1
|
Cantarella S, Vezzoli M, Carnevali D, Morselli M, Zemke NR, Montanini B, Daussy CF, Wodrich H, Teichmann M, Pellegrini M, Berk AJ, Dieci G, Ferrari R. Adenovirus small E1A directs activation of Alu transcription at YAP/TEAD- and AP-1-bound enhancers through interactions with the EP400 chromatin remodeler. Nucleic Acids Res 2024; 52:9481-9500. [PMID: 39011896 PMCID: PMC11381368 DOI: 10.1093/nar/gkae615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 04/29/2024] [Accepted: 07/02/2024] [Indexed: 07/17/2024] Open
Abstract
Alu retrotransposons, which form the largest family of mobile DNA elements in the human genome, have recently come to attention as a potential source of regulatory novelties, most notably by participating in enhancer function. Even though Alu transcription by RNA polymerase III is subjected to tight epigenetic silencing, their expression has long been known to increase in response to various types of stress, including viral infection. Here we show that, in primary human fibroblasts, adenovirus small e1a triggered derepression of hundreds of individual Alus by promoting TFIIIB recruitment by Alu-bound TFIIIC. Epigenome profiling revealed an e1a-induced decrease of H3K27 acetylation and increase of H3K4 monomethylation at derepressed Alus, making them resemble poised enhancers. The enhancer nature of e1a-targeted Alus was confirmed by the enrichment, in their upstream regions, of the EP300/CBP acetyltransferase, EP400 chromatin remodeler and YAP1 and FOS transcription factors. The physical interaction of e1a with EP400 was critical for Alu derepression, which was abrogated upon EP400 ablation. Our data suggest that e1a targets a subset of enhancer Alus whose transcriptional activation, which requires EP400 and is mediated by the e1a-EP400 interaction, may participate in the manipulation of enhancer activity by adenoviruses.
Collapse
Affiliation(s)
- Simona Cantarella
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Marco Vezzoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Davide Carnevali
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Marco Morselli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Nathan R Zemke
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Barbara Montanini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Coralie F Daussy
- Bordeaux University, CNRS UMR 5234, Fundamental Microbiology and Pathogenicity, Bordeaux, France
| | - Harald Wodrich
- Bordeaux University, CNRS UMR 5234, Fundamental Microbiology and Pathogenicity, Bordeaux, France
| | - Martin Teichmann
- Bordeaux University, Inserm U 1312, Bordeaux Institute of Oncology, 33076 Bordeaux, France
| | - Matteo Pellegrini
- Department of Molecular Cellular and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Arnold J Berk
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Giorgio Dieci
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Roberto Ferrari
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| |
Collapse
|
2
|
Ungerleider NA, Roberts C, O’Grady TM, Nguyen TT, Baddoo M, Wang J, Ishaq E, Concha M, Lam M, Bass J, Nguyen T, Van Otterloo N, Wickramarachchige-Dona N, Wyczechowska D, Morales M, Ma T, Dong Y, Flemington E. Viral reprogramming of host transcription initiation. Nucleic Acids Res 2024; 52:5016-5032. [PMID: 38471819 PMCID: PMC11109974 DOI: 10.1093/nar/gkae175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/13/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Viruses are master remodelers of the host cell environment in support of infection and virus production. For example, viruses typically regulate cell gene expression through modulating canonical cell promoter activity. Here, we show that Epstein Barr virus (EBV) replication causes 'de novo' transcription initiation at 29674 new transcription start sites throughout the cell genome. De novo transcription initiation is facilitated in part by the unique properties of the viral pre-initiation complex (vPIC) that binds a TATT[T/A]AA, TATA box-like sequence and activates transcription with minimal support by additional transcription factors. Other de novo promoters are driven by the viral transcription factors, Zta and Rta and are influenced by directional proximity to existing canonical cell promoters, a configuration that fosters transcription through existing promoters and transcriptional interference. These studies reveal a new way that viruses interact with the host transcriptome to inhibit host gene expression and they shed light on primal features driving eukaryotic promoter function.
Collapse
Affiliation(s)
- Nathan A Ungerleider
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, USA
| | - Claire Roberts
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, USA
| | - Tina M O’Grady
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, USA
| | - Trang T Nguyen
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, USA
| | - Melody Baddoo
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, USA
| | - Jia Wang
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, USA
| | - Eman Ishaq
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, USA
| | - Monica Concha
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, USA
| | - Meggie Lam
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, USA
| | - Jordan Bass
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, USA
| | - Truong D Nguyen
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, USA
| | - Nick Van Otterloo
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, USA
| | | | - Dorota Wyczechowska
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | | | - Tianfang Ma
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yan Dong
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, USA
| | - Erik K Flemington
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, USA
| |
Collapse
|
3
|
Sharma H, Valentine MNZ, Toki N, Sueki HN, Gustincich S, Takahashi H, Carninci P. Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation. Nat Commun 2024; 15:1400. [PMID: 38383605 PMCID: PMC10881587 DOI: 10.1038/s41467-024-45517-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
RNA structure folding largely influences RNA regulation by providing flexibility and functional diversity. In silico and in vitro analyses are limited in their ability to capture the intricate relationships between dynamic RNA structure and RNA functional diversity present in the cell. Here, we investigate sequence, structure and functional features of mouse and human SINE-transcribed retrotransposons embedded in SINEUPs long non-coding RNAs, which positively regulate target gene expression post-transcriptionally. In-cell secondary structure probing reveals that functional SINEs-derived RNAs contain conserved short structure motifs essential for SINEUP-induced translation enhancement. We show that SINE RNA structure dynamically changes between the nucleus and cytoplasm and is associated with compartment-specific binding to RBP and related functions. Moreover, RNA-RNA interaction analysis shows that the SINE-derived RNAs interact directly with ribosomal RNAs, suggesting a mechanism of translation regulation. We further predict the architecture of 18 SINE RNAs in three dimensions guided by experimental secondary structure data. Overall, we demonstrate that the conservation of short key features involved in interactions with RBPs and ribosomal RNA drives the convergent function of evolutionarily distant SINE-transcribed RNAs.
Collapse
Affiliation(s)
- Harshita Sharma
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Matthew N Z Valentine
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Naoko Toki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Hiromi Nishiyori Sueki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | | | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
- Human Technopole, Milan, 20157, Italy.
| |
Collapse
|
4
|
Kawase M, Ichiyanagi K. Mouse retrotransposons: sequence structure, evolutionary age, genomic distribution and function. Genes Genet Syst 2024; 98:337-351. [PMID: 37989301 DOI: 10.1266/ggs.23-00221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Retrotransposons are transposable elements that are transposed via transcription and reverse transcription. Their copies have accumulated in the genome of mammals, occupying approximately 40% of mammalian genomic mass. These copies are often involved in numerous phenomena, such as chromatin spatial organization, gene expression, development and disease, and have been recognized as a driving force in evolution. Different organisms have gained specific retrotransposon subfamilies and retrotransposed copies, such as hundreds of Mus-specific subfamilies with diverse sequences and genomic locations. Despite this complexity, basic information is still necessary for present-day genomic and epigenomic studies. Herein, we describe the characteristics of each subfamily of Mus-specific retrotransposons in terms of sequence structure, phylogenetic relationships, evolutionary age, and preference for A or B compartments of chromatin.
Collapse
Affiliation(s)
- Masaki Kawase
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University
| |
Collapse
|
5
|
Hou Y, Diao L, Hu Y, Zhang Q, Lv G, Tao S, Xu W, Xie S, Zhang Q, Xiao Z. The Conserved LncRNA DIO3OS Restricts Hepatocellular Carcinoma Stemness by Interfering with NONO-Mediated Nuclear Export of ZEB1 mRNA. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301983. [PMID: 37271897 PMCID: PMC10427364 DOI: 10.1002/advs.202301983] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/28/2023] [Indexed: 06/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is an aggressive and fatal disease caused by a subset of cancer stem cells (CSCs). It is estimated that there are approximately 100 000 long noncoding RNAs (lncRNAs) in humans. However, the mechanisms by which lncRNAs affect tumor stemness remain poorly understood. In the present study, it is found that DIO3OS is a conserved lncRNA that is generally downregulated in multiple cancers, including HCC, and its low expression correlates with poor clinical outcomes in HCC. In in vitro cancer cell lines and an in vivo spontaneous HCC mouse model, DIO3OS markedly represses tumor development via its suppressive role in CSCs through downregulation of zinc finger E-box binding homeobox 1 (ZEB1). Interestingly, DIO3OS represses ZEB1 post-transcriptionally without affecting its mRNA levels. Subsequent experiments show that DIO3OS interacts with the NONO protein and restricts NONO-mediated nuclear export of ZEB1 mRNA. Overall, these findings demonstrate that the DIO3OS-NONO-ZEB1 axis restricts HCC development and offers a valuable candidate for CSC-targeted therapeutics for HCC.
Collapse
Affiliation(s)
- Ya‐Rui Hou
- Biotherapy CenterThe Third Affiliated HospitalSun Yat‐sen UniversityGuangzhou510630P. R. China
| | - Li‐Ting Diao
- Biotherapy CenterThe Third Affiliated HospitalSun Yat‐sen UniversityGuangzhou510630P. R. China
| | - Yan‐Xia Hu
- Biotherapy CenterThe Third Affiliated HospitalSun Yat‐sen UniversityGuangzhou510630P. R. China
| | - Qian‐Qian Zhang
- School of Life Sciences and BiopharmaceuticsGuangdong Pharmaceutical UniversityGuangzhou510006P. R. China
| | - Guo Lv
- Guangdong Key Laboratory of Liver Disease ResearchThe Third Affiliated HospitalSun Yat‐sen UniversityGuangzhou510630P. R. China
| | - Shuang Tao
- Biotherapy CenterThe Third Affiliated HospitalSun Yat‐sen UniversityGuangzhou510630P. R. China
| | - Wan‐Yi Xu
- Biotherapy CenterThe Third Affiliated HospitalSun Yat‐sen UniversityGuangzhou510630P. R. China
| | - Shu‐Juan Xie
- Institute of VaccineThe Third Affiliated HospitalSun Yat‐sen UniversityGuangzhou510630P. R. China
| | - Qi Zhang
- Biotherapy CenterThe Third Affiliated HospitalSun Yat‐sen UniversityGuangzhou510630P. R. China
- Institute of VaccineThe Third Affiliated HospitalSun Yat‐sen UniversityGuangzhou510630P. R. China
| | - Zhen‐Dong Xiao
- Biotherapy CenterThe Third Affiliated HospitalSun Yat‐sen UniversityGuangzhou510630P. R. China
| |
Collapse
|
6
|
Naesens L, Haerynck F, Gack MU. The RNA polymerase III-RIG-I axis in antiviral immunity and inflammation. Trends Immunol 2023; 44:435-449. [PMID: 37149405 PMCID: PMC10461603 DOI: 10.1016/j.it.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 05/08/2023]
Abstract
Nucleic acid sensors survey subcellular compartments for atypical or mislocalized RNA or DNA, ultimately triggering innate immune responses. Retinoic acid-inducible gene-I (RIG-I) is part of the family of cytoplasmic RNA receptors that can detect viruses. A growing literature demonstrates that mammalian RNA polymerase III (Pol III) transcribes certain viral or cellular DNA sequences into immunostimulatory RIG-I ligands, which elicits antiviral or inflammatory responses. Dysregulation of the Pol III-RIG-I sensing axis can lead to human diseases including severe viral infection outcomes, autoimmunity, and tumor progression. Here, we summarize the newly emerging role of viral and host-derived Pol III transcripts in immunity and also highlight recent advances in understanding how mammalian cells prevent unwanted immune activation by these RNAs to maintain homeostasis.
Collapse
Affiliation(s)
- Leslie Naesens
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium; Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Filomeen Haerynck
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium; Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA.
| |
Collapse
|
7
|
Horton I, Kelly CJ, Dziulko A, Simpson DM, Chuong EB. Mouse B2 SINE elements function as IFN-inducible enhancers. eLife 2023; 12:e82617. [PMID: 37158599 PMCID: PMC10229128 DOI: 10.7554/elife.82617] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 05/08/2023] [Indexed: 05/10/2023] Open
Abstract
Regulatory networks underlying innate immunity continually face selective pressures to adapt to new and evolving pathogens. Transposable elements (TEs) can affect immune gene expression as a source of inducible regulatory elements, but the significance of these elements in facilitating evolutionary diversification of innate immunity remains largely unexplored. Here, we investigated the mouse epigenomic response to type II interferon (IFN) signaling and discovered that elements from a subfamily of B2 SINE (B2_Mm2) contain STAT1 binding sites and function as IFN-inducible enhancers. CRISPR deletion experiments in mouse cells demonstrated that a B2_Mm2 element has been co-opted as an enhancer driving IFN-inducible expression of Dicer1. The rodent-specific B2 SINE family is highly abundant in the mouse genome and elements have been previously characterized to exhibit promoter, insulator, and non-coding RNA activity. Our work establishes a new role for B2 elements as inducible enhancer elements that influence mouse immunity, and exemplifies how lineage-specific TEs can facilitate evolutionary turnover and divergence of innate immune regulatory networks.
Collapse
Affiliation(s)
- Isabella Horton
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Conor J Kelly
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Adam Dziulko
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - David M Simpson
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Edward B Chuong
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| |
Collapse
|
8
|
Lari A, Glaunsinger BA. Murine Gammaherpesvirus 68 ORF45 Stimulates B2 Retrotransposon and Pre-tRNA Activation in a Manner Dependent on Mitogen-Activated Protein Kinase (MAPK) Signaling. Microbiol Spectr 2023; 11:e0017223. [PMID: 36752632 PMCID: PMC10100704 DOI: 10.1128/spectrum.00172-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 01/21/2023] [Indexed: 02/09/2023] Open
Abstract
RNA polymerase III (RNAPIII) transcribes a variety of noncoding RNAs, including tRNA (tRNA) and the B2 family of short interspersed nuclear elements (SINEs). B2 SINEs are noncoding retrotransposons that possess tRNA-like promoters and are normally silenced in healthy somatic tissue. Infection with the murine gammaherpesvirus MHV68 induces transcription of both SINEs and tRNAs, in part through the activity of the viral protein kinase ORF36. Here, we identify the conserved MHV68 tegument protein ORF45 as an additional activator of these RNAPIII loci. MHV68 ORF45 and ORF36 form a complex, resulting in an additive induction RNAPIII and increased ORF45 expression. ORF45-induced RNAPIII transcription is dependent on its activation of the extracellular signal-regulated kinase (ERK) mitogen-activated protein kinase (MAPK) signaling pathway, which in turn increases the abundance of the RNAPIII transcription factor Brf1. Other viral and nonviral activators of MAPK/ERK signaling also increase the levels of Brf1 protein, B2 SINE RNA, and tRNA, suggesting that this is a common strategy to increase RNAPIII activity. IMPORTANCE Gammaherpesviral infection alters the gene expression landscape of a host cell, including through the induction of noncoding RNAs transcribed by RNA polymerase III (RNAPIII). Among these are a class of repetitive genes known as retrotransposons, which are normally silenced elements and can copy and spread throughout the genome, and transfer RNAs (tRNAs), which are fundamental components of protein translation machinery. How these loci are activated during infection is not well understood. Here, we identify ORF45 from the model murine gammaherpesvirus MHV68 as a novel activator of RNAPIII transcription. To do so, it engages the MAPK/ERK signaling pathway, which is a central regulator of cellular response to environmental stimuli. Activation of this pathway leads to the upregulation of a key factor required for RNAPIII activity, Brf1. These findings expand our understanding of the regulation and dysregulation of RNAPIII transcription and highlight how viral cooption of key signaling pathways can impact host gene expression.
Collapse
Affiliation(s)
- Azra Lari
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Britt A. Glaunsinger
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
- Howard Hughes Medical Institute, Berkeley, California, USA
| |
Collapse
|
9
|
Gulyas L, Glaunsinger BA. RNA polymerase II subunit modulation during viral infection and cellular stress. Curr Opin Virol 2022; 56:101259. [PMID: 36162260 PMCID: PMC10150648 DOI: 10.1016/j.coviro.2022.101259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/03/2022]
Abstract
Control of gene expression, including transcription, is central in dictating the outcome of viral infection. One of the profound alterations induced by viruses is modification to the integrity and function of eukaryotic RNA polymerase II (Pol II). Here, we discuss how infection perturbs the Pol II complex by altering subunit phosphorylation and turnover, as well as how cellular genotoxic stress (e.g. DNA damage) elicits similar outcomes. By highlighting emerging parallels and differences in Pol II control during viral infection and abiotic stress, we hope to bolster identification of pathways that target Pol II and regulate the transcriptome.
Collapse
Affiliation(s)
- Leah Gulyas
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Britt A Glaunsinger
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA 94709, USA.
| |
Collapse
|
10
|
Doratt BM, Vance E, Malherbe DC, Ebbert MT, Messaoudi I. Transcriptional response to VZV infection is modulated by RNA polymerase III in lung epithelial cell lines. Front Cell Infect Microbiol 2022; 12:943587. [PMID: 35959363 PMCID: PMC9359802 DOI: 10.3389/fcimb.2022.943587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Ancestral RNA polymerase III (Pol III) is a multi-subunit polymerase responsible for transcription of short non-coding RNA, such as double-stranded short interspersed nuclear elements (SINEs). Although SINE ncRNAs are generally transcriptionally repressed, they can be induced in response to viral infections and can stimulate immune signaling pathways. Indeed, mutations in RNA Pol III have been associated with poor antiviral interferon response following infection with varicella zoster virus (VZV). In this study, we probed the role of Pol III transcripts in the detection and initial immune response to VZV by characterizing the transcriptional response following VZV infection of wild type A549 lung epithelial cells as well as A549 cells lacking specific RNA sensors MAVS and TLR3, or interferon-stimulated genes RNase L and PKR in presence or absence of functional RNA Pol III. Multiple components of the antiviral sensing and interferon signaling pathways were involved in restricting VZV replication in lung epithelial cells thus suggesting an innate defense system with built-in redundancy. In addition, RNA Pol III silencing altered the antiviral transcriptional program indicating that it plays an essential role in the sensing of VZV infection.
Collapse
Affiliation(s)
- Brianna M. Doratt
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Elizabeth Vance
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States
- Department of Internal Medicine, Division of Biomedical Informatics, University of Kentucky, Lexington, KY, United States
- Department of Neuroscience, University of Kentucky, Lexington, KY, United States
| | - Delphine C. Malherbe
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Mark T.W. Ebbert
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States
- Department of Internal Medicine, Division of Biomedical Informatics, University of Kentucky, Lexington, KY, United States
- Department of Neuroscience, University of Kentucky, Lexington, KY, United States
| | - Ilhem Messaoudi
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, United States
- *Correspondence: Ilhem Messaoudi,
| |
Collapse
|
11
|
Price AM, Steinbock RT, Di C, Hayer K, Li Y, Herrmann C, Parenti N, Whelan J, Weiss S, Weitzman M. Adenovirus prevents dsRNA formation by promoting efficient splicing of viral RNA. Nucleic Acids Res 2022; 50:1201-1220. [PMID: 34671803 PMCID: PMC8860579 DOI: 10.1093/nar/gkab896] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/10/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic cells recognize intracellular pathogens through pattern recognition receptors, including sensors of aberrant nucleic acid structures. Sensors of double-stranded RNA (dsRNA) are known to detect replication intermediates of RNA viruses. It has long been suggested that annealing of mRNA from symmetrical transcription of both top and bottom strands of DNA virus genomes can produce dsRNA during infection. Supporting this hypothesis, nearly all DNA viruses encode inhibitors of dsRNA-recognition pathways. However, direct evidence that DNA viruses produce dsRNA is lacking. Contrary to dogma, we show that the nuclear-replicating DNA virus adenovirus (AdV) does not produce detectable levels of dsRNA during infection. In contrast, abundant dsRNA is detected within the nucleus of cells infected with AdV mutants defective for viral RNA processing. In the presence of nuclear dsRNA, the cytoplasmic dsRNA sensor PKR is relocalized and activated within the nucleus. Accumulation of viral dsRNA occurs in the late phase of infection, when unspliced viral transcripts form intron/exon base pairs between top and bottom strand transcripts. We propose that DNA viruses actively limit dsRNA formation by promoting efficient splicing and mRNA processing, thus avoiding detection and restriction by host innate immune sensors of pathogenic nucleic acids.
Collapse
Affiliation(s)
- Alexander M Price
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Robert T Steinbock
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Cell & Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Chao Di
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yize Li
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christin Herrmann
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Cell & Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas A Parenti
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jillian N Whelan
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Susan R Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew D Weitzman
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
12
|
Li CL, Pu M, Wang W, Chaturbedi A, Emerson FJ, Lee SS. Region-specific H3K9me3 gain in aged somatic tissues in Caenorhabditis elegans. PLoS Genet 2021; 17:e1009432. [PMID: 34506495 PMCID: PMC8457455 DOI: 10.1371/journal.pgen.1009432] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 09/22/2021] [Accepted: 08/17/2021] [Indexed: 12/13/2022] Open
Abstract
Epigenetic alterations occur as organisms age, and lead to chromatin deterioration, loss of transcriptional silencing and genomic instability. Dysregulation of the epigenome has been associated with increased susceptibility to age-related disorders. In this study, we aimed to characterize the age-dependent changes of the epigenome and, in turn, to understand epigenetic processes that drive aging phenotypes. We focused on the aging-associated changes in the repressive histone marks H3K9me3 and H3K27me3 in C. elegans. We observed region-specific gain and loss of both histone marks, but the changes are more evident for H3K9me3. We further found alteration of heterochromatic boundaries in aged somatic tissues. Interestingly, we discovered that the most statistically significant changes reflected H3K9me3-marked regions that are formed during aging, and are absent in developing worms, which we termed "aging-specific repressive regions" (ASRRs). These ASRRs preferentially occur in genic regions that are marked by high levels of H3K9me2 and H3K36me2 in larval stages. Maintenance of high H3K9me2 levels in these regions have been shown to correlate with a longer lifespan. Next, we examined whether the changes in repressive histone marks lead to de-silencing of repetitive DNA elements, as reported for several other organisms. We observed increased expression of active repetitive DNA elements but not global re-activation of silent repeats in old worms, likely due to the distributed nature of repetitive elements in the C. elegans genome. Intriguingly, CELE45, a putative short interspersed nuclear element (SINE), was greatly overexpressed at old age and upon heat stress. SINEs have been suggested to regulate transcription in response to various cellular stresses in mammals. It is likely that CELE45 RNAs also play roles in stress response and aging in C. elegans. Taken together, our study revealed significant and specific age-dependent changes in repressive histone modifications and repetitive elements, providing important insights into aging biology.
Collapse
Affiliation(s)
- Cheng-Lin Li
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Mintie Pu
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Wenke Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Amaresh Chaturbedi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Felicity J Emerson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Siu Sylvia Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| |
Collapse
|
13
|
Lytic Infection with Murine Gammaherpesvirus 68 Activates Host and Viral RNA Polymerase III Promoters and Enhances Noncoding RNA Expression. J Virol 2021; 95:e0007921. [PMID: 33910955 PMCID: PMC8223928 DOI: 10.1128/jvi.00079-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA polymerase III (pol III) transcribes multiple noncoding RNAs (ncRNAs) that are essential for cellular function. Pol III-dependent transcription is also engaged during certain viral infections, including those of the gammaherpesviruses (γHVs), where pol III-dependent viral ncRNAs promote pathogenesis. Additionally, several host ncRNAs are upregulated during γHV infection and play integral roles in pathogenesis by facilitating viral establishment and gene expression. Here, we sought to investigate how pol III promoters and transcripts are regulated during gammaherpesvirus infection using the murine gammaherpesvirus 68 (γHV68) system. To compare the transcription of host and viral pol III-dependent ncRNAs, we analyzed a series of pol III promoters for host and viral ncRNAs using a luciferase reporter optimized to measure pol III activity. We measured promoter activity from the reporter gene at the translation level via luciferase activity and at the transcription level via reverse transcription-quantitative PCR (RT-qPCR). We further measured endogenous ncRNA expression at single-cell resolution by flow cytometry. These studies demonstrated that lytic infection with γHV68 increased the transcription from multiple host and viral pol III promoters and further identified the ability of accessory sequences to influence both baseline and inducible promoter activity after infection. RNA flow cytometry revealed the induction of endogenous pol III-derived ncRNAs that tightly correlated with viral gene expression. These studies highlight how lytic gammaherpesvirus infection alters the transcriptional landscape of host cells to increase pol III-derived RNAs, a process that may further modify cellular function and enhance viral gene expression and pathogenesis. IMPORTANCE Gammaherpesviruses are a prime example of how viruses can alter the host transcriptional landscape to establish infection. Despite major insights into how these viruses modify RNA polymerase II-dependent generation of messenger RNAs, how these viruses influence the activity of host RNA polymerase III remains much less clear. Small noncoding RNAs produced by RNA polymerase III are increasingly recognized to play critical regulatory roles in cell biology and virus infection. Studies of RNA polymerase III-dependent transcription are complicated by multiple promoter types and diverse RNAs with variable stability and processing requirements. Here, we characterized a reporter system to directly study RNA polymerase III-dependent responses during gammaherpesvirus infection and utilized single-cell flow cytometry-based methods to reveal that gammaherpesvirus lytic replication broadly induces pol III activity to enhance host and viral noncoding RNA expression within the infected cell.
Collapse
|
14
|
melRNA-seq for Expression Analysis of SINE RNAs and Other Medium-Length Non-Coding RNAs. Mob DNA 2021; 12:15. [PMID: 34134767 PMCID: PMC8210359 DOI: 10.1186/s13100-021-00245-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/04/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Small interspersed elements (SINEs) are transcribed by RNA polymerase III (Pol III) to produce RNAs typically 100-500 nucleotides in length. Although their RNA abundance can be evaluated by Northern blotting and primer extension, the nature (sequence, exact length, and genomic origin) of these RNAs cannot be revealed by these methods. Moreover, mRNA sequencing (mRNA-seq) is not able to distinguish bona fide SINE RNAs or SINE sequences present in longer transcripts. RESULTS To elucidate the abundance, source loci, and sequence nature of SINE RNAs, we established a deep sequencing method, designated as melRNA-seq (medium-length RNA-seq), which can determine whole-length RNA sequences. Total RNA samples were treated with 5' pyrophosphohydrolase (RppH), which allowed ligation of an RNA adaptor to the 5' end of intact SINE RNAs. Similarly, another adaptor was ligated to the 3' end, followed by reverse transcription, PCR amplification, size selection, and single-end deep sequencing. The analysis of two biological replicates of RNAs from mouse spermatogonia showed high reproducibility of SINE expression data both at family and locus levels. CONCLUSIONS This new method can be used for quantification and detailed sequence analysis of medium-length non-coding RNAs, such as rRNA, snRNA, tRNAs, and SINE RNAs. Further, its dynamic range is much wider than Northern blotting and primer extension.
Collapse
|
15
|
Mangiavacchi A, Liu P, Della Valle F, Orlando V. New insights into the functional role of retrotransposon dynamics in mammalian somatic cells. Cell Mol Life Sci 2021; 78:5245-5256. [PMID: 33990851 PMCID: PMC8257530 DOI: 10.1007/s00018-021-03851-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/31/2021] [Accepted: 05/04/2021] [Indexed: 12/18/2022]
Abstract
Retrotransposons are genetic elements present across all eukaryotic genomes. While their role in evolution is considered as a potentially beneficial natural source of genetic variation, their activity is classically considered detrimental due to their potentially harmful effects on genome stability. However, studies are increasingly shedding light on the regulatory function and beneficial role of somatic retroelement reactivation in non-pathological contexts. Here, we review recent findings unveiling the regulatory potential of retrotransposons, including their role in noncoding RNA transcription, as modulators of mammalian transcriptional and epigenome landscapes. We also discuss technical challenges in deciphering the multifaceted activity of retrotransposable elements, highlighting an unforeseen central role of this neglected portion of the genome both in early development and in adult life.
Collapse
Affiliation(s)
- Arianna Mangiavacchi
- Biological Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Peng Liu
- Biological Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Francesco Della Valle
- Biological Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Valerio Orlando
- Biological Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| |
Collapse
|
16
|
Ho JJD, Man JHS, Schatz JH, Marsden PA. Translational remodeling by RNA-binding proteins and noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1647. [PMID: 33694288 DOI: 10.1002/wrna.1647] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022]
Abstract
Responsible for generating the proteome that controls phenotype, translation is the ultimate convergence point for myriad upstream signals that influence gene expression. System-wide adaptive translational reprogramming has recently emerged as a pillar of cellular adaptation. As classic regulators of mRNA stability and translation efficiency, foundational studies established the concept of collaboration and competition between RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) on individual mRNAs. Fresh conceptual innovations now highlight stress-activated, evolutionarily conserved RBP networks and ncRNAs that increase the translation efficiency of populations of transcripts encoding proteins that participate in a common cellular process. The discovery of post-transcriptional functions for long noncoding RNAs (lncRNAs) was particularly intriguing given their cell-type-specificity and historical definition as nuclear-functioning epigenetic regulators. The convergence of RBPs, lncRNAs, and microRNAs on functionally related mRNAs to enable adaptive protein synthesis is a newer biological paradigm that highlights their role as "translatome (protein output) remodelers" and reinvigorates the paradigm of "RNA operons." Together, these concepts modernize our understanding of cellular stress adaptation and strategies for therapeutic development. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Regulation Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
Collapse
Affiliation(s)
- J J David Ho
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Jeffrey H S Man
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Department of Respirology, University Health Network, Latner Thoracic Research Laboratories, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan H Schatz
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Philip A Marsden
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
17
|
Cheng Y, Saville L, Gollen B, Veronesi AA, Mohajerani M, Joseph JT, Zovoilis A. Increased Alu RNA processing in Alzheimer brains is linked to gene expression changes. EMBO Rep 2021; 22:e52255. [PMID: 33645898 PMCID: PMC8097388 DOI: 10.15252/embr.202052255] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/23/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
Despite significant steps in our understanding of Alzheimer's disease (AD), many of the molecular processes underlying its pathogenesis remain largely unknown. Here, we focus on the role of non-coding RNAs produced by small interspersed nuclear elements (SINEs). RNAs from SINE B2 repeats in mouse and SINE Alu repeats in humans, long regarded as "junk" DNA, control gene expression by binding RNA polymerase II and suppressing transcription. They also possess self-cleaving activity that is accelerated through their interaction with certain proteins disabling this suppression. Here, we show that similar to mouse SINE RNAs, human Alu RNAs, are processed, and the processing rate is increased in brains of AD patients. This increased processing correlates with the activation of genes up-regulated in AD patients, while increased intact Alu RNA levels correlate with down-regulated gene expression in AD. In vitro assays show that processing of Alu RNAs is accelerated by HSF1. Overall, our data show that RNAs from SINE elements in the human brain show a similar pattern of deregulation during amyloid beta pathology as in mouse.
Collapse
Affiliation(s)
- Yubo Cheng
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, AB, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Luke Saville
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, AB, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Babita Gollen
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, AB, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Ana Alvarez Veronesi
- Departments of Pathology and Clinical Neurosciences and Calgary Brain Bank, University of Calgary, Calgary, AB, Canada
| | - Majid Mohajerani
- Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Jeffrey T Joseph
- Departments of Pathology and Clinical Neurosciences and Calgary Brain Bank, University of Calgary, Calgary, AB, Canada
| | - Athanasios Zovoilis
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, AB, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| |
Collapse
|
18
|
Differential Expression of Urinary Exosomal Small RNAs in Idiopathic Membranous Nephropathy. BIOMED RESEARCH INTERNATIONAL 2021; 2020:3170927. [PMID: 33457405 PMCID: PMC7785370 DOI: 10.1155/2020/3170927] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/02/2020] [Accepted: 12/13/2020] [Indexed: 11/18/2022]
Abstract
Background Idiopathic membranous nephropathy (IMN) is a major cause of adult nephrotic syndromes, and reliable noninvasive biomarkers for diagnosis and monitoring are urgently needed. In this study, we performed small RNA (sRNA) sequencing to explore sRNA profiles of urinary exosomes derived from IMN patients and healthy controls (CON) to provide clues for identifying novel noninvasive sRNA biomarkers for IMN. Methods Urine samples were collected from five healthy controls and six patients with IMN. High-throughput sequencing was used to screen sRNA expression profiles of urinary exosomes from patients with IMN in two independent cohorts. Results Urinary exosomes were successfully isolated and used to obtain exosomal sRNAs. We screened 131 differentially expressed miRNAs, including 28 specifically expressed miRNAs, then explored the top 10 specifically expressed miRNAs in all IMN individuals. The specifically expressed miRNAs and differentially expressed miRNAs provide potential biomarkers for IMN. Additionally, we discovered numerous sRNAs derived from genomic repetitive sequences, which could represent an exciting new area of research. Conclusion Herein, we revealed significant differences in expression profiles of urinary exosomal miRNAs and repetitive region-derived sRNAs between patients with IMN and healthy controls. The findings could facilitate the development of potential molecular targets for membranous nephropathy.
Collapse
|
19
|
Abstract
Viral infection can dramatically change the gene expression landscape of the host cell, yet little is known regarding changes in noncoding gene transcription by RNA polymerase III (RNAPIII). Among these are transfer RNAs (tRNAs), which are fundamental in protein translation, yet whose gene regulatory features remain largely undefined in mammalian cells. Transfer RNAs (tRNAs) are transcribed by RNA polymerase III (RNAPIII) and play a central role in decoding our genome, yet their expression and noncanonical function remain understudied. Many DNA tumor viruses enhance the activity of RNAPIII, yet whether infection alters tRNA expression is largely unknown. Here, we present the first genome-wide analysis of how viral infection alters the tRNAome. Using a tRNA-specific sequencing method (DM-tRNA-seq), we find that the murine gammaherpesvirus MHV68 induces global changes in premature tRNA (pre-tRNA) expression, with 14% of tRNA genes upregulated more than 3-fold, indicating that differential tRNA gene induction is a characteristic of DNA virus infection. Elevated pre-tRNA expression corresponds to increased RNAPIII occupancy for the subset of tRNA genes tested; additionally, posttranscriptional mechanisms contribute to the accumulation of pre-tRNA species. We find increased abundance of tRNA fragments derived from pre-tRNAs upregulated by viral infection, suggesting that noncanonical tRNA cleavage is also affected. Furthermore, pre-tRNA accumulation, but not RNAPIII recruitment, requires gammaherpesvirus-induced degradation of host mRNAs by the virally encoded mRNA endonuclease muSOX. We hypothesize that depletion of pre-tRNA maturation or turnover machinery contributes to robust accumulation of full-length pre-tRNAs in infected cells. Collectively, these findings reveal pervasive changes to tRNA expression during DNA virus infection and highlight the potential of using viruses to explore tRNA biology.
Collapse
|
20
|
Fan J, Martinez-Arguelles DB, Papadopoulos V. Genome-wide expression analysis of a new class of lncRNAs driven by SINE B2. Gene 2020; 768:145332. [PMID: 33278552 DOI: 10.1016/j.gene.2020.145332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/13/2020] [Accepted: 11/27/2020] [Indexed: 12/30/2022]
Abstract
Repetitive short interspersed elements B2 (SINE B2) have been shown to possess two promoters: polymerase III promoter for producing short B2-S RNAs and polymerase II promoter for driving the expression of long non-coding RNA (B2-AS lncRNAs). Using a B2-antisense (B2-AS) transcript sequence from the SINE B2 resident in mitochondrial translocator protein gene (Tspo) locus, we constructed a B2-AS specific RNA library and identified 96,862 sequences encoding potential B2-mediated lncRNAs, of which 55,592 lncRNAs with more than 390 nt in length possess a feature of potential genomic locus-specific effect. In addition, small RNA-Northern hybridization showed that the new B2-AS lncRNAs are constantly degraded by the Dicer1 enzyme, a finding further confirmed by in vitro Dicer1 enzyme digestion. B2-AS lncRNAs regulate the expression of target genes in a different fashion than B2-S RNAs. Genome-wide cross-comparison with mRNA mapping showed a total of 904 mRNA loci directly targeted by B2-AS lncRNAs, suggesting a locus-specific effect of the B2-AS lncRNAs and a general effect of B2-S RNAs.
Collapse
Affiliation(s)
- Jinjiang Fan
- The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada
| | | | - Vassilios Papadopoulos
- The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada; Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States.
| |
Collapse
|
21
|
Cheng Y, Saville L, Gollen B, Isaac C, Belay A, Mehla J, Patel K, Thakor N, Mohajerani MH, Zovoilis A. Increased processing of SINE B2 ncRNAs unveils a novel type of transcriptome deregulation in amyloid beta neuropathology. eLife 2020; 9:61265. [PMID: 33191914 PMCID: PMC7717908 DOI: 10.7554/elife.61265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/15/2020] [Indexed: 12/18/2022] Open
Abstract
The functional importance of many non-coding RNAs (ncRNAs) generated by repetitive elements and their connection with pathologic processes remains elusive. B2 RNAs, a class of ncRNAs of the B2 family of SINE repeats, mediate through their processing the transcriptional activation of various genes in response to stress. Here, we show that this response is dysfunctional during amyloid beta toxicity and pathology in the mouse hippocampus due to increased levels of B2 RNA processing, leading to constitutively elevated B2 RNA target gene expression and high Trp53 levels. Evidence indicates that Hsf1, a master regulator of stress response, mediates B2 RNA processing in hippocampal cells and is activated during amyloid toxicity, accelerating the processing of SINE RNAs and gene hyper-activation. Our study reveals that in mouse, SINE RNAs constitute a novel pathway deregulated in amyloid beta pathology, with potential implications for similar cases in the human brain, such as Alzheimer’s disease (AD).
Collapse
Affiliation(s)
- Yubo Cheng
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada.,Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Canada
| | - Luke Saville
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada.,Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Canada
| | - Babita Gollen
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada.,Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Canada
| | - Christopher Isaac
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada.,Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Canada
| | - Abel Belay
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada.,Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Canada
| | - Jogender Mehla
- Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada
| | - Kush Patel
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada
| | - Nehal Thakor
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada
| | - Majid H Mohajerani
- Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada
| | - Athanasios Zovoilis
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.,Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada.,Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada.,Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Canada
| |
Collapse
|
22
|
Linker SB, Randolph-Moore L, Kottilil K, Qiu F, Jaeger BN, Barron J, Gage FH. Identification of bona fide B2 SINE retrotransposon transcription through single-nucleus RNA-seq of the mouse hippocampus. Genome Res 2020; 30:1643-1654. [PMID: 33122305 PMCID: PMC7605253 DOI: 10.1101/gr.262196.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022]
Abstract
Currently, researchers rely on generalized methods to quantify transposable element (TE) RNA expression, such as RT-qPCR and RNA-seq, that do not distinguish between TEs expressed from their own promoter (bona fide) and TEs that are transcribed from a neighboring gene promoter such as within an intron or exon. This distinction is important owing to the differing functional roles of TEs depending on whether they are independently transcribed. Here we report a simple strategy to examine bona fide TE expression, termed BonaFide-TEseq. This approach can be used with any template-switch based library such as Smart-seq2 or the single-cell 5' gene expression kit from 10x, extending its utility to single-cell RNA-sequencing. This approach does not require TE-specific enrichment, enabling the simultaneous examination of TEs and protein-coding genes. We show that TEs identified through BonaFide-TEseq are expressed from their own promoter, rather than captured as internal products of genes. We reveal the utility of BonaFide-TEseq in the analysis of single-cell data and show that short-interspersed nuclear elements (SINEs) show cell type-specific expression profiles in the mouse hippocampus. We further show that, in response to a brief exposure of home-cage mice to a novel stimulus, SINEs are activated in dentate granule neurons in a time course that is similar to that of protein-coding immediate early genes. This work provides a simple alternative approach to assess bona fide TE transcription at single-cell resolution and provides a proof-of-concept using this method to identify SINE activation in a context that is relevant for normal learning and memory.
Collapse
Affiliation(s)
- Sara B Linker
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Lynne Randolph-Moore
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Kalyani Kottilil
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Fan Qiu
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Baptiste N Jaeger
- Laboratory of Neural Plasticity, Faculty of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Jerika Barron
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California 94143, USA
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| |
Collapse
|
23
|
Zhang D, Huang P, Sharma M, Keller CA, Giardine B, Zhang H, Gilgenast TG, Phillips-Cremins JE, Hardison RC, Blobel GA. Alteration of genome folding via contact domain boundary insertion. Nat Genet 2020; 52:1076-1087. [PMID: 32868908 PMCID: PMC7541666 DOI: 10.1038/s41588-020-0680-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 07/23/2020] [Indexed: 12/26/2022]
Abstract
Animal chromosomes are partitioned into contact domains. Pathogenic domain disruptions can result from chromosomal rearrangements or perturbation of architectural factors. However, such broad-scale alterations are insufficient to define the minimal requirements for domain formation. Moreover, to what extent domains can be engineered is just beginning to be explored. In an attempt to create contact domains, we inserted a 2-kb DNA sequence underlying a tissue-invariant domain boundary-containing a CTCF-binding site (CBS) and a transcription start site (TSS)-into 16 ectopic loci across 11 chromosomes, and characterized its architectural impact. Depending on local constraints, this fragment variably formed new domains, partitioned existing ones, altered compartmentalization and initiated contacts reflecting chromatin loop extrusion. Deletions of the CBS or the TSS individually or in combination within inserts revealed its distinct contributions to genome folding. Altogether, short DNA insertions can suffice to shape the spatial genome in a manner influenced by chromatin context.
Collapse
Affiliation(s)
- Di Zhang
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Peng Huang
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Malini Sharma
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cheryl A Keller
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Belinda Giardine
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Haoyue Zhang
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Thomas G Gilgenast
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer E Phillips-Cremins
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ross C Hardison
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Gerd A Blobel
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
24
|
Zhao H, Qin Y, Xiao Z, Li Q, Yang N, Pan Z, Gong D, Sun Q, Yang F, Zhang Z, Wu Y, Xu C, Qiu F. Loss of Function of an RNA Polymerase III Subunit Leads to Impaired Maize Kernel Development. PLANT PHYSIOLOGY 2020; 184:359-373. [PMID: 32591429 PMCID: PMC7479876 DOI: 10.1104/pp.20.00502] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/15/2020] [Indexed: 05/03/2023]
Abstract
Kernel size is an important factor determining grain yield. Although a number of genes affecting kernel development in maize (Zea mays) have been identified by analyzing kernel mutants, most of the corresponding mutants cannot be used in maize breeding programs due to low germination or incomplete seed development. Here, we characterized small kernel7, a recessive small-kernel mutant with a mutation in the gene encoding the second-largest subunit of RNA polymerase III (RNAPΙΙΙ; NRPC2). A frame shift in ZmNRPC2 leads to a premature stop codon, resulting in significantly reduced levels of transfer RNAs and 5S ribosomal RNA, which are transcribed by RNAPΙΙΙ. Loss-of-function nrpc2 mutants created by CRISPR/CAS9 showed significantly reduced kernel size due to altered endosperm cell size and number. ZmNRPC2 affects RNAPIII activity and the expression of genes involved in cell proliferation and endoreduplication to control kernel development via physically interacting with RNAPIII subunits RPC53 and AC40, transcription factor class C1 and Floury3. Notably, unlike the semidominant negative mutant floury3, which has defects in starchy endosperm, small kernel7 only affects kernel size but not the composition of kernel storage proteins. Our findings provide novel insights into the molecular network underlying maize kernel size, which could facilitate the genetic improvement of maize in the future.
Collapse
Affiliation(s)
- Hailiang Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | | | - Ziyi Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Li
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Science Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ning Yang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenyuan Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Dianming Gong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qin Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Science Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Cao Xu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Fazhan Qiu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
25
|
Conserved Herpesvirus Kinase ORF36 Activates B2 Retrotransposons during Murine Gammaherpesvirus Infection. J Virol 2020; 94:JVI.00262-20. [PMID: 32404524 DOI: 10.1128/jvi.00262-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 05/04/2020] [Indexed: 12/14/2022] Open
Abstract
Short interspersed nuclear elements (SINEs) are RNA polymerase III (RNAPIII)-transcribed, retrotransposable noncoding RNA (ncRNA) elements ubiquitously spread throughout mammalian genomes. While normally silenced in healthy somatic tissue, SINEs can be induced during infection with DNA viruses, including the model murine gammaherpesvirus 68 (MHV68). Here, we explored the mechanisms underlying MHV68 activation of SINE ncRNAs. We demonstrate that lytic MHV68 infection of B cells, macrophages, and fibroblasts leads to robust activation of the B2 family of SINEs in a cell-autonomous manner. B2 ncRNA induction requires neither host innate immune signaling factors nor involvement of the RNAPIII master regulator Maf1. However, we identified MHV68 ORF36, the conserved herpesviral kinase, as playing a key role in B2 induction during lytic infection. SINE activation is linked to ORF36 kinase activity and can also be induced by inhibition of histone deacetylases 1 and 2 (HCAC 1/2), which is one of the known ORF36 functions. Collectively, our data suggest that ORF36-mediated changes in chromatin modification contribute to B2 activation during MHV68 infection and that this activity is conserved in other herpesviral protein kinase homologs.IMPORTANCE Viral infection dramatically changes the levels of many types of RNA in a cell. In particular, certain oncogenic viruses activate expression of repetitive genes called retrotransposons, which are normally silenced due to their ability to copy and spread throughout the genome. Here, we established that infection with the gammaherpesvirus MHV68 leads to a dramatic induction of a class of noncoding retrotransposons called B2 SINEs in multiple cell types. We then explored how MHV68 activates B2 SINEs, revealing a role for the conserved herpesviral protein kinase ORF36. Both ORF36 kinase-dependent and kinase-independent functions contribute to B2 induction, perhaps through ORF36 targeting of proteins involved in controlling the accessibility of chromatin surrounding SINE loci. Understanding the features underlying induction of these elements following MHV68 infection should provide insight into core elements of SINE regulation, as well as disregulation of SINE elements associated with disease.
Collapse
|
26
|
Zhao Y, Karijolich J. Know Thyself: RIG-I-Like Receptor Sensing of DNA Virus Infection. J Virol 2019; 93:e01085-19. [PMID: 31511389 PMCID: PMC6854496 DOI: 10.1128/jvi.01085-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 09/06/2019] [Indexed: 12/16/2022] Open
Abstract
The RIG-I-like receptors (RLRs) are double-stranded RNA-binding proteins that play a role in initiating and modulating cell intrinsic immunity through the recognition of RNA features typically absent from the host transcriptome. While they are initially characterized in the context of RNA virus infection, evidence has now accumulated establishing the role of RLRs in DNA virus infection. Here, we review recent advances in the RLR-mediated restriction of DNA virus infection with an emphasis on the RLR ligands sensed.
Collapse
Affiliation(s)
- Yang Zhao
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - John Karijolich
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, USA
| |
Collapse
|
27
|
Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts. Int J Mol Sci 2019; 20:ijms20133315. [PMID: 31284509 PMCID: PMC6651528 DOI: 10.3390/ijms20133315] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 12/18/2022] Open
Abstract
Alu retroelements, whose retrotransposition requires prior transcription by RNA polymerase III to generate Alu RNAs, represent the most numerous non-coding RNA (ncRNA) gene family in the human genome. Alu transcription is generally kept to extremely low levels by tight epigenetic silencing, but it has been reported to increase under different types of cell perturbation, such as viral infection and cancer. Alu RNAs, being able to act as gene expression modulators, may be directly involved in the mechanisms determining cellular behavior in such perturbed states. To directly address the regulatory potential of Alu RNAs, we generated IMR90 fibroblasts and HeLa cell lines stably overexpressing two slightly different Alu RNAs, and analyzed genome-wide the expression changes of protein-coding genes through RNA-sequencing. Among the genes that were upregulated or downregulated in response to Alu overexpression in IMR90, but not in HeLa cells, we found a highly significant enrichment of pathways involved in cell cycle progression and mitotic entry. Accordingly, Alu overexpression was found to promote transition from G1 to S phase, as revealed by flow cytometry. Therefore, increased Alu RNA may contribute to sustained cell proliferation, which is an important factor of cancer development and progression.
Collapse
|
28
|
Lyu L, Zhang X, Li C, Yang T, Wang J, Pan L, Jia H, Li Z, Sun Q, Yue L, Chen F, Zhang Z. Small RNA Profiles of Serum Exosomes Derived From Individuals With Latent and Active Tuberculosis. Front Microbiol 2019; 10:1174. [PMID: 31191492 PMCID: PMC6546874 DOI: 10.3389/fmicb.2019.01174] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/08/2019] [Indexed: 12/17/2022] Open
Abstract
Tuberculosis (TB) has been the leading lethal infectious disease worldwide since 2014, and about one third of the world’s population has a latent TB infection (LTBI). This is largely attributed to the difficulties in diagnosis and treatment of TB and LTBI patients. Exosomes offer a new perspective on investigation of the process of TB infection. In this study, we performed small RNA sequencing to explore small RNA profiles of serum exosomes derived from LTBI and TB patients and healthy controls (HC). Our results revealed distinct miRNA profile of the exosomes in the three groups. We screened 250 differentially expressed miRNAs including 130 specifically expressed miRNAs. Some miRNAs were further validated to be specifically expressed in LTBI (hsa-let-7e-5p, hsa-let-7d-5p, hsa-miR-450a-5p, and hsa-miR-140-5p) and TB samples (hsa-miR-1246, hsa-miR-2110, hsa-miR-370-3P, hsa-miR-28-3p, and hsa-miR-193b-5p). Additionally, we demonstrated four expression panels in LTBI and TB groups, and six expression patterns among the three groups. These specifically expressed miRNAs and differentially expressed miRNAs in different panels and patterns provide potential biomarkers for detection/diagnosis of latent and active TB using exosomal miRNAs. Additionally, we also discovered plenty of small RNAs derived from genomic repetitive sequences, which might play roles in host immune responses along with Mtb infection progresses. Overall, our findings provide important reference and an improved understanding about miRNAs and repetitive region-derived small RNAs in exosomes during the Mtb infectious process, and facilitate the development of potential molecular targets for detection/diagnosis of latent and active tuberculosis.
Collapse
Affiliation(s)
- Lingna Lyu
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Xiuli Zhang
- CAS Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Cuidan Li
- CAS Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Tingting Yang
- CAS Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jinghui Wang
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Liping Pan
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Hongyan Jia
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Zihui Li
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Qi Sun
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Liya Yue
- CAS Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Fei Chen
- CAS Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zongde Zhang
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
29
|
Zhao Y, Ye X, Dunker W, Song Y, Karijolich J. RIG-I like receptor sensing of host RNAs facilitates the cell-intrinsic immune response to KSHV infection. Nat Commun 2018; 9:4841. [PMID: 30451863 PMCID: PMC6242832 DOI: 10.1038/s41467-018-07314-7] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 10/26/2018] [Indexed: 02/06/2023] Open
Abstract
The RIG-I like receptors (RLRs) RIG-I and MDA5 are cytosolic RNA helicases best characterized as restriction factors for RNA viruses. However, evidence suggests RLRs participate in innate immune recognition of other pathogens, including DNA viruses. Kaposi's sarcoma-associated herpesvirus (KSHV) is a human gammaherpesvirus and the etiological agent of Kaposi's sarcoma and primary effusion lymphoma (PEL). Here, we demonstrate that RLRs restrict KSHV lytic reactivation and we demonstrate that restriction is facilitated by the recognition of host-derived RNAs. Misprocessed noncoding RNAs represent an abundant class of RIG-I substrates, and biochemical characterizations reveal that an infection-dependent reduction in the cellular triphosphatase DUSP11 results in an accumulation of select triphosphorylated noncoding RNAs, enabling their recognition by RIG-I. These findings reveal an intricate relationship between RNA processing and innate immunity, and demonstrate that an antiviral innate immune response can be elicited by the sensing of misprocessed cellular RNAs.
Collapse
MESH Headings
- Base Sequence
- Cell Line, Tumor
- DEAD Box Protein 58/antagonists & inhibitors
- DEAD Box Protein 58/genetics
- DEAD Box Protein 58/immunology
- Dual-Specificity Phosphatases/genetics
- Dual-Specificity Phosphatases/immunology
- Gene Expression Profiling
- HEK293 Cells
- Herpesvirus 8, Human/genetics
- Herpesvirus 8, Human/immunology
- Host-Pathogen Interactions
- Humans
- Immunity, Innate
- Interferon-Induced Helicase, IFIH1/antagonists & inhibitors
- Interferon-Induced Helicase, IFIH1/genetics
- Interferon-Induced Helicase, IFIH1/immunology
- Lymphocytes/immunology
- Lymphocytes/virology
- Nucleic Acid Conformation
- Phosphorylation
- RNA Processing, Post-Transcriptional
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Untranslated/genetics
- RNA, Untranslated/immunology
- Receptors, Immunologic
- Signal Transduction
- Virus Activation
Collapse
Affiliation(s)
- Yang Zhao
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232-2363, USA
| | - Xiang Ye
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232-2363, USA
| | - William Dunker
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232-2363, USA
| | - Yu Song
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232-2363, USA
- College of Pharmacy, Xinxiang Medical University, Xinxiang, Henan Province, 453000, China
| | - John Karijolich
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232-2363, USA.
- Vanderbilt-Ingram Cancer Center, Nashville, TN, 37232-2363, USA.
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, 37232-2363, USA.
| |
Collapse
|
30
|
Dunker W, Zhao Y, Song Y, Karijolich J. Recognizing the SINEs of Infection: Regulation of Retrotransposon Expression and Modulation of Host Cell Processes. Viruses 2017; 9:v9120386. [PMID: 29258254 PMCID: PMC5744160 DOI: 10.3390/v9120386] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/12/2017] [Accepted: 12/17/2017] [Indexed: 12/16/2022] Open
Abstract
Short interspersed elements (SINEs) are a family of retrotransposons evolutionarily derived from cellular RNA polymerase III transcripts. Over evolutionary time, SINEs have expanded throughout the human genome and today comprise ~11% of total chromosomal DNA. While generally transcriptionally silent in healthy somatic cells, SINE expression increases during a variety of types of stresses, including DNA virus infection. The relevance of SINE expression to viral infection was largely unexplored, however, recent years have seen great progress towards defining the impact of SINE expression on viral replication and host gene expression. Here we review the origin and diversity of SINE elements and their transcriptional control, with an emphasis on how their expression impacts host cell biology during viral infection.
Collapse
Affiliation(s)
- William Dunker
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232-2363, USA.
| | - Yang Zhao
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232-2363, USA.
| | - Yu Song
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232-2363, USA.
- College of Pharmacy, Xinxiang Medical University, Xingxiang 453000, China.
| | - John Karijolich
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232-2363, USA.
- Vanderbilt-Ingram Cancer Center, Nashville, TN 37232-2363, USA.
| |
Collapse
|
31
|
Wegener M, Müller-McNicoll M. Nuclear retention of mRNAs - quality control, gene regulation and human disease. Semin Cell Dev Biol 2017; 79:131-142. [PMID: 29102717 DOI: 10.1016/j.semcdb.2017.11.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 12/21/2022]
Abstract
Nuclear retention of incompletely spliced or mature mRNAs emerges as a novel, previously underappreciated layer of gene regulation, which enables the cell to rapidly respond to stress, viral infection, differentiation cues or changing environmental conditions. Focusing on mammalian cells, we discuss recent insights into the mechanisms and functions of nuclear retention, describe retention-promoting features in protein-coding transcripts and propose mechanisms for their regulated release into the cytoplasm. Moreover, we discuss examples of how aberrant nuclear retention of mRNAs may lead to human diseases.
Collapse
Affiliation(s)
- Marius Wegener
- RNA Regulation Group, Cluster of Excellence 'Macromolecular Complexes', Goethe University Frankfurt, Institute of Cell Biology and Neuroscience, Max-von-Laue-Str. 13, 60438 Frankfurt/Main, Germany
| | - Michaela Müller-McNicoll
- RNA Regulation Group, Cluster of Excellence 'Macromolecular Complexes', Goethe University Frankfurt, Institute of Cell Biology and Neuroscience, Max-von-Laue-Str. 13, 60438 Frankfurt/Main, Germany.
| |
Collapse
|
32
|
Abstract
Our genomes are dominated by repetitive elements. The majority of these elements derive from retrotransposons, which expand throughout the genome through a process of reverse transcription and integration. Short interspersed nuclear elements, or SINEs, are an abundant class of retrotransposons that are transcribed by RNA polymerase III, thus generating exclusively noncoding RNA (ncRNA) that must hijack the machinery required for their transposition. SINE loci are generally transcriptionally repressed in somatic cells but can be robustly induced upon infection with multiple DNA viruses. Recent research has focused on the gene expression and signaling events that are modulated by SINE ncRNAs, particularly during gammaherpesvirus infection. Here, we review the biology of these SINE ncRNAs, explore how DNA virus infection may lead to their induction, and describe how novel gene regulatory and immune-related functions of these ncRNAs may impact the viral life cycle.
Collapse
|