1
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Payen SH, Andrada K, Tara E, Petereit J, Verma SC, Rossetto CC. The cellular paraspeckle component SFPQ associates with the viral processivity factor ORF59 during lytic replication of Kaposi's Sarcoma-associated herpesvirus (KSHV). Virus Res 2024; 349:199456. [PMID: 39214388 PMCID: PMC11406446 DOI: 10.1016/j.virusres.2024.199456] [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: 06/03/2024] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) relies on many cellular proteins to complete replication and generate new virions. Paraspeckle nuclear bodies consisting of core ribonucleoproteins splicing factor proline/glutamine-rich (SFPQ), Non-POU domain-containing octamer-binding protein (NONO), and paraspeckle protein component 1 (PSPC1) along with the long non-coding RNA NEAT1, form a complex that has been speculated to play an important role in viral replication. Paraspeckle bodies are multifunctional and involved in various processes including gene expression, mRNA splicing, and anti-viral defenses. To better understand the role of SFPQ during KSHV replication, we performed SFPQ immunoprecipitation followed by mass spectrometry from KSHV-infected cells. Proteomic analysis showed that during lytic reactivation, SFPQ associates with viral proteins, including ORF10, ORF59, and ORF61. These results are consistent with a previously reported ORF59 proteomics assay identifying SFPQ. To test if the association between ORF59 and SFPQ is important for replication, we first identified the region of ORF59 that associates with SFPQ using a series of 50 amino acid deletion mutants of ORF59 in the KSHV BACmid system. By performing co-immunoprecipitations, we identified the region spanning amino acids 101-150 of ORF59 as the association domain with SFPQ. Using this information, we generated a dominant negative polypeptide of ORF59 encompassing amino acids 101-150, that disrupted the association between SFPQ and full-length ORF59, and decreased virus production. Interestingly, when we tested other human herpesvirus processivity factors (EBV BMRF1, HSV-1 UL42, and HCMV UL44) by transfection of each expression plasmid followed by co-immunoprecipitation, we found a conserved association with SFPQ. These are limited studies that remain to be done in the context of infection but suggest a potential association of SFPQ with processivity factors across multiple herpesviruses.
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Affiliation(s)
- Shannon Harger Payen
- University of Nevada, Reno School of Medicine, Department of Microbiology & Immunology, Reno, NV 89557, USA
| | - Kayla Andrada
- University of Nevada, Reno School of Medicine, Department of Microbiology & Immunology, Reno, NV 89557, USA
| | - Evelyn Tara
- University of Nevada, Reno School of Medicine, Department of Microbiology & Immunology, Reno, NV 89557, USA
| | - Juli Petereit
- University of Nevada, Reno, Nevada Bioinformatics Center (RRID: SCR_017802), Reno, NV 89557, USA
| | - Subhash C Verma
- University of Nevada, Reno School of Medicine, Department of Microbiology & Immunology, Reno, NV 89557, USA
| | - Cyprian C Rossetto
- University of Nevada, Reno School of Medicine, Department of Microbiology & Immunology, Reno, NV 89557, USA.
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2
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Lu Y, Gan L, Di S, Nie F, Shi H, Wang R, Yang F, Qin W, Wen W. The role of phase separation in RNA modification: both cause and effect. Int J Biol Macromol 2024; 280:135907. [PMID: 39322163 DOI: 10.1016/j.ijbiomac.2024.135907] [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: 06/29/2024] [Revised: 09/20/2024] [Accepted: 09/20/2024] [Indexed: 09/27/2024]
Abstract
Phase separation is a critical mechanism for partitioning cellular functions by specific aggregation of biological macromolecules. Recent studies have found that phase separation is widely contributed in various biological functions, particularly in RNA related processes. Over 170 different post-transcriptional modifications occur in RNA, which is considered to be one of the most important physiological and pathogenic epigenetic mechanisms. Here, we discuss the role of phase separation in regulating RNA modification processing to ensure orderly RNA metabolism and function. Enzymes responsible for RNA modification undergo compartmentalization, enabling them to traffic client RNAs and amplify modifying efficacy. Meanwhile, altered RNA affects the formation, dissolution, and biophysical properties of phase separation conversely. These findings deeper our understanding of the interplay between phase separation and RNAs that governs a wide range of cellular processes. Finally, we concluded pathological roles of phase separation in RNA modification towards clinical applications and outlined perspectives to research RNA modification through the lens of phase separation.
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Affiliation(s)
- Yu Lu
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, 710072 Xi'an, China
| | - Lunbiao Gan
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, 710072 Xi'an, China
| | - Sijia Di
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, 710072 Xi'an, China
| | - Fengze Nie
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, 710072 Xi'an, China
| | - Haoxin Shi
- Department of Urology, Xijing Hospital, Fourth Military Medical University, 710032 Xi'an, China
| | - Ruoyu Wang
- Department of Urology, Xijing Hospital, Fourth Military Medical University, 710032 Xi'an, China
| | - Fa Yang
- Department of Urology, Xijing Hospital, Fourth Military Medical University, 710032 Xi'an, China.
| | - Weijun Qin
- Department of Urology, Xijing Hospital, Fourth Military Medical University, 710032 Xi'an, China.
| | - Weihong Wen
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, 710072 Xi'an, China.
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3
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Al-Refaie N, Padovani F, Hornung J, Pudelko L, Binando F, Del Carmen Fabregat A, Zhao Q, Towbin BD, Cenik ES, Stroustrup N, Padeken J, Schmoller KM, Cabianca DS. Fasting shapes chromatin architecture through an mTOR/RNA Pol I axis. Nat Cell Biol 2024:10.1038/s41556-024-01512-w. [PMID: 39300311 DOI: 10.1038/s41556-024-01512-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 08/19/2024] [Indexed: 09/22/2024]
Abstract
Chromatin architecture is a fundamental mediator of genome function. Fasting is a major environmental cue across the animal kingdom, yet how it impacts three-dimensional (3D) genome organization is unknown. Here we show that fasting induces an intestine-specific, reversible and large-scale spatial reorganization of chromatin in Caenorhabditis elegans. This fasting-induced 3D genome reorganization requires inhibition of the nutrient-sensing mTOR pathway, acting through the regulation of RNA Pol I, but not Pol II nor Pol III, and is accompanied by remodelling of the nucleolus. By uncoupling the 3D genome configuration from the animal's nutritional status, we find that the expression of metabolic and stress-related genes increases when the spatial reorganization of chromatin occurs, showing that the 3D genome might support the transcriptional response in fasted animals. Our work documents a large-scale chromatin reorganization triggered by fasting and reveals that mTOR and RNA Pol I shape genome architecture in response to nutrients.
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Affiliation(s)
- Nada Al-Refaie
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Faculty of Medicine, Ludwig-Maximilians Universität München, Munich, Germany
| | - Francesco Padovani
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Johanna Hornung
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Lorenz Pudelko
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Faculty of Medicine, Ludwig-Maximilians Universität München, Munich, Germany
| | - Francesca Binando
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Andrea Del Carmen Fabregat
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Qiuxia Zhao
- Department of Molecular Biosciences, University of Texas Austin, Austin, TX, USA
| | | | - Elif Sarinay Cenik
- Department of Molecular Biosciences, University of Texas Austin, Austin, TX, USA
| | - Nicholas Stroustrup
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Jan Padeken
- Institute of Molecular Biology, Mainz, Germany
| | - Kurt M Schmoller
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Daphne S Cabianca
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.
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4
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Boukoura S, Larsen DH. Nucleolar organization and ribosomal DNA stability in response to DNA damage. Curr Opin Cell Biol 2024; 89:102380. [PMID: 38861757 DOI: 10.1016/j.ceb.2024.102380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/13/2024]
Abstract
Eukaryotic nuclei are structured into sub-compartments orchestrating various cellular functions. The nucleolus is the largest nuclear organelle: a biomolecular condensate with an architecture composed of immiscible fluids facilitating ribosome biogenesis. The nucleolus forms upon the transcription of the repetitive ribosomal RNA genes (rDNA) that cluster in this compartment. rDNA is intrinsically unstable and prone to rearrangements and copy number variation. Upon DNA damage, a specialized nucleolar-DNA Damage Response (n-DDR) is activated: nucleolar transcription is inhibited, the architecture is rearranged, and rDNA is relocated to the nucleolar periphery. Recent data have highlighted how the composition of nucleoli, its structure, chemical and physical properties, contribute to rDNA stability. In this mini-review we focus on recent data that start to reveal how nucleolar composition and the n-DDR work together to ensure rDNA integrity.
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Affiliation(s)
- Stavroula Boukoura
- Nucleolar Stress and Disease Group, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Dorthe Helena Larsen
- Nucleolar Stress and Disease Group, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark.
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5
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Bhattacharya A, Wang K, Penailillo J, Chan CN, Fushimi A, Yamashita N, Daimon T, Haratake N, Ozawa H, Nakashoji A, Shigeta K, Morimoto Y, Miyo M, Kufe DW. MUC1-C regulates NEAT1 lncRNA expression and paraspeckle formation in cancer progression. Oncogene 2024; 43:2199-2214. [PMID: 38802648 PMCID: PMC11226401 DOI: 10.1038/s41388-024-03068-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/08/2024] [Accepted: 05/16/2024] [Indexed: 05/29/2024]
Abstract
The MUC1 gene evolved in mammals for adaptation of barrier tissues in response to infections and damage. Paraspeckles are nuclear bodies formed on the NEAT1 lncRNA in response to loss of homeostasis. There is no known intersection of MUC1 with NEAT1 or paraspeckles. Here, we demonstrate that the MUC1-C subunit plays an essential role in regulating NEAT1 expression. MUC1-C activates the NEAT1 gene with induction of the NEAT1_1 and NEAT1_2 isoforms by NF-κB- and MYC-mediated mechanisms. MUC1-C/MYC signaling also induces expression of the SFPQ, NONO and FUS RNA binding proteins (RBPs) that associate with NEAT1_2 and are necessary for paraspeckle formation. MUC1-C integrates activation of NEAT1 and RBP-encoding genes by recruiting the PBAF chromatin remodeling complex and increasing chromatin accessibility of their respective regulatory regions. We further demonstrate that MUC1-C and NEAT1 form an auto-inductive pathway that drives common sets of genes conferring responses to inflammation and loss of homeostasis. Of functional significance, we find that the MUC1-C/NEAT1 pathway is of importance for the cancer stem cell (CSC) state and anti-cancer drug resistance. These findings identify a previously unrecognized role for MUC1-C in the regulation of NEAT1, RBPs, and paraspeckles that has been co-opted in promoting cancer progression.
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Affiliation(s)
| | - Keyi Wang
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Johany Penailillo
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Chi Ngai Chan
- Tissue Technologies Unit, Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Atsushi Fushimi
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Nami Yamashita
- Breast Surgical Oncology, Breast Oncology Center, The Cancer Institute Hospital of the JFCR, Tokyo, Japan
| | - Tatsuaki Daimon
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Naoki Haratake
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Hiroki Ozawa
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ayako Nakashoji
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Keisuke Shigeta
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yoshihiro Morimoto
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Masaaki Miyo
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Donald W Kufe
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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6
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Trifault B, Mamontova V, Cossa G, Ganskih S, Wei Y, Hofstetter J, Bhandare P, Baluapuri A, Nieto B, Solvie D, Ade CP, Gallant P, Wolf E, Larsen DH, Munschauer M, Burger K. Nucleolar detention of NONO shields DNA double-strand breaks from aberrant transcripts. Nucleic Acids Res 2024; 52:3050-3068. [PMID: 38224452 PMCID: PMC11014278 DOI: 10.1093/nar/gkae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 12/11/2023] [Accepted: 01/04/2024] [Indexed: 01/16/2024] Open
Abstract
RNA-binding proteins emerge as effectors of the DNA damage response (DDR). The multifunctional non-POU domain-containing octamer-binding protein NONO/p54nrb marks nuclear paraspeckles in unperturbed cells, but also undergoes re-localization to the nucleolus upon induction of DNA double-strand breaks (DSBs). However, NONO nucleolar re-localization is poorly understood. Here we show that the topoisomerase II inhibitor etoposide stimulates the production of RNA polymerase II-dependent, DNA damage-inducible antisense intergenic non-coding RNA (asincRNA) in human cancer cells. Such transcripts originate from distinct nucleolar intergenic spacer regions and form DNA-RNA hybrids to tether NONO to the nucleolus in an RNA recognition motif 1 domain-dependent manner. NONO occupancy at protein-coding gene promoters is reduced by etoposide, which attenuates pre-mRNA synthesis, enhances NONO binding to pre-mRNA transcripts and is accompanied by nucleolar detention of a subset of such transcripts. The depletion or mutation of NONO interferes with detention and prolongs DSB signalling. Together, we describe a nucleolar DDR pathway that shields NONO and aberrant transcripts from DSBs to promote DNA repair.
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Affiliation(s)
- Barbara Trifault
- Mildred Scheel Early Career Center for Cancer Research (Mildred-Scheel-Nachwuchszentrum, MSNZ) Würzburg, University Hospital Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Victoria Mamontova
- Mildred Scheel Early Career Center for Cancer Research (Mildred-Scheel-Nachwuchszentrum, MSNZ) Würzburg, University Hospital Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Giacomo Cossa
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Sabina Ganskih
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| | - Yuanjie Wei
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| | - Julia Hofstetter
- Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Pranjali Bhandare
- Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Apoorva Baluapuri
- Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Blanca Nieto
- Nucleolar Stress and Disease Group, Danish Cancer Institute, Strandboulevarden 49, Copenhagen, Denmark
| | - Daniel Solvie
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Carsten P Ade
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Peter Gallant
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Elmar Wolf
- Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Dorthe H Larsen
- Nucleolar Stress and Disease Group, Danish Cancer Institute, Strandboulevarden 49, Copenhagen, Denmark
| | - Mathias Munschauer
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| | - Kaspar Burger
- Mildred Scheel Early Career Center for Cancer Research (Mildred-Scheel-Nachwuchszentrum, MSNZ) Würzburg, University Hospital Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
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7
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Sundara Rajan S, Ebegboni VJ, Pichling P, Ludwig KR, Jones TL, Chari R, Tran A, Kruhlak MJ, Loncarek J, Caplen NJ. Endogenous EWSR1 Exists in Two Visual Modalities That Reflect Its Associations with Nucleic Acids and Concentration at Sites of Active Transcription. Mol Cell Biol 2024; 44:103-122. [PMID: 38506112 PMCID: PMC10986767 DOI: 10.1080/10985549.2024.2315425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/02/2024] [Indexed: 03/21/2024] Open
Abstract
EWSR1 is a member of the FET family of nucleic acid binding proteins that includes FUS and TAF15. Here, we report the systematic analysis of endogenous EWSR1's cellular organization in human cells. We demonstrate that EWSR1, which contains low complexity and nucleic acid binding domains, is present in cells in faster and slower-recovering fractions, indicative of a protein undergoing both rapid exchange and longer-term interactions. The employment of complementary high-resolution imaging approaches shows EWSR1 exists in two visual modalities, a distributed state which is present throughout the nucleoplasm, and a concentrated state consistent with the formation of foci. Both EWSR1 visual modalities localize with nascent RNA. EWSR1 foci concentrate in regions of euchromatin, adjacent to protein markers of transcriptional activation, and significantly colocalize with phosphorylated RNA polymerase II. Our results contribute to bridging the gap between our understanding of the biophysical and biochemical properties of FET proteins, including EWSR1, their functions as transcriptional regulators, and the participation of these proteins in tumorigenesis and neurodegenerative disease.
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Affiliation(s)
- Soumya Sundara Rajan
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Vernon J. Ebegboni
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Patricio Pichling
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Katelyn R. Ludwig
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Tamara L. Jones
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, Maryland, USA
| | - Andy Tran
- CCR Confocal Microscopy Core Facility, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael J. Kruhlak
- CCR Confocal Microscopy Core Facility, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jadranka Loncarek
- Centrosome Biology Section, Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Natasha J. Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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8
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Fakim H, Vande Velde C. The implications of physiological biomolecular condensates in amyotrophic lateral sclerosis. Semin Cell Dev Biol 2024; 156:176-189. [PMID: 37268555 DOI: 10.1016/j.semcdb.2023.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 06/04/2023]
Abstract
In recent years, there has been an emphasis on the role of phase-separated biomolecular condensates, especially stress granules, in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). This is largely due to several ALS-associated mutations occurring in genes involved in stress granule assembly and observations that pathological inclusions detected in ALS patient neurons contain stress granule proteins, including the ALS-linked proteins TDP-43 and FUS. However, protein components of stress granules are also found in numerous other phase-separated biomolecular condensates under physiological conditions which are inadequately discussed in the context of ALS. In this review, we look beyond stress granules and describe the roles of TDP-43 and FUS in physiological condensates occurring in the nucleus and neurites, such as the nucleolus, Cajal bodies, paraspeckles and neuronal RNA transport granules. We also discuss the consequences of ALS-linked mutations in TDP-43 and FUS on their ability to phase separate into these stress-independent biomolecular condensates and perform their respective functions. Importantly, biomolecular condensates sequester multiple overlapping protein and RNA components, and their dysregulation could contribute to the observed pleiotropic effects of both sporadic and familial ALS on RNA metabolism.
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Affiliation(s)
- Hana Fakim
- Department of Neurosciences, Université de Montréal, and CHUM Research Center, Montréal, QC, Canada
| | - Christine Vande Velde
- Department of Neurosciences, Université de Montréal, and CHUM Research Center, Montréal, QC, Canada.
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9
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Huo M, Rai SK, Nakatsu K, Deng Y, Jijiwa M. Subverting the Canon: Novel Cancer-Promoting Functions and Mechanisms for snoRNAs. Int J Mol Sci 2024; 25:2923. [PMID: 38474168 PMCID: PMC10932220 DOI: 10.3390/ijms25052923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Small nucleolar RNAs (snoRNAs) constitute a class of intron-derived non-coding RNAs ranging from 60 to 300 nucleotides. Canonically localized in the nucleolus, snoRNAs play a pivotal role in RNA modifications and pre-ribosomal RNA processing. Based on the types of modifications they involve, such as methylation and pseudouridylation, they are classified into two main families-box C/D and H/ACA snoRNAs. Recent investigations have revealed the unconventional synthesis and biogenesis strategies of snoRNAs, indicating their more profound roles in pathogenesis than previously envisioned. This review consolidates recent discoveries surrounding snoRNAs and provides insights into their mechanistic roles in cancer. It explores the intricate interactions of snoRNAs within signaling pathways and speculates on potential therapeutic solutions emerging from snoRNA research. In addition, it presents recent findings on the long non-coding small nucleolar RNA host gene (lncSNHG), a subset of long non-coding RNAs (lncRNAs), which are the transcripts of parental SNHGs that generate snoRNA. The nucleolus, the functional epicenter of snoRNAs, is also discussed. Through a deconstruction of the pathways driving snoRNA-induced oncogenesis, this review aims to serve as a roadmap to guide future research in the nuanced field of snoRNA-cancer interactions and inspire potential snoRNA-related cancer therapies.
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Affiliation(s)
- Matthew Huo
- Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD 21218, USA;
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA; (S.K.R.); (K.N.)
| | - Sudhir Kumar Rai
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA; (S.K.R.); (K.N.)
| | - Ken Nakatsu
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA; (S.K.R.); (K.N.)
- Emory College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA; (S.K.R.); (K.N.)
| | - Mayumi Jijiwa
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA; (S.K.R.); (K.N.)
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10
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Ganser LR, Niaki AG, Yuan X, Huang E, Deng D, Djaja NA, Ge Y, Craig A, Langlois O, Myong S. The roles of FUS-RNA binding domain and low complexity domain in RNA-dependent phase separation. Structure 2024; 32:177-187.e5. [PMID: 38070499 PMCID: PMC10997494 DOI: 10.1016/j.str.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/24/2023] [Accepted: 11/14/2023] [Indexed: 02/04/2024]
Abstract
Fused in sarcoma (FUS) is an archetypal phase separating protein asymmetrically divided into a low complexity domain (LCD) and an RNA binding domain (RBD). Here, we explore how the two domains contribute to RNA-dependent phase separation, RNA recognition, and multivalent complex formation. We find that RBD drives RNA-dependent phase separation but forms large and irregularly shaped droplets that are rescued by LCD in trans. Electrophoretic mobility shift assay (EMSA) and single-molecule fluorescence assays reveal that, while both LCD and RBD bind RNA, RBD drives RNA engagement and multivalent complex formation. While RBD alone exhibits delayed RNA recognition and a less dynamic RNP complex compared to full-length FUS, LCD in trans rescues full-length FUS activity. Likewise, cell-based data show RBD forms nucleolar condensates while LCD in trans rescues the diffuse nucleoplasm localization of full-length FUS. Our results point to a regulatory role of LCD in tuning the RNP interaction and buffering phase separation.
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Affiliation(s)
- Laura R Ganser
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | | | - Xincheng Yuan
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA; Department of Biology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
| | - Ethan Huang
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Dahlia Deng
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA; Department of Biology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
| | - Nathalie A Djaja
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA; Department of Biology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
| | - Yingda Ge
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alanna Craig
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Olivia Langlois
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA; Department of Biology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA.
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11
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Xiao M, Wang F, Chen N, Zhang H, Cao J, Yu Y, Zhao B, Ji J, Xu P, Li L, Shen L, Lin X, Feng XH. Smad4 sequestered in SFPQ condensates prevents TGF-β tumor-suppressive signaling. Dev Cell 2024; 59:48-63.e8. [PMID: 38103553 DOI: 10.1016/j.devcel.2023.11.020] [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: 05/10/2023] [Revised: 09/18/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023]
Abstract
Loss of TGF-β growth-inhibitory responses is a hallmark of human cancer. However, the molecular mechanisms underlying the TGF-β resistance of cancer cells remain to be fully elucidated. Splicing factor proline- and glutamine-rich (SFPQ) is a prion-like RNA-binding protein that is frequently upregulated in human cancers. In this study, we identified SFPQ as a potent suppressor of TGF-β signaling. The ability of SFPQ to suppress TGF-β responses depends on its prion-like domain (PrLD) that drives liquid-liquid phase separation (LLPS). Mechanistically, SFPQ physically restrained Smad4 in its condensates, which excluded Smad4 from the Smad complex and chromatin occupancy and thus functionally dampened Smad-dependent transcriptional responses. Accordingly, SFPQ deficiency or loss of phase separation activities rendered human cells hypersensitive to TGF-β responses. Together, our data identify an important function of SFPQ through LLPS that suppresses Smad transcriptional activation and TGF-β tumor-suppressive activity.
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Affiliation(s)
- Mu Xiao
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Fei Wang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Nuo Chen
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hanchenxi Zhang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jin Cao
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yi Yu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Bin Zhao
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Junfang Ji
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Pinglong Xu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lei Li
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Li Shen
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xia Lin
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China
| | - Xin-Hua Feng
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China; The Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310009, China.
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12
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Liang J, Cai D. Membrane-less compartments in the nucleus: Separated or connected phases? Curr Opin Cell Biol 2023; 84:102215. [PMID: 37574634 PMCID: PMC10528681 DOI: 10.1016/j.ceb.2023.102215] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023]
Abstract
In recent years, it has become increasingly clear that many nuclear membrane-less compartments have liquid-like properties and may form through the physicochemical process of phase separation. In this review, we will first discuss how various nuclear compartments, such as the genome, transcription compartments, and nuclear bodies are formed through phase separation. Then, we propose that inter-compartmental communications can also be prevalent and may be mediated by inter-compartmental diffusion of macromolecules, fusion among different compartments, and transient or stable contacts among nuclear compartments. Understanding how nuclear compartments communicate with each other represents an exciting new area of research and may reveal important insights about cellular functions and uncover previously under-appreciated disease mechanisms.
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Affiliation(s)
- Jindayi Liang
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Danfeng Cai
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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13
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Wang T, Shi S, Shi Y, Jiang P, Hu G, Ye Q, Shi Z, Yu K, Wang C, Fan G, Zhao S, Ma H, Chang ACY, Li Z, Bian Q, Lin CP. Chemical-induced phase transition and global conformational reorganization of chromatin. Nat Commun 2023; 14:5556. [PMID: 37689690 PMCID: PMC10492836 DOI: 10.1038/s41467-023-41340-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 08/29/2023] [Indexed: 09/11/2023] Open
Abstract
Chemicals or drugs can accumulate within biomolecular condensates formed through phase separation in cells. Here, we use super-resolution imaging to search for chemicals that induce phase transition within chromatin at the microscale. This microscopic screening approach reveals that adriamycin (doxorubicin) - a widely used anticancer drug that is known to interact with chromatin - specifically induces visible local condensation and global conformational change of chromatin in cancer and primary cells. Hi-C and ATAC-seq experiments systematically and quantitatively demonstrate that adriamycin-induced chromatin condensation is accompanied by weakened chromatin interaction within topologically associated domains, compartment A/B switching, lower chromatin accessibility, and corresponding transcriptomic changes. Mechanistically, adriamycin complexes with histone H1 and induces phase transition of H1, forming fibrous aggregates in vitro. These results reveal a phase separation-driven mechanism for a chemotherapeutic drug.
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Affiliation(s)
- Tengfei Wang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Shuxiang Shi
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
- Lingang Laboratory, 200031, Shanghai, China
| | - Yuanyuan Shi
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200125, Shanghai, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Peipei Jiang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200125, Shanghai, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Ganlu Hu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Qinying Ye
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Zhan Shi
- School of Physical Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Kexin Yu
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
- iHuman Institute, ShanghaiTech University, 201010, Shanghai, China
| | - Chenguang Wang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200125, Shanghai, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
- Department of Cardiology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guoping Fan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Suwen Zhao
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
- iHuman Institute, ShanghaiTech University, 201010, Shanghai, China
| | - Hanhui Ma
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Alex C Y Chang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200125, Shanghai, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
- Department of Cardiology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhi Li
- School of Physical Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Qian Bian
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200125, Shanghai, China.
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
| | - Chao-Po Lin
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
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14
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Rajan SS, Ebegboni VJ, Pichling P, Ludwig KR, Jones TL, Chari R, Tran A, Kruhlak MJ, Loncarek J, Caplen NJ. EWSR1's visual modalities are defined by its association with nucleic acids and RNA polymerase II. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553246. [PMID: 37645932 PMCID: PMC10462028 DOI: 10.1101/2023.08.16.553246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
We report systematic analysis of endogenous EWSR1's cellular organization. We demonstrate that EWSR1, which contains low complexity and nucleic acid binding domains, is present in cells in faster and slower-recovering fractions, indicative of a protein undergoing both rapid exchange and longer-term interactions. The employment of complementary high-resolution imaging approaches shows EWSR1 exists in in two visual modalities, a distributed state which is present throughout the nucleoplasm, and a concentrated state consistent with the formation of foci. Both EWSR1 visual modalities localize with nascent RNA. EWSR1 foci concentrate in regions of euchromatin, adjacent to protein markers of transcriptional activation, and significantly colocalize with phosphorylated RNA polymerase II. Interestingly, EWSR1 and FUS, another FET protein, exhibit distinct spatial organizations. Our results contribute to bridging the gap between our understanding of the biophysical and biochemical properties of FET proteins, including EWSR1, their functions as transcriptional regulators, and the participation of these proteins in tumorigenesis and neurodegenerative disease.
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Affiliation(s)
- Soumya Sundara Rajan
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health MD 20892, USA
| | - Vernon J. Ebegboni
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health MD 20892, USA
| | - Patricio Pichling
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health MD 20892, USA
| | - Katelyn R. Ludwig
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health MD 20892, USA
| | - Tamara L. Jones
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health MD 20892, USA
| | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program at the Frederick National Lab for Cancer Research, Frederick, MD 21702, USA
| | - Andy Tran
- CCR Confocal Microscopy Core Facility, Laboratory of Cancer Biology and Genetics, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michael J. Kruhlak
- CCR Confocal Microscopy Core Facility, Laboratory of Cancer Biology and Genetics, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jadranka Loncarek
- Centrosome Biology Section, Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA
| | - Natasha J. Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health MD 20892, USA
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15
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Qin X, Long Y, Bai X, Cao L, Yan H, Zhang K, Wang B, Wu X. The disordered C terminus of ALKBH5 promotes phase separation and paraspeckles assembly. J Biol Chem 2023; 299:105071. [PMID: 37474102 PMCID: PMC10457456 DOI: 10.1016/j.jbc.2023.105071] [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: 05/13/2023] [Revised: 06/19/2023] [Accepted: 07/12/2023] [Indexed: 07/22/2023] Open
Abstract
Paraspeckles (PS) are nuclear structures scaffolded by the long noncoding RNA NEAT1 and protein components such as NONO and SFPQ. We previously found that the upregulation of RNA N6-methyl-adenosine (m6A) demethylase ALKBH5 facilitates hypoxia-induced paraspeckle assembly through erasing m6A marks on NEAT1, thus stabilizing it. However, it remains unclear how these processes are spatiotemporally coordinated. Here we discover that ALKBH5 specifically binds to proteins in PS and forms phase-separated droplets that are incorporated into PS through its C-terminal intrinsically disordered region (cIDR). Upon exposure to hypoxia, rapid ALKBH5 condensation in PS induces m6A demethylation of NEAT1, which further facilitates PS formation before the upregulation of ALKBH5 expression. In cells expressing ALKBH5 lacking cIDR, PS fail to be formed in response to hypoxia, accompanied with insufficient m6A demethylation of NEAT1 and its destabilization. We also demonstrate that ALKBH5-cIDR is indispensable for hypoxia-induced effects such as cancer cell invasion. Therefore, our study has identified the role of ALKBH5 in phase separation as the molecular basis of the positive feedback loop for PS formation between ALKBH5 incorporation into PS and NEAT1 stabilization.
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Affiliation(s)
- Xiaoyang Qin
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Cell Biology, Tianjin Medical University, Tianjin, China
| | - Yan Long
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Cell Biology, Tianjin Medical University, Tianjin, China
| | - Xue Bai
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, China
| | - Lei Cao
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Cell Biology, Tianjin Medical University, Tianjin, China
| | - Han Yan
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Cell Biology, Tianjin Medical University, Tianjin, China
| | - Kai Zhang
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, China
| | - Bo Wang
- Department of Neurosurgery, Tianjin Huanhu Hospital, Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Neurosurgical Institute, Tianjin, China
| | - Xudong Wu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Cell Biology, Tianjin Medical University, Tianjin, China; Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.
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16
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Al-Refaie N, Padovani F, Binando F, Hornung J, Zhao Q, Towbin BD, Cenik ES, Stroustrup N, Schmoller KM, Cabianca DS. An mTOR/RNA pol I axis shapes chromatin architecture in response to fasting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.22.550032. [PMID: 37503059 PMCID: PMC10370172 DOI: 10.1101/2023.07.22.550032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Chromatin architecture is a fundamental mediator of genome function. Fasting is a major environmental cue across the animal kingdom. Yet, how it impacts on 3D genome organization is unknown. Here, we show that fasting induces a reversible and large-scale spatial reorganization of chromatin in C. elegans . This fasting-induced 3D genome reorganization requires inhibition of the nutrient-sensing mTOR pathway, a major regulator of ribosome biogenesis. Remarkably, loss of transcription by RNA Pol I, but not RNA Pol II nor Pol III, induces a similar 3D genome reorganization in fed animals, and prevents the restoration of the fed-state architecture upon restoring nutrients to fasted animals. Our work documents the first large-scale chromatin reorganization triggered by fasting and reveals that mTOR and RNA Pol I shape genome architecture in response to nutrients.
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17
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Schede HH, Natarajan P, Chakraborty AK, Shrinivas K. A model for organization and regulation of nuclear condensates by gene activity. Nat Commun 2023; 14:4152. [PMID: 37438363 DOI: 10.1038/s41467-023-39878-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 07/03/2023] [Indexed: 07/14/2023] Open
Abstract
Condensation by phase separation has recently emerged as a mechanism underlying many nuclear compartments essential for cellular functions. Nuclear condensates enrich nucleic acids and proteins, localize to specific genomic regions, and often promote gene expression. How diverse properties of nuclear condensates are shaped by gene organization and activity is poorly understood. Here, we develop a physics-based model to interrogate how spatially-varying transcription activity impacts condensate properties and dynamics. Our model predicts that spatial clustering of active genes can enable precise localization and de novo nucleation of condensates. Strong clustering and high activity results in aspherical condensate morphologies. Condensates can flow towards distant gene clusters and competition between multiple clusters lead to stretched morphologies and activity-dependent repositioning. Overall, our model predicts and recapitulates morphological and dynamical features of diverse nuclear condensates and offers a unified mechanistic framework to study the interplay between non-equilibrium processes, spatially-varying transcription, and multicomponent condensates in cell biology.
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Affiliation(s)
- Halima H Schede
- School of Life Sciences, École Polytechnique Fédérale Lausanne, CH-1015, Lausanne, Switzerland
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pradeep Natarajan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Krishna Shrinivas
- NSF-Simons Center for Mathematical & Statistical Analysis of Biology, Harvard University, Cambridge, MA, USA.
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18
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Li C, Li Z, Wu Z, Lu H. Phase separation in gene transcription control. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1052-1063. [PMID: 37265348 PMCID: PMC10415188 DOI: 10.3724/abbs.2023099] [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: 03/15/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023] Open
Abstract
Phase separation provides a general mechanism for the formation of biomolecular condensates, and it plays a vital role in regulating diverse cellular processes, including gene expression. Although the role of transcription factors and coactivators in regulating transcription has long been understood, how phase separation is involved in this process is just beginning to be explored. In this review, we highlight recent advance in elucidating the molecular mechanisms and functions of transcriptional condensates in gene expression control. We discuss the different condensates formed at each stage of the transcription cycle and how they are dynamically regulated in response to diverse cellular and extracellular cues that cause rapid changes in gene expression. Furthermore, we present new findings regarding the dysregulation of transcription condensates and their implications in human diseases.
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Affiliation(s)
- Chengyu Li
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell BiologyLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Zhuo Li
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell BiologyLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Zhibing Wu
- Department of OncologyAffiliated Zhejiang HospitalZhejiang University School of MedicineHangzhou310058China
| | - Huasong Lu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell BiologyLife Sciences InstituteZhejiang UniversityHangzhou310058China
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19
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Horii Y, Matsuda S, Toyota C, Morinaga T, Nakaya T, Tsuchiya S, Ohmuraya M, Hironaka T, Yoshiki R, Kasai K, Yamauchi Y, Takizawa N, Nagasaka A, Tanaka A, Kosako H, Nakaya M. VGLL3 is a mechanosensitive protein that promotes cardiac fibrosis through liquid-liquid phase separation. Nat Commun 2023; 14:550. [PMID: 36754961 PMCID: PMC9908974 DOI: 10.1038/s41467-023-36189-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 01/17/2023] [Indexed: 02/10/2023] Open
Abstract
Myofibroblasts cause tissue fibrosis by producing extracellular matrix proteins, such as collagens. Humoral factors like TGF-β, and matrix stiffness are important for collagen production by myofibroblasts. However, the molecular mechanisms regulating their ability to produce collagen remain poorly characterised. Here, we show that vestigial-like family member 3 (VGLL3) is specifically expressed in myofibroblasts from mouse and human fibrotic hearts and promotes collagen production. Further, substrate stiffness triggers VGLL3 translocation into the nucleus through the integrin β1-Rho-actin pathway. In the nucleus, VGLL3 undergoes liquid-liquid phase separation via its low-complexity domain and is incorporated into non-paraspeckle NONO condensates containing EWS RNA-binding protein 1 (EWSR1). VGLL3 binds EWSR1 and suppresses miR-29b, which targets collagen mRNA. Consistently, cardiac fibrosis after myocardial infarction is significantly attenuated in Vgll3-deficient mice, with increased miR-29b expression. Overall, our results reveal an unrecognised VGLL3-mediated pathway that controls myofibroblasts' collagen production, representing a novel therapeutic target for tissue fibrosis.
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Affiliation(s)
- Yuma Horii
- Department of Disease Control, Kyushu University, Fukuoka, Japan.,Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Shoichi Matsuda
- Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Chikashi Toyota
- Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Takumi Morinaga
- Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Takeo Nakaya
- Department of Pathology, Jichi Medical University, Tochigi, Japan
| | - Soken Tsuchiya
- Department of Pharmaceutical Biochemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Masaki Ohmuraya
- Department of Genetics, Hyogo College of Medicine, Hyogo, Japan
| | - Takanori Hironaka
- Department of Disease Control, Kyushu University, Fukuoka, Japan.,Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Ryo Yoshiki
- Department of Disease Control, Kyushu University, Fukuoka, Japan.,Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Kotaro Kasai
- Department of Disease Control, Kyushu University, Fukuoka, Japan.,Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuto Yamauchi
- Department of Disease Control, Kyushu University, Fukuoka, Japan.,Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Noburo Takizawa
- Department of Disease Control, Kyushu University, Fukuoka, Japan.,Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Akiomi Nagasaka
- Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Akira Tanaka
- Department of Pathology, Jichi Medical University, Tochigi, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, Japan
| | - Michio Nakaya
- Department of Disease Control, Kyushu University, Fukuoka, Japan. .,Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan. .,AMED-PRIME, Japan Agency for Medical Research and Development, Tokyo, Japan.
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20
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Stress and the CITI. Mol Cell 2022; 82:2730-2731. [PMID: 35931036 DOI: 10.1016/j.molcel.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Transcription-coupled cellular stress is associated with several physiological and pathological features, including membraneless biomolecular condensates. In the study by Yasuhara et al., the authors have described specific nuclear condensates in multiple cell types upon inhibition of RNA polymerase II transcription, discovered their main constituent proteins, and elucidated their functions.
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