1
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Kumar S, De T, Subramani J, Rangarajan A, Pal D. Combined analysis of somatic mutations and gene expression reveals nuclear speckles-associated enhanced stemness in gingivobuccal carcinoma under DNA damage response. Comput Biol Chem 2025; 119:108513. [PMID: 40424937 DOI: 10.1016/j.compbiolchem.2025.108513] [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: 03/18/2025] [Revised: 05/04/2025] [Accepted: 05/19/2025] [Indexed: 05/29/2025]
Abstract
Smokeless tobacco chewing habits in India lead to a high prevalence of Gingivobuccal oral squamous cell carcinoma (OSCC-GB). Cancer stem cells (CSCs) are a sub-population of cancer cells within a tumor with stem-like properties and are believed to contribute to tumor initiation, progression, increased resistance to drug therapy, and promote post-therapeutic cancer relapse. An RNA-sequencing data-based combined analysis of somatic mutations and gene expression was performed to explore the role of CSCs in disease progression using the novel Indian-origin OSCC-GB cell line 'IIOC019' from a patient with tobacco-chewing habit. The identified DNA damage-related known mutational signature (1 bp T/(A) nucleotide insertions and C>T mutations) indicates the impact of smokeless tobacco-related carcinogens in the IIOC019 cell line. The differentially expressed somatic variants, functional impact predictions, and survival analysis reveal the role of DNA damage response (DDR)-related genes in OSCC-GB, with the SON gene as a significant player. The study suggests that the loss-of-function in a somatic variant of the SON gene is linked to nuclear speckles-associated enhanced stemness and increased risk of disease progression in OSCC-GB under DDR conditions. The newly identified CSC-associated somatic variants appear to promote cancer spread, local recurrence, and resistance to chemotherapy or radiotherapy, contributing to the high mortality rates among Indian OSCC-GB patients.
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Affiliation(s)
- Sachendra Kumar
- IISc Mathematics Initiative, Indian Institute of Science, Bengaluru, Karnataka 560 012, India; Computational and Data Sciences, Indian Institute of Science, Bengaluru, Karnataka 560 012, India
| | - Tamasa De
- Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560 012, India
| | - Janavi Subramani
- Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560 012, India
| | - Annapoorni Rangarajan
- Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, Karnataka 560 012, India.
| | - Debnath Pal
- Computational and Data Sciences, Indian Institute of Science, Bengaluru, Karnataka 560 012, India.
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2
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Kodali S, Sands CM, Guo L, Huang Y, Di Stefano B. Biomolecular condensates in immune cell fate. Nat Rev Immunol 2025:10.1038/s41577-025-01130-z. [PMID: 39875604 DOI: 10.1038/s41577-025-01130-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2025] [Indexed: 01/30/2025]
Abstract
Fate decisions during immune cell development require temporally precise changes in gene expression. Evidence suggests that the dynamic modulation of these changes is associated with the formation of diverse, membrane-less nucleoprotein assemblies that are termed biomolecular condensates. These condensates are thought to orchestrate fate-determining transcriptional and post-transcriptional processes by locally and transiently concentrating DNA or RNA molecules alongside their regulatory proteins. Findings have established a link between condensate formation and the gene regulatory networks that ensure the proper development of immune cells. Conversely, condensate dysregulation has been linked to impaired immune cell fates, including ageing and malignant transformation. This Review explores the putative mechanistic links between condensate assembly and the gene regulatory frameworks that govern normal and pathological development in the immune system.
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Affiliation(s)
- Srikanth Kodali
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Caroline M Sands
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Lei Guo
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
- Department of Translational Medical Sciences, School of Medicine, Texas A&M University, Houston, TX, USA
| | - Yun Huang
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
- Department of Translational Medical Sciences, School of Medicine, Texas A&M University, Houston, TX, USA
| | - Bruno Di Stefano
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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3
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García-Blay Ó, Hu X, Wassermann CL, van Bokhoven T, Struijs FMB, Hansen MMK. Multimodal screen identifies noise-regulatory proteins. Dev Cell 2025; 60:133-151.e12. [PMID: 39406240 DOI: 10.1016/j.devcel.2024.09.015] [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: 11/16/2023] [Revised: 06/11/2024] [Accepted: 09/12/2024] [Indexed: 01/11/2025]
Abstract
Gene-expression noise can influence cell-fate choices across pathology and physiology. However, a crucial question persists: do regulatory proteins or pathways exist that control noise independently of mean expression levels? Our integrative approach, combining single-cell RNA sequencing with proteomics and regulator enrichment analysis, identifies 32 putative noise regulators. SON, a nuclear speckle-associated protein, alters transcriptional noise without changing mean expression levels. Furthermore, SON's noise control can propagate to the protein level. Long-read and total RNA sequencing shows that SON's noise control does not significantly change isoform usage or splicing efficiency. Moreover, SON depletion reduces state switching in pluripotent mouse embryonic stem cells and impacts their fate choice during differentiation. Collectively, we demonstrate a class of proteins that control noise orthogonally to mean expression levels. This work serves as a proof of concept that can identify other functional noise regulators throughout development and disease progression.
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Affiliation(s)
- Óscar García-Blay
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Oncode Institute, Nijmegen, the Netherlands
| | - Xinyu Hu
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Oncode Institute, Nijmegen, the Netherlands
| | - Christin L Wassermann
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Tom van Bokhoven
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Fréderique M B Struijs
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Maike M K Hansen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Oncode Institute, Nijmegen, the Netherlands.
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4
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Soggia G, ElMaghloob Y, Boromangnaeva AK, Al Jord A. Mechanical Remodeling of Nuclear Biomolecular Condensates. Physiology (Bethesda) 2025; 40:0. [PMID: 39109673 DOI: 10.1152/physiol.00027.2024] [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: 06/03/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 08/15/2024] Open
Abstract
Organism health relies on cell proliferation, migration, and differentiation. These universal processes depend on cytoplasmic reorganization driven notably by the cytoskeleton and its force-generating motors. Their activity generates forces that mechanically agitate the cell nucleus and its interior. New evidence from reproductive cell biology revealed that these cytoskeletal forces can be tuned to remodel nuclear membraneless compartments, known as biomolecular condensates, and regulate their RNA processing function for the success of subsequent cell division that is critical for fertility. Both cytoskeletal and nuclear condensate reorganization are common to numerous physiological and pathological contexts, raising the possibility that mechanical remodeling of nuclear condensates may be a much broader mechanism regulating their function. Here, we review this newfound mechanism of condensate remodeling and venture into the contexts of health and disease where it may be relevant, with a focus on reproduction, cancer, and premature aging.
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Affiliation(s)
- Giulia Soggia
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Yasmin ElMaghloob
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Systems Biology and Immunology Lab, Children's Cancer Hospital Egypt, Cairo, Egypt
| | | | - Adel Al Jord
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
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5
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Lederer AR, Leonardi M, Talamanca L, Bobrovskiy DM, Herrera A, Droin C, Khven I, Carvalho HJF, Valente A, Dominguez Mantes A, Mulet Arabí P, Pinello L, Naef F, La Manno G. Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations. Nat Methods 2024; 21:2271-2286. [PMID: 39482463 PMCID: PMC11621032 DOI: 10.1038/s41592-024-02471-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 09/15/2024] [Indexed: 11/03/2024]
Abstract
Across biological systems, cells undergo coordinated changes in gene expression, resulting in transcriptome dynamics that unfold within a low-dimensional manifold. While low-dimensional dynamics can be extracted using RNA velocity, these algorithms can be fragile and rely on heuristics lacking statistical control. Moreover, the estimated vector field is not dynamically consistent with the traversed gene expression manifold. To address these challenges, we introduce a Bayesian model of RNA velocity that couples velocity field and manifold estimation in a reformulated, unified framework, identifying the parameters of an explicit dynamical system. Focusing on the cell cycle, we implement VeloCycle to study gene regulation dynamics on one-dimensional periodic manifolds and validate its ability to infer cell cycle periods using live imaging. We also apply VeloCycle to reveal speed differences in regionally defined progenitors and Perturb-seq gene knockdowns. Overall, VeloCycle expands the single-cell RNA sequencing analysis toolkit with a modular and statistically consistent RNA velocity inference framework.
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Affiliation(s)
- Alex R Lederer
- Laboratory of Brain Development and Biological Data Science, Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Maxine Leonardi
- Laboratory of Computational and Systems Biology, Institute of Bioengineering, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Lorenzo Talamanca
- Laboratory of Computational and Systems Biology, Institute of Bioengineering, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Daniil M Bobrovskiy
- Laboratory of Brain Development and Biological Data Science, Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Antonio Herrera
- Laboratory of Brain Development and Biological Data Science, Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Colas Droin
- Laboratory of Computational and Systems Biology, Institute of Bioengineering, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Irina Khven
- Laboratory of Brain Development and Biological Data Science, Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Hugo J F Carvalho
- Laboratory of Computational and Systems Biology, Institute of Bioengineering, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alessandro Valente
- Laboratory of Brain Development and Biological Data Science, Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Albert Dominguez Mantes
- Laboratory of Brain Development and Biological Data Science, Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Laboratory of Bioimage Analysis and Computational Microscopy, Institute of Bioengineering, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Pau Mulet Arabí
- Laboratory of Computational and Systems Biology, Institute of Bioengineering, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Luca Pinello
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Felix Naef
- Laboratory of Computational and Systems Biology, Institute of Bioengineering, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Gioele La Manno
- Laboratory of Brain Development and Biological Data Science, Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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6
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Dion W, Zhu B. Basic research and opportunities for translational advancement in the field of mammalian ∼12-hour ultradian chronobiology. Front Physiol 2024; 15:1497836. [PMID: 39633646 PMCID: PMC11614809 DOI: 10.3389/fphys.2024.1497836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Accepted: 10/28/2024] [Indexed: 12/07/2024] Open
Abstract
Repetitive variations, such as oscillation, are ubiquitous in biology. In this mini review, we present a general summary of the ∼24 h circadian clock and provide a fundamental overview of another biological timekeeper that maintains ∼12 h oscillations. This ∼12 h oscillator is proposed to function independently of the circadian clock to regulate ultradian biological rhythms relevant to both protein homeostasis and liver health. Recent studies exploring these ∼12 h rhythms in humans are discussed, followed by our proposal that mammary gland physiology represents a promising area for further research. We conclude by highlighting potential translational applications in ∼12 h ultradian chronobiology.
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Affiliation(s)
- William Dion
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, United States
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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7
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Song YJ, Shinn MK, Bangru S, Wang Y, Sun Q, Hao Q, Chaturvedi P, Freier SM, Perez-Pinera P, Nelson ER, Belmont AS, Guttman M, Prasanth SG, Kalsotra A, Pappu RV, Prasanth KV. Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.31.621310. [PMID: 39554052 PMCID: PMC11565956 DOI: 10.1101/2024.10.31.621310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
Abstract
Hypoxia-induced alternative splicing (AS) regulates tumor progression and metastasis. Little is known about how such AS is controlled and whether higher-order genome and nuclear domain (ND) organizations dictate these processes. We observe that hypoxia-responsive alternatively spliced genes position near nuclear speckle (NS), the ND that enhances splicing efficiency. NS-resident MALAT1 long noncoding RNA, induced in response to hypoxia, regulates hypoxia-responsive AS. MALAT1 achieves this by organizing the SR-family of splicing factor, SRSF1, near NS and regulating the binding of SRSF1 to pre-mRNAs. Mechanistically, MALAT1 enhances the recruitment of SRSF1 to elongating RNA polymerase II (pol II) by promoting the formation of phase-separated condensates of SRSF1, which are preferentially recognized by pol II. During hypoxia, MALAT1 regulates spatially organized AS by establishing a threshold SRSF1 concentration near NSs, potentially by forming condensates, critical for pol II-mediated recruitment of SRSF1 to pre-mRNAs.
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8
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Dion W, Tao Y, Chambers M, Zhao S, Arbuckle RK, Sun M, Kubra S, Jamal I, Nie Y, Ye M, Larsen MB, Camarco D, Ickes E, DuPont C, Wang H, Wang B, Liu S, Pi S, Chen BB, Chen Y, Chen X, Zhu B. SON-dependent nuclear speckle rejuvenation alleviates proteinopathies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590103. [PMID: 38659924 PMCID: PMC11042303 DOI: 10.1101/2024.04.18.590103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Current treatments targeting individual protein quality control have limited efficacy in alleviating proteinopathies, highlighting the prerequisite for a common upstream druggable target capable of global proteostasis modulation. Building on our prior research establishing nuclear speckles as a pivotal membrane-less organelle responsible for global proteostasis transcriptional control, we aim to alleviate proteinopathies through nuclear speckle rejuvenation. We identified pyrvinium pamoate as a small-molecule nuclear speckle rejuvenator that enhances protein quality control while suppressing YAP1 signaling via decreasing the surface/interfacial tension of nuclear speckle condensates through interaction with the intrinsically disordered region of nuclear speckle scaffold protein SON. In pre-clinical models, nanomolar pyrvinium pamoate alleviated retina degeneration and reduced tauopathy by promoting autophagy and ubiquitin-proteasome system in a SON-dependent manner without causing cellular stress. Aberrant nuclear speckle morphology, reduced protein quality control and increased YAP1 activity were also observed in human tauopathies. Our study uncovers novel therapeutic targets for tackling protein misfolding disorders within an expanded proteostasis framework encompassing nuclear speckles and YAP1.
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Affiliation(s)
- William Dion
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Yuren Tao
- Department of Neuroscience, School of Medicine, University of California, San Diego, CA, U.S.A
| | - Maci Chambers
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Shanshan Zhao
- Department of Neuroscience, School of Medicine, University of California, San Diego, CA, U.S.A
| | - Riley K. Arbuckle
- Department of Ophthalmology, University of Pittsburgh School of Medicine, PA, U.S.A
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Michelle Sun
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Syeda Kubra
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Imran Jamal
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Yuhang Nie
- Department of Neuroscience, School of Medicine, University of California, San Diego, CA, U.S.A
| | - Megan Ye
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Mads B. Larsen
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Daniel Camarco
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Eleanor Ickes
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Claire DuPont
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Haokun Wang
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Bingjie Wang
- Department of Ophthalmology, University of Pittsburgh School of Medicine, PA, U.S.A
| | - Silvia Liu
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, U.S.A
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Shaohua Pi
- Department of Ophthalmology, University of Pittsburgh School of Medicine, PA, U.S.A
| | - Bill B Chen
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Yuanyuan Chen
- Department of Ophthalmology, University of Pittsburgh School of Medicine, PA, U.S.A
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, PA, U.S.A
| | - Xu Chen
- Department of Neuroscience, School of Medicine, University of California, San Diego, CA, U.S.A
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, U.S.A
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
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9
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Noguchi K, Suzuki H, Abe R, Horiuchi K, Onoguchi-Mizutani R, Akimitsu N, Ogawa S, Akiyama T, Ike Y, Ino Y, Kimura Y, Ryo A, Doi H, Tanaka F, Suzuki Y, Toyoda A, Yamaguchi Y, Takahashi H. Multi-omics analysis using antibody-based in situ biotinylation technique suggests the mechanism of Cajal body formation. Cell Rep 2024; 43:114734. [PMID: 39283744 DOI: 10.1016/j.celrep.2024.114734] [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: 08/20/2023] [Revised: 04/30/2024] [Accepted: 08/23/2024] [Indexed: 09/28/2024] Open
Abstract
Membrane-less subcellular compartments play important roles in various cellular functions. Although techniques exist to identify components of cellular bodies, a comprehensive method for analyzing both static and dynamic states has not been established. Here, we apply an antibody-based in situ biotinylation proximity-labeling technique to identify components of static and dynamic nuclear bodies. Using this approach, we comprehensively identify DNA, RNA, and protein components of Cajal bodies (CBs) and then clarify their interactome. By inhibiting transcription, we capture dynamic changes in CBs. Our analysis reveals that nascent small nuclear RNAs (snRNAs) transcribed in CBs contribute to CB formation by assembling RNA-binding proteins, including frontotemporal dementia-related proteins, RNA-binding motif proteins, and heterogeneous nuclear ribonucleoproteins.
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Affiliation(s)
- Keisuke Noguchi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Hidefumi Suzuki
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Ryota Abe
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Keiko Horiuchi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Rena Onoguchi-Mizutani
- R&D Department, Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Nobuyoshi Akimitsu
- R&D Department, Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Shintaro Ogawa
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Tomohiko Akiyama
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Yoko Ike
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Yoko Ino
- Advance Medical Research Center, Yokohama City University, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 216-0004, Japan
| | - Yayoi Kimura
- Advance Medical Research Center, Yokohama City University, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 216-0004, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 216-0004, Japan; Department of Virology III, National Institute of Infectious Diseases, 4-7-1, Gakuen Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Fumiaki Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Yuki Yamaguchi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, Kanagawa 226-8501, Japan.
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan.
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10
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Zhou S, Lizarazo S, Mouli L, Chorghade S, Cheng R, Rajendra KC, Kalsotra A, Van Bortle K. Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601767. [PMID: 39005375 PMCID: PMC11245037 DOI: 10.1101/2024.07.02.601767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
RNA polymerase III (Pol III) activity in cancer is linked to the production of small noncoding (nc)RNAs that are otherwise silent in most tissues. snaR-A (small NF90-associated RNA isoform A) - a hominid-specific ncRNA shown to enhance cell proliferation, migration, and invasion - is a cancer-emergent Pol III product that remains largely uncharacterized despite promoting growth phenotypes. Here, we applied a combination of genomic and biochemical approaches to study the biogenesis and subsequent protein interactions of snaR-A and to better understand its role as a putative driver of cancer progression. By profiling the chromatin landscapes across a multitude of primary tumor types, we show that predicted snaR-A upregulation is broadly linked with unfavorable outcomes among cancer patients. At the molecular level, we unexpectedly discover widespread interactions between snaR-A and mRNA splicing factors, including SF3B2 - a core component of the U2 small nuclear ribonucleoprotein (snRNP). We find that SF3B2 levels are sensitive to high snaR-A abundance and that depletion of snaR-A alone is sufficient to decrease intron retention levels across subpopulations of mRNA enriched for U2 snRNP occupancy. snaR-A sensitive genes are characterized by high GC content, close spatial proximity to nuclear bodies concentrated in pre-mRNA splicing factors, and functional enrichment for proteins involved in deacetylation and autophagy. We highlight examples of splicing misregulation and increased protein levels following snaR-A depletion for a wide-ranging set of factors, suggesting snaR-A-driven splicing defects may have far-reaching effects that re-shape the cellular proteome. These findings clarify the molecular activities and consequences of snaR-A in cancer, and altogether establish a novel mechanism through which Pol III overactivity may promote tumorigenesis.
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Affiliation(s)
- Sihang Zhou
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Simon Lizarazo
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Leela Mouli
- School of Molecular and Cellular Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Sandip Chorghade
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruiying Cheng
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - K C Rajendra
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Kevin Van Bortle
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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11
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Regan-Fendt KE, Izumi K. Nuclear speckleopathies: developmental disorders caused by variants in genes encoding nuclear speckle proteins. Hum Genet 2024; 143:529-544. [PMID: 36929417 DOI: 10.1007/s00439-023-02540-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/17/2023] [Indexed: 03/18/2023]
Abstract
Nuclear speckles are small, membrane-less organelles that reside within the nucleus. Nuclear speckles serve as a regulatory hub coordinating complex RNA metabolism steps including gene transcription, pre-mRNA splicing, RNA modifications, and mRNA nuclear export. Reflecting the importance of proper nuclear speckle function in regulating normal human development, an increasing number of genetic disorders have been found to result from mutations in the genes encoding nuclear speckle proteins. To denote this growing class of genetic disorders, we propose "nuclear speckleopathies". Notably, developmental disabilities are commonly seen in individuals with nuclear speckleopathies, suggesting the particular importance of nuclear speckles in ensuring normal neurocognitive development. In this review article, a general overview of nuclear speckle function, and the current knowledge of the mechanisms underlying some nuclear speckleopathies, such as ZTTK syndrome, NKAP-related syndrome, TARP syndrome, and TAR syndrome, are discussed. These nuclear speckleopathies represent valuable models to understand the basic function of nuclear speckles and how its functional defects result in human developmental disorders.
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Affiliation(s)
- Kelly E Regan-Fendt
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd., Philadelphia, PA, USA
| | - Kosuke Izumi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd., Philadelphia, PA, USA.
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
- Laboratory of Rare Disease Research, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.
- Division of Genetics and Metabolism, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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12
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Vukadin L, Park B, Mohamed M, Li H, Elkholy A, Torrelli-Diljohn A, Kim JH, Jeong K, Murphy JM, Harvey CA, Dunlap S, Gehrs L, Lee H, Kim HG, Sah JP, Lee SN, Stanford D, Barrington RA, Foote JB, Sorace AG, Welner RS, Hildreth BE, Lim STS, Ahn EYE. A mouse model of Zhu-Tokita-Takenouchi-Kim syndrome reveals indispensable SON functions in organ development and hematopoiesis. JCI Insight 2024; 9:e175053. [PMID: 38290089 PMCID: PMC10972584 DOI: 10.1172/jci.insight.175053] [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: 09/06/2023] [Accepted: 01/25/2024] [Indexed: 02/01/2024] Open
Abstract
Rare diseases are underrepresented in biomedical research, leading to insufficient awareness. Zhu-Tokita-Takenouchi-Kim (ZTTK) syndrome is a rare disease caused by genetic alterations that result in heterozygous loss of function of SON. While patients with ZTTK syndrome live with numerous symptoms, the lack of model organisms hampers our understanding of SON and this complex syndrome. Here, we developed Son haploinsufficiency (Son+/-) mice as a model of ZTTK syndrome and identified the indispensable roles of Son in organ development and hematopoiesis. Son+/- mice recapitulated clinical symptoms of ZTTK syndrome, including growth retardation, cognitive impairment, skeletal abnormalities, and kidney agenesis. Furthermore, we identified hematopoietic abnormalities in Son+/- mice, including leukopenia and immunoglobulin deficiency, similar to those observed in human patients. Surface marker analyses and single-cell transcriptome profiling of hematopoietic stem and progenitor cells revealed that Son haploinsufficiency shifted cell fate more toward the myeloid lineage but compromised lymphoid lineage development by reducing genes required for lymphoid and B cell lineage specification. Additionally, Son haploinsufficiency caused inappropriate activation of erythroid genes and impaired erythropoiesis. These findings highlight the importance of the full gene expression of Son in multiple organs. Our model serves as an invaluable research tool for this rare disease and related disorders associated with SON dysfunction.
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Affiliation(s)
- Lana Vukadin
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Bohye Park
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Mostafa Mohamed
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Huashi Li
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Amr Elkholy
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Alex Torrelli-Diljohn
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jung-Hyun Kim
- Metastasis Branch, Division of Cancer Biology, National Cancer Center, Goyang, Gyeonggi-do, South Korea
| | - Kyuho Jeong
- Department of Medicine, College of Medicine, Dongguk University, Gyeongju, South Korea
| | - James M. Murphy
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Caitlin A. Harvey
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Sophia Dunlap
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Leah Gehrs
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Hanna Lee
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Hyung-Gyoon Kim
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Jay Prakash Sah
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | | | - Denise Stanford
- Department of Medicine, Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Robert A. Barrington
- Department of Microbiology and Immunology, College of Medicine, University of South Alabama, Mobile, Alabama, USA
| | | | - Anna G. Sorace
- Department of Radiology and
- O’Neal Comprehensive Cancer Center, and
| | - Robert S. Welner
- O’Neal Comprehensive Cancer Center, and
- Department of Medicine, Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Blake E. Hildreth
- Department of Pathology, Division of Molecular and Cellular Pathology, and
- O’Neal Comprehensive Cancer Center, and
| | - Ssang-Taek Steve Lim
- Department of Pathology, Division of Molecular and Cellular Pathology, and
- O’Neal Comprehensive Cancer Center, and
| | - Eun-Young Erin Ahn
- Department of Pathology, Division of Molecular and Cellular Pathology, and
- O’Neal Comprehensive Cancer Center, and
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13
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Dumelie JG, Chen Q, Miller D, Attarwala N, Gross SS, Jaffrey SR. Biomolecular condensates create phospholipid-enriched microenvironments. Nat Chem Biol 2024; 20:302-313. [PMID: 37973889 PMCID: PMC10922641 DOI: 10.1038/s41589-023-01474-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/08/2023] [Indexed: 11/19/2023]
Abstract
Proteins and RNA can phase separate from the aqueous cellular environment to form subcellular compartments called condensates. This process results in a protein-RNA mixture that is chemically different from the surrounding aqueous phase. Here, we use mass spectrometry to characterize the metabolomes of condensates. To test this, we prepared mixtures of phase-separated proteins and extracts of cellular metabolites and identified metabolites enriched in the condensate phase. Among the most condensate-enriched metabolites were phospholipids, due primarily to the hydrophobicity of their fatty acyl moieties. We found that phospholipids can alter the number and size of phase-separated condensates and in some cases alter their morphology. Finally, we found that phospholipids partition into a diverse set of endogenous condensates as well as artificial condensates expressed in cells. Overall, these data show that many condensates are protein-RNA-lipid mixtures with chemical microenvironments that are ideally suited to facilitate phospholipid biology and signaling.
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Affiliation(s)
- Jason G Dumelie
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Qiuying Chen
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Dawson Miller
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Nabeel Attarwala
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Steven S Gross
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA.
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14
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Cornelissen G, Gubin D, Otsuka K. Disease Conditions. CHRONOBIOLOGY AND CHRONOMEDICINE 2024:455-475. [DOI: 10.1039/bk9781839167553-00455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/07/2024]
Abstract
Since clock genes are involved in all physiological systems, their role in most disease conditions is not surprising. To complement the information reviewed in Part II for each physiological system considered separately, this chapter illustrates the interdigitating network of interactions taking place within multiple physiological systems in any given disease condition. Circadian disruption, a common factor in disease, is almost inseparable from disturbed sleep, which is present in conditions ranging from psychological to cardio-metabolic and neurodegenerative conditions. Sleep disruption also modifies the immune system. Herein, we highlight the pervasive role played by the circadian system in pathology based on a few examples of selected disease conditions, including some sleep disorders, mental disorders, neurodegenerative conditions, and cancer.
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Affiliation(s)
- Germaine Cornelissen
- aHalberg Chronobiology Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Denis Gubin
- bTyumen State Medical University, Tyumen, Russia
- cTyumen Cardiology Research Center, Tomsk National Research Medical Center, Russian Academy of Science, Tomsk, Russia
| | - Kuniaki Otsuka
- aHalberg Chronobiology Center, University of Minnesota, Minneapolis, Minnesota, USA
- dExecutive Medical Center, Totsuka Royal Clinic, Tokyo Women’s Medical University, Tokyo, Japan
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15
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Lederer AR, Leonardi M, Talamanca L, Herrera A, Droin C, Khven I, Carvalho HJF, Valente A, Mantes AD, Arabí PM, Pinello L, Naef F, Manno GL. Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576093. [PMID: 38328127 PMCID: PMC10849531 DOI: 10.1101/2024.01.18.576093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Across a range of biological processes, cells undergo coordinated changes in gene expression, resulting in transcriptome dynamics that unfold within a low-dimensional manifold. Single-cell RNA-sequencing (scRNA-seq) only measures temporal snapshots of gene expression. However, information on the underlying low-dimensional dynamics can be extracted using RNA velocity, which models unspliced and spliced RNA abundances to estimate the rate of change of gene expression. Available RNA velocity algorithms can be fragile and rely on heuristics that lack statistical control. Moreover, the estimated vector field is not dynamically consistent with the traversed gene expression manifold. Here, we develop a generative model of RNA velocity and a Bayesian inference approach that solves these problems. Our model couples velocity field and manifold estimation in a reformulated, unified framework, so as to coherently identify the parameters of an autonomous dynamical system. Focusing on the cell cycle, we implemented VeloCycle to study gene regulation dynamics on one-dimensional periodic manifolds and validated using live-imaging its ability to infer actual cell cycle periods. We benchmarked RNA velocity inference with sensitivity analyses and demonstrated one- and multiple-sample testing. We also conducted Markov chain Monte Carlo inference on the model, uncovering key relationships between gene-specific kinetics and our gene-independent velocity estimate. Finally, we applied VeloCycle to in vivo samples and in vitro genome-wide Perturb-seq, revealing regionally-defined proliferation modes in neural progenitors and the effect of gene knockdowns on cell cycle speed. Ultimately, VeloCycle expands the scRNA-seq analysis toolkit with a modular and statistically rigorous RNA velocity inference framework.
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16
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Sun W, Zhang X, Bai X, Du K, Chen L, Wang H, Jia X, Lai S. miR-889-3p Facilitates the Browning Process of White Adipocyte Precursors by Targeting the SON Gene. Int J Mol Sci 2023; 24:17580. [PMID: 38139409 PMCID: PMC10743546 DOI: 10.3390/ijms242417580] [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: 10/31/2023] [Revised: 12/02/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
It is well-established that beige/brown adipose tissue can dissipate stored energy through thermogenesis; hence, the browning of white adipocytes (WAT) has garnered significant interest in contemporary research. Our preceding investigations have identified a marked downregulation of miR-889-3p concurrent with the natural maturation of brown adipose tissue. However, the specific role and underlying molecular mechanisms of miR-889-3p in the browning process of white adipose tissue warrant further elucidation. In this research, we initially delved into the potential role of miR-889-3p in preadipocyte growth via flow cytometry and CCK-8 assay, revealing that miR-889-3p can stimulate preadipocyte growth. To validate the potential contribution of miR-889-3p in the browning process of white adipose tissue, we established an in vitro rabbit white adipocyte browning induction, which exhibited a significant upregulation of miR-889-3p during the browning process. RT-qPCR and Western blot analysis indicated that miR-889-3p overexpression significantly amplified the mRNA levels of UCP1, PRDM16, and CIDEA, as well as UCP1 protein levels. Furthermore, miR-889-3p overexpression fostered intracellular triglyceride accumulation. Conversely, the downregulation of miR-889-3p hindered the browning of rabbit preadipocytes. Subsequently, based on target gene prediction and luciferase reporter gene determination, we demonstrated that miR-889-3p directly targets the 3'-UTR region of SON. Lastly, we observed that inhibiting SON could facilitate the browning of rabbit preadipocytes. In conclusion, our findings suggest that miR-889-3p facilitates the browning process of white adipocyte precursors by specifically targeting the SON gene.
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Affiliation(s)
- Wenqiang Sun
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China; (W.S.); (X.Z.); (X.B.); (K.D.); (L.C.); (H.W.); (X.J.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611134, China
| | - Xiaoxiao Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China; (W.S.); (X.Z.); (X.B.); (K.D.); (L.C.); (H.W.); (X.J.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611134, China
| | - Xue Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China; (W.S.); (X.Z.); (X.B.); (K.D.); (L.C.); (H.W.); (X.J.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611134, China
| | - Kun Du
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China; (W.S.); (X.Z.); (X.B.); (K.D.); (L.C.); (H.W.); (X.J.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611134, China
| | - Li Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China; (W.S.); (X.Z.); (X.B.); (K.D.); (L.C.); (H.W.); (X.J.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611134, China
| | - Haoding Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China; (W.S.); (X.Z.); (X.B.); (K.D.); (L.C.); (H.W.); (X.J.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611134, China
| | - Xianbo Jia
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China; (W.S.); (X.Z.); (X.B.); (K.D.); (L.C.); (H.W.); (X.J.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611134, China
| | - Songjia Lai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China; (W.S.); (X.Z.); (X.B.); (K.D.); (L.C.); (H.W.); (X.J.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611134, China
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17
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Wang C, Xu L, Du C, Yun H, Wang K, Liu H, Ye M, Fan J, Zhou Y, Cheng H. CDK11 requires a critical activator SAP30BP to regulate pre-mRNA splicing. EMBO J 2023; 42:e114051. [PMID: 38059508 PMCID: PMC10711644 DOI: 10.15252/embj.2023114051] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 12/08/2023] Open
Abstract
CDK11 is an emerging druggable target for cancer therapy due to its prevalent roles in phosphorylating critical transcription and splicing factors and in facilitating cell cycle progression in cancer cells. Like other cyclin-dependent kinases, CDK11 requires its cognate cyclin, cyclin L1 or cyclin L2, for activation. However, little is known about how CDK11 activities might be modulated by other regulators. In this study, we show that CDK11 forms a tight complex with cyclins L1/L2 and SAP30BP, the latter of which is a poorly characterized factor. Acute degradation of SAP30BP mirrors that of CDK11 in causing widespread and strong defects in pre-mRNA splicing. Furthermore, we demonstrate that SAP30BP facilitates CDK11 kinase activities in vitro and in vivo, through ensuring the stabilities and the assembly of cyclins L1/L2 with CDK11. Together, these findings uncover SAP30BP as a critical CDK11 activator that regulates global pre-mRNA splicing.
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Affiliation(s)
- Changshou Wang
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
| | - Lin Xu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
| | - Chen Du
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Hubei Key Laboratory of Cell HomeostasisWuhan UniversityWuhanChina§
| | - Hao Yun
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
| | - Keyun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalianChina
| | - Hui Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouChina
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalianChina
| | - Jing Fan
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
| | - Yu Zhou
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Hubei Key Laboratory of Cell HomeostasisWuhan UniversityWuhanChina§
| | - Hong Cheng
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouChina
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18
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Vukadin L, Park B, Mohamed M, Li H, Elkholy A, Torrelli-Diljohn A, Kim JH, Jeong K, Murphy JM, Harvey CA, Dunlap S, Gehrs L, Lee H, Kim HG, Lee SN, Stanford D, Barrington RA, Foote JB, Sorace AG, Welner RS, Hildreth BE, Lim STS, Ahn EYE. A mouse model of ZTTK syndrome reveals indispensable SON functions in organ development and hematopoiesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.19.567732. [PMID: 38014320 PMCID: PMC10680872 DOI: 10.1101/2023.11.19.567732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Rare diseases are underrepresented in biomedical research, leading to insufficient awareness. Zhu-Tokita-Takenouchi-Kim (ZTTK) syndrome is a rare disease caused by genetic alterations that result in heterozygous loss-of-function of SON. While ZTTK syndrome patients suffer from numerous symptoms, the lack of model organisms hamper our understanding of both SON and this complex syndrome. Here, we developed Son haploinsufficiency (Son+/-) mice as a model of ZTTK syndrome and identified the indispensable roles of Son in organ development and hematopoiesis. Son+/- mice recapitulated clinical symptoms of ZTTK syndrome, including growth retardation, cognitive impairment, skeletal abnormalities, and kidney agenesis. Furthermore, we identified hematopoietic abnormalities in Son+/- mice, similar to those observed in human patients. Surface marker analyses and single-cell transcriptome profiling of hematopoietic stem and progenitor cells revealed that Son haploinsufficiency inclines cell fate toward the myeloid lineage but compromises lymphoid lineage development by reducing key genes required for lymphoid and B cell lineage specification. Additionally, Son haploinsufficiency causes inappropriate activation of erythroid genes and impaired erythroid maturation. These findings highlight the importance of the full gene dosage of Son in organ development and hematopoiesis. Our model serves as an invaluable research tool for this rare disease and related disorders associated with SON dysfunction.
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Affiliation(s)
- Lana Vukadin
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Bohye Park
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mostafa Mohamed
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Huashi Li
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Amr Elkholy
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alex Torrelli-Diljohn
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jung-Hyun Kim
- Metastasis Branch, Division of Cancer Biology, National Cancer Center, Goyang, Gyeonggi-do, Korea
| | - Kyuho Jeong
- Department of Medicine, College of Medicine, Dongguk University, Gyeongju, Korea
| | - James M Murphy
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Caitlin A. Harvey
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sophia Dunlap
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Leah Gehrs
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hanna Lee
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hyung-Gyoon Kim
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Seth N. Lee
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Denise Stanford
- Department of Medicine, Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert A. Barrington
- Department of Microbiology and Immunology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Jeremy B. Foote
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anna G. Sorace
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert S. Welner
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Medicine, Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Blake E. Hildreth
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ssang-Taek Steve Lim
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Eun-Young Erin Ahn
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
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19
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Otsuka K, Murakami S, Okajima K, Shibata K, Kubo Y, Gubin DG, Beaty LA, Cornelissen G. Appropriate Circadian-Circasemidian Coupling Protects Blood Pressure from Morning Surge and Promotes Human Resilience and Wellbeing. Clin Interv Aging 2023; 18:755-769. [PMID: 37193339 PMCID: PMC10183193 DOI: 10.2147/cia.s398957] [Citation(s) in RCA: 3] [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: 11/24/2022] [Accepted: 05/02/2023] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND Blood pressure (BP) variability is involved in the appraisal of threat and safety, and can serve as a potential marker of psychological resilience against stress. The relationship between biological rhythms of BP and resilience was cross-sectionally assessed by 7-day/24-hour chronobiologic screening in a rural Japanese community (Tosa), with focus on the 12-hour component and the "circadian-circasemidian coupling" of systolic (S) BP. SUBJECTS AND METHODS Tosa residents (N = 239, 147 women, 23-74 years), free of anti-hypertensive medication, completed 7-day/24-hour ambulatory BP monitoring. The circadian-circasemidian coupling was determined individually by computing the difference between the circadian phase and the circasemidian morning-phase of SBP. Participants were classified into three groups: those with a short coupling interval of about 4.5 hours (Group A), those with an intermediate coupling interval of about 6.0 hours (Group B), and those with a long coupling interval of about 8.0 hours (Group C). RESULTS Residents of Group B who showed optimal circadian-circasemidian coordination had less pronounced morning and evening SBP surges, as compared to residents of Group A (10.82 vs 14.29 mmHg, P < 0.0001) and Group C (11.86 vs 15.21 mmHg, P < 0.0001), respectively. The incidence of morning or evening SBP surge was less in Group B than in Group A (P < 0.0001) or Group C (P < 0.0001). Group B residents showed highest measures of wellbeing and psychological resilience, assessed by good relation with friends (P < 0.05), life satisfaction (P < 0.05), and subjective happiness (P < 0.05). A disturbed circadian-circasemidian coupling was associated with elevated BP, dyslipidemia, arteriosclerosis and a depressive mood. CONCLUSION The circadian-circasemidian coupling of SBP could serve as a new biomarker in clinical practice to guide precision medicine interventions aimed at achieving properly timed rhythms, and thereby resilience and wellbeing.
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Affiliation(s)
- Kuniaki Otsuka
- Tokyo Women’s Medical University, Tokyo, Japan
- Halberg Chronobiology Center, University of Minnesota, Minneapolis, MN, USA
| | - Shougo Murakami
- Department of Cardiovascular Medicine, Soseikai General Hospital, Kyoto, Japan
| | - Kiyotaka Okajima
- Cardiovascular Internal Medicine, Higashi Omiya General Hospital, Saitama, Japan
| | | | - Yutaka Kubo
- Department of Medicine, Machida Keisen Hospital, Tokyo, Japan
| | - Denis G Gubin
- Laboratory for Chronobiology and Chronomedicine, Research Institute of Biomedicine and Biomedical Technologies, Medical University, Tyumen, 625023, Russia
- Department of Biology, Medical University, Tyumen, 625023, Russia
- Tyumen Cardiology Research Center, Tomsk National Research Medical Center, Russian Academy of Science, Tomsk, Russia
| | - Larry A Beaty
- Halberg Chronobiology Center, University of Minnesota, Minneapolis, MN, USA
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20
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Wakao S, Saitoh N, Awazu A. Mathematical model of structural changes in nuclear speckle. Biophys Physicobiol 2023; 20:e200020. [PMID: 38496241 PMCID: PMC10941963 DOI: 10.2142/biophysico.bppb-v20.0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/26/2023] [Indexed: 03/19/2024] Open
Abstract
Nuclear speckles are nuclear bodies consisting of populations of small and irregularly shaped droplet-like molecular condensates that contain various splicing factors. Recent experiments have revealed the following structural features of nuclear speckles: (I) Each molecular condensate contains SON and SRRM2 proteins, and MALAT1 non-coding RNA surrounds these condensates; (II) During normal interphase of the cell cycle in multicellular organisms, these condensates are broadly distributed throughout the nucleus. In contrast, when cell transcription is suppressed, the condensates fuse and form strongly condensed spherical droplets; (III) SON is dispersed spatially in MALAT1 knocked-down cells and MALAT1 is dispersed in SON knocked-down cells because of the collapse of the nuclear speckles. However, the detailed interactions among the molecules that are mechanistically responsible for the structural variation remain unknown. In this study, a coarse-grained molecular dynamics model of the nuclear speckle was developed by considering the dynamics of SON, SRRM2, MALAT1, and pre-mRNA as representative components of the condensates. The simulations reproduced the structural changes, which were used to predict the interaction network among the representative components of the condensates.
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Affiliation(s)
- Shingo Wakao
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima 739-8526, Japan
| | - Noriko Saitoh
- Division of Cancer Biology, The Cancer Institute of Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, Japan
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima 739-8526, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Higashihiroshima, Hiroshima 739-8526, Japan
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21
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Voss PG, Wang JL. Liquid-liquid phase separation: Galectin-3 in nuclear speckles and ribonucleoprotein complexes. Exp Cell Res 2023; 427:113571. [PMID: 37003559 DOI: 10.1016/j.yexcr.2023.113571] [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: 01/29/2023] [Revised: 03/19/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023]
Abstract
Nuclear speckles are subcellular structures originally characterized by punctate immunofluorescence staining of the monoclonal antibody SC35, which recognizes an epitope on SRRM2 (serine/arginine repetitive matrix protein 2) and Sfrs2, a member of the SR (serine/arginine-rich) family of splicing factors. Galectin-3 co-localizes with SC35 in nuclear speckles, which represent one group of nuclear bodies that include the nucleolus, Cajal bodies and gems, paraspeckles, etc. Although they appear to have well-delineated physical boundaries, these nuclear bodies are not membrane-bound structures but represent macromolecular assemblies arising from a phenomenon called liquid-liquid phase separation. There has been much recent interest in liquid phase condensation as a newly recognized mechanism by which a cell can organize and compartmentalize subcellular structures with distinct composition. The punctate/speckled staining of galectin-3 with SC3 demonstrates their co-localization in a phase-separated body in vivo, under conditions endogenous to the cell. The purpose of the present review is to summarize the studies that document three key features of galectin-3 for its localization in liquid phase condensates: (a) an intrinsically disordered domain; (b) oligomer formation for multivalent binding; and (c) association with RNA and ribonucleoprotein complexes.
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Affiliation(s)
- Patricia G Voss
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - John L Wang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
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22
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Asher G, Zhu B. Beyond circadian rhythms: emerging roles of ultradian rhythms in control of liver functions. Hepatology 2023; 77:1022-1035. [PMID: 35591797 PMCID: PMC9674798 DOI: 10.1002/hep.32580] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 12/08/2022]
Abstract
The mammalian liver must cope with various metabolic and physiological changes that normally recur every day and primarily stem from daily cycles of rest-activity and fasting-feeding. Although a large body of evidence supports the reciprocal regulation of circadian rhythms and liver function, the research on the hepatic ultradian rhythms have largely been lagging behind. However, with the advent of more cost-effective high-throughput omics technologies, high-resolution time-lapse imaging, and more robust and powerful mathematical tools, several recent studies have shed new light on the presence and functions of hepatic ultradian rhythms. In this review, we will first very briefly discuss the basic principles of circadian rhythms, and then cover in greater details the recent literature related to ultradian rhythms. Specifically, we will highlight the prevalence and mechanisms of hepatic 12-h rhythms, and 8-h rhythms, which cycle at the second and third harmonics of circadian frequency. Finally, we also refer to ultradian rhythms with other frequencies and examine the limitations of the current approaches as well as the challenges related to identifying ultradian rhythm and addressing their molecular underpinnings.
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Affiliation(s)
- Gad Asher
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pennsylvania, USA
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania, USA
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23
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Bhat P, Chow A, Emert B, Ettlin O, Quinodoz SA, Takei Y, Huang W, Blanco MR, Guttman M. 3D genome organization around nuclear speckles drives mRNA splicing efficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.04.522632. [PMID: 36711853 PMCID: PMC9881923 DOI: 10.1101/2023.01.04.522632] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The nucleus is highly organized such that factors involved in transcription and processing of distinct classes of RNA are organized within specific nuclear bodies. One such nuclear body is the nuclear speckle, which is defined by high concentrations of protein and non-coding RNA regulators of pre-mRNA splicing. What functional role, if any, speckles might play in the process of mRNA splicing remains unknown. Here we show that genes localized near nuclear speckles display higher spliceosome concentrations, increased spliceosome binding to their pre-mRNAs, and higher co-transcriptional splicing levels relative to genes that are located farther from nuclear speckles. We show that directed recruitment of a pre-mRNA to nuclear speckles is sufficient to drive increased mRNA splicing levels. Finally, we show that gene organization around nuclear speckles is highly dynamic with differential localization between cell types corresponding to differences in Pol II occupancy. Together, our results integrate the longstanding observations of nuclear speckles with the biochemistry of mRNA splicing and demonstrate a critical role for dynamic 3D spatial organization of genomic DNA in driving spliceosome concentrations and controlling the efficiency of mRNA splicing.
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24
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Pavone P, Saia F, Pappalardo X, Barbagallo M, Prato A, Rizzo R. Novel malformations: Chiari type 1 and hydrocephalus in Zhu-Tokita-Takenouchi-Kim syndrome and novel SON variants. Clin Case Rep 2022; 10:e6529. [PMID: 36540882 PMCID: PMC9755635 DOI: 10.1002/ccr3.6529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 10/13/2022] [Accepted: 10/15/2022] [Indexed: 12/23/2022] Open
Abstract
Zhu-Tokita-Tachenouchi-Kim syndrome (ZTTK) is a recently recognized malformation syndrome presenting with craniofacial dysmorphism, developmental delay/intellectual disability, seizures, anomalies involving brain white matter, and other body-organs. In humans, the disorder is linked to the loss-of-function variants in the SON gene (MIM# 617140). Herewith, a new case of this syndrome is reported in a 2-year-old Caucasian child who presented the classical clinical features of the ZTTK syndrome in association with hydrocephalus and Chiari malformations type 1 an anomaly previously unreported. Exome analysis showed a de novo heterozygous variant in SON gene. Literature review of similar cases is reported.
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Affiliation(s)
- Piero Pavone
- Unit of Clinical Pediatrics, AOU "Policlinico", PO "G. Rodolico"University of CataniaCataniaItaly
| | - Federica Saia
- Child and Adolescent Neurology and Psichiatry, Department of Clinical and Experimental MedicineCatania UniversityCataniaItaly
| | - Xena Pappalardo
- Unit of Catania, Institute for Biomedical Research and InnovationNational Council of ResearchCataniaItaly
| | - Massimo Barbagallo
- Unit of Pediatrics and Pediatrics EmergencyHospital "G. Garibaldi"CataniaItaly
| | - Adriana Prato
- Child and Adolescent Neurology and Psichiatry, Department of Clinical and Experimental MedicineCatania UniversityCataniaItaly
- Department of Cognitive Sciences, Psychology, Education and Cultural StudiesUniversity of MessinaMessinaItaly
| | - Renata Rizzo
- Child and Adolescent Neurology and Psichiatry, Department of Clinical and Experimental MedicineCatania UniversityCataniaItaly
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25
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Cuddleston WH, Fan X, Sloofman L, Liang L, Mossotto E, Moore K, Zipkowitz S, Wang M, Zhang B, Wang J, Sestan N, Devlin B, Roeder K, Sanders SJ, Buxbaum JD, Breen MS. Spatiotemporal and genetic regulation of A-to-I editing throughout human brain development. Cell Rep 2022; 41:111585. [PMID: 36323256 PMCID: PMC9704047 DOI: 10.1016/j.celrep.2022.111585] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 07/06/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Posttranscriptional RNA modifications by adenosine-to-inosine (A-to-I) editing are abundant in the brain, yet elucidating functional sites remains challenging. To bridge this gap, we investigate spatiotemporal and genetically regulated A-to-I editing sites across prenatal and postnatal stages of human brain development. More than 10,000 spatiotemporally regulated A-to-I sites were identified that occur predominately in 3' UTRs and introns, as well as 37 sites that recode amino acids in protein coding regions with precise changes in editing levels across development. Hyper-edited transcripts are also enriched in the aging brain and stabilize RNA secondary structures. These features are conserved in murine and non-human primate models of neurodevelopment. Finally, thousands of cis-editing quantitative trait loci (edQTLs) were identified with unique regulatory effects during prenatal and postnatal development. Collectively, this work offers a resolved atlas linking spatiotemporal variation in editing levels to genetic regulatory effects throughout distinct stages of brain maturation.
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Affiliation(s)
- Winston H Cuddleston
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xuanjia Fan
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura Sloofman
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lindsay Liang
- Department of Psychiatry and Behavioral Sciences and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Enrico Mossotto
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kendall Moore
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sarah Zipkowitz
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Icahn Institute for Genomics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Icahn Institute for Genomics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Jiebiao Wang
- Department of Biostatistics, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261, USA
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Program in Cellular Neuroscience, Neurodegeneration, and Repair and Yale Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Comparative Medicine, Program in Integrative Cell Signaling and Neurobiology of Metabolism, Yale School of Medicine, New Haven, CT 06510, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, 3811 O'Hara Street, Pittsburgh, PA 15213, USA
| | - Kathryn Roeder
- Carnegie Mellon University, Statistics & Data Science Department, Pittsburgh, PA 15213, USA
| | - Stephan J Sanders
- Department of Psychiatry and Behavioral Sciences and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael S Breen
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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26
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Ilık İA, Aktaş T. Nuclear speckles: dynamic hubs of gene expression regulation. FEBS J 2022; 289:7234-7245. [PMID: 34245118 DOI: 10.1111/febs.16117] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/13/2021] [Accepted: 07/08/2021] [Indexed: 01/13/2023]
Abstract
Complex, multistep biochemical reactions that routinely take place in our cells require high concentrations of enzymes, substrates, and other structural components to proceed efficiently and typically require chemical environments that can inhibit other reactions in their immediate vicinity. Eukaryotic cells solve these problems by restricting such reactions into diffusion-restricted compartments within the cell called organelles that can be separated from their environment by a lipid membrane, or into membrane-less compartments that form through liquid-liquid phase separation (LLPS). One of the most easily noticeable and the earliest discovered organelle is the nucleus, which harbors the genetic material in cells where transcription by RNA polymerases produces most of the messenger RNAs and a plethora of noncoding RNAs, which in turn are required for translation of mRNAs in the cytoplasm. The interior of the nucleus is not a uniform soup of biomolecules and rather consists of a variety of membrane-less bodies, such as the nucleolus, nuclear speckles (NS), paraspeckles, Cajal bodies, histone locus bodies, and more. In this review, we will focus on NS with an emphasis on recent developments including our own findings about the formation of NS by two large IDR-rich proteins SON and SRRM2.
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Affiliation(s)
| | - Tuğçe Aktaş
- Max Planck Institute for Molecular Genetics, Berlin, Germany
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27
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Sandlin CW, Gu S, Xu J, Deshpande C, Feldman MD, Good MC. Epithelial cell size dysregulation in human lung adenocarcinoma. PLoS One 2022; 17:e0274091. [PMID: 36201559 PMCID: PMC9536599 DOI: 10.1371/journal.pone.0274091] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 08/22/2022] [Indexed: 11/18/2022] Open
Abstract
Human cells tightly control their dimensions, but in some cancers, normal cell size control is lost. In this study we measure cell volumes of epithelial cells from human lung adenocarcinoma progression in situ. By leveraging artificial intelligence (AI), we reconstruct tumor cell shapes in three dimensions (3D) and find airway type 2 cells display up to 10-fold increases in volume. Surprisingly, cell size increase is not caused by altered ploidy, and up to 80% of near-euploid tumor cells show abnormal sizes. Size dysregulation is not explained by cell swelling or senescence because cells maintain cytoplasmic density and proper organelle size scaling, but is correlated with changes in tissue organization and loss of a novel network of processes that appear to connect alveolar type 2 cells. To validate size dysregulation in near-euploid cells, we sorted cells from tumor single-cell suspensions on the basis of size. Our study provides data of unprecedented detail for cell volume dysregulation in a human cancer. Broadly, loss of size control may be a common feature of lung adenocarcinomas in humans and mice that is relevant to disease and identification of these cells provides a useful model for investigating cell size control and consequences of cell size dysregulation.
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Affiliation(s)
- Clifford W. Sandlin
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (CWS); (MCG)
| | - Song Gu
- Nanjing University of Information Science and Technology, Nanjing, China
| | - Jun Xu
- Nanjing University of Information Science and Technology, Nanjing, China
| | - Charuhas Deshpande
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Michael D. Feldman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew C. Good
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (CWS); (MCG)
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28
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Lee B, Jaberi-Lashkari N, Calo E. A unified view of low complexity regions (LCRs) across species. eLife 2022; 11:e77058. [PMID: 36098382 PMCID: PMC9470157 DOI: 10.7554/elife.77058] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Low complexity regions (LCRs) play a role in a variety of important biological processes, yet we lack a unified view of their sequences, features, relationships, and functions. Here, we use dotplots and dimensionality reduction to systematically define LCR type/copy relationships and create a map of LCR sequence space capable of integrating LCR features and functions. By defining LCR relationships across the proteome, we provide insight into how LCR type and copy number contribute to higher order assemblies, such as the importance of K-rich LCR copy number for assembly of the nucleolar protein RPA43 in vivo and in vitro. With LCR maps, we reveal the underlying structure of LCR sequence space, and relate differential occupancy in this space to the conservation and emergence of higher order assemblies, including the metazoan extracellular matrix and plant cell wall. Together, LCR relationships and maps uncover and identify scaffold-client relationships among E-rich LCR-containing proteins in the nucleolus, and revealed previously undescribed regions of LCR sequence space with signatures of higher order assemblies, including a teleost-specific T/H-rich sequence space. Thus, this unified view of LCRs enables discovery of how LCRs encode higher order assemblies of organisms.
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Affiliation(s)
- Byron Lee
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Nima Jaberi-Lashkari
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Eliezer Calo
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
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29
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Zhu B. Logic of the Temporal Compartmentalization of the Hepatic Metabolic Cycle. Physiology (Bethesda) 2022; 37:0. [PMID: 35658626 PMCID: PMC9394779 DOI: 10.1152/physiol.00003.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/05/2022] [Accepted: 05/28/2022] [Indexed: 12/25/2022] Open
Abstract
The mammalian liver must cope with various metabolic and physiological changes that normally recur every day and result primarily from rest-activity and fasting-feeding cycles. In this article, I present evidence supporting a temporal compartmentalization of rhythmic hepatic metabolic processes into four main clusters: regulation of energy homeostasis, maintenance of information integrity, immune response, and genetic information flow. I further review literatures and discuss how both the circadian and the newly discovered 12-h ultradian clock work together to regulate these four temporally separated processes in mouse liver, which, interestingly, is largely uncoupled from the liver zonation regulation.
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Affiliation(s)
- Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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30
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Cytoplasmic forces functionally reorganize nuclear condensates in oocytes. Nat Commun 2022; 13:5070. [PMID: 36038550 PMCID: PMC9424315 DOI: 10.1038/s41467-022-32675-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/05/2022] [Indexed: 12/21/2022] Open
Abstract
Cells remodel their cytoplasm with force-generating cytoskeletal motors. Their activity generates random forces that stir the cytoplasm, agitating and displacing membrane-bound organelles like the nucleus in somatic and germ cells. These forces are transmitted inside the nucleus, yet their consequences on liquid-like biomolecular condensates residing in the nucleus remain unexplored. Here, we probe experimentally and computationally diverse nuclear condensates, that include nuclear speckles, Cajal bodies, and nucleoli, during cytoplasmic remodeling of female germ cells named oocytes. We discover that growing mammalian oocytes deploy cytoplasmic forces to timely impose multiscale reorganization of nuclear condensates for the success of meiotic divisions. These cytoplasmic forces accelerate nuclear condensate collision-coalescence and molecular kinetics within condensates. Disrupting the forces decelerates nuclear condensate reorganization on both scales, which correlates with compromised condensate-associated mRNA processing and hindered oocyte divisions that drive female fertility. We establish that cytoplasmic forces can reorganize nuclear condensates in an evolutionary conserved fashion in insects. Our work implies that cells evolved a mechanism, based on cytoplasmic force tuning, to functionally regulate a broad range of nuclear condensates across scales. This finding opens new perspectives when studying condensate-associated pathologies like cancer, neurodegeneration and viral infections. Cytoskeletal activity generates mechanical forces known to agitate and displace membrane-bound organelles in the cytoplasm. In oocytes, Al Jord et al. discover that these cytoplasmic forces functionally remodel nuclear RNA-processing condensates across scales for developmental success.
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31
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Faber GP, Nadav-Eliyahu S, Shav-Tal Y. Nuclear speckles - a driving force in gene expression. J Cell Sci 2022; 135:275909. [PMID: 35788677 DOI: 10.1242/jcs.259594] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nuclear speckles are dynamic membraneless bodies located in the cell nucleus. They harbor RNAs and proteins, many of which are splicing factors, that together display complex biophysical properties dictating nuclear speckle formation and maintenance. Although these nuclear bodies were discovered decades ago, only recently has in-depth genomic analysis begun to unravel their essential functions in modulation of gene activity. Major advancements in genomic mapping techniques combined with microscopy approaches have enabled insights into the roles nuclear speckles may play in enhancing gene expression, and how gene positioning to specific nuclear landmarks can regulate gene expression and RNA processing. Some studies have drawn a link between nuclear speckles and disease. Certain maladies either involve nuclear speckles directly or dictate the localization and reorganization of many nuclear speckle factors. This is most striking during viral infection, as viruses alter the entire nuclear architecture and highjack host machinery. As discussed in this Review, nuclear speckles represent a fascinating target of study not only to reveal the links between gene positioning, genome subcompartments and gene activity, but also as a potential target for therapeutics.
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Affiliation(s)
- Gabriel P Faber
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University, Ramat Gan 5290002, Israel.,Institute of Nanotechnology , Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Shani Nadav-Eliyahu
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University, Ramat Gan 5290002, Israel.,Institute of Nanotechnology , Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University, Ramat Gan 5290002, Israel.,Institute of Nanotechnology , Bar-Ilan University, Ramat Gan 5290002, Israel
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32
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Raina K, Rao BJ. Mammalian nuclear speckles exhibit stable association with chromatin: a biochemical study. Nucleus 2022; 13:58-73. [PMID: 35220893 PMCID: PMC8890396 DOI: 10.1080/19491034.2021.2024948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Nuclear Speckles (NS) are phase-separated condensates of protein and RNA whose components dynamically coordinate RNA transcription, splicing, transport and DNA repair. NS, probed largely by imaging studies, remained historically well known as Interchromatin Granule Clusters, and biochemical properties, especially their association with Chromatin have been largely unexplored. In this study, we tested whether NS exhibit any stable association with chromatin and show that limited DNAse-1 nicking of chromatin leads to the collapse of NS into isotropic distribution or aggregates of constituent proteins without affecting other nuclear structures. Further biochemical probing revealed that NS proteins were tightly associated with chromatin, extractable only by high-salt treatment just like histone proteins. NS were also co-released with solubilised mono-dinucleosomal chromatin fraction following the MNase digestion of chromatin. We propose a model that NS-chromatin constitutes a “putative stable association” whose coupling might be subject to the combined regulation from both chromatin and NS changes. Abbreviations: NS: Nuclear speckles; DSB: double strand breaks; PTM: posttranslational modifications; DDR: DNA damage repair; RBP-RNA binding proteins; TAD: topologically associated domains; LCR: low complexity regions; IDR: intrinsically disordered regions.
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Affiliation(s)
- Komal Raina
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
- Department of Biology, Indian Institute of Science Education and Research (Iiser) Tirupati, Transit Campus: Sree Rama Engineering College, Tirupati, India
| | - Basuthkar J Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
- Department of Biology, Indian Institute of Science Education and Research (Iiser) Tirupati, Transit Campus: Sree Rama Engineering College, Tirupati, India
- Department of Animal Biology, University of Hyderabad, Hyderabad, India
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33
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Systematic mapping of nuclear domain-associated transcripts reveals speckles and lamina as hubs of functionally distinct retained introns. Mol Cell 2022; 82:1035-1052.e9. [PMID: 35182477 DOI: 10.1016/j.molcel.2021.12.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 12/22/2022]
Abstract
The nucleus is highly compartmentalized through the formation of distinct classes of membraneless domains. However, the composition and function of many of these structures are not well understood. Using APEX2-mediated proximity labeling and RNA sequencing, we surveyed human transcripts associated with nuclear speckles, several additional domains, and the lamina. Remarkably, speckles and lamina are associated with distinct classes of retained introns enriched in genes that function in RNA processing, translation, and the cell cycle, among other processes. In contrast to the lamina-proximal introns, retained introns associated with speckles are relatively short, GC-rich, and enriched for functional sites of RNA-binding proteins that are concentrated in these domains. They are also highly differentially regulated across diverse cellular contexts, including the cell cycle. Thus, our study provides a resource of nuclear domain-associated transcripts and further reveals speckles and lamina as hubs of distinct populations of retained introns linked to gene regulation and cell cycle progression.
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34
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Dion W, Ballance H, Lee J, Pan Y, Irfan S, Edwards C, Sun M, Zhang J, Zhang X, Liu S, Zhu B. Four-dimensional nuclear speckle phase separation dynamics regulate proteostasis. SCIENCE ADVANCES 2022; 8:eabl4150. [PMID: 34985945 PMCID: PMC8730402 DOI: 10.1126/sciadv.abl4150] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/15/2021] [Indexed: 05/15/2023]
Abstract
Phase separation and biorhythms control biological processes in the spatial and temporal dimensions, respectively, but mechanisms of four-dimensional integration remain elusive. Here, we identified an evolutionarily conserved XBP1s-SON axis that establishes a cell-autonomous mammalian 12-hour ultradian rhythm of nuclear speckle liquid-liquid phase separation (LLPS) dynamics, separate from both the 24-hour circadian clock and the cell cycle. Higher expression of nuclear speckle scaffolding protein SON, observed at early morning/early afternoon, generates diffuse and fluid nuclear speckles, increases their interactions with chromatin proactively, transcriptionally amplifies the unfolded protein response, and protects against proteome stress, whereas the opposites are observed following reduced SON level at early evening/late morning. Correlative Son and proteostasis gene expression dynamics are further observed across the entire mouse life span. Our results suggest that by modulating the temporal dynamics of proteostasis, the nuclear speckle LLPS may represent a previously unidentified (chrono)-therapeutic target for pathologies associated with dysregulated proteostasis.
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Affiliation(s)
- William Dion
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Heather Ballance
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jane Lee
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Saad Irfan
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Casey Edwards
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michelle Sun
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jing Zhang
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Xin Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Silvia Liu
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh
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35
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Larsen K, Heide-Jørgensen MP. Conservation of A-to-I RNA editing in bowhead whale and pig. PLoS One 2021; 16:e0260081. [PMID: 34882682 PMCID: PMC8659423 DOI: 10.1371/journal.pone.0260081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 11/02/2021] [Indexed: 01/18/2023] Open
Abstract
RNA editing is a post-transcriptional process in which nucleotide changes are introduced into an RNA sequence, many of which can contribute to proteomic sequence variation. The most common type of RNA editing, contributing to nearly 99% of all editing events in RNA, is A-to-I (adenosine-to-inosine) editing mediated by double-stranded RNA-specific adenosine deaminase (ADAR) enzymes. A-to-I editing at 'recoding' sites results in non-synonymous substitutions in protein-coding sequences. Here, we present studies of the conservation of A-to-I editing in selected mRNAs between pigs, bowhead whales, humans and two shark species. All examined mRNAs-NEIL1, COG3, GRIA2, FLNA, FLNB, IGFBP7, AZIN1, BLCAP, GLI1, SON, HTR2C and ADAR2 -showed conservation of A-to-I editing of recoding sites. In addition, novel editing sites were identified in NEIL1 and GLI1 in bowhead whales. The A-to-I editing site of human NEIL1 in position 242 was conserved in the bowhead and porcine homologues. A novel editing site was discovered in Tyr244. Differential editing was detected at the two adenosines in the NEIL1 242 codon in both pig and bowhead NEIL1 mRNAs in various tissues and organs. No conservation of editing of KCNB1 and EEF1A mRNAs was seen in bowhead whales. In silico analyses revealed conservation of five adenosines in ADAR2, some of which are subject to A-to-I editing in bowheads and pigs, and conservation of a regulatory sequence in GRIA2 mRNA that is responsible for recognition of the ADAR editing enzyme.
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Affiliation(s)
- Knud Larsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
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36
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Cha HJ, Uyan Ö, Kai Y, Liu T, Zhu Q, Tothova Z, Botten GA, Xu J, Yuan GC, Dekker J, Orkin SH. Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture. Nat Commun 2021; 12:6241. [PMID: 34716321 PMCID: PMC8556400 DOI: 10.1038/s41467-021-26574-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Precise control of gene expression during differentiation relies on the interplay of chromatin and nuclear structure. Despite an established contribution of nuclear membrane proteins to developmental gene regulation, little is known regarding the role of inner nuclear proteins. Here we demonstrate that loss of the nuclear scaffolding protein Matrin-3 (Matr3) in erythroid cells leads to morphological and gene expression changes characteristic of accelerated maturation, as well as broad alterations in chromatin organization similar to those accompanying differentiation. Matr3 protein interacts with CTCF and the cohesin complex, and its loss perturbs their occupancy at a subset of sites. Destabilization of CTCF and cohesin binding correlates with altered transcription and accelerated differentiation. This association is conserved in embryonic stem cells. Our findings indicate Matr3 negatively affects cell fate transitions and demonstrate that a critical inner nuclear protein impacts occupancy of architectural factors, culminating in broad effects on chromatin organization and cell differentiation.
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Affiliation(s)
- Hye Ji Cha
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Özgün Uyan
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Yan Kai
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Tianxin Liu
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Qian Zhu
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Zuzana Tothova
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Giovanni A Botten
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jian Xu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guo-Cheng Yuan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
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37
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Williams LK, Mackay DR, Whitney MA, Couldwell GC, Sundquist WI, Ullman KS. Identification of abscission checkpoint bodies as structures that regulate ESCRT factors to control abscission timing. eLife 2021; 10:63743. [PMID: 34346309 PMCID: PMC8437436 DOI: 10.7554/elife.63743] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 08/03/2021] [Indexed: 11/21/2022] Open
Abstract
The abscission checkpoint regulates the ESCRT membrane fission machinery and thereby delays cytokinetic abscission to protect genomic integrity in response to residual mitotic errors. The checkpoint is maintained by Aurora B kinase, which phosphorylates multiple targets, including CHMP4C, a regulatory ESCRT-III subunit necessary for this checkpoint. We now report the discovery that cytoplasmic abscission checkpoint bodies (ACBs) containing phospho-Aurora B and tri-phospho-CHMP4C develop during an active checkpoint. ACBs are derived from mitotic interchromatin granules, transient mitotic structures whose components are housed in splicing-related nuclear speckles during interphase. ACB formation requires CHMP4C, and the ESCRT factor ALIX also contributes. ACB formation is conserved across cell types and under multiple circumstances that activate the checkpoint. Finally, ACBs retain a population of ALIX, and their presence correlates with delayed abscission and delayed recruitment of ALIX to the midbody where it would normally promote abscission. Thus, a cytoplasmic mechanism helps regulate midbody machinery to delay abscission. When a cell divides, it must first carefully duplicate its genetic information and package these copies into compartments housed in the two new cells. Errors in this process lead to genetic mistakes that trigger cancer or other harmful biological events. Quality control checks exist to catch errors before it is too late. This includes a final ‘abscission’ checkpoint right before the end of division, when the two new cells are still connected by a thin membrane bridge. If cells fail to pass this ‘no cut’ checkpoint, they delay severing their connection until the mistake is fixed. A group of proteins called ESCRTs is responsible for splitting the two cells apart if nothing is amiss. The abscission checkpoint blocks this process by altering certain proteins in the ESCRT complex, but exactly how this works is not yet clear. To find out more, Strohacker et al. imaged ESCRT factors in a new experimental system in which the abscission checkpoint is active in many cells. This showed that, in this context, certain ESCRT components were rerouted from the thread of membrane between the daughter cells to previously unknown structures, which Strohacker et al. named abscission checkpoint bodies. These entities also sequestered other factors that participate in the abscission checkpoint and factors that contribute to gene expression. These results are key to better understand how cells regulate their division; in particular, they provide a new framework to explore when this process goes wrong and contributes to cancer.
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Affiliation(s)
- Lauren K Williams
- Biochemistry and Oncological Sciences, University of Utah, Salt Lake City, United States
| | - Douglas R Mackay
- Oncological Sciences, University of Utah, Salt Lake City, United States
| | | | | | - Wesley I Sundquist
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
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38
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Scoca V, Di Nunzio F. Membraneless organelles restructured and built by pandemic viruses: HIV-1 and SARS-CoV-2. J Mol Cell Biol 2021; 13:259-268. [PMID: 33760045 PMCID: PMC8083626 DOI: 10.1093/jmcb/mjab020] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 12/13/2022] Open
Abstract
Viruses hijack host functions to invade their target cells and spread to new cells. Specifically, viruses learned to usurp liquid‒liquid phase separation (LLPS), a newly exploited mechanism, used by the cell to concentrate enzymes to accelerate and confine a wide variety of cellular processes. LLPS gives rise to actual membraneless organelles (MLOs), which do not only increase reaction rates but also act as a filter to select molecules to be retained or to be excluded from the liquid droplet. This is exactly what seems to happen with the condensation of SARS-CoV-2 nucleocapsid protein to favor the packaging of intact viral genomes, excluding viral subgenomic or host cellular RNAs. Another older pandemic virus, HIV-1, also takes advantage of LLPS in the host cell during the viral cycle. Recent discoveries highlighted that HIV-1 RNA genome condensates in nuclear MLOs accompanied by specific host and viral proteins, breaking the dogma of retroviruses that limited viral synthesis exclusively to the cytoplasmic compartment. Intriguing fundamental properties of viral/host LLPS remain still unclear. Future studies will contribute to deeply understanding the role of pathogen-induced MLOs in the epidemic invasion of pandemic viruses.
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Affiliation(s)
- Viviana Scoca
- Advanced Molecular Virology and Retroviral Dynamics Group, Department of Virology, Pasteur Institute, Paris, France
- BioSPC Doctoral School, Universitè de Paris, Paris, France
| | - Francesca Di Nunzio
- Advanced Molecular Virology and Retroviral Dynamics Group, Department of Virology, Pasteur Institute, Paris, France
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39
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Abstract
Viral infection is intrinsically linked to the capacity of the virus to generate progeny. Many DNA and some RNA viruses need to access the nuclear machinery and therefore transverse the nuclear envelope barrier through the nuclear pore complex. Viral genomes then become chromatinized either in their episomal form or upon integration into the host genome. Interactions with host DNA, transcription factors or nuclear bodies mediate their replication. Often interfering with nuclear functions, viruses use nuclear architecture to ensure persistent infections. Discovering these multiple modes of replication and persistence served in unraveling many important nuclear processes, such as nuclear trafficking, transcription, and splicing. Here, by using examples of DNA and RNA viral families, we portray the nucleus with the virus inside.
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Affiliation(s)
- Bojana Lucic
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital and German Center for Infection Research, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Ines J de Castro
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital and German Center for Infection Research, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Marina Lusic
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital and German Center for Infection Research, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
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40
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Yildirim A, Mozaffari-Jovin S, Wallisch AK, Schäfer J, Ludwig SEJ, Urlaub H, Lührmann R, Wolfrum U. SANS (USH1G) regulates pre-mRNA splicing by mediating the intra-nuclear transfer of tri-snRNP complexes. Nucleic Acids Res 2021; 49:5845-5866. [PMID: 34023904 PMCID: PMC8191790 DOI: 10.1093/nar/gkab386] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/22/2021] [Accepted: 04/28/2021] [Indexed: 02/06/2023] Open
Abstract
Splicing is catalyzed by the spliceosome, a compositionally dynamic complex assembled stepwise on pre-mRNA. We reveal links between splicing machinery components and the intrinsically disordered ciliopathy protein SANS. Pathogenic mutations in SANS/USH1G lead to Usher syndrome—the most common cause of deaf-blindness. Previously, SANS was shown to function only in the cytosol and primary cilia. Here, we have uncovered molecular links between SANS and pre-mRNA splicing catalyzed by the spliceosome in the nucleus. We show that SANS is found in Cajal bodies and nuclear speckles, where it interacts with components of spliceosomal sub-complexes such as SF3B1 and the large splicing cofactor SON but also with PRPFs and snRNAs related to the tri-snRNP complex. SANS is required for the transfer of tri-snRNPs between Cajal bodies and nuclear speckles for spliceosome assembly and may also participate in snRNP recycling back to Cajal bodies. SANS depletion alters the kinetics of spliceosome assembly, leading to accumulation of complex A. SANS deficiency and USH1G pathogenic mutations affects splicing of genes related to cell proliferation and human Usher syndrome. Thus, we provide the first evidence that splicing dysregulation may participate in the pathophysiology of Usher syndrome.
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Affiliation(s)
- Adem Yildirim
- Molecular Cell Biology, Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Germany
| | - Sina Mozaffari-Jovin
- Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany.,Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Bioanalytical Mass Spectrometry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany
| | - Ann-Kathrin Wallisch
- Molecular Cell Biology, Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Germany
| | - Jessica Schäfer
- Molecular Cell Biology, Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Germany
| | - Sebastian E J Ludwig
- Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany.,Bioanalytics, Department of Clinical Chemistry, University Medical Center Goettingen, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany
| | - Uwe Wolfrum
- Molecular Cell Biology, Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Germany
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41
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Onoguchi-Mizutani R, Kirikae Y, Ogura Y, Gutschner T, Diederichs S, Akimitsu N. Identification of a heat-inducible novel nuclear body containing the long noncoding RNA MALAT1. J Cell Sci 2021; 134:268337. [PMID: 34028540 DOI: 10.1242/jcs.253559] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 03/29/2021] [Indexed: 11/20/2022] Open
Abstract
The heat-shock response is critical for the survival of all organisms. Metastasis-associated long adenocarcinoma transcript 1 (MALAT1) is a long noncoding RNA localized in nuclear speckles, but its physiological role remains elusive. Here, we show that heat shock induces translocation of MALAT1 to a distinct nuclear body named the heat shock-inducible noncoding RNA-containing nuclear (HiNoCo) body in mammalian cells. MALAT1-knockout A549 cells showed reduced proliferation after heat shock. The HiNoCo body, which is formed adjacent to nuclear speckles, is distinct from any other known nuclear bodies, including the nuclear stress body, Cajal body, germs, paraspeckles, nucleoli and promyelocytic leukemia body. The formation of HiNoCo body is reversible and independent of heat shock factor 1, the master transcription regulator of the heat-shock response. Our results suggest the HiNoCo body participates in heat shock factor 1-independent heat-shock responses in mammalian cells.
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Affiliation(s)
| | - Yoshitaka Kirikae
- Isotope Science Center, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Yoko Ogura
- Isotope Science Center, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Tony Gutschner
- Junior Research Group 'RNA Biology and Pathogenesis', Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany
| | - Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, 79106 Freiburg, Germany.,Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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42
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p53 mediates target gene association with nuclear speckles for amplified RNA expression. Mol Cell 2021; 81:1666-1681.e6. [PMID: 33823140 DOI: 10.1016/j.molcel.2021.03.006] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/05/2021] [Accepted: 03/03/2021] [Indexed: 01/01/2023]
Abstract
Nuclear speckles are prominent nuclear bodies that contain proteins and RNA involved in gene expression. Although links between nuclear speckles and gene activation are emerging, the mechanisms regulating association of genes with speckles are unclear. We find that speckle association of p53 target genes is driven by the p53 transcription factor. Focusing on p21, a key p53 target, we demonstrate that speckle association boosts expression by elevating nascent RNA amounts. p53-regulated speckle association did not depend on p53 transactivation functions but required an intact proline-rich domain and direct DNA binding, providing mechanisms within p53 for regulating gene-speckle association. Beyond p21, a substantial subset of p53 targets have p53-regulated speckle association. Strikingly, speckle-associating p53 targets are more robustly activated and occupy a distinct niche of p53 biology compared with non-speckle-associating p53 targets. Together, our findings illuminate regulated speckle association as a mechanism used by a transcription factor to boost gene expression.
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CLK1 reorganizes the splicing factor U1-70K for early spliceosomal protein assembly. Proc Natl Acad Sci U S A 2021; 118:2018251118. [PMID: 33811140 DOI: 10.1073/pnas.2018251118] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Early spliceosome assembly requires phosphorylation of U1-70K, a constituent of the U1 small nuclear ribonucleoprotein (snRNP), but it is unclear which sites are phosphorylated, and by what enzyme, and how such modification regulates function. By profiling the proteome, we found that the Cdc2-like kinase 1 (CLK1) phosphorylates Ser-226 in the C terminus of U1-70K. This releases U1-70K from subnuclear granules facilitating interaction with U1 snRNP and the serine-arginine (SR) protein SRSF1, critical steps in establishing the 5' splice site. CLK1 breaks contacts between the C terminus and the RNA recognition motif (RRM) in U1-70K releasing the RRM to bind SRSF1. This reorganization also permits stable interactions between U1-70K and several proteins associated with U1 snRNP. Nuclear induction of the SR protein kinase 1 (SRPK1) facilitates CLK1 dissociation from U1-70K, recycling the kinase for catalysis. These studies demonstrate that CLK1 plays a vital, signal-dependent role in early spliceosomal protein assembly by contouring U1-70K for protein-protein multitasking.
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Gordon JM, Phizicky DV, Neugebauer KM. Nuclear mechanisms of gene expression control: pre-mRNA splicing as a life or death decision. Curr Opin Genet Dev 2021; 67:67-76. [PMID: 33291060 PMCID: PMC8084925 DOI: 10.1016/j.gde.2020.11.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/26/2020] [Accepted: 11/03/2020] [Indexed: 02/06/2023]
Abstract
Thousands of genes produce polyadenylated mRNAs that still contain one or more introns. These transcripts are known as retained intron RNAs (RI-RNAs). In the past 10 years, RI-RNAs have been linked to post-transcriptional alternative splicing in a variety of developmental contexts, but they can also be dead-end products fated for RNA decay. Here we discuss the role of intron retention in shaping gene expression programs, as well as recent evidence suggesting that the biogenesis and fate of RI-RNAs is regulated by nuclear organization. We discuss the possibility that proximity of RNA to nuclear speckles - biomolecular condensates that are highly enriched in splicing factors and other RNA binding proteins - is associated with choices ranging from efficient co-transcriptional splicing, export and stability to regulated post-transcriptional splicing and possible vulnerability to decay.
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Affiliation(s)
- Jackson M Gordon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - David V Phizicky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
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Dopie J, Sweredoski MJ, Moradian A, Belmont AS. Tyramide signal amplification mass spectrometry (TSA-MS) ratio identifies nuclear speckle proteins. J Cell Biol 2021; 219:151914. [PMID: 32609799 PMCID: PMC7480118 DOI: 10.1083/jcb.201910207] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 04/03/2020] [Accepted: 05/13/2020] [Indexed: 12/11/2022] Open
Abstract
We present a simple ratio method to infer protein composition within cellular structures using proximity labeling approaches but compensating for the diffusion of free radicals. We used tyramide signal amplification (TSA) and label-free mass spectrometry (MS) to compare proteins in nuclear speckles versus centromeres. Our “TSA-MS ratio” approach successfully identified known nuclear speckle proteins. For example, 96% and 67% of proteins in the top 30 and 100 sorted proteins, respectively, are known nuclear speckle proteins, including proteins that we validated here as enriched in nuclear speckles. We show that MFAP1, among the top 20 in our list, forms droplets under certain circumstances and that MFAP1 expression levels modulate the size, stability, and dynamics of nuclear speckles. Localization of MFAP1 and its binding partner, PRPF38A, in droplet-like nuclear bodies precedes formation of nuclear speckles during telophase. Our results update older proteomic studies of nuclear speckles and should provide a useful reference dataset to guide future experimental dissection of nuclear speckle structure and function.
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Affiliation(s)
- Joseph Dopie
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Department of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, CA
| | - Annie Moradian
- Proteome Exploration Laboratory, Department of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, CA
| | - Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL
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Belmonte RL, Engbretson IL, Kim JH, Cajias I, Ahn EYE, Stachura DL. son is necessary for proper vertebrate blood development. PLoS One 2021; 16:e0247489. [PMID: 33630943 PMCID: PMC7906411 DOI: 10.1371/journal.pone.0247489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 02/08/2021] [Indexed: 12/15/2022] Open
Abstract
The gene SON is on human chromosome 21 (21q22.11) and is thought to be associated with hematopoietic disorders that accompany Down syndrome. Additionally, SON is an RNA splicing factor that plays a role in the transcription of leukemia-associated genes. Previously, we showed that mutations in SON cause malformations in human and zebrafish spines and brains during early embryonic development. To examine the role of SON in normal hematopoiesis, we reduced expression of the zebrafish homolog of SON in zebrafish at the single-cell developmental stage with specific morpholinos. In addition to the brain and spinal malformations we also observed abnormal blood cell levels upon son knockdown. We then investigated how blood production was altered when levels of son were reduced. Decreased levels of son resulted in lower amounts of red blood cells when visualized with lcr:GFP transgenic fish. There were also reduced thrombocytes seen with cd41:GFP fish, and myeloid cells when mpx:GFP fish were examined. We also observed a significant decrease in the quantity of T cells, visualized with lck:GFP fish. However, when we examined their hematopoietic stem and progenitor cells (HSPCs), we saw no difference in colony-forming capability. These studies indicate that son is essential for the proper differentiation of the innate and adaptive immune system, and further investigation determining the molecular pathways involved during blood development should elucidate important information about vertebrate HSPC generation, proliferation, and differentiation.
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Affiliation(s)
- Rebecca L. Belmonte
- Department of Biological Sciences, California State University Chico, Chico, California, United States of America
| | - Isabella L. Engbretson
- Department of Biological Sciences, California State University Chico, Chico, California, United States of America
| | - Jung-Hyun Kim
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, United States of America
| | - Illiana Cajias
- Department of Biological Sciences, California State University Chico, Chico, California, United States of America
| | - Eun-Young Erin Ahn
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - David L. Stachura
- Department of Biological Sciences, California State University Chico, Chico, California, United States of America
- * E-mail:
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Hoboth P, Sztacho M, Šebesta O, Schätz M, Castano E, Hozák P. Nanoscale mapping of nuclear phosphatidylinositol phosphate landscape by dual-color dSTORM. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158890. [PMID: 33513445 DOI: 10.1016/j.bbalip.2021.158890] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/10/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
Current models of gene expression, which are based on single-molecule localization microscopy, acknowledge protein clustering and the formation of transcriptional condensates as a driving force of gene expression. However, these models largely omit the role of nuclear lipids and amongst them nuclear phosphatidylinositol phosphates (PIPs) in particular. Moreover, the precise distribution of nuclear PIPs in the functional sub-nuclear domains remains elusive. The direct stochastic optical reconstruction microscopy (dSTORM) provides an unprecedented resolution in biological imaging. Therefore, its use for imaging in the densely crowded cell nucleus is desired but also challenging. Here we present a dual-color dSTORM imaging and image analysis of nuclear PI(4,5)P2, PI(3,4)P2 and PI(4)P distribution while preserving the context of nuclear architecture. In the nucleoplasm, PI(4,5)P2 and PI(3,4)P2 co-pattern in close proximity with the subset of RNA polymerase II foci. PI(4,5)P2 is surrounded by fibrillarin in the nucleoli and all three PIPs are dispersed within the matrix formed by the nuclear speckle protein SON. PI(4,5)P2 is the most abundant nuclear PIP, while PI(4)P is a precursor for the biosynthesis of PI(4,5)P2 and PI(3,4)P2. Therefore, our data are relevant for the understanding the roles of nuclear PIPs and provide further evidence for the model in which nuclear PIPs represent a localization signal for the formation of lipo-ribonucleoprotein hubs in the nucleus. The discussed experimental pipeline is applicable for further functional studies on the role of other nuclear PIPs in the regulation of gene expression and beyond.
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Affiliation(s)
- Peter Hoboth
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Martin Sztacho
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Ondřej Šebesta
- Faculty of Science, Charles University, Albertov 6, 128 00 Prague, Czech Republic
| | - Martin Schätz
- Faculty of Science, Charles University, Albertov 6, 128 00 Prague, Czech Republic
| | - Enrique Castano
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic; Biochemistry and Molecular Plant Biology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatán, Mexico
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic; Department of Epigenetics of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, division BIOCEV, Průmyslová 595, 252 20 Vestec, Czech Republic; Microscopy Centre, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
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Herdlevær I, Kråkenes T, Schubert M, Vedeler CA. Localization of CDR2L and CDR2 in paraneoplastic cerebellar degeneration. Ann Clin Transl Neurol 2020; 7:2231-2242. [PMID: 33009713 PMCID: PMC7664253 DOI: 10.1002/acn3.51212] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/07/2020] [Accepted: 09/11/2020] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVE Identify the subcellular location and potential binding partners of two cerebellar degeneration-related proteins, CDR2L and CDR2, associated with anti-Yo-mediated paraneoplastic cerebellar degeneration. METHODS Cancer cells, rat Purkinje neuron cultures, and human cerebellar sections were exposed to cerebrospinal fluid and serum from patients with paraneoplastic cerebellar degeneration with Yo antibodies and with several antibodies against CDR2L and CDR2. We used mass spectrometry-based proteomics, super-resolution microscopy, proximity ligation assay, and co-immunoprecipitation to verify the antibodies and to identify potential binding partners. RESULTS We confirmed the CDR2L specificity of Yo antibodies by mass spectrometry-based proteomics and found that CDR2L localized to the cytoplasm and CDR2 to the nucleus. CDR2L co-localized with the 40S ribosomal protein S6, while CDR2 co-localized with the nuclear speckle proteins SON, eukaryotic initiation factor 4A-III, and serine/arginine-rich splicing factor 2. INTERPRETATION We showed that Yo antibodies specifically bind to CDR2L in Purkinje neurons of PCD patients where they potentially interfere with the function of the ribosomal machinery resulting in disrupted mRNA translation and/or protein synthesis. Our findings demonstrating that CDR2L interacts with ribosomal proteins and CDR2 with nuclear speckle proteins is an important step toward understanding PCD pathogenesis.
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Affiliation(s)
- Ida Herdlevær
- Department of Clinical MedicineUniversity of BergenBergenNorway
- Department of NeurologyHaukeland University HospitalBergenNorway
| | | | - Manja Schubert
- Department of NeurologyHaukeland University HospitalBergenNorway
| | - Christian A. Vedeler
- Department of Clinical MedicineUniversity of BergenBergenNorway
- Department of NeurologyHaukeland University HospitalBergenNorway
- Departments of Neurology and Clinical MedicineNeuro‐SysMed ‐ Centre of Excellence for Experimental Therapy in NeurologyBergenNorway
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Ilik İA, Malszycki M, Lübke AK, Schade C, Meierhofer D, Aktaş T. SON and SRRM2 are essential for nuclear speckle formation. eLife 2020; 9:60579. [PMID: 33095160 PMCID: PMC7671692 DOI: 10.7554/elife.60579] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/20/2020] [Indexed: 12/17/2022] Open
Abstract
Nuclear speckles (NS) are among the most prominent biomolecular condensates. Despite their prevalence, research on the function of NS is virtually restricted to colocalization analyses, since an organizing core, without which NS cannot form, remains unidentified. The monoclonal antibody SC35, raised against a spliceosomal extract, is frequently used to mark NS. Unexpectedly, we found that this antibody was mischaracterized and the main target of SC35 mAb is SRRM2, a spliceosome-associated protein that sharply localizes to NS. Here we show that, the core of NS is likely formed by SON and SRRM2, since depletion of SON leads only to a partial disassembly of NS, while co-depletion of SON and SRRM2 or depletion of SON in a cell-line where intrinsically disordered regions (IDRs) of SRRM2 are genetically deleted, leads to a near-complete dissolution of NS. This work, therefore, paves the way to study the role of NS under diverse physiological and stress conditions. Most cells store their genetic material inside a compartment called the nucleus, which helps to separate DNA from other molecules in the cell. Inside the nucleus, DNA is tightly packed together with proteins that can read the cell’s genetic code and convert into the RNA molecules needed to build proteins. However, the contents of the nucleus are not randomly arranged, and these proteins are often clustered into specialized areas where they perform their designated roles. One of the first nuclear territories to be identified were granular looking structures named Nuclear Speckles (or NS for short), which are thought to help process RNA before it leaves the nucleus. Structures like NS often contain a number of different factors held together by a core group of proteins known as a scaffold. Although NS were discovered over a century ago, little is known about their scaffold proteins, making it difficult to understand the precise role of these speckles. Typically, researchers visualize NS using a substance called SC35 which targets specific sites in these structures. However, it was unclear which parts of the NS this marker binds to. To answer this question, Ilik et al. studied NS in human cells grown in the lab. The analysis revealed that SC35 attaches to certain parts of a large, flexible protein called SRRM2. Ilik et al. discovered that although the structure and sequence of SRMM2 varies between different animal species, a small region of this protein remained unchanged throughout evolution. Studying the evolutionary history of SRRM2 led to the identification of another protein with similar properties called SON. Ilik et al. found that depleting SON and SRRM2 from human cells caused other proteins associated with the NS to diffuse away from their territories and become dispersed within the nucleus. This suggests that SRMM2 and SON make up the scaffold that holds the proteins in NS together. Nuclear speckles have been associated with certain viral infections, and seem to help prevent the onset of diseases such as Huntington’s and spinocerebellar ataxia. These newly discovered core proteins could therefore further our understanding of the role NS play in disease.
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Affiliation(s)
| | - Michal Malszycki
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Freie Universität Berlin, Berlin, Germany
| | - Anna Katharina Lübke
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Freie Universität Berlin, Berlin, Germany
| | - Claudia Schade
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Tuğçe Aktaş
- Max Planck Institute for Molecular Genetics, Berlin, Germany
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Alkalay E, Gam Ze Letova Refael C, Shoval I, Kinor N, Sarid R, Shav-Tal Y. The Sub-Nuclear Localization of RNA-Binding Proteins in KSHV-Infected Cells. Cells 2020; 9:cells9091958. [PMID: 32854341 PMCID: PMC7564026 DOI: 10.3390/cells9091958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 08/21/2020] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins, particularly splicing factors, localize to sub-nuclear domains termed nuclear speckles. During certain viral infections, as the nucleus fills up with replicating virus compartments, host cell chromatin distribution changes, ending up condensed at the nuclear periphery. In this study we wished to determine the fate of nucleoplasmic RNA-binding proteins and nuclear speckles during the lytic cycle of the Kaposi's sarcoma associated herpesvirus (KSHV). We found that nuclear speckles became fewer and dramatically larger, localizing at the nuclear periphery, adjacent to the marginalized chromatin. Enlarged nuclear speckles contained splicing factors, whereas other proteins were nucleoplasmically dispersed. Polyadenylated RNA, typically found in nuclear speckles under regular conditions, was also found in foci separated from nuclear speckles in infected cells. Poly(A) foci did not contain lncRNAs known to colocalize with nuclear speckles but contained the poly(A)-binding protein PABPN1. Examination of the localization of spliced viral RNAs revealed that some spliced transcripts could be detected within the nuclear speckles. Since splicing is required for the maturation of certain KSHV transcripts, we suggest that the infected cell does not dismantle nuclear speckles but rearranges their components at the nuclear periphery to possibly serve in splicing and transport of viral RNAs into the cytoplasm.
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