1
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Barger SR, Penfield L, Bahmanyar S. Nuclear envelope assembly relies on CHMP-7 in the absence of BAF-LEM-mediated hole closure. J Cell Sci 2023; 136:jcs261385. [PMID: 37795681 PMCID: PMC10668030 DOI: 10.1242/jcs.261385] [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: 06/04/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
Barrier-to-autointegration factor (BAF) protein is a DNA-binding protein that crosslinks chromatin to allow mitotic nuclear envelope (NE) assembly. The LAP2-emerin-MAN1 (LEM)-domain protein LEMD2 and ESCRT-II/III hybrid protein CHMP7 close NE holes surrounding spindle microtubules (MTs). BAF binds LEM-domain family proteins to repair NE ruptures in interphase, but whether BAF-LEM binding participates in NE hole closure around spindle MTs is not known. Here, we took advantage of the stereotypical event of NE formation in fertilized Caenorhabditis elegans oocytes to show that BAF-LEM binding and LEM-2-CHMP-7 have distinct roles in NE closure around spindle MTs. LEM-2 and EMR-1 (homologs of LEMD2 and emerin) function redundantly with BAF-1 (the C. elegans BAF protein) in NE closure. Compromising BAF-LEM binding revealed an additional role for EMR-1 in the maintenance of the NE permeability barrier. In the absence of BAF-LEM binding, LEM-2-CHMP-7 was required for NE assembly and embryo survival. The winged helix domain of LEM-2 recruits CHMP-7 to the NE in C. elegans and a LEM-2-independent nucleoplasmic pool of CHMP-7 also contributes to NE stability. Thus, NE hole closure surrounding spindle MTs requires redundant mechanisms that safeguard against failure in NE assembly to support embryogenesis.
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Affiliation(s)
- Sarah R. Barger
- Yale University, Department of Molecular, Cellular, Developmental Biology, 266 Whitney Ave., New Haven, CT 06511, USA
| | - Lauren Penfield
- Yale University, Department of Molecular, Cellular, Developmental Biology, 266 Whitney Ave., New Haven, CT 06511, USA
| | - Shirin Bahmanyar
- Yale University, Department of Molecular, Cellular, Developmental Biology, 266 Whitney Ave., New Haven, CT 06511, USA
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2
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Cheng LC, Zhang X, Abhinav K, Nguyen JA, Baboo S, Martinez-Bartolomé S, Branon TC, Ting AY, Loose E, Yates JR, Gerace L. Shared and Distinctive Neighborhoods of Emerin and Lamin B Receptor Revealed by Proximity Labeling and Quantitative Proteomics. J Proteome Res 2022; 21:2197-2210. [PMID: 35972904 PMCID: PMC9442789 DOI: 10.1021/acs.jproteome.2c00281] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Emerin and lamin B receptor (LBR) are abundant transmembrane
proteins
of the nuclear envelope that are concentrated at the inner nuclear
membrane (INM). Although both proteins interact with chromatin and
nuclear lamins, they have distinctive biochemical and functional properties.
Here, we have deployed proximity labeling using the engineered biotin
ligase TurboID (TbID) and quantitative proteomics to compare the neighborhoods
of emerin and LBR in cultured mouse embryonic fibroblasts. Our analysis
revealed 232 high confidence proximity partners that interact selectively
with emerin and/or LBR, 49 of which are shared by both. These included
previously characterized NE-concentrated proteins, as well as a host
of additional proteins not previously linked to emerin or LBR functions.
Many of these are TM proteins of the ER, including two E3 ubiquitin
ligases. Supporting these results, we found that 11/12 representative
proximity relationships identified by TbID also were detected at the
NE with the proximity ligation assay. Overall, this work presents
methodology that may be used for large-scale mapping of the landscape
of the INM and reveals a group of new proteins with potential functional
connections to emerin and LBR.
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Affiliation(s)
- Li-Chun Cheng
- Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
| | - Xi Zhang
- Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
| | - Kanishk Abhinav
- Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
| | - Julie A Nguyen
- Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
| | - Sabyasachi Baboo
- Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
| | - Salvador Martinez-Bartolomé
- Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
| | - Tess C Branon
- Department of Genetics, Stanford University, Stanford, California 94305, United States
| | - Alice Y Ting
- Department of Genetics, Stanford University, Stanford, California 94305, United States
| | - Esther Loose
- Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
| | - John R Yates
- Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
| | - Larry Gerace
- Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
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3
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Nuclear Dynamics and Chromatin Structure: Implications for Pancreatic Cancer. Cells 2021; 10:cells10102624. [PMID: 34685604 PMCID: PMC8534098 DOI: 10.3390/cells10102624] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 12/14/2022] Open
Abstract
Changes in nuclear shape have been extensively associated with the dynamics and functionality of cancer cells. In most normal cells, nuclei have a regular ellipsoid shape and minimal variation in nuclear size; however, an irregular nuclear contour and abnormal nuclear size is often observed in cancer, including pancreatic cancer. Furthermore, alterations in nuclear morphology have become the 'gold standard' for tumor staging and grading. Beyond the utility of altered nuclear morphology as a diagnostic tool in cancer, the implications of altered nuclear structure for the biology and behavior of cancer cells are profound as changes in nuclear morphology could impact cellular responses to physical strain, adaptation during migration, chromatin organization, and gene expression. Here, we aim to highlight and discuss the factors that regulate nuclear dynamics and their implications for pancreatic cancer biology.
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4
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Rouhi L, Cheedipudi SM, Chen SN, Fan S, Lombardi R, Chen X, Coarfa C, Robertson MJ, Gurha P, Marian AJ. Haploinsufficiency of Tmem43 in cardiac myocytes activates the DNA damage response pathway leading to a late-onset senescence-associated pro-fibrotic cardiomyopathy. Cardiovasc Res 2021; 117:2377-2394. [PMID: 33070193 PMCID: PMC8861264 DOI: 10.1093/cvr/cvaa300] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/18/2020] [Accepted: 10/06/2020] [Indexed: 02/06/2023] Open
Abstract
AIMS Arrhythmogenic cardiomyopathy (ACM) encompasses a genetically heterogeneous group of myocardial diseases whose manifestations are sudden cardiac death, cardiac arrhythmias, heart failure, and in a subset fibro-adipogenic infiltration of the myocardium. Mutations in the TMEM43 gene, encoding transmembrane protein 43 (TMEM43) are known to cause ACM. The purpose of the study was to gain insights into the molecular pathogenesis of ACM caused by TMEM43 haploinsufficiency. METHODS AND RESULTS The Tmem43 gene was specifically deleted in cardiac myocytes by crossing the Myh6-Cre and floxed Tmem43 mice. Myh6-Cre:Tmem43W/F mice showed an age-dependent phenotype characterized by an increased mortality, cardiac dilatation and dysfunction, myocardial fibrosis, adipogenesis, and apoptosis. Sequencing of cardiac myocyte transcripts prior to and after the onset of cardiac phenotype predicted early activation of the TP53 pathway. Increased TP53 activity was associated with increased levels of markers of DNA damage response (DDR), and a subset of senescence-associated secretary phenotype (SASP). Activation of DDR, TP53, SASP, and their selected downstream effectors, including phospho-SMAD2 and phospho-SMAD3 were validated by alternative methods, including immunoblotting. Expression of SASP was associated with epithelial-mesenchymal transition and age-dependent expression of myocardial fibrosis and apoptosis in the Myh6-Cre:Tmem43W/F mice. CONCLUSION TMEM43 haploinsufficiency is associated with activation of the DDR and the TP53 pathways, which lead to increased expression of SASP and an age-dependent expression of a pro-fibrotic cardiomyopathy. Given that TMEM43 is a nuclear envelope protein and our previous data showing deficiency of another nuclear envelope protein, namely lamin A/C, activates the DDR/TP53 pathway, we surmise that DNA damage is a shared mechanism in the pathogenesis of cardiomyopathies caused by mutations involving nuclear envelope proteins.
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Affiliation(s)
- Leila Rouhi
- Center for Cardiovascular Genetics, Institute of Molecular Medicine and Department of Medicine University of Texas Health Sciences Center at Houston, 6770 Bertner Street, Suite C900A, TX 77030, USA
| | - Sirisha M Cheedipudi
- Center for Cardiovascular Genetics, Institute of Molecular Medicine and Department of Medicine University of Texas Health Sciences Center at Houston, 6770 Bertner Street, Suite C900A, TX 77030, USA
| | - Suet Nee Chen
- Center for Cardiovascular Genetics, Institute of Molecular Medicine and Department of Medicine University of Texas Health Sciences Center at Houston, 6770 Bertner Street, Suite C900A, TX 77030, USA
| | - Siyang Fan
- Center for Cardiovascular Genetics, Institute of Molecular Medicine and Department of Medicine University of Texas Health Sciences Center at Houston, 6770 Bertner Street, Suite C900A, TX 77030, USA
| | - Raffaella Lombardi
- Center for Cardiovascular Genetics, Institute of Molecular Medicine and Department of Medicine University of Texas Health Sciences Center at Houston, 6770 Bertner Street, Suite C900A, TX 77030, USA
| | - Xiaofan Chen
- Center for Cardiovascular Genetics, Institute of Molecular Medicine and Department of Medicine University of Texas Health Sciences Center at Houston, 6770 Bertner Street, Suite C900A, TX 77030, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew J Robertson
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Priyatansh Gurha
- Center for Cardiovascular Genetics, Institute of Molecular Medicine and Department of Medicine University of Texas Health Sciences Center at Houston, 6770 Bertner Street, Suite C900A, TX 77030, USA
| | - Ali J Marian
- Center for Cardiovascular Genetics, Institute of Molecular Medicine and Department of Medicine University of Texas Health Sciences Center at Houston, 6770 Bertner Street, Suite C900A, TX 77030, USA
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5
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Pawar S, Kutay U. The Diverse Cellular Functions of Inner Nuclear Membrane Proteins. Cold Spring Harb Perspect Biol 2021; 13:a040477. [PMID: 33753404 PMCID: PMC8411953 DOI: 10.1101/cshperspect.a040477] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The nuclear compartment is delimited by a specialized expanded sheet of the endoplasmic reticulum (ER) known as the nuclear envelope (NE). Compared to the outer nuclear membrane and the contiguous peripheral ER, the inner nuclear membrane (INM) houses a unique set of transmembrane proteins that serve a staggering range of functions. Many of these functions reflect the exceptional position of INM proteins at the membrane-chromatin interface. Recent research revealed that numerous INM proteins perform crucial roles in chromatin organization, regulation of gene expression, genome stability, and mediation of signaling pathways into the nucleus. Other INM proteins establish mechanical links between chromatin and the cytoskeleton, help NE remodeling, or contribute to the surveillance of NE integrity and homeostasis. As INM proteins continue to gain prominence, we review these advancements and give an overview on the functional versatility of the INM proteome.
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Affiliation(s)
- Sumit Pawar
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ulrike Kutay
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
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6
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Burgess JT, Cheong CM, Suraweera A, Sobanski T, Beard S, Dave K, Rose M, Boucher D, Croft LV, Adams MN, O'Byrne K, Richard DJ, Bolderson E. Barrier-to-autointegration-factor (Banf1) modulates DNA double-strand break repair pathway choice via regulation of DNA-dependent kinase (DNA-PK) activity. Nucleic Acids Res 2021; 49:3294-3307. [PMID: 33660778 PMCID: PMC8034644 DOI: 10.1093/nar/gkab110] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 02/04/2021] [Accepted: 02/23/2021] [Indexed: 01/07/2023] Open
Abstract
DNA repair pathways are essential to maintain the integrity of the genome and prevent cell death and tumourigenesis. Here, we show that the Barrier-to-Autointegration Factor (Banf1) protein has a role in the repair of DNA double-strand breaks. Banf1 is characterized as a nuclear envelope protein and mutations in Banf1 are associated with the severe premature aging syndrome, Néstor–Guillermo Progeria Syndrome. We have previously shown that Banf1 directly regulates the activity of PARP1 in the repair of oxidative DNA lesions. Here, we show that Banf1 also has a role in modulating DNA double-strand break repair through regulation of the DNA-dependent Protein Kinase catalytic subunit, DNA-PKcs. Specifically, we demonstrate that Banf1 relocalizes from the nuclear envelope to sites of DNA double-strand breaks. We also show that Banf1 can bind to and directly inhibit the activity of DNA-PKcs. Supporting this, cellular depletion of Banf1 leads to an increase in non-homologous end-joining and a decrease in homologous recombination, which our data suggest is likely due to unrestrained DNA-PKcs activity. Overall, this study identifies how Banf1 regulates double-strand break repair pathway choice by modulating DNA-PKcs activity to control genome stability within the cell.
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Affiliation(s)
- Joshua T Burgess
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Chee Man Cheong
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Amila Suraweera
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Thais Sobanski
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Sam Beard
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Keyur Dave
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Maddison Rose
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Didier Boucher
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Laura V Croft
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Mark N Adams
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Kenneth O'Byrne
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia.,Princess Alexandra Hospital, Ipswich Road, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Derek J Richard
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
| | - Emma Bolderson
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health at the Translational Research Institute (TRI), Brisbane, Australia
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7
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Drosophila female germline stem cells undergo mitosis without nuclear breakdown. Curr Biol 2021; 31:1450-1462.e3. [PMID: 33548191 DOI: 10.1016/j.cub.2021.01.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/18/2020] [Accepted: 01/11/2021] [Indexed: 02/02/2023]
Abstract
Stem cell homeostasis requires nuclear lamina (NL) integrity. In Drosophila germ cells, compromised NL integrity activates the ataxia telangiectasia and Rad3-related (ATR) and checkpoint kinase 2 (Chk2) checkpoint kinases, blocking germ cell differentiation and causing germline stem cell (GSC) loss. Checkpoint activation occurs upon loss of either the NL protein emerin or its partner barrier-to-autointegration factor, two proteins required for nuclear reassembly at the end of mitosis. Here, we examined how mitosis contributes to NL structural defects linked to checkpoint activation. These analyses led to the unexpected discovery that wild-type female GSCs utilize a non-canonical mode of mitosis, one that retains a permeable but intact nuclear envelope and NL. We show that the interphase NL is remodeled during mitosis for insertion of centrosomes that nucleate the mitotic spindle within the confines of the nucleus. We show that depletion or loss of NL components causes mitotic defects, including compromised chromosome segregation associated with altered centrosome positioning and structure. Further, in emerin mutant GSCs, centrosomes remain embedded in the interphase NL. Notably, these embedded centrosomes carry large amounts of pericentriolar material and nucleate astral microtubules, revealing a role for emerin in the regulation of centrosome structure. Epistasis studies demonstrate that defects in centrosome structure are upstream of checkpoint activation, suggesting that these centrosome defects might trigger checkpoint activation and GSC loss. Connections between NL proteins and centrosome function have implications for mechanisms associated with NL dysfunction in other stem cell populations, including NL-associated diseases, such as laminopathies.
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8
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High-Throughput Identification of Nuclear Envelope Protein Interactions in Schizosaccharomyces pombe Using an Arrayed Membrane Yeast-Two Hybrid Library. G3-GENES GENOMES GENETICS 2020; 10:4649-4663. [PMID: 33109728 PMCID: PMC7718735 DOI: 10.1534/g3.120.401880] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The nuclear envelope (NE) contains a specialized set of integral membrane proteins that maintain nuclear shape and integrity and influence chromatin organization and gene expression. Advances in proteomics techniques and studies in model organisms have identified hundreds of proteins that localize to the NE. However, the function of many of these proteins at the NE remains unclear, in part due to a lack of understanding of the interactions that these proteins participate in at the NE membrane. To assist in the characterization of NE transmembrane protein interactions we developed an arrayed library of integral and peripheral membrane proteins from the fission yeast Schizosaccharomyces pombe for high-throughput screening using the split-ubiquitin based membrane yeast two -hybrid system. We used this approach to characterize protein interactions for three conserved proteins that localize to the inner nuclear membrane: Cut11/Ndc1, Lem2 and Ima1/Samp1/Net5. Additionally, we determined how the interaction network for Cut11 is altered in canonical temperature-sensitive cut11-ts mutants. This library and screening approach is readily applicable to characterizing the interactomes of integral membrane proteins localizing to various subcellular compartments.
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9
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Sears RM, Roux KJ. Diverse cellular functions of barrier-to-autointegration factor and its roles in disease. J Cell Sci 2020; 133:133/16/jcs246546. [PMID: 32817163 DOI: 10.1242/jcs.246546] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Barrier-to-autointegration factor (BAF; encoded by BANF1) is a small highly conserved, ubiquitous and self-associating protein that coordinates with numerous binding partners to accomplish several key cellular processes. By interacting with double-stranded DNA, histones and various other nuclear proteins, including those enriched at the nuclear envelope, BAF appears to be essential for replicating cells to protect the genome and enable cell division. Cellular processes, such as innate immunity, post-mitotic nuclear reformation, repair of interphase nuclear envelope rupture, genomic regulation, and the DNA damage and repair response have all been shown to depend on BAF. This Review focuses on the regulation of the numerous interactions of BAF, which underlie the mechanisms by which BAF accomplishes its essential cellular functions. We will also discuss how perturbation of BAF function may contribute to human disease.
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Affiliation(s)
- Rhiannon M Sears
- Enabling Technologies Group, Sanford Research, Sioux Falls, SD 57104, USA.,Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD 57069, USA
| | - Kyle J Roux
- Enabling Technologies Group, Sanford Research, Sioux Falls, SD 57104, USA .,Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57069, USA
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10
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Cenni V, Squarzoni S, Loi M, Mattioli E, Lattanzi G, Capanni C. Emerin Phosphorylation during the Early Phase of the Oxidative Stress Response Influences Emerin-BAF Interaction and BAF Nuclear Localization. Cells 2020; 9:cells9061415. [PMID: 32517247 PMCID: PMC7349582 DOI: 10.3390/cells9061415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/04/2020] [Accepted: 06/04/2020] [Indexed: 02/07/2023] Open
Abstract
Reactive Oxygen Species (ROS) are reactive molecules required for the maintenance of physiological functions. Oxidative stress arises when ROS production exceeds the cellular ability to eliminate such molecules. In this study, we showed that oxidative stress induces post-translational modification of the inner nuclear membrane protein emerin. In particular, emerin is phosphorylated at the early stages of the oxidative stress response, while protein phosphorylation is abolished upon recovery from stress. A finely tuned balance between emerin phosphorylation and O-GlcNAcylation seems to govern this dynamic and modulates emerin–BAF interaction and BAF nucleoplasmic localization during the oxidative stress response. Interestingly, emerin post-translational modifications, similar to those observed during the stress response, are detected in cells bearing LMNA gene mutations and are characterized by a free radical generating environment. On the other hand, under oxidative stress conditions, a delay in DNA damage repair and cell cycle progression is found in cells from Emery–Dreifuss Muscular Dystrophy type 1, which do not express emerin. These results suggest a role of the emerin–BAF protein platform in the DNA damage response aimed at counteracting the detrimental effects of elevated levels of ROS.
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Affiliation(s)
- Vittoria Cenni
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, Unit of Bologna, 40136 Bologna, Italy; (V.C.); (S.S.); (M.L.); (E.M.); (G.L.)
- IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Stefano Squarzoni
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, Unit of Bologna, 40136 Bologna, Italy; (V.C.); (S.S.); (M.L.); (E.M.); (G.L.)
- IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Manuela Loi
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, Unit of Bologna, 40136 Bologna, Italy; (V.C.); (S.S.); (M.L.); (E.M.); (G.L.)
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40127 Bologna, Italy
| | - Elisabetta Mattioli
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, Unit of Bologna, 40136 Bologna, Italy; (V.C.); (S.S.); (M.L.); (E.M.); (G.L.)
- IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Giovanna Lattanzi
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, Unit of Bologna, 40136 Bologna, Italy; (V.C.); (S.S.); (M.L.); (E.M.); (G.L.)
- IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Cristina Capanni
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, Unit of Bologna, 40136 Bologna, Italy; (V.C.); (S.S.); (M.L.); (E.M.); (G.L.)
- IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
- Correspondence: ; Tel.: +39-051-6366856; Fax: +39-051-4689922
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11
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Ummethum H, Hamperl S. Proximity Labeling Techniques to Study Chromatin. Front Genet 2020; 11:450. [PMID: 32477404 PMCID: PMC7235407 DOI: 10.3389/fgene.2020.00450] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/14/2020] [Indexed: 12/19/2022] Open
Abstract
Mammals contain over 200 different cell types, yet nearly all have the same genomic DNA sequence. It is a key question in biology how the genetic instructions in DNA are selectively interpreted by cells to specify various transcriptional programs and therefore cellular identity. The structural and functional organization of chromatin governs the transcriptional state of individual genes. To understand how genomic loci adopt different levels of gene expression, it is critical to characterize all local chromatin factors as well as long-range interactions in the 3D nuclear compartment. Much of our current knowledge regarding protein interactions in a chromatin context is based on affinity purification of chromatin components coupled to mass spectrometry (AP-MS). AP-MS has been invaluable to map strong protein-protein interactions in the nucleus. However, the interaction is detected after cell lysis and biochemical enrichment, allowing for loss or gain of false positive or negative interaction partners. Recently, proximity-dependent labeling methods have emerged as powerful tools for studying chromatin in its native context. These methods take advantage of engineered enzymes that are fused to a chromatin factor of interest and can directly label all factors in proximity. Subsequent pull-down assays followed by mass spectrometry or sequencing approaches provide a comprehensive snapshot of the proximal chromatin interactome. By combining this method with dCas9, this approach can also be extended to study chromatin at specific genomic loci. Here, we review and compare current proximity-labeling approaches available for studying chromatin, with a particular focus on new emerging technologies that can provide important insights into the transcriptional and chromatin interaction networks essential for cellular identity.
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Affiliation(s)
- Henning Ummethum
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Stephan Hamperl
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
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