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Wang J, Nakato R. Churros: a Docker-based pipeline for large-scale epigenomic analysis. DNA Res 2024; 31:dsad026. [PMID: 38102723 PMCID: PMC11389749 DOI: 10.1093/dnares/dsad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/23/2023] [Accepted: 12/13/2023] [Indexed: 12/17/2023] Open
Abstract
The epigenome, which reflects the modifications on chromatin or DNA sequences, provides crucial insight into gene expression regulation and cellular activity. With the continuous accumulation of epigenomic datasets such as chromatin immunoprecipitation followed by sequencing (ChIP-seq) data, there is a great demand for a streamlined pipeline to consistently process them, especially for large-dataset comparisons involving hundreds of samples. Here, we present Churros, an end-to-end epigenomic analysis pipeline that is environmentally independent and optimized for handling large-scale data. We successfully demonstrated the effectiveness of Churros by analyzing large-scale ChIP-seq datasets with the hg38 or Telomere-to-Telomere (T2T) human reference genome. We found that applying T2T to the typical analysis workflow has important impacts on read mapping, quality checks, and peak calling. We also introduced a useful feature to study context-specific epigenomic landscapes. Churros will contribute a comprehensive and unified resource for analyzing large-scale epigenomic data.
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Affiliation(s)
- Jiankang Wang
- School of Biomedical Sciences, Hunan University, Changsha, Hunan, China
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ryuichiro Nakato
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Seifritz T, Brunner M, Camarillo Retamosa E, Maciukiewicz M, Krošel M, Moser L, Züllig T, Tomšič M, Distler O, Ospelt C, Klein K. BRD3 Regulates the Inflammatory and Stress Response in Rheumatoid Arthritis Synovial Fibroblasts. Biomedicines 2023; 11:3188. [PMID: 38137409 PMCID: PMC10741099 DOI: 10.3390/biomedicines11123188] [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: 11/07/2023] [Revised: 11/18/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND Individual functions of members of the bromodomain (BRD) and extra-terminal (BET) protein family underlying the anti-inflammatory effects of BET inhibitors in rheumatoid arthritis (RA) are incompletely understood. Here, we aimed to analyze the regulatory functions of BRD3, an understudied member of the BET protein family, in RA synovial fibroblasts (FLS). METHODS BRD3 was silenced in FLS prior to stimulation with TNF. Alternatively, FLS were treated with I-BET. Transcriptomes were analyzed by RNA sequencing (RNAseq), followed by pathway enrichment analysis. We confirmed results for selective target genes by real-time PCR, ELISA, and Western blotting. RESULTS BRD3 regulates the expression of several cytokines and chemokines in FLS, and positively correlates with inflammatory scores in the RA synovium. In addition, RNAseq pointed to a profound role of BRD3 in regulating FLS proliferation, metabolic adaption, and response to stress, including oxidative stress, and autophagy. CONCLUSIONS BRD3 acts as an upstream regulatory factor that integrates the response to inflammatory stimuli and stress conditions in FLS and executes many functions of BET proteins that have previously been identified using pan-BET inhibitors.
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Affiliation(s)
- Tanja Seifritz
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland (E.C.R.)
| | - Matthias Brunner
- Department of Rheumatology and Immunology, Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Eva Camarillo Retamosa
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland (E.C.R.)
| | - Malgorzata Maciukiewicz
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland (E.C.R.)
- Department of Rheumatology and Immunology, Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Monika Krošel
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland (E.C.R.)
- Department of Rheumatology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Larissa Moser
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland (E.C.R.)
| | - Thomas Züllig
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland (E.C.R.)
| | - Matija Tomšič
- Department of Rheumatology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Oliver Distler
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland (E.C.R.)
| | - Caroline Ospelt
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland (E.C.R.)
| | - Kerstin Klein
- Department of Rheumatology and Immunology, Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
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3
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Mokin YI, Gavrilova AA, Fefilova AS, Kuznetsova IM, Turoverov KK, Uversky VN, Fonin AV. Nucleolar- and Nuclear-Stress-Induced Membrane-Less Organelles: A Proteome Analysis through the Prism of Liquid-Liquid Phase Separation. Int J Mol Sci 2023; 24:11007. [PMID: 37446185 DOI: 10.3390/ijms241311007] [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: 04/30/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Radical changes in the idea of the organization of intracellular space that occurred in the early 2010s made it possible to consider the formation and functioning of so-called membrane-less organelles (MLOs) based on a single physical principle: the liquid-liquid phase separation (LLPS) of biopolymers. Weak non-specific inter- and intramolecular interactions of disordered polymers, primarily intrinsically disordered proteins, and RNA, play a central role in the initiation and regulation of these processes. On the other hand, in some cases, the "maturation" of MLOs can be accompanied by a "liquid-gel" phase transition, where other types of interactions can play a significant role in the reorganization of their structure. In this work, we conducted a bioinformatics analysis of the propensity of the proteomes of two membrane-less organelles, formed in response to stress in the same compartment, for spontaneous phase separation and examined their intrinsic disorder predispositions. These MLOs, amyloid bodies (A-bodies) formed in the response to acidosis and heat shock and nuclear stress bodies (nSBs), are characterized by a partially overlapping composition, but show different functional activities and morphologies. We show that the proteomes of these biocondensates are differently enriched in proteins, and many have high potential for spontaneous LLPS that correlates with the different morphology and function of these organelles. The results of these analyses allowed us to evaluate the role of weak interactions in the formation and functioning of these important organelles.
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Affiliation(s)
- Yakov I Mokin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Anastasia A Gavrilova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Anna S Fefilova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Alexander V Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
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4
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Gavrilova AA, Fefilova AS, Vishnyakov IE, Kuznetsova IM, Turoverov KK, Uversky VN, Fonin AV. On the Roles of the Nuclear Non-Coding RNA-Dependent Membrane-Less Organelles in the Cellular Stress Response. Int J Mol Sci 2023; 24:ijms24098108. [PMID: 37175815 PMCID: PMC10179167 DOI: 10.3390/ijms24098108] [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: 03/26/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
At the beginning of the 21st century, it became obvious that radical changes had taken place in the concept of living matter and, in particular, in the concept of the organization of intracellular space. The accumulated data testify to the essential importance of phase transitions of biopolymers (first of all, intrinsically disordered proteins and RNA) in the spatiotemporal organization of the intracellular space. Of particular interest is the stress-induced reorganization of the intracellular space. Examples of organelles formed in response to stress are nuclear A-bodies and nuclear stress bodies. The formation of these organelles is based on liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) and non-coding RNA. Despite their overlapping composition and similar mechanism of formation, these organelles have different functional activities and physical properties. In this review, we will focus our attention on these membrane-less organelles (MLOs) and describe their functions, structure, and mechanism of formation.
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Affiliation(s)
- Anastasia A Gavrilova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
| | - Anna S Fefilova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
| | - Innokentii E Vishnyakov
- Group of Molecular Cytology of Prokaryotes and Bacterial Invasion, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Alexander V Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
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5
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Timcheva K, Dufour S, Touat-Todeschini L, Burnard C, Carpentier MC, Chuffart F, Merret R, Helsmoortel M, Ferré S, Grézy A, Couté Y, Rousseaux S, Khochbin S, Vourc'h C, Bousquet-Antonelli C, Kiernan R, Seigneurin-Berny D, Verdel A. Chromatin-associated YTHDC1 coordinates heat-induced reprogramming of gene expression. Cell Rep 2022; 41:111784. [PMID: 36516773 DOI: 10.1016/j.celrep.2022.111784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 08/01/2022] [Accepted: 11/15/2022] [Indexed: 12/15/2022] Open
Abstract
Heat stress (HS) induces a cellular response leading to profound changes in gene expression. Here, we show that human YTHDC1, a reader of N6-methyladenosine (m6A) RNA modification, mostly associates to the chromatin fraction and that HS induces a redistribution of YTHDC1 across the genome, including to heat-induced heat shock protein (HSP) genes. YTHDC1 binding to m6A-modified HSP transcripts co-transcriptionally promotes expression of HSPs. In parallel, hundreds of the genes enriched in YTHDC1 during HS have their transcripts undergoing YTHDC1- and m6A-dependent intron retention. Later, YTHDC1 concentrates within nuclear stress bodies (nSBs) where it binds to m6A-modified SATIII non-coding RNAs, produced in an HSF1-dependent manner upon HS. These findings reveal that YTHDC1 plays a central role in a chromatin-associated m6A-based reprogramming of gene expression during HS. Furthermore, they support the model where the subsequent and temporary sequestration of YTHDC1 within nSBs calibrates the timing of this YTHDC1-dependent gene expression reprogramming.
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Affiliation(s)
- Kalina Timcheva
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Solenne Dufour
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Leila Touat-Todeschini
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Callum Burnard
- Gene Regulation Laboratory, Institut de Génétique Humaine, UMR9002, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Marie-Christine Carpentier
- University Perpignan Via Domitia, LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; CNRS LGDP-UMR5096, UPVD, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - Florent Chuffart
- Epigenetic Regulations, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Rémy Merret
- University Perpignan Via Domitia, LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; CNRS LGDP-UMR5096, UPVD, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - Marion Helsmoortel
- Gene Regulation Laboratory, Institut de Génétique Humaine, UMR9002, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Sabrina Ferré
- University Grenoble Alpes, Inserm, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Aude Grézy
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Yohann Couté
- University Grenoble Alpes, Inserm, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Sophie Rousseaux
- Epigenetic Regulations, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Saadi Khochbin
- Epigenetic Regulations, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Claire Vourc'h
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Cécile Bousquet-Antonelli
- University Perpignan Via Domitia, LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; CNRS LGDP-UMR5096, UPVD, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - Rosemary Kiernan
- Gene Regulation Laboratory, Institut de Génétique Humaine, UMR9002, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Daphné Seigneurin-Berny
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France.
| | - André Verdel
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France.
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6
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Ugarković Đ, Sermek A, Ljubić S, Feliciello I. Satellite DNAs in Health and Disease. Genes (Basel) 2022; 13:genes13071154. [PMID: 35885937 PMCID: PMC9324158 DOI: 10.3390/genes13071154] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/20/2022] [Accepted: 06/24/2022] [Indexed: 12/10/2022] Open
Abstract
Tandemly repeated satellite DNAs are major components of centromeres and pericentromeric heterochromatin which are crucial chromosomal elements responsible for accurate chromosome segregation. Satellite DNAs also contribute to genome evolution and the speciation process and are important for the maintenance of the entire genome inside the nucleus. In addition, there is increasing evidence for active and tightly regulated transcription of satellite DNAs and for the role of their transcripts in diverse processes. In this review, we focus on recent discoveries related to the regulation of satellite DNA expression and the role of their transcripts, either in heterochromatin establishment and centromere function or in gene expression regulation under various biological contexts. We discuss the role of satellite transcripts in the stress response and environmental adaptation as well as consequences of the dysregulation of satellite DNA expression in cancer and their potential use as cancer biomarkers.
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Affiliation(s)
- Đurđica Ugarković
- Department of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia; (A.S.); (S.L.)
- Correspondence: (Đ.U.); (I.F.); Tel.: +385-1-4561-083 (D.U.); +39-081-746-4317 (I.F.)
| | - Antonio Sermek
- Department of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia; (A.S.); (S.L.)
| | - Sven Ljubić
- Department of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia; (A.S.); (S.L.)
| | - Isidoro Feliciello
- Department of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia; (A.S.); (S.L.)
- Department of Clinical Medicine and Surgery, School of Medicine, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy
- Correspondence: (Đ.U.); (I.F.); Tel.: +385-1-4561-083 (D.U.); +39-081-746-4317 (I.F.)
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7
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Vourc’h C, Dufour S, Timcheva K, Seigneurin-Berny D, Verdel A. HSF1-Activated Non-Coding Stress Response: Satellite lncRNAs and Beyond, an Emerging Story with a Complex Scenario. Genes (Basel) 2022; 13:genes13040597. [PMID: 35456403 PMCID: PMC9032817 DOI: 10.3390/genes13040597] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/18/2022] [Accepted: 03/19/2022] [Indexed: 12/21/2022] Open
Abstract
In eukaryotes, the heat shock response is orchestrated by a transcription factor named Heat Shock Factor 1 (HSF1). HSF1 is mostly characterized for its role in activating the expression of a repertoire of protein-coding genes, including the heat shock protein (HSP) genes. Remarkably, a growing set of reports indicate that, upon heat shock, HSF1 also targets various non-coding regions of the genome. Focusing primarily on mammals, this review aims at reporting the identity of the non-coding genomic sites directly bound by HSF1, and at describing the molecular function of the long non-coding RNAs (lncRNAs) produced in response to HSF1 binding. The described non-coding genomic targets of HSF1 are pericentric Satellite DNA repeats, (sub)telomeric DNA repeats, Short Interspersed Nuclear Element (SINE) repeats, transcriptionally active enhancers and the NEAT1 gene. This diverse set of non-coding genomic sites, which already appears to be an integral part of the cellular response to stress, may only represent the first of many. Thus, the study of the evolutionary conserved heat stress response has the potential to emerge as a powerful cellular context to study lncRNAs, produced from repeated or unique DNA regions, with a regulatory function that is often well-documented but a mode of action that remains largely unknown.
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Affiliation(s)
- Claire Vourc’h
- Université de Grenoble Alpes (UGA), 38700 La Tronche, France
- Correspondence: (C.V.); (A.V.)
| | - Solenne Dufour
- Institute for Advanced Biosciences (IAB), Centre de Recherche UGA/Inserm U 1209/CNRS UMR 5309, Site Santé-Allée des Alpes, 38700 La Tronche, France; (S.D.); (K.T.); (D.S.-B.)
| | - Kalina Timcheva
- Institute for Advanced Biosciences (IAB), Centre de Recherche UGA/Inserm U 1209/CNRS UMR 5309, Site Santé-Allée des Alpes, 38700 La Tronche, France; (S.D.); (K.T.); (D.S.-B.)
| | - Daphné Seigneurin-Berny
- Institute for Advanced Biosciences (IAB), Centre de Recherche UGA/Inserm U 1209/CNRS UMR 5309, Site Santé-Allée des Alpes, 38700 La Tronche, France; (S.D.); (K.T.); (D.S.-B.)
| | - André Verdel
- Institute for Advanced Biosciences (IAB), Centre de Recherche UGA/Inserm U 1209/CNRS UMR 5309, Site Santé-Allée des Alpes, 38700 La Tronche, France; (S.D.); (K.T.); (D.S.-B.)
- Correspondence: (C.V.); (A.V.)
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8
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Dicer promotes genome stability via the bromodomain transcriptional co-activator BRD4. Nat Commun 2022; 13:1001. [PMID: 35194019 PMCID: PMC8863982 DOI: 10.1038/s41467-022-28554-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 01/14/2022] [Indexed: 01/01/2023] Open
Abstract
RNA interference is required for post-transcriptional silencing, but also has additional roles in transcriptional silencing of centromeres and genome stability. However, these roles have been controversial in mammals. Strikingly, we found that Dicer-deficient embryonic stem cells have strong proliferation and chromosome segregation defects as well as increased transcription of centromeric satellite repeats, which triggers the interferon response. We conducted a CRISPR-Cas9 genetic screen to restore viability and identified transcriptional activators, histone H3K9 methyltransferases, and chromosome segregation factors as suppressors, resembling Dicer suppressors identified in independent screens in fission yeast. The strongest suppressors were mutations in the transcriptional co-activator Brd4, which reversed the strand-specific transcription of major satellite repeats suppressing the interferon response, and in the histone acetyltransferase Elp3. We show that identical mutations in the second bromodomain of Brd4 rescue Dicer-dependent silencing and chromosome segregation defects in both mammalian cells and fission yeast. This remarkable conservation demonstrates that RNA interference has an ancient role in transcriptional silencing and in particular of satellite repeats, which is essential for cell cycle progression and proper chromosome segregation. Our results have pharmacological implications for cancer and autoimmune diseases characterized by unregulated transcription of satellite repeats. While RNA interference is conserved across species, small RNA pathways are very diverse. In this study, Gutbrod et al. find that non-canonical roles of Dicer in genome stability are in fact deeply conserved from yeast to humans.
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9
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Zhou N, Zhang Y, Lei G, Chen Y, Lin T, Liu Q, Zhao Y, Mao J, Jiang Y, Mao R. Inhibition of BETs prevents heat shock-induced cell death via upregulating HSPs in SV40 large T antigen transfected cells. Genes Genomics 2022; 44:1259-1269. [PMID: 35175516 DOI: 10.1007/s13258-022-01228-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/31/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Heat shock response is a protected mechanism against environmental changes for the organism, which must be tightly regulated. Bromodomain and extra terminal-containing protein family (BETs) regulate numerous gene expression in many physiological and pathological conditions, including viral infection. SV40 is considered as a highly human disease-associated virus. OBJECTIVE We aimed to explore whether BETs play a role in heat shock in SV40 large T antigen transfected cells. METHODS SV40LTA was transfected in HeLa cells using the Lipofectamine 8000. BETs inhibitor JQ1 and I-BET-762 was employed to treat transfected cells and HEK-293 T cells. Heat shock treatment was performed to determine the effect of JQ1 and I-BET-762 on these cells. Western blot and quantitative RT-PCR were carried out to assess the expression of HSP70 and other HSPs. RESULTS We found that inhibition of BETs by JQ1 and I-BET-762 protects cells from heat shock-induced death in HEK293T cells. Both JQ1 and I-BET-762 induce the expression of HSPs and HSF1 in HEK-293 T cells. However, neither JQ1 nor I-BET-762 fail to induce the expression of HSPs in either HeLa or HBL-1 cells. When SV40 large T antigen was transfected into HeLa cells, the induction of HSP70 expressing and the protection of heat shock-induced cell death are reproduced by JQ1 and IBET treatment in these transfected cells. CONCLUSIONS Inhibition of BETs by JQ1 and I-BET-762 prevents heat shock-induced cell death via upregulating HSPs in SV40 large T antigen transfected cells. Our data indicate a novel function of BETs in SV40 large T antigen transformed cells, affecting HSPs and HSF1 as well as its function on heat shock response.
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Affiliation(s)
- Nan Zhou
- Department of Pathophysiology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China
| | - Ye Zhang
- Department of Pathophysiology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China
| | - Gongyun Lei
- Department of Pathophysiology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China
| | - Yifan Chen
- Department of Pathophysiology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China
| | - Ting Lin
- Department of Pathophysiology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China
| | - Qin Liu
- Department of Pathophysiology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China
| | - Yinshuang Zhao
- Department of Pathophysiology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China.,Department of Pediatric Surgery, Affiliated Hospital of Nantong University, Nantong University, Nantong, 226001, Jiangsu, People's Republic of China
| | - Jiahui Mao
- Department of Pathophysiology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China
| | - Yongying Jiang
- Department of Pathophysiology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China.
| | - Renfang Mao
- Department of Pathophysiology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China.
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10
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Vertii A. Stress as a Chromatin Landscape Architect. Front Cell Dev Biol 2021; 9:790138. [PMID: 34970548 PMCID: PMC8712864 DOI: 10.3389/fcell.2021.790138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
The exponential development of methods investigating different levels of spatial genome organization leads to the appreciation of the chromatin landscape's contribution to gene regulation and cell fate. Multiple levels of 3D chromatin organization include chromatin loops and topologically associated domains, followed by euchromatin and heterochromatin compartments, chromatin domains associated with nuclear bodies, and culminate with the chromosome territories. 3D chromatin architecture is exposed to multiple factors such as cell division and stress, including but not limited to mechanical, inflammatory, and environmental challenges. How exactly the stress exposure shapes the chromatin landscape is a new and intriguing area of research. In this mini-review, the developments that motivate the exploration of this field are discussed.
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Affiliation(s)
- Anastassiia Vertii
- Department of Molecular, Cellular and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, United States
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11
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Iyer H, Wahul AB, P K A, Sawant BS, Kumar A. A BRD's (BiRD's) eye view of BET and BRPF bromodomains in neurological diseases. Rev Neurosci 2021; 32:403-426. [PMID: 33661583 DOI: 10.1515/revneuro-2020-0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/11/2020] [Indexed: 01/18/2023]
Abstract
Neurological disorders (NLDs) are among the top leading causes for disability worldwide. Dramatic changes in the epigenetic topography of the brain and nervous system have been found in many NLDs. Histone lysine acetylation has prevailed as one of the well characterised epigenetic modifications in these diseases. Two instrumental components of the acetylation machinery are the evolutionarily conserved Bromodomain and PHD finger containing (BRPF) and Bromo and Extra terminal domain (BET) family of proteins, also referred to as acetylation 'readers'. Several reasons, including their distinct mechanisms of modulation of gene expression and their property of being highly tractable small molecule targets, have increased their translational relevance. Thus, compounds which demonstrated promising results in targeting these proteins have advanced to clinical trials. They have been established as key role players in pathologies of cancer, cardiac diseases, renal diseases and rheumatic diseases. In addition, studies implicating the role of these bromodomains in NLDs are gaining pace. In this review, we highlight the findings of these studies, and reason for the plausible roles of all BET and BRPF members in NLDs. A comprehensive understanding of their multifaceted functions would be radical in the development of therapeutic interventions.
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Affiliation(s)
- Harish Iyer
- Epigenetics and Neuropsychiatric Disorders' Laboratory, CSIR - Centre for Cellular and Molecular Biology (CCMB), Hyderabad500007, India
| | - Abhipradnya B Wahul
- Epigenetics and Neuropsychiatric Disorders' Laboratory, CSIR - Centre for Cellular and Molecular Biology (CCMB), Hyderabad500007, India
| | - Annapoorna P K
- Epigenetics and Neuropsychiatric Disorders' Laboratory, CSIR - Centre for Cellular and Molecular Biology (CCMB), Hyderabad500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
| | - Bharvi S Sawant
- Epigenetics and Neuropsychiatric Disorders' Laboratory, CSIR - Centre for Cellular and Molecular Biology (CCMB), Hyderabad500007, India
| | - Arvind Kumar
- Epigenetics and Neuropsychiatric Disorders' Laboratory, CSIR - Centre for Cellular and Molecular Biology (CCMB), Hyderabad500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
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12
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Feliciello I, Pezer Ž, Sermek A, Bruvo Mađarić B, Ljubić S, Ugarković Đ. Satellite DNA-Mediated Gene Expression Regulation: Physiological and Evolutionary Implication. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 60:145-167. [PMID: 34386875 DOI: 10.1007/978-3-030-74889-0_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Satellite DNAs are tandemly repeated sequences organized in large clusters within (peri)centromeric and/or subtelomeric heterochromatin. However, in many species, satellite DNAs are not restricted to heterochromatin but are also dispersed as short arrays within euchromatin. Such genomic organization together with transcriptional activity seems to be a prerequisite for the gene-modulatory effect of satellite DNAs which was first demonstrated in the beetle Tribolium castaneum upon heat stress. Namely, enrichment of a silent histone mark at euchromatic repeats of a major beetle satellite DNA results in epigenetic silencing of neighboring genes. In addition, human satellite III transcripts induced by heat shock contribute to genome-wide gene silencing, providing protection against stress-induced cell death. Gene silencing mediated by satellite RNA was also shown to be fundamental for the early embryonic development of the mosquito Aedes aegypti. Apart from a physiological role during embryogenesis and heat stress response, activation of satellite DNAs in terms of transcription and proliferation can have an evolutionary impact. Spreading of satellite repeats throughout euchromatin promotes the variation of epigenetic landscapes and gene expression diversity, contributing to the evolution of gene regulatory networks and to genome adaptation in fluctuating environmental conditions.
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Affiliation(s)
- Isidoro Feliciello
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia.,Dipartimento di Medicina Clinica e Chirurgia, Universita' degli Studi di Napoli Federico II, Naples, Italy
| | - Željka Pezer
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Antonio Sermek
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | | | - Sven Ljubić
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Đurđica Ugarković
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia.
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13
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Ishikura S, Nakabayashi K, Nagai M, Tsunoda T, Shirasawa S. ZFAT binds to centromeres to control noncoding RNA transcription through the KAT2B-H4K8ac-BRD4 axis. Nucleic Acids Res 2020; 48:10848-10866. [PMID: 32997115 PMCID: PMC7641738 DOI: 10.1093/nar/gkaa815] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/09/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023] Open
Abstract
Centromeres are genomic regions essential for faithful chromosome segregation. Transcription of noncoding RNA (ncRNA) at centromeres is important for their formation and functions. Here, we report the molecular mechanism by which the transcriptional regulator ZFAT controls the centromeric ncRNA transcription in human and mouse cells. Chromatin immunoprecipitation with high-throughput sequencing analysis shows that ZFAT binds to centromere regions at every chromosome. We find a specific 8-bp DNA sequence for the ZFAT-binding motif that is highly conserved and widely distributed at whole centromere regions of every chromosome. Overexpression of ZFAT increases the centromeric ncRNA levels at specific chromosomes, whereas its silencing reduces them, indicating crucial roles of ZFAT in centromeric transcription. Overexpression of ZFAT increases the centromeric levels of both the histone acetyltransferase KAT2B and the acetylation at the lysine 8 in histone H4 (H4K8ac). siRNA-mediated knockdown of KAT2B inhibits the overexpressed ZFAT-induced increase in centromeric H4K8ac levels, suggesting that ZFAT recruits KAT2B to centromeres to induce H4K8ac. Furthermore, overexpressed ZFAT recruits the bromodomain-containing protein BRD4 to centromeres through KAT2B-mediated H4K8ac, leading to RNA polymerase II-dependent ncRNA transcription. Thus, ZFAT binds to centromeres to control ncRNA transcription through the KAT2B-H4K8ac-BRD4 axis.
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Affiliation(s)
- Shuhei Ishikura
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka 814-0180, Japan.,Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Fukuoka 814-0180, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Masayoshi Nagai
- Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Fukuoka 814-0180, Japan
| | - Toshiyuki Tsunoda
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka 814-0180, Japan.,Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Fukuoka 814-0180, Japan
| | - Senji Shirasawa
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka 814-0180, Japan.,Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Fukuoka 814-0180, Japan
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14
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Leo L, Marchetti M, Giunta S, Fanti L. Epigenetics as an Evolutionary Tool for Centromere Flexibility. Genes (Basel) 2020; 11:genes11070809. [PMID: 32708654 PMCID: PMC7397245 DOI: 10.3390/genes11070809] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 12/31/2022] Open
Abstract
Centromeres are the complex structures responsible for the proper segregation of chromosomes during cell division. Structural or functional alterations of the centromere cause aneuploidies and other chromosomal aberrations that can induce cell death with consequences on health and survival of the organism as a whole. Because of their essential function in the cell, centromeres have evolved high flexibility and mechanisms of tolerance to preserve their function following stress, whether it is originating from within or outside the cell. Here, we review the main epigenetic mechanisms of centromeres’ adaptability to preserve their functional stability, with particular reference to neocentromeres and holocentromeres. The centromere position can shift in response to altered chromosome structures, but how and why neocentromeres appear in a given chromosome region are still open questions. Models of neocentromere formation developed during the last few years will be hereby discussed. Moreover, we will discuss the evolutionary significance of diffuse centromeres (holocentromeres) in organisms such as nematodes. Despite the differences in DNA sequences, protein composition and centromere size, all of these diverse centromere structures promote efficient chromosome segregation, balancing genome stability and adaptability, and ensuring faithful genome inheritance at each cellular generation.
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Affiliation(s)
- Laura Leo
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy; (L.L.); (M.M.); (S.G.)
| | - Marcella Marchetti
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy; (L.L.); (M.M.); (S.G.)
| | - Simona Giunta
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy; (L.L.); (M.M.); (S.G.)
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Laura Fanti
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy; (L.L.); (M.M.); (S.G.)
- Correspondence:
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15
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Heat Stress Affects H3K9me3 Level at Human Alpha Satellite DNA Repeats. Genes (Basel) 2020; 11:genes11060663. [PMID: 32570830 PMCID: PMC7348797 DOI: 10.3390/genes11060663] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/10/2020] [Accepted: 06/16/2020] [Indexed: 12/19/2022] Open
Abstract
Satellite DNAs are tandemly repeated sequences preferentially assembled into large arrays within constitutive heterochromatin and their transcription is often activated by stress conditions, particularly by heat stress. Bioinformatic analyses of sequenced genomes however reveal single repeats or short arrays of satellite DNAs dispersed in the vicinity of genes within euchromatin. Here, we analyze transcription of a major human alpha satellite DNA upon heat stress and follow the dynamics of “silent” H3K9me3 and “active” H3K4me2/3 histone marks at dispersed euchromatic and tandemly arranged heterochromatic alpha repeats. The results show H3K9me3 enrichment at alpha repeats upon heat stress, which correlates with the dynamics of alpha satellite DNA transcription activation, while no change in H3K4me2/3 level is detected. Spreading of H3K9me3 up to 1–2 kb from the insertion sites of the euchromatic alpha repeats is detected, revealing the alpha repeats as modulators of local chromatin structure. In addition, expression of genes containing alpha repeats within introns as well as of genes closest to the intergenic alpha repeats is downregulated upon heat stress. Further studies are necessary to reveal the possible contribution of H3K9me3 enriched alpha repeats, in particular those located within introns, to the silencing of their associated genes.
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16
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Abo1 is required for the H3K9me2 to H3K9me3 transition in heterochromatin. Sci Rep 2020; 10:6055. [PMID: 32269268 PMCID: PMC7142091 DOI: 10.1038/s41598-020-63209-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 03/26/2020] [Indexed: 01/24/2023] Open
Abstract
Heterochromatin regulation is critical for genomic stability. Different H3K9 methylation states have been discovered, with distinct roles in heterochromatin formation and silencing. However, how the transition from H3K9me2 to H3K9me3 is controlled is still unclear. Here, we investigate the role of the conserved bromodomain AAA-ATPase, Abo1, involved in maintaining global nucleosome organisation in fission yeast. We identified several key factors involved in heterochromatin silencing that interact genetically with Abo1: histone deacetylase Clr3, H3K9 methyltransferase Clr4, and HP1 homolog Swi6. Cells lacking Abo1 cultivated at 30 °C exhibit an imbalance of H3K9me2 and H3K9me3 in heterochromatin. In abo1∆ cells, the centromeric constitutive heterochromatin has increased H3K9me2 but decreased H3K9me3 levels compared to wild-type. In contrast, facultative heterochromatin regions exhibit reduced H3K9me2 and H3K9me3 levels in abo1∆. Genome-wide analysis showed that abo1∆ cells have silencing defects in both the centromeres and subtelomeres, but not in a subset of heterochromatin islands in our condition. Thus, our work uncovers a role of Abo1 in stabilising directly or indirectly Clr4 recruitment to allow the H3K9me2 to H3K9me3 transition in heterochromatin.
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17
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Kainth AS, Meduri R, Pandit V, Rubio LS, Gross DS. Shugoshin 2-a new guardian for heat shock transcription. EMBO J 2020; 39:e104077. [PMID: 31886561 PMCID: PMC6960451 DOI: 10.15252/embj.2019104077] [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] [Indexed: 11/09/2022] Open
Abstract
Takii et al (2019) demonstrate in a recent issue of The EMBO Journal that the pericentromeric protein, SGO2, serves as a novel transcriptional coactivator of HSF1, contributing to PIC assembly and expression of Heat Shock Protein (HSP) genes. This finding highlights repurposing of a protein with a nuclear function to drive transcription of proteotoxic stress machinery genes.
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Affiliation(s)
- Amoldeep S Kainth
- Department of Biochemistry and Molecular BiologyLouisiana State University Health Sciences CenterShreveportLAUSA
| | - Rajyalakshmi Meduri
- Department of Biochemistry and Molecular BiologyLouisiana State University Health Sciences CenterShreveportLAUSA
| | - Vickky Pandit
- Department of Biochemistry and Molecular BiologyLouisiana State University Health Sciences CenterShreveportLAUSA
| | - Linda S Rubio
- Department of Biochemistry and Molecular BiologyLouisiana State University Health Sciences CenterShreveportLAUSA
| | - David S Gross
- Department of Biochemistry and Molecular BiologyLouisiana State University Health Sciences CenterShreveportLAUSA
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18
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Zhang L, Hu Z, Zhang Y, Huang J, Yang X, Wang J. Proteomics analysis of proteins interacting with heat shock factor 1 in squamous cell carcinoma of the cervix. Oncol Lett 2019; 18:2568-2575. [PMID: 31402952 DOI: 10.3892/ol.2019.10539] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 03/07/2019] [Indexed: 01/08/2023] Open
Abstract
Protein interactions are crucial for maintaining homeostasis. Heat shock factor 1 (HSF1), a transcription factor that interacts with various proteins, is highly expressed in squamous cell carcinoma (SCC) of the cervix. The aim of the present study was to investigate the protein interaction profile of HSF1 in cervical SCC. Proteins interacting with HSF1 in SCC tissue and non-cancerous control (Ctrl) tissue were obtained by immunoprecipitation, separated by SDS-PAGE, identified by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry and analyzed using bioinformatics methods. A total of 220 and 241 proteins were identified by mass spectrometry in the tissues of Ctrl and SCC samples, respectively, among which 172 were detected exclusively in SCC (Pro-S), 151 exclusively in Ctrl (Pro-C) and 69 in both groups (Pro-B). The protein interaction profiles were different in each group; the STRING database identified three proteins that interacted with HSF1 directly, including insulin-like growth factor 1 receptor and small nuclear RNA-activating protein complex subunit 4 in Pro-C and small ubiquitin-related modifier 1 in Pro-S. Functional enrichment analysis of Gene Ontology revealed that the top terms were alternative splicing in Pro-S and polymorphism in Pro-C. In Pro-S, more categories were related to protein modification, such as phosphorylation, ubiquitination and acetylation. Therefore, HSF1 may influence the occurrence and development of cervical SCC by interacting with specific proteins.
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Affiliation(s)
- Lingli Zhang
- Department of Gynaecology and Obstetrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
| | - Zhe Hu
- Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
| | - Ying Zhang
- Department of Gynaecology and Obstetrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
| | - Jinzhi Huang
- Department of Gynaecology and Obstetrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
| | - Xuefen Yang
- Department of Gynaecology and Obstetrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
| | - Jiafeng Wang
- Stem Cell Research and Cellular Therapy Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
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19
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Furlan A, Agbazahou F, Henry M, Gonzalez-Pisfil M, Le Nézet C, Champelovier D, Fournier M, Vandenbunder B, Bidaux G, Héliot L. P-TEFb et Brd4. Med Sci (Paris) 2018; 34:685-692. [DOI: 10.1051/medsci/20183408015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
La physiologie d’une cellule est dictée par l’intégration des signaux qu’elle reçoit et la mise en place de réponses adaptées par le biais, entre autres, de programmes transcriptionnels adéquats. Pour assurer un contrôle optimal de ces réponses, des mécanismes de régulation ont été sélectionnés, dont un processus de pause transcriptionnelle et de levée de cette pause par P-TEFb (positive transcription elongation factor) et Brd4 (bromodomain-containing protein 4). Le dérèglement de ce processus peut conduire à l’apparition de pathologies. P-TEFb et Brd4 ont ainsi émergé au cours des dernières années comme des cibles thérapeutiques potentielles dans le cadre des cancers et du syndrome d‘immunodéficience acquise (sida) notamment.
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20
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Liu X, Li Q, Huang P, Tong D, Wu H, Zhang F. EGFR-mediated signaling pathway influences the sensitivity of oral squamous cell carcinoma to JQ1. J Cell Biochem 2018; 119:8368-8377. [PMID: 30687956 DOI: 10.1002/jcb.26920] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 04/04/2018] [Indexed: 12/25/2022]
Abstract
Inhibiting BRD4 has emerged as a promising anticancer strategy, and inhibitors such as JQ1 can suppress cell growth in oral squamous cell carcinoma (OSCC). However, the mechanism through which JQ1 exerts its anticancer activity has not been reported. Moreover, JQ1 does not markedly inhibit proliferation and increase apoptosis in OSCC when used as a monotherapy. Herein, we explore the mechanism of JQ1 in OSCC and probe ways to increase its therapeutic potential. In this study, we used two cell lines, Cal27, and Scc25. We found that BRD4 was highly expressed in OSCC tissues when compared with adjacent non-tumor tissues, and JQ1 worked through the EGFR-mediated signaling pathway in tumor cells. Furthermore, we demonstrated that JQ1 induced an increased treatment effect in vitro and in vivo when combined with a PI3K inhibitor. Interestingly, subsequent mechanistic analyses indicated that further suppressing EGFR and BRD4 expression was instrumental to this functional synergism. Moreover, we found that upregulating EGFR expression by EGF stimulation protected cells treated with JQ1 from apoptosis, while knockdown of EGFR before addition of JQ1 successfully mimicked the combination treatment results. In summary, our findings revealed that JQ1 can act by inhibiting the EGFR-mediated signaling pathway, and EGFR expression influences the sensitivity of OSCC to JQ1. Regarding clinical use, this study demonstrates that BRD4 is a novel therapeutic target and EGFR can be used as a biomarker to identify the most appropriate anti-BRD4 treatment strategy in OSCC.
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Affiliation(s)
- Xiaojing Liu
- School of Stomatology, Shandong University, Jinan, Shandong Province, China
- Shandong Provincial Key Laboratory of Oral Tissue Regeneration, Jinan, Shandong Province, China
| | - Qing Li
- School of Stomatology, Shandong University, Jinan, Shandong Province, China
- Shandong Provincial Key Laboratory of Oral Tissue Regeneration, Jinan, Shandong Province, China
| | - Ping Huang
- Department of Stomatology, Qilu hospital, Jinan, Shandong Province, China
| | - Dongdong Tong
- School of Stomatology, Shandong University, Jinan, Shandong Province, China
- Shandong Provincial Key Laboratory of Oral Tissue Regeneration, Jinan, Shandong Province, China
| | - Haitao Wu
- School of Stomatology, Shandong University, Jinan, Shandong Province, China
- Shandong Provincial Key Laboratory of Oral Tissue Regeneration, Jinan, Shandong Province, China
| | - Fenghe Zhang
- School of Stomatology, Shandong University, Jinan, Shandong Province, China
- Shandong Provincial Key Laboratory of Oral Tissue Regeneration, Jinan, Shandong Province, China
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21
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Podgornaya OI, Ostromyshenskii DI, Enukashvily NI. Who Needs This Junk, or Genomic Dark Matter. BIOCHEMISTRY (MOSCOW) 2018; 83:450-466. [PMID: 29626931 DOI: 10.1134/s0006297918040156] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Centromeres (CEN), pericentromeric regions (periCEN), and subtelomeric regions (subTel) comprise the areas of constitutive heterochromatin (HChr). Tandem repeats (TRs or satellite DNA) are the main components of HChr forming no less than 10% of the mouse and human genome. HChr is assembled within distinct structures in the interphase nuclei of many species - chromocenters. In this review, the main classes of HChr repeat sequences are considered in the order of their number increase in the sequencing reads of the mouse chromocenters (ChrmC). TRs comprise ~70% of ChrmC occupying the first place. Non-LTR (-long terminal repeat) retroposons (mainly LINE, long interspersed nuclear element) are the next (~11%), and endogenous retroviruses (ERV; LTR-containing) are in the third position (~9%). HChr is not enriched with ERV in comparison with the whole genome, but there are differences in distribution of certain elements: while MaLR-like elements (ERV3) are dominant in the whole genome, intracisternal A-particles and corresponding LTR (ERV2) are prevalent in HChr. Most of LINE in ChrmC is represented by the 2-kb fragment at the end of the 2nd open reading frame and its flanking regions. Almost all tandem repeats classified as CEN or periCEN are contained in ChrmC. Our previous classification revealed 60 new mouse TR families with 29 of them being absent in ChrmC, which indicates their location on chromosome arms. TR transcription is necessary for maintenance of heterochromatic status of the HChr genome part. A burst of TR transcription is especially important in embryogenesis and other cases of radical changes in the cell program, including carcinogenesis. The recently discovered mechanism of epigenetic regulation with noncoding sequences transcripts, long noncoding RNA, and its role in embryogenesis and pluripotency maintenance is discussed.
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Affiliation(s)
- O I Podgornaya
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia.
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22
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Garrido-Ramos MA. Satellite DNA: An Evolving Topic. Genes (Basel) 2017; 8:genes8090230. [PMID: 28926993 PMCID: PMC5615363 DOI: 10.3390/genes8090230] [Citation(s) in RCA: 232] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022] Open
Abstract
Satellite DNA represents one of the most fascinating parts of the repetitive fraction of the eukaryotic genome. Since the discovery of highly repetitive tandem DNA in the 1960s, a lot of literature has extensively covered various topics related to the structure, organization, function, and evolution of such sequences. Today, with the advent of genomic tools, the study of satellite DNA has regained a great interest. Thus, Next-Generation Sequencing (NGS), together with high-throughput in silico analysis of the information contained in NGS reads, has revolutionized the analysis of the repetitive fraction of the eukaryotic genomes. The whole of the historical and current approaches to the topic gives us a broad view of the function and evolution of satellite DNA and its role in chromosomal evolution. Currently, we have extensive information on the molecular, chromosomal, biological, and population factors that affect the evolutionary fate of satellite DNA, knowledge that gives rise to a series of hypotheses that get on well with each other about the origin, spreading, and evolution of satellite DNA. In this paper, I review these hypotheses from a methodological, conceptual, and historical perspective and frame them in the context of chromosomal organization and evolution.
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Affiliation(s)
- Manuel A Garrido-Ramos
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
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