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Nowak J, Lenartowski R, Kalita K, Lehka L, Karatsai O, Lenartowska M, Rędowicz MJ. Myosin VI in the nucleolus of neurosecretory PC12 cells: its involvement in the maintenance of nucleolar structure and ribosome organization. Front Physiol 2024; 15:1368416. [PMID: 38774650 PMCID: PMC11106421 DOI: 10.3389/fphys.2024.1368416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/01/2024] [Indexed: 05/24/2024] Open
Abstract
We have previously shown that unconventional myosin VI (MVI), a unique actin-based motor protein, shuttles between the cytoplasm and nucleus in neurosecretory PC12 cells in a stimulation-dependent manner and interacts with numerous proteins involved in nuclear processes. Among the identified potential MVI partners was nucleolin, a major nucleolar protein implicated in rRNA processing and ribosome assembly. Several other nucleolar proteins such as fibrillarin, UBF (upstream binding factor), and B23 (also termed nucleophosmin) have been shown to interact with MVI. A bioinformatics tool predicted the presence of the nucleolar localization signal (NoLS) within the MVI globular tail domain, and immunostaining confirmed the presence of MVI within the nucleolus. Depletion of MVI, previously shown to impair PC12 cell proliferation and motility, caused disorganization of the nucleolus and rough endoplasmic reticulum (rER). However, lack of MVI does not affect nucleolar transcription. In light of these data, we propose that MVI is important for nucleolar and ribosome maintenance but not for RNA polymerase 1-related transcription.
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Affiliation(s)
- Jolanta Nowak
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Robert Lenartowski
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, Torun, Poland
| | - Katarzyna Kalita
- Laboratory of Neurobiology, Nencki-EMBL Partnership for Neural Plasticity and Brain Disorders—BRAINCITY, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Lilya Lehka
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Olena Karatsai
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Marta Lenartowska
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, Torun, Poland
| | - Maria Jolanta Rędowicz
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
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2
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Shahid-Fuente IW, Toseland CP. Myosin in chromosome organisation and gene expression. Biochem Soc Trans 2023; 51:1023-1034. [PMID: 37171068 PMCID: PMC10317160 DOI: 10.1042/bst20220939] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 04/05/2023] [Accepted: 04/18/2023] [Indexed: 05/13/2023]
Abstract
The importance of myosin motor protein is well-characterised within the cytoplasm and cytoskeleton. However, mounting evidence on four nuclear myosins highlights the central role these proteins have in maintaining genomic stability and gene expression. This review focuses on each of their critical roles in chromatin structure, chromosome translocation, transcription regulation, and DNA damage repair in terms of maintaining chromosome and chromatin integrity.
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3
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O’Grady TM, Baddoo M, Flemington SA, Ishaq EY, Ungerleider NA, Flemington EK. Reversal of splicing infidelity is a pre-activation step in B cell differentiation. Front Immunol 2022; 13:1060114. [PMID: 36601126 PMCID: PMC9806119 DOI: 10.3389/fimmu.2022.1060114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction B cell activation and differentiation is central to the adaptive immune response. Changes in exon usage can have major impacts on cellular signaling and differentiation but have not been systematically explored in differentiating B cells. Methods We analyzed exon usage and intron retention in RNA-Seq data from subsets of human B cells at various stages of differentiation, and in an in vitro laboratory model of B cell activation and differentiation (Epstein Barr virus infection). Results Blood naïve B cells were found to have an unusual splicing profile, with unannotated splicing events in over 30% of expressed genes. Splicing changed substantially upon naïve B cell entry into secondary lymphoid tissue and before activation, involving significant increases in exon commitment and reductions in intron retention. These changes preferentially involved short introns with weak splice sites and were likely mediated by an overall increase in splicing efficiency induced by the lymphoid environment. The majority of transcripts affected by splicing changes showed restoration of encoded conserved protein domains and/or reduced targeting to the nonsense-mediated decay pathway. Affected genes were enriched in functionally important immune cell activation pathways such as antigen-mediated signaling, cell cycle control and mRNA processing and splicing. Discussion Functional observations from donor B cell subsets in progressive states of differentiation and from timecourse experiments using the in vitro model suggest that these widespread changes in mRNA splicing play a role in preparing naïve B cells for the decisive step of antigen-mediated activation and differentiation.
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Affiliation(s)
- Tina M. O’Grady
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States,*Correspondence: Tina M. O’Grady, ; Erik K. Flemington,
| | - Melody Baddoo
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Samuel A. Flemington
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, United States
| | - Eman Y. Ishaq
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Nathan A. Ungerleider
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Erik K. Flemington
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States,*Correspondence: Tina M. O’Grady, ; Erik K. Flemington,
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4
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Dupont S, Wickström SA. Mechanical regulation of chromatin and transcription. Nat Rev Genet 2022; 23:624-643. [DOI: 10.1038/s41576-022-00493-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2022] [Indexed: 01/14/2023]
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5
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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] [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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6
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Kneussel M, Sánchez-Rodríguez N, Mischak M, Heisler FF. Dynein and muskelin control myosin VI delivery towards the neuronal nucleus. iScience 2021; 24:102416. [PMID: 33997696 PMCID: PMC8099778 DOI: 10.1016/j.isci.2021.102416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 02/15/2021] [Accepted: 04/07/2021] [Indexed: 11/30/2022] Open
Abstract
Protein transport toward the nucleus is important for translating molecular signals into gene expression changes. Interestingly, the unconventional motor protein myosin VI regulates RNA polymerase II-dependent gene transcription. Whether actin-filament-dependent myosins are actively transported to nuclear compartments remains unknown. Here, we report that neurons also contain myosin VI inside their nucleus. Notably, nuclear appearance of this actin-dependent motor depends on functional cytoplasmic dynein, a minus end-directed microtubule motor. We find that the trafficking factor muskelin assists in the formation of dynein-myosin VI interactions and further localizes to nuclear foci, enriched in the myosin. Impairment of dynein, but not myosin VI function, reduces nuclear muskelin levels. In turn, muskelin represents a critical determinant in regulating myosin VI nuclear targeting. Our data reveal that minus end-directed microtubule transport determines myosin VI subcellular localization. They suggest a pathway of cytoplasm-to-nucleus trafficking that requires muskelin and is based on dynein-myosin cross talk.
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Affiliation(s)
- Matthias Kneussel
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany
| | - Noelia Sánchez-Rodríguez
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany
| | - Michaela Mischak
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany
| | - Frank F. Heisler
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany
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7
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dos Santos Á, Toseland CP. Regulation of Nuclear Mechanics and the Impact on DNA Damage. Int J Mol Sci 2021; 22:3178. [PMID: 33804722 PMCID: PMC8003950 DOI: 10.3390/ijms22063178] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 02/06/2023] Open
Abstract
In eukaryotic cells, the nucleus houses the genomic material of the cell. The physical properties of the nucleus and its ability to sense external mechanical cues are tightly linked to the regulation of cellular events, such as gene expression. Nuclear mechanics and morphology are altered in many diseases such as cancer and premature ageing syndromes. Therefore, it is important to understand how different components contribute to nuclear processes, organisation and mechanics, and how they are misregulated in disease. Although, over the years, studies have focused on the nuclear lamina-a mesh of intermediate filament proteins residing between the chromatin and the nuclear membrane-there is growing evidence that chromatin structure and factors that regulate chromatin organisation are essential contributors to the physical properties of the nucleus. Here, we review the main structural components that contribute to the mechanical properties of the nucleus, with particular emphasis on chromatin structure. We also provide an example of how nuclear stiffness can both impact and be affected by cellular processes such as DNA damage and repair.
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Affiliation(s)
- Ália dos Santos
- Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
| | - Christopher P. Toseland
- Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
- Insigneo Institute for in Silico Medicine, University of Sheffield, Sheffield S10 2RX, UK
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8
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Peng AYT, Kolhe JA, Behrens LD, Freeman BC. Genome organization: Tag it, move it, place it. Curr Opin Cell Biol 2020; 68:90-97. [PMID: 33166737 DOI: 10.1016/j.ceb.2020.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/28/2020] [Accepted: 10/08/2020] [Indexed: 12/14/2022]
Abstract
Chromosomes are selectively organized within the nuclei of interphase cells reflecting the current fate of each cell and are reorganized in response to various physiological cues to maintain homeostasis. Although substantial progress is being made to establish the various patterns of genome architecture, less is understood on how chromosome folding/positioning is achieved. Here, we discuss recent insights into the cellular mechanisms dictating chromatin movements including the use of epigenetic modifications and allosterically regulated transcription factors, as well as a nucleoskeleton system comprised of actin, myosin, and actin-binding proteins. Together, these nuclear factors help coordinate the positioning of both general and cell-specific genomic architectural features.
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Affiliation(s)
- Audrey Yi Tyan Peng
- University of Illinois, Urbana-Champaign, Department of Cell and Developmental Biology, Urbana, IL, 61801, USA
| | - Janhavi A Kolhe
- University of Illinois, Urbana-Champaign, Department of Cell and Developmental Biology, Urbana, IL, 61801, USA
| | - Lindsey D Behrens
- University of Illinois, Urbana-Champaign, Department of Cell and Developmental Biology, Urbana, IL, 61801, USA
| | - Brian C Freeman
- University of Illinois, Urbana-Champaign, Department of Cell and Developmental Biology, Urbana, IL, 61801, USA.
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9
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Cook AW, Gough RE, Toseland CP. Nuclear myosins - roles for molecular transporters and anchors. J Cell Sci 2020; 133:133/11/jcs242420. [PMID: 32499319 DOI: 10.1242/jcs.242420] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The myosin family of molecular motors are well-characterised cytoskeletal proteins. However, myosins are also present in the nucleus, where they have been shown to have roles in transcription, DNA repair and viral infections. Despite their involvement in these fundamental cellular processes, our understanding of these functions and their regulation remains limited. Recently, research on nuclear myosins has been gathering pace, and this Review will evaluate the current state of the field. Here, we will focus on the variation in structure of nuclear myosins, their nuclear import and their roles within transcription, DNA damage, chromatin organisation and viral infections. We will also consider both the biochemical and biophysical properties and restraints that are placed on these multifunctional motors, and how they link to their cytoplasmic counterparts. By highlighting these properties and processes, we show just how integral nuclear myosins are for cellular survival.
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Affiliation(s)
- Alexander W Cook
- Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
| | - Rosemarie E Gough
- Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
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10
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Guh CY, Hsieh YH, Chu HP. Functions and properties of nuclear lncRNAs-from systematically mapping the interactomes of lncRNAs. J Biomed Sci 2020; 27:44. [PMID: 32183863 PMCID: PMC7079490 DOI: 10.1186/s12929-020-00640-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/06/2020] [Indexed: 02/07/2023] Open
Abstract
Protein and DNA have been considered as the major components of chromatin. But beyond that, an increasing number of studies show that RNA occupies a large amount of chromatin and acts as a regulator of nuclear architecture. A significant fraction of long non-coding RNAs (lncRNAs) prefers to stay in the nucleus and cooperate with protein complexes to modulate epigenetic regulation, phase separation, compartment formation, and nuclear organization. An RNA strand also can invade into double-stranded DNA to form RNA:DNA hybrids (R-loops) in living cells, contributing to the regulation of gene expression and genomic instability. In this review, we discuss how nuclear lncRNAs orchestrate cellular processes through their interactions with proteins and DNA and summarize the recent genome-wide techniques to study the functions of lncRNAs by revealing their interactomes in vivo.
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Affiliation(s)
- Chia-Yu Guh
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan, Republic of China
| | - Yu-Hung Hsieh
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan, Republic of China
| | - Hsueh-Ping Chu
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan, Republic of China.
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11
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12
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Abstract
Cells must fine-tune their gene expression programs for optimal cellular activities in their natural growth conditions. Transcriptional memory, a unique transcriptional response, plays a pivotal role in faster reactivation of genes upon environmental changes, and is facilitated if genes were previously in an active state. Hyper-activation of gene expression by transcriptional memory is critical for cellular differentiation, development, and adaptation. TREM (Transcriptional REpression Memory), a distinct type of transcriptional memory, promoting hyper-repression of unnecessary genes, upon environmental changes has been recently reported. These two transcriptional responses may optimize specific gene expression patterns, in rapidly changing environments. Emerging evidence suggests that they are also critical for immune responses. In addition to memory B and T cells, innate immune cells are transcriptionally hyperactivated by restimulation, with the same or different pathogens known as trained immunity. In this review, we briefly summarize recent progress in chromatin-based regulation of transcriptional memory, and its potential role in immune responses. [BMB Reports 2019; 52(2): 127-132].
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Affiliation(s)
- Min Young Kim
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Ji Eun Lee
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Lark Kyun Kim
- Severance Biomedical Science Institute and BK21 PLUS Project to Medical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06230, Korea
| | - TaeSoo Kim
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
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13
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Majewski L, Nowak J, Sobczak M, Karatsai O, Havrylov S, Lenartowski R, Suszek M, Lenartowska M, Redowicz MJ. Myosin VI in the nucleus of neurosecretory PC12 cells: Stimulation-dependent nuclear translocation and interaction with nuclear proteins. Nucleus 2018; 9:125-141. [PMID: 29293066 PMCID: PMC5973263 DOI: 10.1080/19491034.2017.1421881] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/23/2017] [Accepted: 12/18/2017] [Indexed: 02/07/2023] Open
Abstract
Myosin VI (MVI) is a unique actin-based motor protein moving towards the minus end of actin filaments, in the opposite direction than other known myosins. Besides well described functions of MVI in endocytosis and maintenance of Golgi apparatus, there are few reports showing its involvement in transcription. We previously demonstrated that in neurosecretory PC12 cells MVI was present in the cytoplasm and nucleus, and its depletion caused substantial inhibition of cell migration and proliferation. Here, we show an increase in nuclear localization of MVI upon cell stimulation, and identification of potential nuclear localization (NLS) and nuclear export (NES) signals within MVI heavy chain. These signals seem to be functional as the MVI nuclear presence was affected by the inhibitors of nuclear import (ivermectin) and export (leptomycin B). In nuclei of stimulated cells, MVI colocalized with active RNA polymerase II, BrUTP-containing transcription sites and transcription factor SP1 as well as SC35 and PML proteins, markers of nuclear speckles and PML bodies, respectively. Mass spectrometry analysis of samples of a GST-pull-down assay with the MVI tail domain as a "bait" identified several new potential MVI binding partners. Among them are proteins involved in transcription and post-transcriptional processes. We confirmed interaction of MVI with heterogeneous nuclear ribonucleoprotein U (hnRNPU) and nucleolin, proteins involved in pre-mRNA binding and transport, and nucleolar function, respectively. Our data provide an insight into mechanisms of involvement of MVI in nuclear processes via interaction with nuclear proteins and support a notion for important role(s) for MVI in gene expression.
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Affiliation(s)
- Lukasz Majewski
- Laboratory of Molecular Basis of Cell Motility, Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Jolanta Nowak
- Laboratory of Molecular Basis of Cell Motility, Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Magdalena Sobczak
- Laboratory of Molecular Basis of Cell Motility, Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Olena Karatsai
- Laboratory of Molecular Basis of Cell Motility, Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Serhiy Havrylov
- Laboratory of Molecular Basis of Cell Motility, Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Robert Lenartowski
- Laboratory of Isotope and Instrumental Analysis, Department of Cellular and Molecular Biology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University in Torun, Torun, Poland
| | - Malgorzata Suszek
- Laboratory of Molecular Basis of Cell Motility, Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Marta Lenartowska
- Laboratory of Developmental Biology, Department of Cellular and Molecular Biology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University in Torun, Torun, Poland
| | - Maria Jolanta Redowicz
- Laboratory of Molecular Basis of Cell Motility, Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
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14
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Fili N, Hari-Gupta Y, Dos Santos Á, Cook A, Poland S, Ameer-Beg SM, Parsons M, Toseland CP. NDP52 activates nuclear myosin VI to enhance RNA polymerase II transcription. Nat Commun 2017; 8:1871. [PMID: 29187741 PMCID: PMC5707354 DOI: 10.1038/s41467-017-02050-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 10/30/2017] [Indexed: 11/09/2022] Open
Abstract
Myosin VI (MVI) has been found to be overexpressed in ovarian, breast and prostate cancers. Moreover, it has been shown to play a role in regulating cell proliferation and migration, and to interact with RNA Polymerase II (RNAPII). Here, we find that backfolding of MVI regulates its ability to bind DNA and that a putative transcription co-activator NDP52 relieves the auto-inhibition of MVI to enable DNA binding. Additionally, we show that the MVI-NDP52 complex binds RNAPII, which is critical for transcription, and that depletion of NDP52 or MVI reduces steady-state mRNA levels. Lastly, we demonstrate that MVI directly interacts with nuclear receptors to drive expression of target genes, thereby suggesting a link to cell proliferation and migration. Overall, we suggest MVI may function as an auxiliary motor to drive transcription.
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Affiliation(s)
- Natalia Fili
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Yukti Hari-Gupta
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Ália Dos Santos
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Alexander Cook
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Simon Poland
- Randall Division of Cell and Molecular Biophysics, King's College London, Guys Campus, London, SE1 1UL, UK
| | - Simon M Ameer-Beg
- Randall Division of Cell and Molecular Biophysics, King's College London, Guys Campus, London, SE1 1UL, UK
| | - Maddy Parsons
- Randall Division of Cell and Molecular Biophysics, King's College London, Guys Campus, London, SE1 1UL, UK
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15
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Bhat J, Helmuth J, Chitadze G, Kouakanou L, Peters C, Vingron M, Ammerpohl O, Kabelitz D. Stochastics of Cellular Differentiation Explained by Epigenetics: The Case of T-Cell Differentiation and Functional Plasticity. Scand J Immunol 2017; 86:184-195. [PMID: 28799233 DOI: 10.1111/sji.12589] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 08/06/2017] [Indexed: 12/19/2022]
Abstract
Epigenetic marks including histone modifications and DNA methylation are associated with the regulation of gene expression and activity. In addition, an increasing number of non-coding RNAs with regulatory activity on gene expression have been identified. Alongside, technological advancements allow for the analysis of these mechanisms with high resolution up to the single-cell level. For instance, the assay for transposase-accessible chromatin using sequencing (ATAC-seq) simultaneously probes for chromatin accessibility and nucleosome positioning. Thus, it provides information on two levels of epigenetic regulation. Development and differentiation of T cells into functional subset cells including memory T cells are dynamic processes driven by environmental signals. Here, we briefly review the current knowledge of how epigenetic regulation contributes to subset specification, differentiation and memory development in T cells. Specifically, we focus on epigenetic mechanisms differentially active in the two distinct T cell populations expressing αβ or γδ T cell receptors. We also discuss examples of epigenetic alterations of T cells in autoimmune diseases. DNA methylation and histone acetylation are subject to modification by several classes of 'epigenetic modifiers', some of which are in clinical use or in preclinical development. Therefore, we address the impact of some epigenetic modifiers on T-cell activation and differentiation, and discuss possible synergies with T cell-based immunotherapeutic strategies.
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Affiliation(s)
- J Bhat
- Institute of Immunology, University of Kiel and University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - J Helmuth
- Otto-Warburg-Laboratories: Epigenomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - G Chitadze
- Institute of Immunology, University of Kiel and University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - L Kouakanou
- Institute of Immunology, University of Kiel and University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - C Peters
- Institute of Immunology, University of Kiel and University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - M Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - O Ammerpohl
- Institute of Human Genetics, University of Kiel and University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - D Kabelitz
- Institute of Immunology, University of Kiel and University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
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16
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Heissler SM, Chinthalapudi K, Sellers JR. Kinetic signatures of myosin-5B, the motor involved in microvillus inclusion disease. J Biol Chem 2017; 292:18372-18385. [PMID: 28882893 DOI: 10.1074/jbc.m117.801456] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/29/2017] [Indexed: 11/06/2022] Open
Abstract
Myosin-5B is a ubiquitous molecular motor that transports cargo vesicles of the endomembrane system in intracellular recycling pathways. Myosin-5B malfunction causes the congenital enteropathy microvillus inclusion disease, underlining its importance in cellular homeostasis. Here we describe the interaction of myosin-5B with F-actin, nucleotides, and the pyrazolopyrimidine compound myoVin-1. We show that single-headed myosin-5B is an intermediate duty ratio motor with a kinetic ATPase cycle that is rate-limited by the release of phosphate. The presence of a second head generates strain and gating in the myosin-5B dimer that alters the kinetic signature by reducing the actin-activated ADP release rate to become rate-limiting. This kinetic transition into a high-duty ratio motor is a prerequisite for the proposed transport function of myosin-5B in cellular recycling pathways. Moreover, we show that the small molecule compound myoVin-1 inhibits the enzymatic and functional activity of myosin-5B in vitro Partial inhibition of the actin-activated steady-state ATPase activity and sliding velocity suggests that caution should be used when probing the effect of myoVin-1 on myosin-5-dependent transport processes in cells.
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Affiliation(s)
- Sarah M Heissler
- From the Laboratory of Molecular Physiology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892-8015 and
| | - Krishna Chinthalapudi
- the Cell Adhesion Laboratory, Department of Integrative Structural and Computational Biology, Scripps Research Institute, Jupiter, Florida 33458
| | - James R Sellers
- From the Laboratory of Molecular Physiology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892-8015 and
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17
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Krivega I, Dean A. A tetrad of chromatin interactions for chromosome pairing in X inactivation. Nat Struct Mol Biol 2017; 24:607-608. [PMID: 28771462 PMCID: PMC6247907 DOI: 10.1038/nsmb.3447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
An unusual pairing of homologous X chromosomes occurs during X inactivation. A new study in mouse embryonic stem cells shows that telomeres and the telomeric RNA PAR-TERRA are responsible for additional pairwise interactions that guide Xic–Xic pairing.
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Affiliation(s)
- Ivan Krivega
- Laboratory of Cellular and Developmental Biology at the National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA.
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology at the National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA.
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18
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Chu HP, Froberg JE, Kesner B, Oh HJ, Ji F, Sadreyev R, Pinter SF, Lee JT. PAR-TERRA directs homologous sex chromosome pairing. Nat Struct Mol Biol 2017; 24:620-631. [PMID: 28692038 PMCID: PMC5553554 DOI: 10.1038/nsmb.3432] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 06/09/2017] [Indexed: 12/25/2022]
Abstract
In mammals, homologous chromosomes rarely pair outside of meiosis. An exception is the X-chromosome, which transiently pairs during X-chromosome inactivation (XCI). How two chromosomes find each other in 3D space is not known. Here, we reveal a required interaction between the X-inactivation center (Xic) and the telomere in mouse embryonic stem cells. The sub-telomeric, pseudoautosomal region (PAR) of both sex chromosomes (X,Y) also undergoes pairing. PAR transcribes a class of telomeric RNA, dubbed “PAR-TERRA”, which accounts for a vast majority of all TERRA transcripts. PAR-TERRA binds throughout the genome, including PAR and Xic. PAR-TERRA anchors the Xic to PAR, creating a “tetrad” of pairwise homologous interactions (Xic:Xic, PAR:PAR, Xic:PAR). Xic pairing occurs within the tetrad. Depleting PAR-TERRA abrogates pairing and blocks initiation of XCI, whereas autosomal PAR-TERRA induces ectopic pairing. We proposed a Constrained Diffusion Model in which PAR-TERRA creates an interaction hub to guide Xic homology searching during XCI.
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Affiliation(s)
- Hsueh-Ping Chu
- Howard Hughes Medical Institute, Boston, Massachusetts, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - John E Froberg
- Howard Hughes Medical Institute, Boston, Massachusetts, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Barry Kesner
- Howard Hughes Medical Institute, Boston, Massachusetts, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Hyun Jung Oh
- Howard Hughes Medical Institute, Boston, Massachusetts, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Stefan F Pinter
- Howard Hughes Medical Institute, Boston, Massachusetts, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeannie T Lee
- Howard Hughes Medical Institute, Boston, Massachusetts, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
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19
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Abstract
Extensive 3D folding is required to package a genome into the tiny nuclear space, and this packaging must be compatible with proper gene expression. Thus, in the well-hierarchized nucleus, chromosomes occupy discrete territories and adopt specific 3D organizational structures that facilitate interactions between regulatory elements for gene expression. The mammalian X chromosome exemplifies this structure-function relationship. Recent studies have shown that, upon X-chromosome inactivation, active and inactive X chromosomes localize to different subnuclear positions and adopt distinct chromosomal architectures that reflect their activity states. Here, we review the roles of long non-coding RNAs, chromosomal organizational structures and the subnuclear localization of chromosomes as they relate to X-linked gene expression.
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20
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Epigenetic Regulation of Adaptive NK Cell Diversification. Trends Immunol 2016; 37:451-461. [PMID: 27160662 DOI: 10.1016/j.it.2016.04.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 04/11/2016] [Accepted: 04/14/2016] [Indexed: 01/08/2023]
Abstract
Natural killer (NK) cells were previously considered to represent short-lived, innate lymphocytes. However, mouse models have revealed expansion and persistence of differentiated NK cell subsets in response to cytomegalovirus (CMV) infection, paralleling antigen-specific T cell differentiation. Congruently, analyses of humans have uncovered CMV-associated NK cell subsets characterized by epigenetic diversification processes that lead to altered target cell specificities and functional capacities. Here, focusing on responses to viruses, we review similarities and differences between mouse and human adaptive NK cells, identifying molecular analogies that may be key to transcriptional reprogramming and functional alterations. We discuss possible molecular mechanisms underlying epigenetic diversification and hypothesize that processes driving epigenetic diversification may represent a more widespread mechanism for fine-tuning and optimization of cellular immunity.
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21
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He F, Wollscheid HP, Nowicka U, Biancospino M, Valentini E, Ehlinger A, Acconcia F, Magistrati E, Polo S, Walters KJ. Myosin VI Contains a Compact Structural Motif that Binds to Ubiquitin Chains. Cell Rep 2016; 14:2683-94. [PMID: 26971995 DOI: 10.1016/j.celrep.2016.01.079] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 11/24/2015] [Accepted: 01/27/2016] [Indexed: 12/13/2022] Open
Abstract
Myosin VI is critical for cargo trafficking and sorting during early endocytosis and autophagosome maturation, and abnormalities in these processes are linked to cancers, neurodegeneration, deafness, and hypertropic cardiomyopathy. We identify a structured domain in myosin VI, myosin VI ubiquitin-binding domain (MyUb), that binds to ubiquitin chains, especially those linked via K63, K11, and K29. Herein, we solve the solution structure of MyUb and MyUb:K63-linked diubiquitin. MyUb folds as a compact helix-turn-helix-like motif and nestles between the ubiquitins of K63-linked diubiquitin, interacting with distinct surfaces of each. A nine-amino-acid extension at the C-terminal helix (Helix2) of MyUb is required for myosin VI interaction with endocytic and autophagic adaptors. Structure-guided mutations revealed that a functional MyUb is necessary for optineurin interaction. In addition, we found that an isoform-specific helix restricts MyUb binding to ubiquitin chains. This work provides fundamental insights into myosin VI interaction with ubiquitinated cargo and functional adaptors.
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Affiliation(s)
- Fahu He
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Hans-Peter Wollscheid
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milano, Italy
| | - Urszula Nowicka
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Matteo Biancospino
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milano, Italy
| | - Eleonora Valentini
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milano, Italy
| | - Aaron Ehlinger
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Filippo Acconcia
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milano, Italy
| | - Elisa Magistrati
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milano, Italy
| | - Simona Polo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milano, Italy; DIPO, Dipartimento di Oncologia ed Emato-oncologia, Università degli Studi di Milano, Via di Rudinì 8, 20122 Milan, Italy.
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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