1
|
Chen Y, Lei X, Jiang Z, Humphries F, Parsi KM, Mustone NJ, Ramos I, Mutetwa T, Fernandez-Sesma A, Maehr R, Caffrey DR, Fitzgerald KA. Cellular nucleic acid-binding protein restricts SARS-CoV-2 by regulating interferon and disrupting RNA-protein condensates. Proc Natl Acad Sci U S A 2023; 120:e2308355120. [PMID: 37963251 PMCID: PMC10666094 DOI: 10.1073/pnas.2308355120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/10/2023] [Indexed: 11/16/2023] Open
Abstract
A detailed understanding of the innate immune mechanisms involved in restricting SARS-CoV-2 infection and how the virus disrupts these processes could reveal new strategies to boost antiviral mechanisms and develop therapeutics for COVID-19. Here, we identify cellular nucleic acid-binding protein (CNBP) as a key host factor controlling SARS-CoV-2 infection. In response to RNA-sensing pathways, CNBP is phosphorylated and translocates from the cytosol to the nucleus where it binds to the interferon-β enhancer to initiate transcription. Because SARS-CoV-2 evades immune detection by the host's RNA-sensing pathways, CNBP is largely retained in the cytosol where it restricts SARS-CoV-2 directly, leading to a battle between the host and SARS-CoV-2 that extends beyond antiviral immune signaling pathways. We further demonstrated that CNBP binds SARS-CoV-2 viral RNA directly and competes with the viral nucleocapsid protein to prevent viral RNA and nucleocapsid protein from forming liquid-liquid phase separation (LLPS) condensates critical for viral replication. Consequently, cells and animals lacking CNBP have higher viral loads, and CNBP-deficient mice succumb rapidly to infection. Altogether, these findings identify CNBP as a key antiviral factor for SARS-CoV-2, functioning both as a regulator of antiviral IFN gene expression and a cell-intrinsic restriction factor that disrupts LLPS to limit viral replication and spread. In addition, our studies also highlight viral condensates as important targets and strategies for the development of drugs to combat COVID-19.
Collapse
Affiliation(s)
- Yongzhi Chen
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01605
| | - Xuqiu Lei
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01605
| | - Zhaozhao Jiang
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01605
| | - Fiachra Humphries
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01605
| | - Krishna Mohan Parsi
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA01605
| | - Nicholas J. Mustone
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01605
| | - Irene Ramos
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY10029
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY10029
| | - Tinaye Mutetwa
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY10029
| | - Ana Fernandez-Sesma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY10029
| | - René Maehr
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA01605
| | - Daniel R. Caffrey
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01605
| | - Katherine A. Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01605
| |
Collapse
|
2
|
Hariharan VN, Shin M, Chang CW, O’Reilly D, Biscans A, Yamada K, Guo Z, Somasundaran M, Tang Q, Monopoli K, Krishnamurthy PM, Devi G, McHugh N, Cooper DA, Echeverria D, Cruz J, Chan IL, Liu P, Lim SY, McConnell J, Singh SP, Hildebrand S, Sousa J, Davis SM, Kennedy Z, Ferguson C, Godinho BMDC, Thillier Y, Caiazzi J, Ly S, Muhuri M, Kelly K, Humphries F, Cousineau A, Parsi KM, Li Q, Wang Y, Maehr R, Gao G, Korkin D, McDougall WM, Finberg RW, Fitzgerald KA, Wang JP, Watts JK, Khvorova A. Divalent siRNAs are bioavailable in the lung and efficiently block SARS-CoV-2 infection. Proc Natl Acad Sci U S A 2023; 120:e2219523120. [PMID: 36893269 PMCID: PMC10089225 DOI: 10.1073/pnas.2219523120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/05/2023] [Indexed: 03/11/2023] Open
Abstract
The continuous evolution of SARS-CoV-2 variants complicates efforts to combat the ongoing pandemic, underscoring the need for a dynamic platform for the rapid development of pan-viral variant therapeutics. Oligonucleotide therapeutics are enhancing the treatment of numerous diseases with unprecedented potency, duration of effect, and safety. Through the systematic screening of hundreds of oligonucleotide sequences, we identified fully chemically stabilized siRNAs and ASOs that target regions of the SARS-CoV-2 genome conserved in all variants of concern, including delta and omicron. We successively evaluated candidates in cellular reporter assays, followed by viral inhibition in cell culture, with eventual testing of leads for in vivo antiviral activity in the lung. Previous attempts to deliver therapeutic oligonucleotides to the lung have met with only modest success. Here, we report the development of a platform for identifying and generating potent, chemically modified multimeric siRNAs bioavailable in the lung after local intranasal and intratracheal delivery. The optimized divalent siRNAs showed robust antiviral activity in human cells and mouse models of SARS-CoV-2 infection and represent a new paradigm for antiviral therapeutic development for current and future pandemics.
Collapse
Affiliation(s)
- Vignesh N. Hariharan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Minwook Shin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Ching-Wen Chang
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Daniel O’Reilly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Zhiru Guo
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Mohan Somasundaran
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Qi Tang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Kathryn Monopoli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | | | - Gitali Devi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - David A. Cooper
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - John Cruz
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Io Long Chan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Ping Liu
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Sun-Young Lim
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jill McConnell
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Satya Prakash Singh
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Samuel Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jacquelyn Sousa
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Sarah M. Davis
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Zachary Kennedy
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Chantal Ferguson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Bruno M. D. C. Godinho
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Yann Thillier
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jillian Caiazzi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Socheata Ly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Manish Muhuri
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Karen Kelly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Fiachra Humphries
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Alyssa Cousineau
- Diabetes Center of Excellence and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Krishna Mohan Parsi
- Diabetes Center of Excellence and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Qi Li
- MassBiologics, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Yang Wang
- MassBiologics, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - René Maehr
- Diabetes Center of Excellence and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Guangping Gao
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA01655
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Dmitry Korkin
- Department of Computer Science, and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA01609
| | - William M. McDougall
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Robert W. Finberg
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Katherine A. Fitzgerald
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jennifer P. Wang
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jonathan K. Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| |
Collapse
|
3
|
Landshammer A, Bolondi A, Kretzmer H, Much C, Buschow R, Rose A, Wu HJ, Mackowiak SD, Braendl B, Giesselmann P, Tornisiello R, Parsi KM, Huey J, Mielke T, Meierhofer D, Maehr R, Hnisz D, Michor F, Rinn JL, Meissner A. T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation. eLife 2023; 12:e83077. [PMID: 36719724 PMCID: PMC9889090 DOI: 10.7554/elife.83077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/06/2023] [Indexed: 02/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as fundamental regulators in various biological processes, including embryonic development and cellular differentiation. Despite much progress over the past decade, the genome-wide annotation of lncRNAs remains incomplete and many known non-coding loci are still poorly characterized. Here, we report the discovery of a previously unannotated lncRNA that is transcribed 230 kb upstream of the SOX17 gene and located within the same topologically associating domain. We termed it T-REX17 (Transcript Regulating Endoderm and activated by soX17) and show that it is induced following SOX17 activation but its expression is more tightly restricted to early definitive endoderm. Loss of T-REX17 affects crucial functions independent of SOX17 and leads to an aberrant endodermal transcriptome, signaling pathway deregulation and epithelial to mesenchymal transition defects. Consequently, cells lacking the lncRNA cannot further differentiate into more mature endodermal cell types. Taken together, our study identified and characterized T-REX17 as a transiently expressed and essential non-coding regulator in early human endoderm differentiation.
Collapse
Affiliation(s)
- Alexandro Landshammer
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
- Institute of Chemistry and Biochemistry, Freie Universität BerlinBerlinGermany
| | - Adriano Bolondi
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
- Institute of Chemistry and Biochemistry, Freie Universität BerlinBerlinGermany
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Christian Much
- Department of Biochemistry, University of Colorado Boulder and BioFrontiers InstituteBoulderUnited States
| | - René Buschow
- Max Planck Institute for Molecular Genetics, Microscopy Core FacilityBerlinGermany
| | - Alina Rose
- Helmholtz Institute for Metabolic, Obesity and Vascular ResearchLeipzigGermany
| | - Hua-Jun Wu
- Department of Data Science, Dana-Farber Cancer Institute, Department of Biostatistics, Harvard T. H. Chan School of Public HealthBostonUnited States
- Center for Precision Medicine Multi-Omics Research, School of Basic Medical Sciences, Peking University Health Science Center and Peking University Cancer Hospital and InstituteBeijingChina
| | - Sebastian D Mackowiak
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Bjoern Braendl
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Pay Giesselmann
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Rosaria Tornisiello
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Krishna Mohan Parsi
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Jack Huey
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Thorsten Mielke
- Max Planck Institute for Molecular Genetics, Microscopy Core FacilityBerlinGermany
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Mass Spectrometry Core FacilityBerlinGermany
| | - René Maehr
- Center for Precision Medicine Multi-Omics Research, School of Basic Medical Sciences, Peking University Health Science Center and Peking University Cancer Hospital and InstituteBeijingChina
- Diabetes Center of Excellence, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Franziska Michor
- Department of Stem Cell and Regenerative Biology, Harvard UniversityCambridgeUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Data Science, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard T. H. Chan School of Public HealthBostonUnited States
- The Ludwig Center at Harvard, Boston, MA 02215, USA, and Center for Cancer Evolution, Dana-Farber Cancer InstituteBostonUnited States
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder and BioFrontiers InstituteBoulderUnited States
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
- Institute of Chemistry and Biochemistry, Freie Universität BerlinBerlinGermany
- Department of Stem Cell and Regenerative Biology, Harvard UniversityCambridgeUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
| |
Collapse
|
4
|
Akgol Oksuz B, Yang L, Abraham S, Venev SV, Krietenstein N, Parsi KM, Ozadam H, Oomen ME, Nand A, Mao H, Genga RMJ, Maehr R, Rando OJ, Mirny LA, Gibcus JH, Dekker J. Systematic evaluation of chromosome conformation capture assays. Nat Methods 2021; 18:1046-1055. [PMID: 34480151 PMCID: PMC8446342 DOI: 10.1038/s41592-021-01248-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 07/18/2021] [Indexed: 01/05/2023]
Abstract
Chromosome conformation capture (3C) assays are used to map chromatin interactions genome-wide. Chromatin interaction maps provide insights into the spatial organization of chromosomes and the mechanisms by which they fold. Hi-C and Micro-C are widely used 3C protocols that differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a systematic evaluation of 3C experimental parameters. We identified optimal protocol variants for either loop or compartment detection, optimizing fragment size and cross-linking chemistry. We used this knowledge to develop a greatly improved Hi-C protocol (Hi-C 3.0) that can detect both loops and compartments relatively effectively. In addition to providing benchmarked protocols, this work produced ultra-deep chromatin interaction maps using Micro-C, conventional Hi-C and Hi-C 3.0 for key cell lines used by the 4D Nucleome project. This analysis systematically evaluates cross-linking chemistry and chromatin fragmentation strategies commonly used in 3C assays and introduces an improved Hi-C protocol for detecting loops and compartments.
Collapse
Affiliation(s)
- Betul Akgol Oksuz
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Liyan Yang
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sameer Abraham
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sergey V Venev
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Nils Krietenstein
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Krishna Mohan Parsi
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.,Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Hakan Ozadam
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Marlies E Oomen
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ankita Nand
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Hui Mao
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.,Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ryan M J Genga
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.,Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Rene Maehr
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.,Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Leonid A Mirny
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA
| | - Johan H Gibcus
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| |
Collapse
|
5
|
Koupenova M, Corkrey HA, Vitseva O, Tanriverdi K, Somasundaran M, Liu P, Soofi S, Bhandari R, Godwin M, Parsi KM, Cousineau A, Maehr R, Wang JP, Cameron SJ, Rade J, Finberg RW, Freedman JE. SARS-CoV-2 Initiates Programmed Cell Death in Platelets. Circ Res 2021; 129:631-646. [PMID: 34293929 PMCID: PMC8409903 DOI: 10.1161/circresaha.121.319117] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Supplemental Digital Content is available in the text. Coronavirus disease 2019 (COVID-19) is characterized by increased incidence of microthrombosis with hyperactive platelets sporadically containing viral RNA. It is unclear if SARS-CoV-2 (severe acute respiratory syndrome, corona virus-2) directly alters platelet activation or if these changes are a reaction to infection-mediated global inflammatory alterations. Importantly, the direct effect of SARS-CoV-2 on platelets has yet to be studied.
Collapse
Affiliation(s)
- Milka Koupenova
- Department of Medicine, Division of Cardiovascular Medicine (M.K., H.A.C., O.V., K.T., J.R., J.E.F.), University of Massachusetts Medical School, Worcester, MA
| | - Heather A Corkrey
- Department of Medicine, Division of Cardiovascular Medicine (M.K., H.A.C., O.V., K.T., J.R., J.E.F.), University of Massachusetts Medical School, Worcester, MA
| | - Olga Vitseva
- Department of Medicine, Division of Cardiovascular Medicine (M.K., H.A.C., O.V., K.T., J.R., J.E.F.), University of Massachusetts Medical School, Worcester, MA
| | - Kahraman Tanriverdi
- Department of Medicine, Division of Cardiovascular Medicine (M.K., H.A.C., O.V., K.T., J.R., J.E.F.), University of Massachusetts Medical School, Worcester, MA
| | - Mohan Somasundaran
- Department of Biochemistry and Molecular Pharmacology (M.S.), University of Massachusetts Medical School, Worcester, MA
| | - Ping Liu
- Department of Medicine, Division of Infectious Disease and Immunology Department of Medicine (P.L., S.S., J.P.W., R.W.F.), University of Massachusetts Medical School, Worcester, MA
| | - Shaukat Soofi
- Department of Medicine, Division of Infectious Disease and Immunology Department of Medicine (P.L., S.S., J.P.W., R.W.F.), University of Massachusetts Medical School, Worcester, MA
| | - Rohan Bhandari
- Heart, Vascular and Thoracic Institute (R.B., S.J.C.).,Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, OH (R.B., M.G., S.J.C.)
| | - Matthew Godwin
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, OH (R.B., M.G., S.J.C.)
| | - Krishna Mohan Parsi
- Diabetes Center of Excellence (K.M.P., A.C., R.M.), University of Massachusetts Medical School, Worcester, MA.,Program in Molecular Medicine (K.M.P., R.M.), University of Massachusetts Medical School, Worcester, MA
| | - Alyssa Cousineau
- Diabetes Center of Excellence (K.M.P., A.C., R.M.), University of Massachusetts Medical School, Worcester, MA
| | - René Maehr
- Diabetes Center of Excellence (K.M.P., A.C., R.M.), University of Massachusetts Medical School, Worcester, MA.,Program in Molecular Medicine (K.M.P., R.M.), University of Massachusetts Medical School, Worcester, MA
| | - Jennifer P Wang
- Department of Medicine, Division of Infectious Disease and Immunology Department of Medicine (P.L., S.S., J.P.W., R.W.F.), University of Massachusetts Medical School, Worcester, MA
| | - Scott J Cameron
- Heart, Vascular and Thoracic Institute (R.B., S.J.C.).,Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, OH (R.B., M.G., S.J.C.).,Case Western Reserve University Lerner College of Medicine, Cleveland, OH (S.J.C.)
| | - Jeffrey Rade
- Department of Medicine, Division of Cardiovascular Medicine (M.K., H.A.C., O.V., K.T., J.R., J.E.F.), University of Massachusetts Medical School, Worcester, MA
| | - Robert W Finberg
- Department of Medicine, Division of Infectious Disease and Immunology Department of Medicine (P.L., S.S., J.P.W., R.W.F.), University of Massachusetts Medical School, Worcester, MA
| | - Jane E Freedman
- Department of Medicine, Division of Cardiovascular Medicine (M.K., H.A.C., O.V., K.T., J.R., J.E.F.), University of Massachusetts Medical School, Worcester, MA
| |
Collapse
|
6
|
Krietenstein N, Abraham S, Venev SV, Abdennur N, Gibcus J, Hsieh THS, Parsi KM, Yang L, Maehr R, Mirny LA, Dekker J, Rando OJ. Ultrastructural Details of Mammalian Chromosome Architecture. Mol Cell 2020; 78:554-565.e7. [PMID: 32213324 DOI: 10.1016/j.molcel.2020.03.003] [Citation(s) in RCA: 259] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 02/11/2020] [Accepted: 03/02/2020] [Indexed: 11/18/2022]
Abstract
Over the past decade, 3C-related methods have provided remarkable insights into chromosome folding in vivo. To overcome the limited resolution of prior studies, we extend a recently developed Hi-C variant, Micro-C, to map chromosome architecture at nucleosome resolution in human ESCs and fibroblasts. Micro-C robustly captures known features of chromosome folding including compartment organization, topologically associating domains, and interactions between CTCF binding sites. In addition, Micro-C provides a detailed map of nucleosome positions and localizes contact domain boundaries with nucleosomal precision. Compared to Hi-C, Micro-C exhibits an order of magnitude greater dynamic range, allowing the identification of ∼20,000 additional loops in each cell type. Many newly identified peaks are localized along extrusion stripes and form transitive grids, consistent with their anchors being pause sites impeding cohesin-dependent loop extrusion. Our analyses comprise the highest-resolution maps of chromosome folding in human cells to date, providing a valuable resource for studies of chromosome organization.
Collapse
Affiliation(s)
- Nils Krietenstein
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Sameer Abraham
- Insitute for Medical Engineering and Sciences and Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Center for 3D Structure and Physics of the Genome, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Sergey V Venev
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nezar Abdennur
- Insitute for Medical Engineering and Sciences and Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Center for 3D Structure and Physics of the Genome, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Johan Gibcus
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Tsung-Han S Hsieh
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Krishna Mohan Parsi
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Liyan Yang
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - René Maehr
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Leonid A Mirny
- Insitute for Medical Engineering and Sciences and Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Center for 3D Structure and Physics of the Genome, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Job Dekker
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| |
Collapse
|
7
|
Shuaib M, Parsi KM, Thimma M, Adroub SA, Kawaji H, Seridi L, Ghosheh Y, Fort A, Fallatah B, Ravasi T, Carninci P, Orlando V. Nuclear AGO1 Regulates Gene Expression by Affecting Chromatin Architecture in Human Cells. Cell Syst 2019; 9:446-458.e6. [PMID: 31629687 DOI: 10.1016/j.cels.2019.09.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/29/2019] [Accepted: 09/12/2019] [Indexed: 12/21/2022]
Abstract
The impact of mammalian RNA interference components, particularly, Argonaute proteins, on chromatin organization is unexplored. Recent reports indicate that AGO1 association with chromatin appears to influence gene expression. To uncover the role of AGO1 in the nucleus, we used a combination of genome-wide approaches in control and AGO1-depleted HepG2 cells. We found that AGO1 strongly associates with active enhancers and RNA being produced at those sites. Hi-C analysis revealed AGO1 enrichment at the boundaries of topologically associated domains (TADs). By Hi-C in AGO1 knockdown cells, we observed changes in chromatin organization, including TADs and A/B compartment mixing, specifically in AGO1-bound regions. Distinct groups of genes and especially eRNA transcripts located within differentially interacting loci showed altered expression upon AGO1 depletion. Moreover, AGO1 association with enhancers is dependent on eRNA transcription. Collectively, our data suggest that enhancer-associated AGO1 contributes to the fine-tuning of chromatin architecture and gene expression in human cells.
Collapse
Affiliation(s)
- Muhammad Shuaib
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
| | - Krishna Mohan Parsi
- IRCSS Fondazione, Santa Lucia, Epigenetics and Genome Reprogramming, Rome, Italy
| | - Manjula Thimma
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
| | - Sabir Abdu Adroub
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
| | - Hideya Kawaji
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Loqmane Seridi
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
| | - Yanal Ghosheh
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
| | - Alexandre Fort
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Bodor Fallatah
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Valerio Orlando
- King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia; IRCSS Fondazione, Santa Lucia, Epigenetics and Genome Reprogramming, Rome, Italy.
| |
Collapse
|
8
|
Parsi KM, Hennessy E, Kearns N, Maehr R. Using an Inducible CRISPR-dCas9-KRAB Effector System to Dissect Transcriptional Regulation in Human Embryonic Stem Cells. Methods Mol Biol 2017; 1507:221-233. [PMID: 27832543 DOI: 10.1007/978-1-4939-6518-2_16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
CRISPR-Cas9 effector systems have wide applications for the stem cell and regenerative medicine field. The ability to dissect the functional gene regulatory networks in pluripotency and potentially in differentiation intermediates of all three germ layers makes this a valuable tool for the stem cell community. Catalytically inactive Cas9 fused to transcriptional/chromatin effector domains allows for silencing or activation of a genomic region of interest. Here, we describe the application of an inducible, RNA-guided, nuclease-deficient (d) Cas9-KRAB system (adapted from Streptococcus pyogenes) to silence target gene expression in human embryonic stem cells, via KRAB repression at the promoter region. This chapter outlines a detailed protocol for generation of a stable human embryonic stem cell line containing both Sp-dCas9-KRAB and sgRNA, followed by inducible expression of Sp-dCas9-KRAB to analyze functional effects of dCas9-KRAB at target loci in human embryonic stem cells.
Collapse
Affiliation(s)
- Krishna Mohan Parsi
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Erica Hennessy
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Nicola Kearns
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - René Maehr
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
| |
Collapse
|