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Venit T, Sapkota O, Abdrabou WS, Loganathan P, Pasricha R, Mahmood SR, El Said NH, Sherif S, Thomas S, Abdelrazig S, Amin S, Bedognetti D, Idaghdour Y, Magzoub M, Percipalle P. Author Correction: Positive regulation of oxidative phosphorylation by nuclear myosin 1 protects cells from metabolic reprogramming and tumorigenesis in mice. Nat Commun 2023; 14:7878. [PMID: 38036530 PMCID: PMC10689722 DOI: 10.1038/s41467-023-43936-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023] Open
Affiliation(s)
- Tomas Venit
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Oscar Sapkota
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Wael Said Abdrabou
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Palanikumar Loganathan
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Renu Pasricha
- Core Technology Platforms, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Syed Raza Mahmood
- Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Nadine Hosny El Said
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Shimaa Sherif
- Translational Medicine Department, Research Branch, Sidra Medicine, Doha, Qatar
| | - Sneha Thomas
- Core Technology Platforms, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Salah Abdelrazig
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Shady Amin
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Davide Bedognetti
- Translational Medicine Department, Research Branch, Sidra Medicine, Doha, Qatar
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genoa, Italy
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Youssef Idaghdour
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Mazin Magzoub
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Piergiorgio Percipalle
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates.
- Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates.
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden.
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Venit T, Sapkota O, Abdrabou WS, Loganathan P, Pasricha R, Mahmood SR, El Said NH, Sherif S, Thomas S, Abdelrazig S, Amin S, Bedognetti D, Idaghdour Y, Magzoub M, Percipalle P. Positive regulation of oxidative phosphorylation by nuclear myosin 1 protects cells from metabolic reprogramming and tumorigenesis in mice. Nat Commun 2023; 14:6328. [PMID: 37816864 PMCID: PMC10564744 DOI: 10.1038/s41467-023-42093-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/29/2023] [Indexed: 10/12/2023] Open
Abstract
Metabolic reprogramming is one of the hallmarks of tumorigenesis. Here, we show that nuclear myosin 1 (NM1) serves as a key regulator of cellular metabolism. NM1 directly affects mitochondrial oxidative phosphorylation (OXPHOS) by regulating mitochondrial transcription factors TFAM and PGC1α, and its deletion leads to underdeveloped mitochondria inner cristae and mitochondrial redistribution within the cell. These changes are associated with reduced OXPHOS gene expression, decreased mitochondrial DNA copy number, and deregulated mitochondrial dynamics, which lead to metabolic reprogramming of NM1 KO cells from OXPHOS to aerobic glycolysis.This, in turn, is associated with a metabolomic profile typical for cancer cells, namely increased amino acid-, fatty acid-, and sugar metabolism, and increased glucose uptake, lactate production, and intracellular acidity. NM1 KO cells form solid tumors in a mouse model, suggesting that the metabolic switch towards aerobic glycolysis provides a sufficient carcinogenic signal. We suggest that NM1 plays a role as a tumor suppressor and that NM1 depletion may contribute to the Warburg effect at the onset of tumorigenesis.
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Affiliation(s)
- Tomas Venit
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Oscar Sapkota
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Wael Said Abdrabou
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Palanikumar Loganathan
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Renu Pasricha
- Core Technology Platforms, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Syed Raza Mahmood
- Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Nadine Hosny El Said
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Shimaa Sherif
- Translational Medicine Department, Research Branch, Sidra Medicine, Doha, Qatar
| | - Sneha Thomas
- Core Technology Platforms, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Salah Abdelrazig
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Shady Amin
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Davide Bedognetti
- Translational Medicine Department, Research Branch, Sidra Medicine, Doha, Qatar
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genoa, Italy
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Youssef Idaghdour
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Mazin Magzoub
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Piergiorgio Percipalle
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates.
- Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates.
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden.
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Gallardo-Dodd CJ, Oertlin C, Record J, Galvani RG, Sommerauer C, Kuznetsov NV, Doukoumopoulos E, Ali L, Oliveira MMS, Seitz C, Percipalle M, Nikić T, Sadova AA, Shulgina SM, Shmarov VA, Kutko OV, Vlasova DD, Orlova KD, Rykova MP, Andersson J, Percipalle P, Kutter C, Ponomarev SA, Westerberg LS. Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. Sci Adv 2023; 9:eadg1610. [PMID: 37624890 PMCID: PMC10456848 DOI: 10.1126/sciadv.adg1610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 07/25/2023] [Indexed: 08/27/2023]
Abstract
The next steps of deep space exploration are manned missions to Moon and Mars. For safe space missions for crew members, it is important to understand the impact of space flight on the immune system. We studied the effects of 21 days dry immersion (DI) exposure on the transcriptomes of T cells isolated from blood samples of eight healthy volunteers. Samples were collected 7 days before DI, at day 7, 14, and 21 during DI, and 7 days after DI. RNA sequencing of CD3+ T cells revealed transcriptional alterations across all time points, with most changes occurring 14 days after DI exposure. At day 21, T cells showed evidence of adaptation with a transcriptional profile resembling that of 7 days before DI. At 7 days after DI, T cells again changed their transcriptional profile. These data suggest that T cells adapt by rewiring their transcriptomes in response to simulated weightlessness and that remodeling cues persist when reexposed to normal gravity.
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Affiliation(s)
- Carlos J. Gallardo-Dodd
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Christian Oertlin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Julien Record
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Rômulo G. Galvani
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
- Universidade Veiga de Almeida, Rio de Janeiro, Brazil
- Laboratory for Thymus Research (LPT), Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Christian Sommerauer
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Nikolai V. Kuznetsov
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Russian Federation State Research Center Institute of Biomedical Problems RAS, Moscow, Russia
| | | | - Liaqat Ali
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
- Core Technology Platform, NYUAD, Abu Dhabi, United Arab Emirates
| | - Mariana M. S. Oliveira
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Christina Seitz
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Mathias Percipalle
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tijana Nikić
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Anastasia A. Sadova
- Russian Federation State Research Center Institute of Biomedical Problems RAS, Moscow, Russia
| | - Sofia M. Shulgina
- Russian Federation State Research Center Institute of Biomedical Problems RAS, Moscow, Russia
| | - Vjacheslav A. Shmarov
- Russian Federation State Research Center Institute of Biomedical Problems RAS, Moscow, Russia
| | - Olga V. Kutko
- Russian Federation State Research Center Institute of Biomedical Problems RAS, Moscow, Russia
| | - Daria D. Vlasova
- Russian Federation State Research Center Institute of Biomedical Problems RAS, Moscow, Russia
| | - Kseniya D. Orlova
- Russian Federation State Research Center Institute of Biomedical Problems RAS, Moscow, Russia
| | - Marina P. Rykova
- Russian Federation State Research Center Institute of Biomedical Problems RAS, Moscow, Russia
| | - John Andersson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Piergiorgio Percipalle
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology, NYUAD, Abu Dhabi, United Arab Emirates
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Claudia Kutter
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Sergey A. Ponomarev
- Russian Federation State Research Center Institute of Biomedical Problems RAS, Moscow, Russia
| | - Lisa S. Westerberg
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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Fukuda N, Fukuda T, Percipalle P, Oda K, Takei N, Czaplinski K, Touhara K, Yoshihara Y, Sasaoka T. Axonal mRNA binding of hnRNP A/B is crucial for axon targeting and maturation of olfactory sensory neurons. Cell Rep 2023; 42:112398. [PMID: 37083330 DOI: 10.1016/j.celrep.2023.112398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 01/26/2023] [Accepted: 03/29/2023] [Indexed: 04/22/2023] Open
Abstract
Spatiotemporal control of gene expression is important for neural development and function. Here, we show that heterogeneous nuclear ribonucleoprotein (hnRNP) A/B is highly expressed in developing olfactory sensory neurons (OSNs), and its knockout results in reduction in mature OSNs and aberrant targeting of OSN axons to the olfactory bulb. RNA immunoprecipitation analysis reveals that hnRNP A/B binds to a group of mRNAs that are highly related to axon projections and synapse assembly. Approximately 11% of the identified hnRNP A/B targets, including Pcdha and Ncam2, encode cell adhesion molecules. In Hnrnpab knockout mice, PCDHA and NCAM2 levels are significantly reduced at the axon terminals of OSNs. Furthermore, deletion of the hnRNP A/B-recognition motif in the 3' UTR of Pcdha leads to impaired PCDHA expression at the OSN axon terminals. Therefore, we propose that hnRNP A/B facilitates OSN maturation and axon projection by regulating the local expression of its target genes at axon terminals.
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Affiliation(s)
- Nanaho Fukuda
- Brain Research Institute, Niigata University, Niigata 951-8585, Japan; Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma 630-0192, Japan.
| | - Tomoyuki Fukuda
- Niigata University Graduate School of Medical and Dental Science, Niigata 951-8510, Japan
| | - Piergiorgio Percipalle
- Science Division, Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, UAE; Department of Molecular Bioscience, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Kanako Oda
- Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Nobuyuki Takei
- Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | | | - Kazushige Touhara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | | | - Toshikuni Sasaoka
- Brain Research Institute, Niigata University, Niigata 951-8585, Japan
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Mahmood SR, Said NHE, Gunsalus KC, Percipalle P. β-actin mediated H3K27ac changes demonstrate the link between compartment switching and enhancer-dependent transcriptional regulation. Genome Biol 2023; 24:18. [PMID: 36698204 PMCID: PMC9875490 DOI: 10.1186/s13059-023-02853-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 01/09/2023] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Recent work has demonstrated that three-dimensional genome organization is directly affected by changes in the levels of nuclear cytoskeletal proteins such as β-actin. The mechanisms which translate changes in 3D genome structure into changes in transcription, however, are not fully understood. Here, we use a comprehensive genomic analysis of cells lacking nuclear β-actin to investigate the mechanistic links between compartment organization, enhancer activity, and gene expression. RESULTS Using HiC-Seq, ATAC-Seq, and RNA-Seq, we first demonstrate that transcriptional and chromatin accessibility changes observed upon β-actin loss are highly enriched in compartment-switching regions. Accessibility changes within compartment switching genes, however, are mainly observed in non-promoter regions which potentially represent distal regulatory elements. Our results also show that β-actin loss induces widespread accumulation of the enhancer-specific epigenetic mark H3K27ac. Using the ABC model of enhancer annotation, we then establish that these epigenetic changes have a direct impact on enhancer activity and underlie transcriptional changes observed upon compartment switching. A complementary analysis of fibroblasts undergoing reprogramming into pluripotent stem cells further confirms that this relationship between compartment switching and enhancer-dependent transcriptional change is not specific to β-actin knockout cells but represents a general mechanism linking compartment-level genome organization to gene expression. CONCLUSIONS We demonstrate that enhancer-dependent transcriptional regulation plays a crucial role in driving gene expression changes observed upon compartment-switching. Our results also reveal a novel function of nuclear β-actin in regulating enhancer function by influencing H3K27 acetylation levels.
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Affiliation(s)
- Syed Raza Mahmood
- grid.440573.10000 0004 1755 5934Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates ,grid.137628.90000 0004 1936 8753Department of Biology, New York University, New York, NY 10003 USA
| | - Nadine Hosny El Said
- grid.440573.10000 0004 1755 5934Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Kristin C. Gunsalus
- grid.440573.10000 0004 1755 5934Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates ,grid.137628.90000 0004 1936 8753Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003 USA
| | - Piergiorgio Percipalle
- grid.440573.10000 0004 1755 5934Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates ,grid.440573.10000 0004 1755 5934Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates ,grid.10548.380000 0004 1936 9377Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
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Hunashal Y, Percipalle M, Molnár T, Kardos J, Percipalle P, Esposito G. Approaching Protein Aggregation and Structural Dynamics by Equilibrium and Nonequilibrium Paramagnetic Perturbation. Anal Chem 2022; 94:10949-10958. [PMID: 35877130 DOI: 10.1021/acs.analchem.2c00751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
PENELOP (Paramagnetic Equilibrium vs Nonequilibrium magnetization Enhancement or LOss Perturbation) is the presented nuclear magnetic resonance (NMR) approach to identify at once the location of proteins' exposed surface, hindered accessibility, and exchange processes occurring on a μs-ms time scale. In addition to mapping the protein surface accessibility, the application of this method under specific conditions makes it possible to distinguish conformational mobility and chemical exchange processes, thereby providing an alternative to characterization by more demanding techniques (transverse relaxation dispersion, saturation transfer, and high-pressure NMR). Moreover, its high sensitivity enables studying samples at low, physiologically more relevant concentrations. Association, dynamics, and oligomerization are addressed by PENELOP for a component of SARS-CoV-2 replication transcription complex and an amyloidogenic protein.
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Affiliation(s)
- Yamanappa Hunashal
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates.,Dipartimento di Area Medica, Universita' di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Mathias Percipalle
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates.,Department of Chemistry and Magnetic Resonance Center, University of Florence, 50019 Florence, Italy
| | - Tamás Molnár
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary
| | - Jòzsef Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary
| | - Piergiorgio Percipalle
- Biology Program, Science Division, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates.,Department of Molecular Bioscience, The Wenner Gren Institute Stockholm University, Stockholm SE-106 91, Sweden
| | - Gennaro Esposito
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates.,INBB, Viale Medaglie d'Oro 305, Roma 00136, Italy
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Hari-Gupta Y, Fili N, dos Santos Á, Cook AW, Gough RE, Reed HCW, Wang L, Aaron J, Venit T, Wait E, Grosse-Berkenbusch A, Gebhardt JCM, Percipalle P, Chew TL, Martin-Fernandez M, Toseland CP. Myosin VI regulates the spatial organisation of mammalian transcription initiation. Nat Commun 2022; 13:1346. [PMID: 35292632 PMCID: PMC8924246 DOI: 10.1038/s41467-022-28962-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/21/2022] [Indexed: 12/19/2022] Open
Abstract
During transcription, RNA Polymerase II (RNAPII) is spatially organised within the nucleus into clusters that correlate with transcription activity. While this is a hallmark of genome regulation in mammalian cells, the mechanisms concerning the assembly, organisation and stability remain unknown. Here, we have used combination of single molecule imaging and genomic approaches to explore the role of nuclear myosin VI (MVI) in the nanoscale organisation of RNAPII. We reveal that MVI in the nucleus acts as the molecular anchor that holds RNAPII in high density clusters. Perturbation of MVI leads to the disruption of RNAPII localisation, chromatin organisation and subsequently a decrease in gene expression. Overall, we uncover the fundamental role of MVI in the spatial regulation of gene expression.
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Affiliation(s)
- Yukti Hari-Gupta
- grid.9759.20000 0001 2232 2818School of Biosciences, University of Kent, Canterbury, UK ,grid.83440.3b0000000121901201Present Address: MRC LMCB, University College London, London, UK
| | - Natalia Fili
- grid.11835.3e0000 0004 1936 9262Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK ,grid.36511.300000 0004 0420 4262Present Address: School of Life Sciences, University of Lincoln, Lincoln, UK
| | - Ália dos Santos
- grid.11835.3e0000 0004 1936 9262Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Alexander W. Cook
- grid.11835.3e0000 0004 1936 9262Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Rosemarie E. Gough
- grid.11835.3e0000 0004 1936 9262Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Hannah C. W. Reed
- grid.9759.20000 0001 2232 2818School of Biosciences, University of Kent, Canterbury, UK
| | - Lin Wang
- grid.76978.370000 0001 2296 6998Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Didcot, Oxford, UK
| | - Jesse Aaron
- grid.443970.dAdvanced Imaging Center, HHMI Janelia Research Campus, Ashburn, VA USA
| | - Tomas Venit
- grid.440573.10000 0004 1755 5934Science Division, Biology Program, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
| | - Eric Wait
- grid.443970.dAdvanced Imaging Center, HHMI Janelia Research Campus, Ashburn, VA USA
| | | | | | - Piergiorgio Percipalle
- grid.440573.10000 0004 1755 5934Science Division, Biology Program, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates ,grid.10548.380000 0004 1936 9377Department of Molecular Bioscience, The Wenner Gren Institute, Stockholm University, Stockholm, SE Sweden
| | - Teng-Leong Chew
- grid.443970.dAdvanced Imaging Center, HHMI Janelia Research Campus, Ashburn, VA USA
| | - Marisa Martin-Fernandez
- grid.76978.370000 0001 2296 6998Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Didcot, Oxford, UK
| | - Christopher P. Toseland
- grid.11835.3e0000 0004 1936 9262Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
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8
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Mahmood SR, El Said NH, Percipalle P. The Role of Nuclear Actin in Genome Organization and Gene Expression Regulation During Differentiation. Results Probl Cell Differ 2022; 70:607-624. [PMID: 36348124 DOI: 10.1007/978-3-031-06573-6_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In the cell nucleus, actin participates in numerous essential processes. Actin is involved in chromatin as part of specific ATP-dependent chromatin remodeling complexes and associates with the RNA polymerase machinery to regulate transcription at multiple levels. Emerging evidence has also shown that the nuclear actin pool controls the architecture of the mammalian genome playing an important role in its hierarchical organization into transcriptionally active and repressed compartments, contributing to the clustering of RNA polymerase II into transcriptional hubs. Here, we review the most recent literature and discuss how actin involvement in genome organization impacts the regulation of gene programs that are activated or repressed during differentiation and development. As in the cytoplasm, we propose that nuclear actin is involved in key nuclear tasks in complex with different types of actin-binding proteins that regulate actin function and bridge interactions between actin and various nuclear components.
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Affiliation(s)
- Syed Raza Mahmood
- Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
- Department of Biology, New York University, New York, NY, USA
| | - Nadine Hosny El Said
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
| | - Piergiorgio Percipalle
- Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates.
- Department of Biology, New York University, New York, NY, USA.
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates.
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9
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Esposito G, Hunashal Y, Percipalle M, Venit T, Dieng MM, Fogolari F, Hassanzadeh G, Piano F, Gunsalus KC, Idaghdour Y, Percipalle P. NMR-Based Analysis of Nanobodies to SARS-CoV-2 Nsp9 Reveals a Possible Antiviral Strategy Against COVID-19. Adv Biol (Weinh) 2021; 5:e2101113. [PMID: 34705339 PMCID: PMC8646926 DOI: 10.1002/adbi.202101113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/16/2021] [Indexed: 11/17/2022]
Abstract
Following the entry into the host cell, SARS-CoV-2 replication is mediated by the replication transcription complex (RTC) assembled through a number of nonstructural proteins (Nsps). A monomeric form of Nsp9 is particularly important for RTC assembly and function. In the present study, 136 unique nanobodies targeting Nsp9 are generated. Several nanobodies belonging to different B-cell lineages are expressed, purified, and characterized. Results from immunoassays applied to purified Nsp9 and neat saliva from coronavirus disease (COVID-19) patients show that these nanobodies effectively and specifically recognize both recombinant and endogenous Nsp9. Nuclear magnetic resonance analyses supported by molecular dynamics reveal a composite Nsp9 oligomerization pattern and demonstrate that both nanobodies stabilize the tetrameric form of wild-type Nsp9 also identifying the epitopes on the tetrameric assembly. These results can have important implications in the potential use of these nanobodies to combat viral replication.
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Affiliation(s)
- Gennaro Esposito
- Chemistry Program, Science DivisionNew York University Abu DhabiAbu Dhabi129188United Arab Emirates
- Istituto Nazionale Biostrutture e BiosistemiRoma00136Italy
| | - Yamanappa Hunashal
- Chemistry Program, Science DivisionNew York University Abu DhabiAbu Dhabi129188United Arab Emirates
| | - Mathias Percipalle
- Chemistry Program, Science DivisionNew York University Abu DhabiAbu Dhabi129188United Arab Emirates
- Department of Chemistry and Magnetic Resonance CenterUniversity of FlorenceFlorence50019Italy
| | - Tomas Venit
- Biology Program, Science DivisionNew York University Abu DhabiAbu Dhabi129188United Arab Emirates
| | - Mame Massar Dieng
- Biology Program, Science DivisionNew York University Abu DhabiAbu Dhabi129188United Arab Emirates
| | - Federico Fogolari
- Istituto Nazionale Biostrutture e BiosistemiRoma00136Italy
- Dipartimento di Scienze Matematiche, Informatiche, e FisicheUdine UniversityUdine33100Italy
| | | | - Fabio Piano
- Biology Program, Science DivisionNew York University Abu DhabiAbu Dhabi129188United Arab Emirates
- Public Health Research CenterNew York University Abu DhabiAbu Dhabi129188United Arab Emirates
| | - Kristin C. Gunsalus
- Center for Genomics and Systems BiologyNew York University Abu Dhabi (NYUAD)P.O. Box 129188Abu DhabiUnited Arab Emirates
- Department of BiologyCenter for Genomics and Systems Biology New York UniversityNew YorkNY10003USA
| | - Youssef Idaghdour
- Biology Program, Science DivisionNew York University Abu DhabiAbu Dhabi129188United Arab Emirates
- Public Health Research CenterNew York University Abu DhabiAbu Dhabi129188United Arab Emirates
| | - Piergiorgio Percipalle
- Biology Program, Science DivisionNew York University Abu DhabiAbu Dhabi129188United Arab Emirates
- Department of Molecular BioscienceThe Wenner Gren InstituteStockholm UniversityStockholmS‐106 91Sweden
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10
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Di Conza G, Tsai CH, Gallart-Ayala H, Yu YR, Franco F, Zaffalon L, Xie X, Li X, Xiao Z, Raines LN, Falquet M, Jalil A, Locasale JW, Percipalle P, Masson D, Huang SCC, Martinon F, Ivanisevic J, Ho PC. Tumor-induced reshuffling of lipid composition on the endoplasmic reticulum membrane sustains macrophage survival and pro-tumorigenic activity. Nat Immunol 2021; 22:1403-1415. [PMID: 34686867 PMCID: PMC7611917 DOI: 10.1038/s41590-021-01047-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 09/14/2021] [Indexed: 01/20/2023]
Abstract
Tumor-associated macrophages (TAMs) display pro-tumorigenic phenotypes for supporting tumor progression in response to microenvironmental cues imposed by tumor and stromal cells. However, the underlying mechanisms by which tumor cells instruct TAM behavior remain elusive. Here, we uncover that tumor-cell-derived glucosylceramide stimulated unconventional endoplasmic reticulum (ER) stress responses by inducing reshuffling of lipid composition and saturation on the ER membrane in macrophages, which induced IRE1-mediated spliced XBP1 production and STAT3 activation. The cooperation of spliced XBP1 and STAT3 reinforced the pro-tumorigenic phenotype and expression of immunosuppressive genes. Ablation of XBP1 expression with genetic manipulation or ameliorating ER stress responses by facilitating LPCAT3-mediated incorporation of unsaturated lipids to the phosphatidylcholine hampered pro-tumorigenic phenotype and survival in TAMs. Together, we uncover the unexpected roles of tumor-cell-produced lipids that simultaneously orchestrate macrophage polarization and survival in tumors via induction of ER stress responses and reveal therapeutic targets for sustaining host antitumor immunity.
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Affiliation(s)
- Giusy Di Conza
- Department of Oncology, University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Chin-Hsien Tsai
- Department of Oncology, University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Hector Gallart-Ayala
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Yi-Ru Yu
- Department of Oncology, University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Fabien Franco
- Department of Oncology, University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Lea Zaffalon
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Xin Xie
- Program in Biology, Division of Science and Mathematics, New York University, Abu Dhabi, United Arab Emirates
| | - Xiaoyun Li
- Department of Oncology, University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Zhengtao Xiao
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Institute of Infections and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Lydia N Raines
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Maryline Falquet
- Department of Oncology, University of Lausanne, Epalinges, Switzerland
| | - Antoine Jalil
- Lipids Nutrition Cancer-LNC, INSERM-Université de Bourgogne, Dijon, France
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Piergiorgio Percipalle
- Program in Biology, Division of Science and Mathematics, New York University, Abu Dhabi, United Arab Emirates
- Department of Molecular Bioscience, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - David Masson
- Lipids Nutrition Cancer-LNC, INSERM-Université de Bourgogne, Dijon, France
| | - Stanley Ching-Cheng Huang
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Fabio Martinon
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Julijana Ivanisevic
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Ping-Chih Ho
- Department of Oncology, University of Lausanne, Epalinges, Switzerland.
- Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland.
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11
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Record J, Saeed MB, Venit T, Percipalle P, Westerberg LS. Journey to the Center of the Cell: Cytoplasmic and Nuclear Actin in Immune Cell Functions. Front Cell Dev Biol 2021; 9:682294. [PMID: 34422807 PMCID: PMC8375500 DOI: 10.3389/fcell.2021.682294] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/06/2021] [Indexed: 12/12/2022] Open
Abstract
Actin cytoskeletal dynamics drive cellular shape changes, linking numerous cell functions to physiological and pathological cues. Mutations in actin regulators that are differentially expressed or enriched in immune cells cause severe human diseases known as primary immunodeficiencies underscoring the importance of efficienct actin remodeling in immune cell homeostasis. Here we discuss recent findings on how immune cells sense the mechanical properties of their environement. Moreover, while the organization and biochemical regulation of cytoplasmic actin have been extensively studied, nuclear actin reorganization is a rapidly emerging field that has only begun to be explored in immune cells. Based on the critical and multifaceted contributions of cytoplasmic actin in immune cell functionality, nuclear actin regulation is anticipated to have a large impact on our understanding of immune cell development and functionality.
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Affiliation(s)
- Julien Record
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Mezida B. Saeed
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Tomas Venit
- Science Division, Biology Program, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
| | - Piergiorgio Percipalle
- Science Division, Biology Program, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Lisa S. Westerberg
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
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12
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Venit T, El Said NH, Mahmood SR, Percipalle P. A dynamic actin-dependent nucleoskeleton and cell identity. J Biochem 2021; 169:243-257. [PMID: 33351909 DOI: 10.1093/jb/mvaa133] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 10/27/2020] [Indexed: 12/19/2022] Open
Abstract
Actin is an essential regulator of cellular functions. In the eukaryotic cell nucleus, actin regulates chromatin as a bona fide component of chromatin remodelling complexes, it associates with nuclear RNA polymerases to regulate transcription and is involved in co-transcriptional assembly of nascent RNAs into ribonucleoprotein complexes. Actin dynamics are, therefore, emerging as a major regulatory factor affecting diverse cellular processes. Importantly, the involvement of actin dynamics in nuclear functions is redefining the concept of nucleoskeleton from a rigid scaffold to a dynamic entity that is likely linked to the three-dimensional organization of the nuclear genome. In this review, we discuss how nuclear actin, by regulating chromatin structure through phase separation may contribute to the architecture of the nuclear genome during cell differentiation and facilitate the expression of specific gene programs. We focus specifically on mitochondrial genes and how their dysregulation in the absence of actin raises important questions about the role of cytoskeletal proteins in regulating chromatin structure. The discovery of a novel pool of mitochondrial actin that serves as 'mitoskeleton' to facilitate organization of mtDNA supports a general role for actin in genome architecture and a possible function of distinct actin pools in the communication between nucleus and mitochondria.
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Affiliation(s)
- Tomas Venit
- Science Division, Biology Program, New York University Abu Dhabi (NYUAD), PO Box 129188, Abu Dhabi United Arab Emirates
| | - Nadine Hosny El Said
- Science Division, Biology Program, New York University Abu Dhabi (NYUAD), PO Box 129188, Abu Dhabi United Arab Emirates
| | - Syed Raza Mahmood
- Science Division, Biology Program, New York University Abu Dhabi (NYUAD), PO Box 129188, Abu Dhabi United Arab Emirates.,Department of Biology, New York University, 100 Washington Square East, 1009 Silver Center, New York, NY 10003, USA
| | - Piergiorgio Percipalle
- Science Division, Biology Program, New York University Abu Dhabi (NYUAD), PO Box 129188, Abu Dhabi United Arab Emirates.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 114 18 Stockholm, Sweden
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13
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Bajusz C, Kristó I, Abonyi C, Venit T, Vedelek V, Lukácsovich T, Farkas A, Borkúti P, Kovács Z, Bajusz I, Marton A, Vizler C, Lipinszki Z, Sinka R, Percipalle P, Vilmos P. The nuclear activity of the actin-binding Moesin protein is necessary for gene expression in Drosophila. FEBS J 2021; 288:4812-4832. [PMID: 33606336 DOI: 10.1111/febs.15779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/22/2021] [Accepted: 02/18/2021] [Indexed: 11/30/2022]
Abstract
Ezrin-Radixin-Moesin (ERM) proteins play an essential role in the cytoplasm by cross-linking actin filaments with plasma membrane proteins. Research has identified the nuclear localization of ERMs, as well as the involvement of a single Drosophila ERM protein, Moesin, in nuclear mRNA exports. However, the question of how important the nuclear activity of ERM proteins are for the life of an organism has so far not been explored. Here, we present the first attempt to reveal the in vivo relevance of nuclear localization of Moesin in Drosophila. With the help of a nuclear export signal, we decreased the amount of Moesin in the nuclei of the animals. Furthermore, we observed various developmental defects, demonstrating the importance of ERM function in the nucleus for the first time. Transcriptome analysis of the mutant flies revealed that the lack of nuclear Moesin function leads to expression changes in nearly 700 genes, among them heat-shock genes. This result together with additional findings revealed that in Drosophila the expression of protein chaperones requires the nuclear functions of Moesin. DATABASE: GEO accession number: GSE155778.
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Affiliation(s)
- Csaba Bajusz
- Eötvös Loránd Research Network (ELKH), Biological Research Centre, Szeged, Hungary.,Doctoral School of Biology, University of Szeged, Hungary
| | - Ildikó Kristó
- Eötvös Loránd Research Network (ELKH), Biological Research Centre, Szeged, Hungary
| | - Csilla Abonyi
- Eötvös Loránd Research Network (ELKH), Biological Research Centre, Szeged, Hungary
| | - Tomáš Venit
- Biology Program, Science Division, New York University Abu Dhabi, UAE
| | | | | | - Attila Farkas
- Eötvös Loránd Research Network (ELKH), Biological Research Centre, Szeged, Hungary
| | - Péter Borkúti
- Eötvös Loránd Research Network (ELKH), Biological Research Centre, Szeged, Hungary.,Doctoral School of Multidisciplinary Medical Science, University of Szeged, Hungary
| | - Zoltán Kovács
- Eötvös Loránd Research Network (ELKH), Biological Research Centre, Szeged, Hungary.,Doctoral School of Multidisciplinary Medical Science, University of Szeged, Hungary
| | - Izabella Bajusz
- Eötvös Loránd Research Network (ELKH), Biological Research Centre, Szeged, Hungary
| | - Annamária Marton
- Eötvös Loránd Research Network (ELKH), Biological Research Centre, Szeged, Hungary
| | - Csaba Vizler
- Eötvös Loránd Research Network (ELKH), Biological Research Centre, Szeged, Hungary
| | - Zoltán Lipinszki
- Lendület Laboratory of Cell Cycle Regulation, ELKH, Biological Research Centre, Szeged, Hungary
| | - Rita Sinka
- Department of Genetics, University of Szeged, Hungary
| | - Piergiorgio Percipalle
- Biology Program, Science Division, New York University Abu Dhabi, UAE.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Péter Vilmos
- Eötvös Loránd Research Network (ELKH), Biological Research Centre, Szeged, Hungary
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14
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Xie X, Mahmood SR, Gjorgjieva T, Percipalle P. Emerging roles of cytoskeletal proteins in regulating gene expression and genome organization during differentiation. Nucleus 2020; 11:53-65. [PMID: 32212905 PMCID: PMC7289583 DOI: 10.1080/19491034.2020.1742066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In the eukaryotic cell nucleus, cytoskeletal proteins are emerging as essential players in nuclear function. In particular, actin regulates chromatin as part of ATP-dependent chromatin remodeling complexes, it modulates transcription and it is incorporated into nascent ribonucleoprotein complexes, accompanying them from the site of transcription to polyribosomes. The nuclear actin pool is undistinguishable from the cytoplasmic one in terms of its ability to undergo polymerization and it has also been implicated in the dynamics of chromatin, regulating heterochromatin segregation at the nuclear lamina and maintaining heterochromatin levels in the nuclear interiors. One of the next frontiers is, therefore, to determine a possible involvement of nuclear actin in the functional architecture of the cell nucleus by regulating the hierarchical organization of chromatin and, thus, genome organization. Here, we discuss the repertoire of these potential actin functions and how they are likely to play a role in the context of cellular differentiation.
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Affiliation(s)
- Xin Xie
- Science Division, Biology Program, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
| | - S Raza Mahmood
- Science Division, Biology Program, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates.,Department of Biology, New York University, New York, NY, USA
| | - Tamara Gjorgjieva
- Science Division, Biology Program, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
| | - Piergiorgio Percipalle
- Science Division, Biology Program, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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15
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Gjorgjieva T, Xie X, Commins P, Pasricha R, Mahmood SR, Gunsalus KC, Naumov P, Percipalle P. Loss of β-Actin Leads to Accelerated Mineralization and Dysregulation of Osteoblast-Differentiation Genes during Osteogenic Reprogramming. Adv Sci (Weinh) 2020; 7:2002261. [PMID: 33304760 PMCID: PMC7709978 DOI: 10.1002/advs.202002261] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/29/2020] [Indexed: 06/12/2023]
Abstract
Actin plays fundamental roles in both the cytoplasm and the cell nucleus. In the nucleus, β-actin regulates neuronal reprogramming by consolidating a heterochromatin landscape required for transcription of neuronal gene programs, yet it remains unknown whether it has a role in other differentiation models. To explore the potential roles of β-actin in osteogenesis, β-actin wild-type (WT) and β-actin knockout (KO) mouse embryonic fibroblasts (MEFs) are reprogrammed to osteoblast-like cells using small molecules in vitro. It is discovered that loss of β-actin leads to an accelerated mineralization phenotype (hypermineralization), accompanied with enhanced formation of extracellular hydroxyapatite microcrystals, which originate in the mitochondria in the form of microgranules. This phenotype is a consequence of rapid upregulation of mitochondrial genes including those involved in oxidative phosphorylation (OXPHOS) in reprogrammed KO cells. It is further found that osteogenic gene programs are differentially regulated between WT and KO cells, with clusters of genes exhibiting different temporal expression patterns. A novel function for β-actin in osteogenic reprogramming through a mitochondria-based mechanism that controls cell-mediated mineralization is proposed.
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Affiliation(s)
- Tamara Gjorgjieva
- Program in BiologyDivision of Science and MathematicsNew York University Abu Dhabi (NYUAD)P.O. Box 129188Abu DhabiUnited Arab Emirates
| | - Xin Xie
- Program in BiologyDivision of Science and MathematicsNew York University Abu Dhabi (NYUAD)P.O. Box 129188Abu DhabiUnited Arab Emirates
- Center for Genomics and Systems BiologyNew York University Abu Dhabi (NYUAD)P.O. Box 129188Abu DhabiUnited Arab Emirates
| | - Patrick Commins
- Program in ChemistryDivision of Science and MathematicsNew York University Abu Dhabi (NYUAD)P.O. Box 129188Abu DhabiUnited Arab Emirates
| | - Renu Pasricha
- Core Technology PlatformsNew York University Abu Dhabi (NYUAD)P.O. Box 129188Abu DhabiUnited Arab Emirates
| | - Syed Raza Mahmood
- Program in BiologyDivision of Science and MathematicsNew York University Abu Dhabi (NYUAD)P.O. Box 129188Abu DhabiUnited Arab Emirates
- Department of BiologyNew York UniversityNew YorkNY10003USA
| | - Kristin C. Gunsalus
- Center for Genomics and Systems BiologyNew York University Abu Dhabi (NYUAD)P.O. Box 129188Abu DhabiUnited Arab Emirates
- Department of BiologyNew York UniversityNew YorkNY10003USA
| | - Panče Naumov
- Program in ChemistryDivision of Science and MathematicsNew York University Abu Dhabi (NYUAD)P.O. Box 129188Abu DhabiUnited Arab Emirates
| | - Piergiorgio Percipalle
- Program in BiologyDivision of Science and MathematicsNew York University Abu Dhabi (NYUAD)P.O. Box 129188Abu DhabiUnited Arab Emirates
- Department of Molecular BiosciencesThe Wenner‐Gren InstituteStockholm UniversityStockholmSE‐106 91Sweden
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16
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Al-Sayegh MA, Mahmood SR, Khair SBA, Xie X, El Gindi M, Kim T, Almansoori A, Percipalle P. β-actin contributes to open chromatin for activation of the adipogenic pioneer factor CEBPA during transcriptional reprograming. Mol Biol Cell 2020; 31:2511-2521. [PMID: 32877276 PMCID: PMC7851876 DOI: 10.1091/mbc.e19-11-0628] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Adipogenesis is regulated by a cascade of signals that drive transcriptional reprogramming in adipocytes. Here, we report that nuclear actin regulates the chromatin states that establish tissue- specific expression during adipogenesis. To study the role of β-actin in adipocyte differentiation, we conducted RNA sequencing on wild-type and β-actin knockout mouse embryonic fibroblasts (MEFs) after reprograming to adipocytes. We found that β-actin depletion affects induction of several adipogenic genes during transcriptional reprograming. This impaired regulation of adipogenic genes is linked to reduced expression of the pioneer factor Cebpa and is rescued by reintroducing NLS-tagged β-actin. ATAC-Seq in knockout MEFs revealed that actin-dependent reduction of Cebpa expression correlates with decreased chromatin accessibility and loss of chromatin association of the ATPase Brg1. This, in turn, impairs CEBPB's association with its Cebpa promoter-proximal binding site during adipogenesis. We propose a role for the nuclear β-actin pool in maintaining open chromatin for transcriptional reprogramming during adipogenic differentiation.
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Affiliation(s)
- M A Al-Sayegh
- Biology Program, Science Division, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
| | - S R Mahmood
- Biology Program, Science Division, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates.,Department of Biology, New York University, New York, NY 10003
| | - S B Abul Khair
- Biology Program, Science Division, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
| | - X Xie
- Biology Program, Science Division, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
| | - M El Gindi
- Biology Program, Science Division, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
| | - T Kim
- Biology Program, Science Division, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
| | - A Almansoori
- Biology Program, Science Division, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
| | - P Percipalle
- Biology Program, Science Division, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
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17
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Abstract
The emerging role of cytoskeletal proteins in the cell nucleus has become a new frontier in cell biology. Actin and actin-binding proteins regulate chromatin and gene expression, but importantly they are beginning to be essential players in genome organization. These actin-based functions contribute to genome stability and integrity while affecting DNA replication and global transcription patterns. This is likely to occur through interactions of actin with nuclear components including nuclear lamina and subnuclear organelles. An exciting future challenge is to understand how these actin-based genome-wide mechanisms may regulate development and differentiation by interfering with the mechanical properties of the cell nucleus and how regulated actin polymerization plays a role in maintaining nuclear architecture. With a special focus on actin, here we summarize how cytoskeletal proteins operate in the nucleus and how they may be important to consolidate nuclear architecture for sustained gene expression or silencing.
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Affiliation(s)
- Piergiorgio Percipalle
- Biology Program, Science Division, New York University Abu Dhabi, 12988 Abu Dhabi, United Arab Emirates.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Maria Vartiainen
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
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18
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Venit T, Mahmood SR, Endara-Coll M, Percipalle P. Nuclear actin and myosin in chromatin regulation and maintenance of genome integrity. International Review of Cell and Molecular Biology 2020; 355:67-108. [DOI: 10.1016/bs.ircmb.2020.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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19
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Prakash V, Carson BB, Feenstra JM, Dass RA, Sekyrova P, Hoshino A, Petersen J, Guo Y, Parks MM, Kurylo CM, Batchelder JE, Haller K, Hashimoto A, Rundqivst H, Condeelis JS, Allis CD, Drygin D, Nieto MA, Andäng M, Percipalle P, Bergh J, Adameyko I, Farrants AKÖ, Hartman J, Lyden D, Pietras K, Blanchard SC, Vincent CT. Ribosome biogenesis during cell cycle arrest fuels EMT in development and disease. Nat Commun 2019; 10:2110. [PMID: 31068593 PMCID: PMC6506521 DOI: 10.1038/s41467-019-10100-8] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 04/16/2019] [Indexed: 12/15/2022] Open
Abstract
Ribosome biogenesis is a canonical hallmark of cell growth and proliferation. Here we show that execution of Epithelial-to-Mesenchymal Transition (EMT), a migratory cellular program associated with development and tumor metastasis, is fueled by upregulation of ribosome biogenesis during G1/S arrest. This unexpected EMT feature is independent of species and initiating signal, and is accompanied by release of the repressive nucleolar chromatin remodeling complex (NoRC) from rDNA, together with recruitment of the EMT-driving transcription factor Snai1 (Snail1), RNA Polymerase I (Pol I) and the Upstream Binding Factor (UBF). EMT-associated ribosome biogenesis is also coincident with increased nucleolar recruitment of Rictor, an essential component of the EMT-promoting mammalian target of rapamycin complex 2 (mTORC2). Inhibition of rRNA synthesis in vivo differentiates primary tumors to a benign, Estrogen Receptor-alpha (ERα) positive, Rictor-negative phenotype and reduces metastasis. These findings implicate the EMT-associated ribosome biogenesis program with cellular plasticity, de-differentiation, cancer progression and metastatic disease.
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Affiliation(s)
- Varsha Prakash
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Brittany B Carson
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Jennifer M Feenstra
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Randall A Dass
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Petra Sekyrova
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Ayuko Hoshino
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA.,Department of Pediatrics and Cell and Developmental Biology, Weill Cornell Medicine College, New York, NY, 10065, USA
| | - Julian Petersen
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden.,Department for Brain Research, Medical University of Vienna, 1090, Vienna, Austria
| | - Yuan Guo
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691, Stockholm, Sweden
| | - Matthew M Parks
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.,Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Chad M Kurylo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.,Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Jake E Batchelder
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.,Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Kristian Haller
- Department of Laboratory Medicine, Center for Molecular Pathology, Lund University, Lund, SE-223 81, Sweden
| | - Ayako Hashimoto
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA.,Department of Pediatrics and Cell and Developmental Biology, Weill Cornell Medicine College, New York, NY, 10065, USA
| | - Helene Rundqivst
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, SE-171 77, Sweden
| | - John S Condeelis
- Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, 10461, NY, USA.,Department of Pathology, Montefiore Medical Center, Bronx, 10461, NY, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Denis Drygin
- Pimera, Inc, 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - M Angela Nieto
- Instituto de Neurociencias, CSIC-UMH, Alicante, 03550, Spain
| | - Michael Andäng
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Piergiorgio Percipalle
- Science Division, Biology Program, New York University Abu Dhabi, Abu Dhabi, 129188, UAE
| | - Jonas Bergh
- Department of Oncology and Pathology, Karolinska Institutet and University Hospital, S-171 76, Solna, Sweden
| | - Igor Adameyko
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden.,Department for Brain Research, Medical University of Vienna, 1090, Vienna, Austria
| | - Ann-Kristin Östlund Farrants
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691, Stockholm, Sweden
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institutet and University Hospital, S-171 76, Solna, Sweden
| | - David Lyden
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA.,Department of Pediatrics and Cell and Developmental Biology, Weill Cornell Medicine College, New York, NY, 10065, USA
| | - Kristian Pietras
- Department of Laboratory Medicine, Center for Molecular Pathology, Lund University, Lund, SE-223 81, Sweden
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA. .,Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA. .,Tri-Institutional Training Program in Chemical Biology, Weill Cornell Medicine, New York, NY, 10065, USA.
| | - C Theresa Vincent
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden. .,Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden. .,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA. .,Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA.
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20
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Xie X, Liu PS, Percipalle P. Analysis of Global Transcriptome Change in Mouse Embryonic Fibroblasts After dsDNA and dsRNA Viral Mimic Stimulation. Front Immunol 2019; 10:836. [PMID: 31057555 PMCID: PMC6478819 DOI: 10.3389/fimmu.2019.00836] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 04/01/2019] [Indexed: 01/01/2023] Open
Abstract
The activation of innate immunity by viral nucleic acids present in the cytoplasm plays an essential role in controlling viral infection in both immune and non-immune cells. The dsDNA and dsRNA viral mimics can stimulate the cytosolic nucleic acids sensors and activate the antiviral innate immunity. In this study, taking advantage of dsDNA and dsRNA viral mimics, we investigated the global transcriptome changes after the antiviral immunity activation in mouse embryonic fibroblasts. Results from our data identified a positive feedback up-regulation of sensors (e.g., Tlr2, Tlr3, Ddx58, cGAS), transducers (e.g., Traf2, Tbk1) and transcription factors (e.g., Irf7, Jun, Stat1, Stat2) in multiple pathways involved in detecting viral or microbial infections upon viral mimic stimulation. A group of genes involved in DNA damage response and DNA repair such as Parp9, Dtx3l, Rad52 were also up-regulated, implying the involvement of these genes in antiviral immunity. Molecular function analysis further showed that groups of helicase genes (e.g., Dhx58, Helz2), nuclease genes (e.g., Dnase1l3, Rsph10b), methyltransferase genes (e.g., histone methyltransferase Prdm9, Setdb2; RNA methyltransferase Mettl3, Mttl14), and protein ubiquitin-ligase genes (e.g., Trim genes and Rnf genes) were up-regulated upon antiviral immunity activation. In contrast, viral mimic stimulation down-regulated genes involved in a broad range of general biological processes (e.g., cell division, metabolism), cellular components (e.g., mitochondria and ribosome), and molecular functions (e.g., cell-cell adhesion, microtubule binding). In summary, our study provides valuable information about the global transcriptome changes upon antiviral immunity activation. The identification of novel groups of genes up-regulated upon antiviral immunity activation serves as useful resource for mining new antiviral sensors and effectors.
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Affiliation(s)
- Xin Xie
- Biology Program, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
| | - Pu-Ste Liu
- Institute of Cellular and System Medicine, National Health Research Institutes, Zhunan, Taiwan
| | - Piergiorgio Percipalle
- Biology Program, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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21
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Cook A, Hari Gupta Y, Venit T, Percipalle P, Toseland CP. Myosin VI and its Role in the DNA Damage Response. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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22
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Abstract
In eukaryotic cells, gene expression is highly regulated at many layers. Nascent RNA molecules are assembled into ribonucleoprotein complexes that are then released into the nucleoplasmic milieu and transferred to the nuclear pore complex for nuclear export. RNAs are then either translated or transported to the cellular periphery. Emerging evidence indicates that RNA-binding proteins play an essential role throughout RNA biogenesis, from the gene to polyribosomes. However, the sorting mechanisms that regulate whether an RNA molecule is immediately translated or sent to specialized locations for translation are unclear. This question is highly relevant during development and differentiation when cells acquire a specific identity. Here, we focus on the RNA-binding properties of heterogeneous nuclear ribonucleoproteins (hnRNPs) and how these mechanisms are believed to play an essential role in RNA trafficking in polarized cells. Further, by focusing on the specific hnRNP protein CBF-A/hnRNPab and its naturally occurring isoforms, we propose a model on how hnRNP proteins are capable of regulating gene expression both spatially and temporally throughout the RNA biogenesis pathway, impacting both healthy and diseased cells.
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Affiliation(s)
- Nathalie Neriec
- Biology Department, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Piergiorgio Percipalle
- Biology Department, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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23
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Xie X, Percipalle P. Elevated transforming growth factor β signaling activation in β-actin-knockout mouse embryonic fibroblasts enhances myofibroblast features. J Cell Physiol 2018; 233:8884-8895. [PMID: 29851084 PMCID: PMC6220129 DOI: 10.1002/jcp.26808] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 05/30/2018] [Indexed: 01/08/2023]
Abstract
Signaling by the transforming growth factor‐β (TGF‐β) is an essential pathway regulating a variety of cellular events. TGF‐β is produced as a latent protein complex and is required to be activated before activating the receptor. The mechanical force at the cell surface is believed to be a mechanism for latent TGF‐β activation. Using β‐actin null mouse embryonic fibroblasts as a model, in which actin cytoskeleton and cell‐surface biophysical features are dramatically altered, we reveal increased TGF‐β1 activation and the upregulation of TGF‐β target genes. In β‐actin null cells, we show evidence that the enhanced TGF‐β signaling relies on the active utilization of latent TGF‐β1 in the cell culture medium. TGF‐β signaling activation contributes to the elevated reactive oxygen species production, which is likely mediated by the upregulation of Nox4. The previously observed myofibroblast phenotype of β‐actin null cells is inhibited by TGF‐β signaling inhibition, while the expression of actin cytoskeleton genes and angiogenic phenotype are not affected. Together, our study shows a scenario that the alteration of the actin cytoskeleton and the consequent changes in cellular biophysical features lead to changes in cell signaling process such as TGF‐β activation, which in turn contributes to the enhanced myofibroblast phenotype.
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Affiliation(s)
- Xin Xie
- Biology Program, Science Division, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
| | - Piergiorgio Percipalle
- Biology Program, Science Division, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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24
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Xie X, Deliorman M, Qasaimeh MA, Percipalle P. The relative composition of actin isoforms regulates cell surface biophysical features and cellular behaviors. Biochim Biophys Acta Gen Subj 2018; 1862:1079-1090. [PMID: 29410074 DOI: 10.1016/j.bbagen.2018.01.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 01/28/2018] [Accepted: 01/31/2018] [Indexed: 11/16/2022]
Abstract
BACKGROUND Cell surface mechanics is able to physically and biomechanically affect cell shape and motility, vesicle trafficking and actin dynamics. The biophysical properties of cell surface are strongly influenced by cytoskeletal elements. In mammals, tissue-specific expression of six actin isoforms is thought to confer differential biomechanical properties. However, the relative contribution of actin isoforms to cell surface properties is not well understood. Here, we sought to investigate whether and how the composition of endogenous actin isoforms directly affects the biomechanical features of cell surface and cellular behavior. METHODS We used fibroblasts isolated from wild type (WT), heterozygous (HET) and from knockout (KO) mouse embryos where both β-actin alleles are not functional. We applied a combination of genome-wide analysis and biophysical methods such as RNA-seq and atomic force microscopy. RESULTS We found that endogenous β-actin levels are essential in controlling cell surface stiffness and pull-off force, which was not compensated by the up-regulation of other actin isoforms. The variations of surface biophysical features and actin contents were associated with distinct cell behaviors in 2D and 3D WT, HET and KO cell cultures. Since β-actin in WT cells and smooth muscle α-actin up-regulated in KO cells showed different organization patterns, our data support the differential localization and organization as a mechanism to regulate the biophysical properties of cell surface by actin isoforms. CONCLUSIONS We propose that variations in actin isoforms composition impact on the biophysical features of cell surface and cause the changes in cell behavior.
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Affiliation(s)
- Xin Xie
- Science Division, Biology Program, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Muhammedin Deliorman
- Engineering Division, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Mohammad A Qasaimeh
- Engineering Division, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates; Department of Mechanical and Aerospace Engineering, New York University, USA
| | - Piergiorgio Percipalle
- Science Division, Biology Program, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates; Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden.
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25
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Xie X, Almuzzaini B, Drou N, Kremb S, Yousif A, Farrants AKÖ, Gunsalus K, Percipalle P. β-Actin-dependent global chromatin organization and gene expression programs control cellular identity. FASEB J 2018; 32:1296-1314. [PMID: 29101221 DOI: 10.1096/fj.201700753r] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
During differentiation and development, cell fate and identity are established by waves of genetic reprogramming. Although the mechanisms are largely unknown, during these events, dynamic chromatin reorganization is likely to ensure that multiple genes involved in the same cellular functions are coregulated, depending on the nuclear environment. In this study, using high-content screening of embryonic fibroblasts from a β-actin knockout (KO) mouse, we found major chromatin rearrangements and changes in histone modifications, such as methylated histone (H)3-lysine-(K)9. Genome-wide H3K9 trimethylation-(Me)3 landscape changes correlate with gene up- and down-regulation in β-actin KO cells. Mechanistically, we found loss of chromatin association by the Brahma-related gene ( Brg)/Brahma-associated factor (BAF) chromatin remodeling complex subunit Brg1 in the absence of β-actin. This actin-dependent chromatin reorganization was concomitant with the up-regulation of sets of genes involved in angiogenesis, cytoskeletal organization, and myofibroblast features in β-actin KO cells. Some of these genes and phenotypes were gained in a β-actin dose-dependent manner. Moreover, reintroducing a nuclear localization signal-containing β-actin in the knockout cells affected nuclear features and gene expression. Our results suggest that, by affecting the genome-wide organization of heterochromatin through the chromatin-binding activity of the BAF complex, β-actin plays an essential role in the determination of gene expression programs and cellular identity.-Xie, X., Almuzzaini, B., Drou, N., Kremb, S., Yousif, A., Östlund Farrants, A.-K., Gunsalus, K., Percipalle, P. β-Actin-dependent global chromatin organization and gene expression programs control cellular identity.
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Affiliation(s)
- Xin Xie
- Biology Program, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
| | - Bader Almuzzaini
- Medical Genomic Research Department, King Abdullah International Medical Research Center/King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Nizar Drou
- NYUAD Center for Genomics and Systems Biology, Abu Dhabi, United Arab Emirates
| | - Stephan Kremb
- NYUAD Center for Genomics and Systems Biology, Abu Dhabi, United Arab Emirates
| | - Ayman Yousif
- NYUAD Center for Genomics and Systems Biology, Abu Dhabi, United Arab Emirates
| | | | - Kristin Gunsalus
- Biology Program, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates.,NYUAD Center for Genomics and Systems Biology, Abu Dhabi, United Arab Emirates.,Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - Piergiorgio Percipalle
- Biology Program, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden; and
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26
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Kuznetsov NV, Almuzzaini B, Kritikou JS, Baptista MAP, Oliveira MMS, Keszei M, Snapper SB, Percipalle P, Westerberg LS. Nuclear Wiskott-Aldrich syndrome protein co-regulates T cell factor 1-mediated transcription in T cells. Genome Med 2017; 9:91. [PMID: 29078804 PMCID: PMC5660450 DOI: 10.1186/s13073-017-0481-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/11/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The Wiskott-Aldrich syndrome protein (WASp) family of actin-nucleating factors are present in the cytoplasm and in the nucleus. The role of nuclear WASp for T cell development remains incompletely defined. METHODS We performed WASp chromatin immunoprecipitation and deep sequencing (ChIP-seq) in thymocytes and spleen CD4+ T cells. RESULTS WASp was enriched at genic and intergenic regions and associated with the transcription start sites of protein-coding genes. Thymocytes and spleen CD4+ T cells showed 15 common WASp-interacting genes, including the gene encoding T cell factor (TCF)12. WASp KO thymocytes had reduced nuclear TCF12 whereas thymocytes expressing constitutively active WASpL272P and WASpI296T had increased nuclear TCF12, suggesting that regulated WASp activity controlled nuclear TCF12. We identify a putative DNA element enriched in WASp ChIP-seq samples identical to a TCF1-binding site and we show that WASp directly interacted with TCF1 in the nucleus. CONCLUSIONS These data place nuclear WASp in proximity with TCF1 and TCF12, essential factors for T cell development.
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Affiliation(s)
- Nikolai V Kuznetsov
- Department of Microbiology Tumor and Cell biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Bader Almuzzaini
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, 171 77, Sweden.,King Abdullah International Medical Research Center/King Saud bin Abdulaziz University for Health Sciences Medical Genomic Research Department, MNGHA, Riyadh, Saudi Arabia
| | - Joanna S Kritikou
- Department of Microbiology Tumor and Cell biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Marisa A P Baptista
- Department of Microbiology Tumor and Cell biology, Karolinska Institutet, Stockholm, 171 77, Sweden.,Institute for Virology and Immunobiology, University of Würzburg, 97078, Würzburg, Germany
| | - Mariana M S Oliveira
- Department of Microbiology Tumor and Cell biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Marton Keszei
- Department of Microbiology Tumor and Cell biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Scott B Snapper
- Gastroenterology Division, Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Piergiorgio Percipalle
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, 171 77, Sweden.,Biology Program, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - Lisa S Westerberg
- Department of Microbiology Tumor and Cell biology, Karolinska Institutet, Stockholm, 171 77, Sweden.
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27
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Assadi G, Vesterlund L, Bonfiglio F, Mazzurana L, Cordeddu L, Schepis D, Mjösberg J, Ruhrmann S, Fabbri A, Vukojevic V, Percipalle P, Salomons FA, Laurencikiene J, Törkvist L, Halfvarson J, D’Amato M. Functional Analyses of the Crohn's Disease Risk Gene LACC1. PLoS One 2016; 11:e0168276. [PMID: 27959965 PMCID: PMC5154582 DOI: 10.1371/journal.pone.0168276] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/28/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Genetic variation in the Laccase (multicopper oxidoreductase) domain-containing 1 (LACC1) gene has been shown to affect the risk of Crohn's disease, leprosy and, more recently, ulcerative colitis and juvenile idiopathic arthritis. LACC1 function appears to promote fatty-acid oxidation, with concomitant inflammasome activation, reactive oxygen species production, and anti-bacterial responses in macrophages. We sought to contribute to elucidating LACC1 biological function by extensive characterization of its expression in human tissues and cells, and through preliminary analyses of the regulatory mechanisms driving such expression. METHODS We implemented Western blot, quantitative real-time PCR, immunofluorescence microscopy, and flow cytometry analyses to investigate fatty acid metabolism-immune nexus (FAMIN; the LACC1 encoded protein) expression in subcellular compartments, cell lines and relevant human tissues. Gene-set enrichment analyses were performed to initially investigate modulatory mechanisms of LACC1 expression. A small-interference RNA knockdown in vitro model system was used to study the effect of FAMIN depletion on peroxisome function. RESULTS FAMIN expression was detected in macrophage-differentiated THP-1 cells and several human tissues, being highest in neutrophils, monocytes/macrophages, myeloid and plasmacytoid dendritic cells among peripheral blood cells. Subcellular co-localization was exclusively confined to peroxisomes, with some additional positivity for organelle endomembrane structures. LACC1 co-expression signatures were enriched for genes involved in peroxisome proliferator-activated receptors (PPAR) signaling pathways, and PPAR ligands downregulated FAMIN expression in in vitro model systems. CONCLUSION FAMIN is a peroxisome-associated protein with primary role(s) in macrophages and other immune cells, where its metabolic functions may be modulated by PPAR signaling events. However, the precise molecular mechanisms through which FAMIN exerts its biological effects in immune cells remain to be elucidated.
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Affiliation(s)
- Ghazaleh Assadi
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| | - Liselotte Vesterlund
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Ferdinando Bonfiglio
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Luca Mazzurana
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Lina Cordeddu
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Danika Schepis
- Rheumatology unit, Department of Medicine Solna, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Jenny Mjösberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Sabrina Ruhrmann
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Alessia Fabbri
- Department of Therapeutic Research and Medicines Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Vladana Vukojevic
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Piergiorgio Percipalle
- Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Florian A. Salomons
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jurga Laurencikiene
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Leif Törkvist
- Gastrocentrum, Karolinska University Hospital, Stockholm, Sweden
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Mauro D’Amato
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- BioDonostia Health Research Institute, San Sebastian and IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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28
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Dass RA, Sarshad AA, Carson BB, Feenstra JM, Kaur A, Obrdlik A, Parks MM, Prakash V, Love DK, Pietras K, Serra R, Blanchard SC, Percipalle P, Brown AMC, Vincent CT. Wnt5a Signals through DVL1 to Repress Ribosomal DNA Transcription by RNA Polymerase I. PLoS Genet 2016; 12:e1006217. [PMID: 27500936 PMCID: PMC4976976 DOI: 10.1371/journal.pgen.1006217] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 07/05/2016] [Indexed: 11/19/2022] Open
Abstract
Ribosome biogenesis is essential for cell growth and proliferation and is commonly elevated in cancer. Accordingly, numerous oncogene and tumor suppressor signaling pathways target rRNA synthesis. In breast cancer, non-canonical Wnt signaling by Wnt5a has been reported to antagonize tumor growth. Here, we show that Wnt5a rapidly represses rDNA gene transcription in breast cancer cells and generates a chromatin state with reduced transcription of rDNA by RNA polymerase I (Pol I). These effects were specifically dependent on Dishevelled1 (DVL1), which accumulates in nucleolar organizer regions (NORs) and binds to rDNA regions of the chromosome. Upon DVL1 binding, the Pol I transcription activator and deacetylase Sirtuin 7 (SIRT7) releases from rDNA loci, concomitant with disassembly of Pol I transcription machinery at the rDNA promoter. These findings reveal that Wnt5a signals through DVL1 to suppress rRNA transcription. This provides a novel mechanism for how Wnt5a exerts tumor suppressive effects and why disruption of Wnt5a signaling enhances mammary tumor growth in vivo.
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Affiliation(s)
- Randall A. Dass
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York, United States of America
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, United States of America
| | - Aishe A. Sarshad
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
- Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Brittany B. Carson
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Jennifer M. Feenstra
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Amanpreet Kaur
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York, United States of America
| | - Ales Obrdlik
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
- Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Matthew M. Parks
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, United States of America
| | - Varsha Prakash
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Damon K. Love
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York, United States of America
| | - Kristian Pietras
- Department of Laboratory Medicine, Center for Molecular Pathology, Lund University, Lund, Sweden
| | - Rosa Serra
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Scott C. Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, United States of America
- Tri-Institutional PhD program in Chemical Biology, Weill Cornell Medical College, New York, New York, United States of America
| | - Piergiorgio Percipalle
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
- Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- * E-mail: (PP); (AMCB); (CTV)
| | - Anthony M. C. Brown
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail: (PP); (AMCB); (CTV)
| | - C. Theresa Vincent
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York, United States of America
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, United States of America
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
- * E-mail: (PP); (AMCB); (CTV)
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Almuzzaini B, Sarshad AA, Rahmanto AS, Hansson ML, Von Euler A, Sangfelt O, Visa N, Farrants AKÖ, Percipalle P. In β-actin knockouts, epigenetic reprogramming and rDNA transcription inactivation lead to growth and proliferation defects. FASEB J 2016; 30:2860-73. [PMID: 27127100 DOI: 10.1096/fj.201600280r] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/18/2016] [Indexed: 12/18/2022]
Abstract
Actin and nuclear myosin 1 (NM1) are regulators of transcription and chromatin organization. Using a genome-wide approach, we report here that β-actin binds intergenic and genic regions across the mammalian genome, associated with both protein-coding and rRNA genes. Within the rDNA, the distribution of β-actin correlated with NM1 and the other subunits of the B-WICH complex, WSTF and SNF2h. In β-actin(-/-) mouse embryonic fibroblasts (MEFs), we found that rRNA synthesis levels decreased concomitantly with drops in RNA polymerase I (Pol I) and NM1 occupancies across the rRNA gene. Reintroduction of wild-type β-actin, in contrast to mutated forms with polymerization defects, efficiently rescued rRNA synthesis underscoring the direct role for a polymerization-competent form of β-actin in Pol I transcription. The rRNA synthesis defects in the β-actin(-/-) MEFs are a consequence of epigenetic reprogramming with up-regulation of the repressive mark H3K4me1 (monomethylation of lys4 on histone H3) and enhanced chromatin compaction at promoter-proximal enhancer (T0 sequence), which disturb binding of the transcription factor TTF1. We propose a novel genome-wide mechanism where the polymerase-associated β-actin synergizes with NM1 to coordinate permissive chromatin with Pol I transcription, cell growth, and proliferation.-Almuzzaini, B., Sarshad, A. A. , Rahmanto, A. S., Hansson, M. L., Von Euler, A., Sangfelt, O., Visa, N., Farrants, A.-K. Ö., Percipalle, P. In β-actin knockouts, epigenetic reprogramming and rDNA transcription inactivation lead to growth and proliferation defects.
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Affiliation(s)
- Bader Almuzzaini
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden; Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden; and
| | - Aishe A Sarshad
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Aldwin S Rahmanto
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Magnus L Hansson
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Anne Von Euler
- King Abdullah International Medical Research Center, National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Olle Sangfelt
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Neus Visa
- King Abdullah International Medical Research Center, National Guard Health Affairs, Riyadh, Saudi Arabia
| | | | - Piergiorgio Percipalle
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden; King Abdullah International Medical Research Center, National Guard Health Affairs, Riyadh, Saudi Arabia Division of Science, Department of Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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Almuzzaini B, Sarshad AA, Farrants AKÖ, Percipalle P. Nuclear myosin 1 contributes to a chromatin landscape compatible with RNA polymerase II transcription activation. BMC Biol 2015; 13:35. [PMID: 26044184 PMCID: PMC4486089 DOI: 10.1186/s12915-015-0147-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 06/02/2015] [Indexed: 12/11/2022] Open
Abstract
Background Nuclear myosin 1c (NM1) is emerging as a regulator of transcription and chromatin organization. Results Using chromatin immunoprecipitation and deep sequencing (ChIP-Seq) in combination with molecular analyses, we investigated the global association of NM1 with the mammalian genome. Analysis of the ChIP-Seq data demonstrates that NM1 binds across the entire mammalian genome with occupancy peaks correlating with distributions of RNA Polymerase II (Pol II) and active epigenetic marks at class II gene promoters. In mouse embryonic fibroblasts subjected to RNAi mediated NM1 gene silencing, we show that NM1 synergizes with polymerase-associated actin to maintain active Pol II at the promoter. NM1 also co-localizes with the nucleosome remodeler SNF2h at class II promoters where they assemble together with WSTF as part of the B-WICH complex. A high resolution micrococcal nuclease (MNase) assay and quantitative real time PCR shows that this mechanism is required for local chromatin remodeling. Following B-WICH assembly, NM1 mediates physical recruitment of the histone acetyl transferase PCAF and the histone methyl transferase Set1/Ash2 to maintain and preserve H3K9acetylation and H3K4trimethylation for active transcription. Conclusions We propose a novel genome-wide mechanism where myosin synergizes with Pol II-associated actin to link the polymerase machinery with permissive chromatin for transcription activation. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0147-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bader Almuzzaini
- Department of Cell and Molecular Biology, Karolinska Institute, Box 285, SE-171 77, Stockholm, Sweden.
| | - Aishe A Sarshad
- Department of Cell and Molecular Biology, Karolinska Institute, Box 285, SE-171 77, Stockholm, Sweden. .,Present address: National Institute of Health, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, 20892-3675, USA.
| | - Ann-Kristin Östlund Farrants
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden.
| | - Piergiorgio Percipalle
- Department of Cell and Molecular Biology, Karolinska Institute, Box 285, SE-171 77, Stockholm, Sweden.
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Percipalle P. New insights into co-transcriptional sorting of mRNA for cytoplasmic transport during development. Semin Cell Dev Biol 2014; 32:55-62. [DOI: 10.1016/j.semcdb.2014.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 03/11/2014] [Indexed: 12/01/2022]
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Sarshad AA, Corcoran M, Al-Muzzaini B, Borgonovo-Brandter L, Von Euler A, Lamont D, Visa N, Percipalle P. Glycogen synthase kinase (GSK) 3β phosphorylates and protects nuclear myosin 1c from proteasome-mediated degradation to activate rDNA transcription in early G1 cells. PLoS Genet 2014; 10:e1004390. [PMID: 24901984 PMCID: PMC4046919 DOI: 10.1371/journal.pgen.1004390] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 04/03/2014] [Indexed: 11/17/2022] Open
Abstract
Nuclear myosin 1c (NM1) mediates RNA polymerase I (pol I) transcription activation and cell cycle progression by facilitating PCAF-mediated H3K9 acetylation, but the molecular mechanism by which NM1 is regulated remains unclear. Here, we report that at early G1 the glycogen synthase kinase (GSK) 3β phosphorylates and stabilizes NM1, allowing for NM1 association with the chromatin. Genomic analysis by ChIP-Seq showed that this mechanism occurs on the rDNA as active GSK3β selectively occupies the gene. ChIP assays and transmission electron microscopy in GSK3β−/− mouse embryonic fibroblasts indicated that at G1 rRNA synthesis is suppressed due to decreased H3K9 acetylation leading to a chromatin state incompatible with transcription. We found that GSK3β directly phosphorylates the endogenous NM1 on a single serine residue (Ser-1020) located within the NM1 C-terminus. In G1 this phosphorylation event stabilizes NM1 and prevents NM1 polyubiquitination by the E3 ligase UBR5 and proteasome-mediated degradation. We conclude that GSK3β-mediated phosphorylation of NM1 is required for pol I transcription activation. Nuclear actin and myosin are essential regulators of gene expression. At the exit of mitosis, nuclear myosin 1c (NM1) mediates RNA polymerase I (pol I) transcription activation and cell cycle progression by modulating assembly of the chromatin remodeling complex WICH with the subunits WSTF and SNF2h and, crucially, facilitating H3K9 acetylation by the histone acetyl transferase PCAF. The molecular mechanism by which NM1 is regulated remains however unknown. Here, we conducted a genome-wide screen and demonstrate that GSK3β is selectively coupled to the rDNA transcription unit. In embryonic fibroblasts lacking GSK3β there is a significant drop in rRNA synthesis levels and the rDNA is devoid of actin, NM1 and SNF2h. Concomitantly with a transcriptional block we reveal decreased levels of histone H3 acetylation by the histone acetyl transferase PCAF. At G1, transcriptional repression in the GSK3β knockout mouse embryonic fibroblasts, leads to NM1 ubiquitination by the E3 ligase UBR5 and proteasome-mediated degradation. We conclude that GSK3β suppresses NM1 degradation through the ubiquitin-proteasome system, facilitates NM1 association with the rDNA chromatin and transcription activation at G1. We therefore propose a novel and fundamental role for GSK3β as essential regulator of rRNA synthesis and cell cycle progression.
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Affiliation(s)
- Aishe A Sarshad
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Martin Corcoran
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Bader Al-Muzzaini
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | | | - Anne Von Euler
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Douglas Lamont
- FingerPrints Proteomics Facility, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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Sarshad AA, Percipalle P. New Insight into Role of Myosin Motors for Activation of RNA Polymerases. International Review of Cell and Molecular Biology 2014; 311:183-230. [DOI: 10.1016/b978-0-12-800179-0.00004-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Fukuda N, Fukuda T, Sinnamon J, Hernandez-Hernandez A, Izadi M, Raju CS, Czaplinski K, Percipalle P. The transacting factor CBF-A/Hnrnpab binds to the A2RE/RTS element of protamine 2 mRNA and contributes to its translational regulation during mouse spermatogenesis. PLoS Genet 2013; 9:e1003858. [PMID: 24146628 PMCID: PMC3798277 DOI: 10.1371/journal.pgen.1003858] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 08/20/2013] [Indexed: 11/29/2022] Open
Abstract
During spermatogenesis, mRNA localization and translation are believed to be regulated in a stage-specific manner. We report here that the Protamine2 (Prm2) mRNA transits through chromatoid bodies of round spermatids and localizes to cytosol of elongating spermatids for translation. The transacting factor CBF-A, also termed Hnrnpab, contributes to temporal regulation of Prm2 translation. We found that CBF-A co-localizes with the Prm2 mRNA during spermatogenesis, directly binding to the A2RE/RTS element in the 3′ UTR. Although both p37 and p42 CBF-A isoforms interacted with RTS, they associated with translationally repressed and de-repressed Prm2 mRNA, respectively. Only p42 was found to interact with the 5′cap complex, and to co-sediment with the Prm2 mRNA in polysomes. In CBF-A knockout mice, expression of protamine 2 (PRM2) was reduced and the Prm2 mRNA was prematurely translated in a subset of elongating spermatids. Moreover, a high percentage of sperm from the CBF-A knockout mouse showed abnormal DNA morphology. We suggest that CBF-A plays an important role in spermatogenesis by regulating stage-specific translation of testicular mRNAs. During eukaryotic gene expression, a fraction of newly exported mRNA molecules is transported to the cellular periphery for translation. The underlying mechanisms are not fully understood even though they likely affect specialized functions in many cell types including oligodendrocyets, neurons and germ cells. We discovered that the heterogeneous nuclear ribonucleoprotein CBF-A, interacts with a conserved sequence, the RNA trafficking sequence (RTS), located in the untranslated region of transported mRNAs. This interaction facilitates transport of myelin basic protein mRNA and dendritic mRNAs in oligodendrocytes and neurons, respectively. Here we investigated whether RTS-recognition by CBF-A coordinates transport and localized translation of the Protamine 2 mRNA in spermatogenic cells. During spermatogenesis the Protamine 2 mRNAs is synthesized and kept in a silent form to be translated at later stages. We show that by interacting with the RTS of the Protamine 2 mRNA both CBF-A isoforms contribute to regulate the transcript at the translational level. In a CBF-A knockout mouse model, we demonstrate that the interplay between the CBF-A isoforms in translation regulation of the Protamine 2 mRNA and other testicular transcripts has an impact on spermatogenesis.
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Affiliation(s)
- Nanaho Fukuda
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tomoyuki Fukuda
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - John Sinnamon
- Program in Neuroscience, Stony Brook University Center for Nervous System Disorders, Stony Brook, New York, United States of America
- Department of Biochemistry and Cell Biology, Stony Brook University Center for Nervous System Disorders, Stony Brook, New York, United States of America
| | | | - Manizheh Izadi
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Kevin Czaplinski
- Program in Neuroscience, Stony Brook University Center for Nervous System Disorders, Stony Brook, New York, United States of America
- Department of Biochemistry and Cell Biology, Stony Brook University Center for Nervous System Disorders, Stony Brook, New York, United States of America
| | - Piergiorgio Percipalle
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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Sarshad A, Sadeghifar F, Louvet E, Mori R, Böhm S, Al-Muzzaini B, Vintermist A, Fomproix N, Östlund AK, Percipalle P. Nuclear myosin 1c facilitates the chromatin modifications required to activate rRNA gene transcription and cell cycle progression. PLoS Genet 2013; 9:e1003397. [PMID: 23555303 PMCID: PMC3605103 DOI: 10.1371/journal.pgen.1003397] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 02/04/2013] [Indexed: 11/18/2022] Open
Abstract
Actin and nuclear myosin 1c (NM1) cooperate in RNA polymerase I (pol I) transcription. NM1 is also part of a multiprotein assembly, B-WICH, which is involved in transcription. This assembly contains the chromatin remodeling complex WICH with its subunits WSTF and SNF2h. We report here that NM1 binds SNF2h with enhanced affinity upon impairment of the actin-binding function. ChIP analysis revealed that NM1, SNF2h, and actin gene occupancies are cell cycle-dependent and require intact motor function. At the onset of cell division, when transcription is temporarily blocked, B-WICH is disassembled due to WSTF phosphorylation, to be reassembled on the active gene at exit from mitosis. NM1 gene knockdown and motor function inhibition, or stable expression of NM1 mutants that do not interact with actin or chromatin, overall repressed rRNA synthesis by stalling pol I at the gene promoter, led to chromatin alterations by changing the state of H3K9 acetylation at gene promoter, and delayed cell cycle progression. These results suggest a unique structural role for NM1 in which the interaction with SNF2h stabilizes B-WICH at the gene promoter and facilitates recruitment of the HAT PCAF. This leads to a permissive chromatin structure required for transcription activation.
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Affiliation(s)
- Aishe Sarshad
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
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Abstract
Actin is a key player for nuclear structure and function regulating both chromosome organization and gene activity. In the cell nucleus actin interacts with many different proteins. Among these proteins several studies have identified classical nuclear factors involved in chromatin structure and function, transcription and RNA processing as well as proteins that are normally involved in controlling the actin cytoskeleton. These discoveries have raised the possibility that nuclear actin performs its multi task activities through tight interactions with different sets of proteins. This high degree of promiscuity in the spectrum of protein-to-protein interactions correlates well with the conformational plasticity of actin and the ability to undergo regulated changes in its polymerization states. Several of the factors involved in controlling head-to-tail actin polymerization have been shown to be in the nucleus where they seem to regulate gene activity. By focusing on the multiple tasks performed by actin and actin-binding proteins, possible models of how actin dynamics controls the different phases of the RNA polymerase II transcription cycle are being identified.
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Obrdlik A, Percipalle P. The F-actin severing protein cofilin-1 is required for RNA polymerase II transcription elongation. Nucleus 2012; 2:72-9. [PMID: 21647301 DOI: 10.4161/nucl.2.1.14508] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 12/10/2010] [Accepted: 12/17/2010] [Indexed: 11/19/2022] Open
Abstract
In mammals actin contributes to transcription elongation by facilitating establishment of permissive chromatin. Here we report that the F-actin severing protein cofilin-1 is part of the same complex with actin and phosphorylated RNA polymerase (pol) II. In chromatin immunoprecipitation assays cofilin-1 was found selectively associated with transcribed regions of active genes, its occupancy being influenced by the polymerization state of actin. Cofilin-1 gene silencing led to a drop in FUrd incorporation into nascent transcripts. In cofilin-1 silenced cells chromatin immunoprecipitations showed that active genes were devoid of actin, phosphorylated pol II and displayed low histone H3 acetylation levels on K9. These findings suggest that cofilin-1 plays a major role in pol II transcription, facilitating association of elongating pol II and actin with active genes. We speculate that cofilin-1 performs its function in pol II transcription by regulating polymerization of gene-associated actin.
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Affiliation(s)
- Ales Obrdlik
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
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Abstract
Biochemical methods have provided mechanistic insights into the different transcription phases during which the RNA polymerase is assembled at gene promoter and becomes engaged in the elongation of nascent transcripts. Evidence that transcription takes place in specific regions of the nucleus has fuelled the need to develop assays that can be performed in living cells and provide information on the location of the specific foci, where transcription takes place. In this chapter, we describe a method that is based on the incorporation of a fluorine-conjugated uridine analogue, incorporation that can be monitored by immunofluorescence and light microscopy using specific fluorochrome-conjugated monoclonal antibodies. This assay allows direct monitoring of active transcription foci in living cells. When coupled to suitable software, the method outlined here also provides a semiquantitative approach to measure the number of active transcription foci that correlate with the proliferation state of the cell. Therefore, the assay we present here is a sensitive analytical tool to monitor the topology of transcription foci in the eukaryotic cell nucleus and to gain insight into transcription rates.
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Raju CS, Fukuda N, López-Iglesias C, Göritz C, Visa N, Percipalle P. In neurons, activity-dependent association of dendritically transported mRNA transcripts with the transacting factor CBF-A is mediated by A2RE/RTS elements. Mol Biol Cell 2011; 22:1864-77. [PMID: 21471000 PMCID: PMC3103402 DOI: 10.1091/mbc.e10-11-0904] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We report that the transacting factor CArG Box binding Factor A (CBF-A) binds the RNA trafficking sequences found in activity-regulated cytoskeleton-associated protein, calmodulin-dependent protein kinase II, and brain-derived neurotrophic factor mRNAs in an activity-dependent manner and accompanies the transcripts from gene to dendrites. CBF-A gene silencing impaired dendritic mRNA localization. We propose that CBF-A is important for trafficking of RNA trafficking sequence–containing neuronal mRNAs. In neurons certain mRNA transcripts are transported to synapses through mechanisms that are not fully understood. Here we report that the heterogeneous nuclear ribonucleoprotein CBF-A (CArG Box binding Factor A) facilitates dendritic transport and localization of activity-regulated cytoskeleton-associated protein (Arc), brain-derived neurotrophic factor (BDNF), and calmodulin-dependent protein kinase II (CaMKIIα) mRNAs. We discovered that, in the adult mouse brain, CBF-A has a broad distribution. In the nucleus, CBF-A was found at active transcription sites and interchromosomal spaces and close to nuclear pores. In the cytoplasm, CBF-A localized to dendrites as well as pre- and postsynaptic sites. CBF-A was found in synaptosomal fractions, associated with Arc, BDNF, and CaMKIIα mRNAs. Electrophoretic mobility shift assays demonstrated a direct interaction mediated via their hnRNP A2 response element (A2RE)/RNA trafficking sequence (RTS) elements located in the 3′ untranslated regions. In situ hybridization and microscopy on live hippocampal neurons showed that CBF-A is in dynamic granules containing Arc, BDNF, and CaMKIIα mRNAs. N-methyl-d-aspartate (NMDA) and α-amino-3-hydroxyl-5-methyl-4-isoxazole-propionate (AMPA) postsynaptic receptor stimulation led to CBF-A accumulation in dendrites; increased Arc, BDNF, and CaMKIIα mRNA levels; and increased amounts of transcripts coprecipitating with CBF-A. Finally, CBF-A gene knockdown led to decreased mRNA levels. We propose that CBF-A cotranscriptionally binds RTSs in Arc, BDNF, and CaMKIIα mRNAs and follows the transcripts from genes to dendrites, promoting activity-dependent nuclear sorting of transport-competent mRNAs.
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Affiliation(s)
- Chandrasekhar S Raju
- Department of Cell and Molecular Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden
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Obrdlik A, Louvet E, Kukalev A, Naschekin D, Kiseleva E, Fahrenkrog B, Percipalle P. Nuclear myosin 1 is in complex with mature rRNA transcripts and associates with the nuclear pore basket. FASEB J 2009; 24:146-57. [PMID: 19729515 DOI: 10.1096/fj.09-135863] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In rRNA biogenesis, nuclear myosin 1 (NM1) and actin synergize to activate rRNA gene transcription. Evidence that actin is in preribosomal subunits and NM1 may control rRNA biogenesis post-transcriptionally prompted us to investigate whether NM1 associates with and accompanies rRNA to nuclear pores (NPC). Ultracentrifugation on HeLa nucleolar extracts showed RNA-dependent NM1 coelution with preribosomal subunits. In RNA immunoprecipitations (RIPs), NM1 coprecipitated with pre-rRNAs and 18S, 5.8S, and 28S rRNAs, but failed to precipitate 5S rRNA and 7SL RNA. In isolated nuclei and living HeLa cells, NM1 or actin inhibition and selective alterations in actin polymerization impaired 36S pre-rRNA processing. Immunoelectron microscopy (IEM) on sections of manually isolated Xenopus oocyte nuclei showed NM1 localization at the NPC basket. Field emission scanning IEM on isolated nuclear envelopes and intranuclear content confirmed basket localization and showed that NM1 decorates actin-rich pore-linked filaments. Finally, RIP and successive RIPs (reRIPs) on cross-linked HeLa cells demonstrated that NM1, CRM1, and Nup153 precipitate same 18S and 28S rRNAs but not 5S rRNA. We conclude that NM1 facilitates maturation and accompanies export-competent preribosomal subunits to the NPC, thus modulating export.
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Affiliation(s)
- Ales Obrdlik
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
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Ameyar-Zazoua M, Souidi M, Fritsch L, Robin P, Thomas A, Hamiche A, Percipalle P, Ait-Si-Ali S, Harel-Bellan A. Physical and functional interaction between heterochromatin protein 1alpha and the RNA-binding protein heterogeneous nuclear ribonucleoprotein U. J Biol Chem 2009; 284:27974-27979. [PMID: 19617346 DOI: 10.1074/jbc.m109.037929] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
By combining biochemical purification and mass spectrometry, we identified proteins associated with human heterochromatin protein 1alpha (HP1alpha) both in the nucleoplasm and in chromatin. Some of these are RNA-binding proteins, and among them is the protein heterogeneous nuclear ribonucleoprotein U (hnRNP U)/SAF-A, which is linked to chromatin organization and transcriptional regulation. Here, we demonstrate that hnRNP U is a bona fide HP1alpha-interacting molecule. More importantly, hnRNP U depletion reduces HP1alpha-dependent gene silencing and disturbs HP1alpha subcellular localization. Thus, our data demonstrate that hnRNP U is involved in HP1alpha function, shedding new light on the mode of action of HP1alpha and on the function of hnRNP U.
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Affiliation(s)
- Maya Ameyar-Zazoua
- CNRS FRE 2944, Institut André Lwoff; Université Paris-Sud, Villejuif F-94801, France
| | - Mouloud Souidi
- CNRS FRE 2944, Institut André Lwoff; Université Paris-Sud, Villejuif F-94801, France
| | - Lauriane Fritsch
- CNRS FRE 2944, Institut André Lwoff; Université Paris-Sud, Villejuif F-94801, France
| | - Philippe Robin
- CNRS FRE 2944, Institut André Lwoff; Université Paris-Sud, Villejuif F-94801, France
| | - Audrey Thomas
- CNRS FRE 2944, Institut André Lwoff; Université Paris-Sud, Villejuif F-94801, France
| | - Ali Hamiche
- CNRS FRE 2944, Institut André Lwoff; Université Paris-Sud, Villejuif F-94801, France
| | - Piergiorgio Percipalle
- Department of Cell and Molecular Biology, Karolinska Institute, S-171 77 Stockholm, Sweden
| | - Slimane Ait-Si-Ali
- CNRS FRE 2944, Institut André Lwoff; Université Paris-Sud, Villejuif F-94801, France
| | - Annick Harel-Bellan
- CNRS FRE 2944, Institut André Lwoff; Université Paris-Sud, Villejuif F-94801, France.
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Kukalev AS, Lobov IB, Percipalle P, Podgornaya OI. SAF-A/hnRNP-U localization in interphase and metaphase. Cytogenet Genome Res 2009; 124:288-97. [PMID: 19556781 DOI: 10.1159/000218133] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Indexed: 11/19/2022] Open
Abstract
SAF-A/hnRNP U is an abundant nuclear protein that interacts specifically with nuclear matrix attachment region DNA (MAR) and RNA as a component of hnRNPs. SAF-A/hnRNP U was also shown to specifically bind mouse major satellite DNA (satMa). Antibodies against SAF-A and GFP-fusion constructs were used in the current work in order to trace SAF-A localization. In accordance with its diverse nucleic acid binding specificity, SAF-A was found to be localized in three different domains: outside the chromosomes, on the surface of the chromosome arms (probably MARs), and in the centromere region where it apparently binds specifically to the satMa. GFP-fusion constructs with different SAF-A/hnRNP U domains confirms the functional significance of the protein's functional domains in interphase cells. In telophase cells, the anti-SAF-A antibody signal appeared as a kind of network covering unfolded chromosomes.
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Affiliation(s)
- A S Kukalev
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
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Percipalle P, Raju CS, Fukuda N. Actin-associated hnRNP proteins as transacting factors in the control of mRNA transport and localization. RNA Biol 2009; 6:171-4. [PMID: 19276667 DOI: 10.4161/rna.6.2.8195] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Upon nuclear export, RNP particles are either localized to polysomes or further assembled into larger RNA granules which are transported to the cellular periphery for localized translation. These mechanisms are important for asymmetric mRNA and protein distribution and have profound impact on cellular physiology. mRNA transport and localization requires cis-acting elements and cellular transacting factors. hnRNP A2 functions as transacting factor for MBP mRNA transport in myelin-producing oligodendrocytes processes through a mechanism of direct RTS recognition. Here we examine the molecular mechanisms which regulate MBP mRNA transport in mouse oligodendrocytes in view of the recent discovery of CBF-A as novel transacting factor. CBF-A is highly conserved and in humans it is referred to as hnRNP A/B. Since actin has a key role in mRNA biogenesis and it is associated with both CBF-A and hnRNP A2 in pre-mRNP/mRNP complexes, we discuss integrative models underscoring the importance of actin-associated hnRNPs in mRNA biogenesis control at the post-transcriptional level.
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Abstract
Biochemical methods to analyze co-transcriptional recruitment of co-activators to nascent RNA molecules have lagged behind for many years. Most of the information on co-transcriptional regulation of nascent RNA came from invaluable in situ studies using single-cell model systems. More recently, the chromatin RNA immunoprecipitation technique has been developed to evaluate at the molecular level the association of proteins with nascent RNA which is still coupled to chromatin. Similar to chromatin immunoprecipitation, the chromatin RNA immunoprecipitation method is suitable to study events along specific genes, and it has been successfully used in numerous applications to demonstrate the cross-talk between transcription and RNA processing. This technique has a considerable margin of technological development especially in high-throughput screening experiments in combination with microarrays. In this chapter, we describe a RIP protocol optimized in our laboratory to study association of RNA binding proteins with specific nascent mRNA transcripts.
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Raju CS, Göritz C, Nord Y, Hermanson O, López-Iglesias C, Visa N, Castelo-Branco G, Percipalle P. In cultured oligodendrocytes the A/B-type hnRNP CBF-A accompanies MBP mRNA bound to mRNA trafficking sequences. Mol Biol Cell 2008; 19:3008-19. [PMID: 18480411 DOI: 10.1091/mbc.e07-10-1083] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Heterogeneous ribonucleoproteins (hnRNPs) have key roles in RNA biogenesis, including pre-mRNP assembly, transport and cytoplasmic localization. Here we show by biochemical fractionation of nuclear extracts and protein-protein interaction assays that the A/B-type hnRNP CBF-A is in a multiprotein complex with hnRNP A2 and A3 and hnRNP U. Using RNA affinity chromatography and gel retardation assays, CBF-A was found to bind directly to RNA trafficking sequences in the 3'-UTR of the myelin basic protein (MBP) mRNA. In primary oligodendrocytes, astrocytes, neurons, and mouse forebrain sections, CBF-A revealed a characteristic granular cytoplasmic distribution. In mouse forebrain CBF-A-positive granules were preferentially found in regions with loosely bundled myelin fibers. In cultured oligodendrocytes, CBF-A was found to be specifically associated with endogenous MBP mRNA and CBF-A gene silencing resulted in the retention of MBP granules in the cell body. Finally, immunoelectron microscopy in differentiating oligodendrocytes showed that CBF-A is located in cytoplasmic granules that are often associated with the cytoskeleton. The results suggest that CBF-A is a novel transacting factor required for cytoplasmic mRNA transport and localization.
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Affiliation(s)
- Chandrasekhar S Raju
- Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institute, Stockholm SE-171 77, Sweden
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Abstract
Recent years have witnessed a new turn in the field of gene expression regulation. Actin and an ever-growing family of actin-associated proteins have been accepted as members of the nuclear crew, regulating eukaryotic gene transcription. In complex with heterogeneous nuclear ribonucleoproteins and certain myosin species, actin has been shown to be an important regulator in RNA polymerase II transcription. Furthermore, actin-based molecular motors are believed to facilitate RNA polymerase I transcription and possibly downstream events during rRNA biogenesis. Probably these findings represent the tip of the iceberg of a rapidly expanding area within the functional architecture of the cell nucleus. Further studies will contribute to clarify how actin mediates nuclear functions with a glance to cytoplasmic signalling. These discoveries have the potential to define novel regulatory networks required to control gene expression at multiple levels.
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Affiliation(s)
- Emilie Louvet
- Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institutet, S-171 77 Stockholm, Sweden
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Abstract
Recent developments in the field of gene transcription regulation have unfolded a key role for actin as an important co-factor for all three eukaryotic RNA polymerases. In this review article we discuss the latest findings on actin in transcription of protein-coding and ribosomal genes, in complex with specific hnRNP proteins and a form of myosin 1beta which is entirely localized to the cell nucleus. Based on these recent studies, we propose a general model where actin may function in basal gene transcription as an allosteric regulator, to recruit transcriptional co-activators on active genes. A future challenge will be the identification of the polymerization state of actin in gene transcription and how it is mechanistically regulated.
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Affiliation(s)
- A Obrdlik
- Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institute, Stockholm, Sweden
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Abstract
Actin is a key protein in numerous cellular functions. One recent study has identified a large set of genes, associated with the actin cytoskeleton, which could be grouped into a wide spectrum of cytoplasmic and nuclear functions, such as protein biosynthesis and gene transcription. Deletions of many of the identified genes affected cellular actin organization, suggesting a functional link between different actin fractions probably regulated through changes in actin dynamics. The data are very exciting; speculations on the crosstalk between cytoplasmic and nuclear actin fractions in different cellular contexts may help placing the results in perspective to further understand how actin-mediated signalling affects cellular functions, such as gene expression.
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Affiliation(s)
- Piergiorgio Percipalle
- Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institute, Box 285, Stockholm SE-171 77, Sweden.
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