Results: Our results from cell viability assays indicated a significant reduction at 72-hour post CNOT8 siRNA transfection (p= 0.04). Western blot analysis showed slightly alteration in the phosphorylation of DNA damage response (DDR) proteins in CNOT8-depleted HeLa cells following treatment with ionizing radiation (IR). Increased foci formation of H2AX, RPA, 53BP1, and RAD51 foci was observed after IR in CNOT8-depleted cells compared to the control cells. Conclusions: We conclude that CNOT8 deadenylase subunit is involved in the cellular response to DNA damage. Keywords: CNOT complex, CNOT8, DNA damage response, SiRNA.
    [Show full text]
  • Genome Sequencing: Then & Now
    “Aint you got an ‘ome to go to?” Genomics Transcriptomics Proteomics Metabolomics Physiomics toxicogenomics pharmacogenomics ecotoxicopharmacogenomics phosphatome, glycome, secretome metronome, mobilome, gardenome, etc… http://omics.org/index.php/Alphabetically_ordered_list_of_omes_and_omics --A-- Alignmentome: conceived before 2003. The whole set of Bacteriome: an organelle of bacteria. (Bacteriome.org). Also Carbome: BiO center. 2003. The whole set of carbone multiple sequence and structure alignments in the totality of baterial genes and proteins. based living organisms in the universe. (Carbome.org) bioinformatics. Alignments are the most important Bacterome: The totality of (Bacterome.org) Carbomics: BiO center. 2003. (Carbomics.org) representation in bioinformatics especially for homology and Behaviorome: The totality of (Behaviorome.org) Cardiogenomics: The omics approach research of evolution study. (Alignmentome.org) Behavioromics: The omics approach research of Cardiogenome (Cardiogenomics.org) in biology Alignmentomics: conceived before 2003. The study of Behavioromics (Behavioromics.org) in biology Cellome: concept is derived from the understanding that aligning strings and sequences especially in bioinformatics. Behaviourome: The totality of (Behaviourome.org) cells as a whole can be used for therapeutic purposes. As an (Alignmentomics.org) Behaviouromics: The omics approach research of important bioresource, cells are kept for biotechnology. As Alignome: 2003 . The whole set of string alignment Behaviouromics (Behaviouromics.org) in biology a distinct group concept, cellome refers to such cells and algorithms such as FASTA, BLAST and HMMER. Bibliome: 1999. EBI (European Bioinformatics Institute). their genetic materials. (Cellome.org) (Alignome.org) The whole of biological science and technology literature. Cellomics: The study of Cellome. Cellomics is also a Alignomics: The omics approach research of Alignomics Within bibliome, each word and context is interconnected company name Cellomics, Inc.
    [Show full text]
  • Identification of a Primitive Intestinal Transcription Factor Network Shared Between Esophageal Adenocarcinoma and Its Precancerous Precursor State
    Downloaded from genome.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Research Identification of a primitive intestinal transcription factor network shared between esophageal adenocarcinoma and its precancerous precursor state Connor Rogerson,1 Edward Britton,1 Sarah Withey,2 Neil Hanley,2,3 Yeng S. Ang,2,4 and Andrew D. Sharrocks1 1School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom; 2School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, United Kingdom; 3Endocrinology Department, Central Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WU, United Kingdom; 4GI Science Centre, Salford Royal NHS FT, University of Manchester, Salford M6 8HD, United Kingdom Esophageal adenocarcinoma (EAC) is one of the most frequent causes of cancer death, and yet compared to other common cancers, we know relatively little about the molecular composition of this tumor type. To further our understanding of this cancer, we have used open chromatin profiling to decipher the transcriptional regulatory networks that are operational in EAC. We have uncovered a transcription factor network that is usually found in primitive intestinal cells during embryonic development, centered on HNF4A and GATA6. These transcription factors work together to control the EAC transcrip- tome. We show that this network is activated in Barrett’s esophagus, the putative precursor state to EAC, thereby providing novel molecular evidence in support of stepwise malignant transition. Furthermore, we show that HNF4A alone is sufficient to drive chromatin opening and activation of a Barrett’s-like chromatin signature when expressed in normal human epithe- lial cells.
    [Show full text]
  • Renoprotective Effect of Combined Inhibition of Angiotensin-Converting Enzyme and Histone Deacetylase
    BASIC RESEARCH www.jasn.org Renoprotective Effect of Combined Inhibition of Angiotensin-Converting Enzyme and Histone Deacetylase † ‡ Yifei Zhong,* Edward Y. Chen, § Ruijie Liu,*¶ Peter Y. Chuang,* Sandeep K. Mallipattu,* ‡ ‡ † | ‡ Christopher M. Tan, § Neil R. Clark, § Yueyi Deng, Paul E. Klotman, Avi Ma’ayan, § and ‡ John Cijiang He* ¶ *Department of Medicine, Mount Sinai School of Medicine, New York, New York; †Department of Nephrology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China; ‡Department of Pharmacology and Systems Therapeutics and §Systems Biology Center New York, Mount Sinai School of Medicine, New York, New York; |Baylor College of Medicine, Houston, Texas; and ¶Renal Section, James J. Peters Veterans Affairs Medical Center, New York, New York ABSTRACT The Connectivity Map database contains microarray signatures of gene expression derived from approximately 6000 experiments that examined the effects of approximately 1300 single drugs on several human cancer cell lines. We used these data to prioritize pairs of drugs expected to reverse the changes in gene expression observed in the kidneys of a mouse model of HIV-associated nephropathy (Tg26 mice). We predicted that the combination of an angiotensin-converting enzyme (ACE) inhibitor and a histone deacetylase inhibitor would maximally reverse the disease-associated expression of genes in the kidneys of these mice. Testing the combination of these inhibitors in Tg26 mice revealed an additive renoprotective effect, as suggested by reduction of proteinuria, improvement of renal function, and attenuation of kidney injury. Furthermore, we observed the predicted treatment-associated changes in the expression of selected genes and pathway components. In summary, these data suggest that the combination of an ACE inhibitor and a histone deacetylase inhibitor could have therapeutic potential for various kidney diseases.
    [Show full text]