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Rankin BD, Rankin S. The MCM2-7 Complex: Roles beyond DNA Unwinding. BIOLOGY 2024; 13:258. [PMID: 38666870 PMCID: PMC11048021 DOI: 10.3390/biology13040258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/07/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024]
Abstract
The MCM2-7 complex is a hexameric protein complex that serves as a DNA helicase. It unwinds the DNA double helix during DNA replication, thereby providing the single-stranded replication template. In recent years, it has become clear that the MCM2-7 complex has additional functions that extend well beyond its role in DNA replication. Through physical and functional interactions with different pathways, it impacts other nuclear events and activities, including folding of the genome, histone inheritance, chromosome segregation, DNA damage sensing and repair, and gene transcription. Collectively, the diverse roles of the MCM2-7 complex suggest it plays a critical role in maintaining genome integrity by integrating the regulation of DNA replication with other pathways in the nucleus.
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Affiliation(s)
- Brooke D. Rankin
- Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA;
- Cell Biology Department, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Susannah Rankin
- Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA;
- Cell Biology Department, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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2
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Qu HQ, Glessner JT, Qu J, Liu Y, Watson D, Chang X, Saeidian AH, Qiu H, Mentch FD, Connolly JJ, Hakonarson H. High Comorbidity of Pediatric Cancers in Patients with Birth Defects: Insights from Whole Genome Sequencing Analysis of Copy Number Variations. Transl Res 2024; 266:49-56. [PMID: 37989391 DOI: 10.1016/j.trsl.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/01/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Patients with birth defects (BD) exhibit an elevated risk of cancer. We aimed to investigate the potential link between pediatric cancers and BDs, exploring the hypothesis of shared genetic defects contributing to the coexistence of these conditions. METHODS This study included 1454 probands with BDs (704 females and 750 males), including 619 (42.3%) with and 845 (57.7%) without co-occurrence of pediatric onset cancers. Whole genome sequencing (WGS) was done at 30X coverage through the Kids First/Gabriella Miller X01 Program. RESULTS 8211 CNV loci were called from the 1454 unrelated individuals. 191 CNV loci classified as pathogenic/likely pathogenic (P/LP) were identified in 309 (21.3%) patients, with 124 (40.1%) of these patients having pediatric onset cancers. The most common group of CNVs are pathogenic deletions covering the region ChrX:52,863,011-55,652,521, seen in 162 patients including 17 males. Large recurrent P/LP duplications >5MB were detected in 33 patients. CONCLUSIONS This study revealed that P/LP CNVs were common in a large cohort of BD patients with high rate of pediatric cancers. We present a comprehensive spectrum of P/LP CNVs in patients with BDs and various cancers. Notably, deletions involving E2F target genes and genes implicated in mitotic spindle assembly and G2/M checkpoint were identified, potentially disrupting cell-cycle progression and providing mechanistic insights into the concurrent occurrence of BDs and cancers.
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Affiliation(s)
- Hui-Qi Qu
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Joseph T Glessner
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Jingchun Qu
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Yichuan Liu
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Deborah Watson
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Xiao Chang
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Amir Hossein Saeidian
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Haijun Qiu
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Frank D Mentch
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - John J Connolly
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA; Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA; Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
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3
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Pati D. Role of chromosomal cohesion and separation in aneuploidy and tumorigenesis. Cell Mol Life Sci 2024; 81:100. [PMID: 38388697 PMCID: PMC10884101 DOI: 10.1007/s00018-024-05122-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/28/2023] [Accepted: 01/09/2024] [Indexed: 02/24/2024]
Abstract
Cell division is a crucial process, and one of its essential steps involves copying the genetic material, which is organized into structures called chromosomes. Before a cell can divide into two, it needs to ensure that each newly copied chromosome is paired tightly with its identical twin. This pairing is maintained by a protein complex known as cohesin, which is conserved in various organisms, from single-celled ones to humans. Cohesin essentially encircles the DNA, creating a ring-like structure to handcuff, to keep the newly synthesized sister chromosomes together in pairs. Therefore, chromosomal cohesion and separation are fundamental processes governing the attachment and segregation of sister chromatids during cell division. Metaphase-to-anaphase transition requires dissolution of cohesins by the enzyme Separase. The tight regulation of these processes is vital for safeguarding genomic stability. Dysregulation in chromosomal cohesion and separation resulting in aneuploidy, a condition characterized by an abnormal chromosome count in a cell, is strongly associated with cancer. Aneuploidy is a recurring hallmark in many cancer types, and abnormalities in chromosomal cohesion and separation have been identified as significant contributors to various cancers, such as acute myeloid leukemia, myelodysplastic syndrome, colorectal, bladder, and other solid cancers. Mutations within the cohesin complex have been associated with these cancers, as they interfere with chromosomal segregation, genome organization, and gene expression, promoting aneuploidy and contributing to the initiation of malignancy. In summary, chromosomal cohesion and separation processes play a pivotal role in preserving genomic stability, and aberrations in these mechanisms can lead to aneuploidy and cancer. Gaining a deeper understanding of the molecular intricacies of chromosomal cohesion and separation offers promising prospects for the development of innovative therapeutic approaches in the battle against cancer.
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Affiliation(s)
- Debananda Pati
- Texas Children's Cancer Center, Department of Pediatrics Hematology/Oncology, Molecular and Cellular Biology, Baylor College of Medicine, 1102 Bates Avenue, Houston, TX, 77030, USA.
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4
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Abarca-Barriga HH, Punil Luciano R, Vásquez Sotomayor F. Cornelia de Lange Syndrome Caused by an Intragenic Heterozygous Deletion in RAD21 Detected through Very-High-Resolution Chromosomal Microarray Analysis. Genes (Basel) 2023; 14:2212. [PMID: 38137034 PMCID: PMC10742884 DOI: 10.3390/genes14122212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 12/24/2023] Open
Abstract
Cornelia de Lange syndrome is a genetic and clinically heterogeneous entity, caused by at least five genes. It is characterized by short stature, gestalt facies, microcephaly, neurodevelopmental disorders, and other anomalies. In this report, we present a 13-year-old female patient with microcephaly, cleft palate, polydactyly, short stature, triangular facies, frontal bossing, a bulbous nose, an overfolded helix, limited pronosupination, and an anomalous uterus. No neurodevelopmental disorders were reported. A chromosomal microarray analysis of 6.5 million markers was performed in the proband and her parents. The results showed a de novo heterozygous microdeletion of exons 9-14 within RAD21, which confirmed the diagnosis of Cornelia de Lange syndrome type 4. Our patient did not show any neurologic phenotype (until the time of diagnosis), although neurodevelopmental disorders are frequently present in patients with Cornelia de Lange syndrome type 4, and despite carrying a deletion that was larger than previously reported. Therefore, unknown genetic modifiers or intrinsic mechanisms of RAD21 variants may exist and should be studied.
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Affiliation(s)
- Hugo H. Abarca-Barriga
- Instituto de Investigaciones de Ciencias Biomédicas, Universidad Ricardo Palma, Lima 15039, Peru;
- Servicio de Genética & Errores Innatos del Metabolismo, Instituto Nacional de Salud del Niño Breña, Lima 15083, Peru;
| | - Renzo Punil Luciano
- Servicio de Genética & Errores Innatos del Metabolismo, Instituto Nacional de Salud del Niño Breña, Lima 15083, Peru;
| | - Flor Vásquez Sotomayor
- Instituto de Investigaciones de Ciencias Biomédicas, Universidad Ricardo Palma, Lima 15039, Peru;
- Servicio de Genética & Errores Innatos del Metabolismo, Instituto Nacional de Salud del Niño Breña, Lima 15083, Peru;
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5
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Nagasaka K, Davidson IF, Stocsits RR, Tang W, Wutz G, Batty P, Panarotto M, Litos G, Schleiffer A, Gerlich DW, Peters JM. Cohesin mediates DNA loop extrusion and sister chromatid cohesion by distinct mechanisms. Mol Cell 2023; 83:3049-3063.e6. [PMID: 37591243 DOI: 10.1016/j.molcel.2023.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 05/28/2023] [Accepted: 07/25/2023] [Indexed: 08/19/2023]
Abstract
Cohesin connects CTCF-binding sites and other genomic loci in cis to form chromatin loops and replicated DNA molecules in trans to mediate sister chromatid cohesion. Whether cohesin uses distinct or related mechanisms to perform these functions is unknown. Here, we describe a cohesin hinge mutant that can extrude DNA into loops but is unable to mediate cohesion in human cells. Our results suggest that the latter defect arises during cohesion establishment. The observation that cohesin's cohesion and loop extrusion activities can be partially separated indicates that cohesin uses distinct mechanisms to perform these two functions. Unexpectedly, the same hinge mutant can also not be stopped by CTCF boundaries as well as wild-type cohesin. This suggests that cohesion establishment and cohesin's interaction with CTCF boundaries depend on related mechanisms and raises the possibility that both require transient hinge opening to entrap DNA inside the cohesin ring.
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Affiliation(s)
- Kota Nagasaka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Roman R Stocsits
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Gordana Wutz
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Paul Batty
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, Vienna 1030, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna 1030, Austria
| | - Melanie Panarotto
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna 1030, Austria
| | - Gabriele Litos
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, Vienna 1030, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, Vienna 1030, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna 1030, Austria.
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6
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Carmo C, Coelho J, Silva RD, Tavares A, Boavida A, Gaetani P, Guilgur LG, Martinho RG, Oliveira RA. A dual-function SNF2 protein drives chromatid resolution and nascent transcripts removal in mitosis. EMBO Rep 2023; 24:e56463. [PMID: 37462213 PMCID: PMC10481674 DOI: 10.15252/embr.202256463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 09/07/2023] Open
Abstract
Mitotic chromatin is largely assumed incompatible with transcription due to changes in the transcription machinery and chromosome architecture. However, the mechanisms of mitotic transcriptional inactivation and their interplay with chromosome assembly remain largely unknown. By monitoring ongoing transcription in Drosophila early embryos, we reveal that eviction of nascent mRNAs from mitotic chromatin occurs after substantial chromosome compaction and is not promoted by condensin I. Instead, we show that the timely removal of transcripts from mitotic chromatin is driven by the SNF2 helicase-like protein Lodestar (Lds), identified here as a modulator of sister chromatid cohesion defects. In addition to the eviction of nascent transcripts, we uncover that Lds cooperates with Topoisomerase 2 to ensure efficient sister chromatid resolution and mitotic fidelity. We conclude that the removal of nascent transcripts upon mitotic entry is not a passive consequence of cell cycle progression and/or chromosome compaction but occurs via dedicated mechanisms with functional parallelisms to sister chromatid resolution.
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Affiliation(s)
| | - João Coelho
- Instituto Gulbenkian de CiênciaOeirasPortugal
| | - Rui D Silva
- Algarve Biomedical Center Research Institute (ABC‐RI) and Faculty of Medicine and Biomedical Sciences (FMCB)Universidade do AlgarveFaroPortugal
| | | | - Ana Boavida
- Instituto Gulbenkian de CiênciaOeirasPortugal
- Present address:
Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle RicercheNaplesItaly
| | | | | | - Rui Gonçalo Martinho
- Algarve Biomedical Center Research Institute (ABC‐RI) and Faculty of Medicine and Biomedical Sciences (FMCB)Universidade do AlgarveFaroPortugal
- Department of Medical Sciences (DCM) and Institute for Biomedicine (iBiMED)Universidade de AveiroAveiroPortugal
| | - Raquel A Oliveira
- Instituto Gulbenkian de CiênciaOeirasPortugal
- Católica Biomedical Research Centre, Católica Medical SchoolUniversidade Católica PortuguesaLisbonPortugal
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7
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Salvato I, Ricciardi L, Dal Col J, Nigro A, Giurato G, Memoli D, Sellitto A, Lamparelli EP, Crescenzi MA, Vitale M, Vatrella A, Nucera F, Brun P, Caicci F, Dama P, Stiff T, Castellano L, Idrees S, Johansen MD, Faiz A, Wark PA, Hansbro PM, Adcock IM, Caramori G, Stellato C. Expression of targets of the RNA-binding protein AUF-1 in human airway epithelium indicates its role in cellular senescence and inflammation. Front Immunol 2023; 14:1192028. [PMID: 37483631 PMCID: PMC10360199 DOI: 10.3389/fimmu.2023.1192028] [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: 03/22/2023] [Accepted: 06/06/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction The RNA-binding protein AU-rich-element factor-1 (AUF-1) participates to posttranscriptional regulation of genes involved in inflammation and cellular senescence, two pathogenic mechanisms of chronic obstructive pulmonary disease (COPD). Decreased AUF-1 expression was described in bronchiolar epithelium of COPD patients versus controls and in vitro cytokine- and cigarette smoke-challenged human airway epithelial cells, prompting the identification of epithelial AUF-1-targeted transcripts and function, and investigation on the mechanism of its loss. Results RNA immunoprecipitation-sequencing (RIP-Seq) identified, in the human airway epithelial cell line BEAS-2B, 494 AUF-1-bound mRNAs enriched in their 3'-untranslated regions for a Guanine-Cytosine (GC)-rich binding motif. AUF-1 association with selected transcripts and with a synthetic GC-rich motif were validated by biotin pulldown. AUF-1-targets' steady-state levels were equally affected by partial or near-total AUF-1 loss induced by cytomix (TNFα/IL1β/IFNγ/10 nM each) and siRNA, respectively, with differential transcript decay rates. Cytomix-mediated decrease in AUF-1 levels in BEAS-2B and primary human small-airways epithelium (HSAEC) was replicated by treatment with the senescence- inducer compound etoposide and associated with readouts of cell-cycle arrest, increase in lysosomal damage and senescence-associated secretory phenotype (SASP) factors, and with AUF-1 transfer in extracellular vesicles, detected by transmission electron microscopy and immunoblotting. Extensive in-silico and genome ontology analysis found, consistent with AUF-1 functions, enriched RIP-Seq-derived AUF-1-targets in COPD-related pathways involved in inflammation, senescence, gene regulation and also in the public SASP proteome atlas; AUF-1 target signature was also significantly represented in multiple transcriptomic COPD databases generated from primary HSAEC, from lung tissue and from single-cell RNA-sequencing, displaying a predominant downregulation of expression. Discussion Loss of intracellular AUF-1 may alter posttranscriptional regulation of targets particularly relevant for protection of genomic integrity and gene regulation, thus concurring to airway epithelial inflammatory responses related to oxidative stress and accelerated aging. Exosomal-associated AUF-1 may in turn preserve bound RNA targets and sustain their function, participating to spreading of inflammation and senescence to neighbouring cells.
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Affiliation(s)
- Ilaria Salvato
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Luca Ricciardi
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Jessica Dal Col
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Annunziata Nigro
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Giorgio Giurato
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Domenico Memoli
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Assunta Sellitto
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Erwin Pavel Lamparelli
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Maria Assunta Crescenzi
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Monica Vitale
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Alessandro Vatrella
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Francesco Nucera
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Paola Brun
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | | | - Paola Dama
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Thomas Stiff
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Leandro Castellano
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Sobia Idrees
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Matt D. Johansen
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Alen Faiz
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Peter A. Wark
- Immune Health, Hunter Medical Research Institute and The University of Newcastle, Newcastle, NSW, Australia
| | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
- Immune Health, Hunter Medical Research Institute and The University of Newcastle, Newcastle, NSW, Australia
| | - Ian M. Adcock
- National Heart and Lung Institute, Imperial College London and the National Institute for Health and Care Research (NIHR) Imperial Biomedical Research Centre, London, United Kingdom
| | - Gaetano Caramori
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Cristiana Stellato
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
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8
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Langer CCH, Mitter M, Stocsits RR, Gerlich DW. HiCognition: a visual exploration and hypothesis testing tool for 3D genomics. Genome Biol 2023; 24:158. [PMID: 37408019 DOI: 10.1186/s13059-023-02996-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 06/25/2023] [Indexed: 07/07/2023] Open
Abstract
Genome browsers facilitate integrated analysis of multiple genomics datasets yet visualize only a few regions at a time and lack statistical functions for extracting meaningful information. We present HiCognition, a visual exploration and machine-learning tool based on a new genomic region set concept, enabling detection of patterns and associations between 3D chromosome conformation and collections of 1D genomics profiles of any type. By revealing how transcription and cohesion subunit isoforms contribute to chromosome conformation, we showcase how the flexible user interface and machine learning tools of HiCognition help to understand the relationship between the structure and function of the genome.
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Affiliation(s)
- Christoph C H Langer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Michael Mitter
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Roman R Stocsits
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.
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9
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Martin L, Neguembor MV, Cosma MP. Women’s contribution in understanding how topoisomerases, supercoiling, and transcription control genome organization. Front Mol Biosci 2023; 10:1155825. [PMID: 37051322 PMCID: PMC10083264 DOI: 10.3389/fmolb.2023.1155825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/15/2023] [Indexed: 03/28/2023] Open
Abstract
One of the biggest paradoxes in biology is that human genome is roughly 2 m long, while the nucleus containing it is almost one million times smaller. To fit into the nucleus, DNA twists, bends and folds into several hierarchical levels of compaction. Still, DNA has to maintain a high degree of accessibility to be readily replicated and transcribed by proteins. How compaction and accessibility co-exist functionally in human cells is still a matter of debate. Here, we discuss how the torsional stress of the DNA helix acts as a buffer, regulating both chromatin compaction and accessibility. We will focus on chromatin supercoiling and on the emerging role of topoisomerases as pivotal regulators of genome organization. We will mainly highlight the major breakthrough studies led by women, with the intention of celebrating the work of this group that remains a minority within the scientific community.
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Affiliation(s)
- Laura Martin
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Technical Contact, Guangzhou, China
- *Correspondence: Maria Victoria Neguembor, ; Maria Pia Cosma,
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- ICREA, Barcelona, Spain
- Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Lead Contact, Guangzhou, China
- *Correspondence: Maria Victoria Neguembor, ; Maria Pia Cosma,
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10
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Shin H, Kim Y. Regulation of loop extrusion on the interphase genome. Crit Rev Biochem Mol Biol 2023; 58:1-18. [PMID: 36921088 DOI: 10.1080/10409238.2023.2182273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
In the human cell nucleus, dynamically organized chromatin is the substrate for gene regulation, DNA replication, and repair. A central mechanism of DNA loop formation is an ATPase motor cohesin-mediated loop extrusion. The cohesin complexes load and unload onto the chromosome under the control of other regulators that physically interact and affect motor activity. Regulation of the dynamic loading cycle of cohesin influences not only the chromatin structure but also genome-associated human disorders and aging. This review focuses on the recently spotlighted genome organizing factors and the mechanism by which their dynamic interactions shape the genome architecture in interphase.
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Affiliation(s)
- Hyogyung Shin
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
| | - Yoori Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea.,New Biology Research Center, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
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11
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Choudhary K, Kupiec M. The cohesin complex of yeasts: sister chromatid cohesion and beyond. FEMS Microbiol Rev 2023; 47:6825453. [PMID: 36370456 DOI: 10.1093/femsre/fuac045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022] Open
Abstract
Each time a cell divides, it needs to duplicate the genome and then separate the two copies. In eukaryotes, which usually have more than one linear chromosome, this entails tethering the two newly replicated DNA molecules, a phenomenon known as sister chromatid cohesion (SCC). Cohesion ensures proper chromosome segregation to separate poles during mitosis. SCC is achieved by the presence of the cohesin complex. Besides its canonical function, cohesin is essential for chromosome organization and DNA damage repair. Surprisingly, yeast cohesin is loaded in G1 before DNA replication starts but only acquires its binding activity during DNA replication. Work in microorganisms, such as Saccharomyces cerevisiae and Schizosaccharomyces pombe has greatly contributed to the understanding of cohesin composition and functions. In the last few years, much progress has been made in elucidating the role of cohesin in chromosome organization and compaction. Here, we discuss the different functions of cohesin to ensure faithful chromosome segregation and genome stability during the mitotic cell division in yeast. We describe what is known about its composition and how DNA replication is coupled with SCC establishment. We also discuss current models for the role of cohesin in chromatin loop extrusion and delineate unanswered questions about the activity of this important, conserved complex.
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Affiliation(s)
- Karan Choudhary
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
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12
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Yu D, Chen G, Wang Y, Wang Y, Lin R, Liu N, Zhu P, Liu H, Hu T, Feng R, Feng H, Lan F, Cai J, Chen H. Regulation of cohesin-mediated chromosome folding by PDS5 in mammals. EMBO Rep 2022; 23:e54853. [PMID: 36129789 PMCID: PMC9638874 DOI: 10.15252/embr.202254853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 09/04/2022] [Accepted: 09/08/2022] [Indexed: 09/23/2023] Open
Abstract
Cohesin regulates sister chromatid cohesion but also contributes to chromosome folding by promoting the formation of chromatin loops, a process mediated by loop extrusion. Although PDS5 regulates cohesin dynamics on chromatin, the exact function of PDS5 in cohesin-mediated chromatin looping remains unclear. Two paralogs of PDS5 exist in vertebrates, PDS5A and PDS5B. Here we show that PDS5A and PDS5B co-localize with RAD21 and CTCF at loop anchors. Rapid PDS5A or PDS5B degradation in liver cancer cells using an inducible degron system reduces chromatin loops and increases loop size. RAD21 enrichment at loop anchors is decreased upon depletion of PDS5A or PDS5B. PDS5B loss also reduces CTCF signals at loop anchors and has a stronger effect on loop enlargement compared with PDS5A. Co-depletion of PDS5A and PDS5B reduces RAD21 levels at loop anchors although the amount of cohesin on chromatin is increased. Our study provides insight into how PDS5 proteins regulate cohesin-mediated chromatin looping.
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Affiliation(s)
- Dingdang Yu
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical SciencesFudan UniversityShanghaiChina
- Department of Human Cell Biology and Genetics, School of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Guoyu Chen
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer InstituteRenji HospitalShanghaiChina
- Renji‐Med X Clinical Stem Cell Research Center, Ren Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yuci Wang
- Department of Human Cell Biology and Genetics, School of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Yining Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Risheng Lin
- Department of Human Cell Biology and Genetics, School of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Nanbo Liu
- Department of Cardiac Surgery, and Department of Medical Sciences, Guangdong Cardiovascular Institute, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Ping Zhu
- Department of Cardiac Surgery, and Department of Medical Sciences, Guangdong Cardiovascular Institute, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Hang Liu
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical SciencesFudan UniversityShanghaiChina
| | - Tao Hu
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical SciencesFudan UniversityShanghaiChina
| | - Rui Feng
- Department of Human Cell Biology and Genetics, School of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Haizhong Feng
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer InstituteRenji HospitalShanghaiChina
- Renji‐Med X Clinical Stem Cell Research Center, Ren Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Fei Lan
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical SciencesFudan UniversityShanghaiChina
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Jiabin Cai
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical SciencesFudan UniversityShanghaiChina
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Hao Chen
- Department of Human Cell Biology and Genetics, School of MedicineSouthern University of Science and TechnologyShenzhenChina
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13
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Sun X, Zhang J, Cao C. CTCF and Its Partners: Shaper of 3D Genome during Development. Genes (Basel) 2022; 13:genes13081383. [PMID: 36011294 PMCID: PMC9407368 DOI: 10.3390/genes13081383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 02/06/2023] Open
Abstract
The 3D genome organization and its dynamic modulate genome function, playing a pivotal role in cell differentiation and development. CTCF and cohesin, acting as the core architectural components involved in chromatin looping and genome folding, can also recruit other protein or RNA partners to fine-tune genome structure during development. Moreover, systematic screening for partners of CTCF has been performed through high-throughput approaches. In particular, several novel protein and RNA partners, such as BHLHE40, WIZ, MAZ, Aire, MyoD, YY1, ZNF143, and Jpx, have been identified, and these partners are mostly implicated in transcriptional regulation and chromatin remodeling, offering a unique opportunity for dissecting their roles in higher-order chromatin organization by collaborating with CTCF and cohesin. Here, we review the latest advancements with an emphasis on features of CTCF partners and also discuss the specific functions of CTCF-associated complexes in chromatin structure modulation, which may extend our understanding of the functions of higher-order chromatin architecture in developmental processes.
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Affiliation(s)
- Xiaoyue Sun
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Jing Zhang
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Chunwei Cao
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Guangzhou Laboratory, Guangzhou 510320, China
- Correspondence:
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14
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Abstract
Meiotic crossover recombination is required for faithful chromosome segregation and promotes genetic diversity by reshuffling alleles between parental chromosomes. Meiotic chromosomes are organized into arrays of loops that are anchored to the proteinaceous axes. The length of the meiotic chromosome axis is intimately associated with crossover frequencies in yeast and higher eukaryotes. However, how chromosome axis length is regulated in meiosis is unknown. Here, we demonstrate that cohesin regulator Pds5 interacts with proteasomes to regulate meiotic chromosome axis length by modulating ubiquitination. This regulatory mechanism also includes two ubiquitin E3 ligases, SCF (Skp–Cullin–F-box) and Ufd4. These findings identify a molecular pathway in regulating chromosome organization and reveal an unexpected function of the ubiquitin–proteasome system in meiosis. Meiotic crossover (CO) recombination is tightly regulated by chromosome architecture to ensure faithful chromosome segregation and to reshuffle alleles between parental chromosomes for genetic diversity of progeny. However, regulation of the meiotic chromosome loop/axis organization is poorly understood. Here, we identify a molecular pathway for axis length regulation. We show that the cohesin regulator Pds5 can interact with proteasomes. Meiosis-specific depletion of proteasomes and/or Pds5 results in a similarly shortened chromosome axis, suggesting proteasomes and Pds5 regulate axis length in the same pathway. Protein ubiquitination is accumulated in pds5 and proteasome mutants. Moreover, decreased chromosome axis length in these mutants can be largely rescued by decreasing ubiquitin availability and thus decreasing protein ubiquitination. Further investigation reveals that two ubiquitin E3 ligases, SCF (Skp–Cullin–F-box) and Ufd4, are involved in this Pds5–ubiquitin/proteasome pathway to cooperatively control chromosome axis length. These results support the hypothesis that ubiquitination of chromosome proteins results in a shortened chromosome axis, and cohesin–Pds5 recruits proteasomes onto chromosomes to regulate ubiquitination level and thus axis length. These findings reveal an unexpected role of the ubiquitin–proteasome system in meiosis and contribute to our knowledge of how Pds5 regulates meiotic chromosome organization. A conserved regulatory mechanism probably exists in higher eukaryotes.
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15
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Zuilkoski CM, Skibbens RV. Integrating Sister Chromatid Cohesion Establishment to DNA Replication. Genes (Basel) 2022; 13:genes13040625. [PMID: 35456431 PMCID: PMC9032331 DOI: 10.3390/genes13040625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 02/01/2023] Open
Abstract
The intersection through which two fundamental processes meet provides a unique vantage point from which to view cellular regulation. On the one hand, DNA replication is at the heart of cell division, generating duplicate chromosomes that allow each daughter cell to inherit a complete copy of the parental genome. Among other factors, the PCNA (proliferating cell nuclear antigen) sliding clamp ensures processive DNA replication during S phase and is essential for cell viability. On the other hand, the process of chromosome segregation during M phase—an act that occurs long after DNA replication—is equally fundamental to a successful cell division. Eco1/Ctf7 ensures that chromosomes faithfully segregate during mitosis, but functions during DNA replication to activate cohesins and thereby establish cohesion between sister chromatids. To achieve this, Eco1 binds PCNA and numerous other DNA replication fork factors that include MCM helicase, Chl1 helicase, and the Rtt101-Mms1-Mms22 E3 ubiquitin ligase. Here, we review the multi-faceted coordination between cohesion establishment and DNA replication. SUMMARY STATEMENT: New findings provide important insights into the mechanisms through which DNA replication and the establishment of sister chromatid cohesion are coupled.
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Affiliation(s)
- Caitlin M. Zuilkoski
- Department of Biological Sciences, Lehigh University, 111 Research Drive, Bethlehem, PA 18015, USA;
- Department of Biology, Indiana University, 1001 E. Third Street, Bloomington, IN 47401, USA
| | - Robert V. Skibbens
- Department of Biological Sciences, Lehigh University, 111 Research Drive, Bethlehem, PA 18015, USA;
- Correspondence: ; Tel.: +610-758-6162
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16
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Lafta IJ, Kudhair BK, Iyiola OA, Ahmed EA, Chou T. Evaluating Expression of the STAG1 Gene as a Potential Breast Cancer Biomarker. THE IRAQI JOURNAL OF VETERINARY MEDICINE 2021. [DOI: 10.30539/ijvm.v45i2.1255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
STAG proteins, which are part of the cohesin complex and encoded by the STAG genes, are known as Irr1/Scc3 in yeast and as SA/STAG/stromalin in mammals. There are more variants as there are alternate splice sites, maybe three open reading frames (ORFs) code for three main proteins, including: SA1 (STAG1), SA2 (STAG2) and SA3 (STAG3). The cohesin protein complex has various essential roles in eukaryotic cell biology. This study compared the expression of the STAG1 gene in four different breast cancer cell lines, including: MCF-7, T-47D, MDA-MB-468, and MDA-MB-231 and normal breast tissue. RNA was extracted from these cell lines and mRNA was converted to cDNA, and then expression of the STAG1 gene was quantified by three sets of specific primer pairs using Real Time-quantitative PCR (RT-qPCR). The findings show significantly different over-expression of STAG1 in these cancer cell lines in comparison with the normal tissue, and the cell lines were different in their expression levels. In conclusion, the STAG1 gene can be postulated as a candidate breast cancer biomarker that needs to be further evaluated in breast tumor biopsies.
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17
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Ciecko AE, Schauder DM, Foda B, Petrova G, Kasmani MY, Burns R, Lin CW, Drobyski WR, Cui W, Chen YG. Self-Renewing Islet TCF1 + CD8 T Cells Undergo IL-27-Controlled Differentiation to Become TCF1 - Terminal Effectors during the Progression of Type 1 Diabetes. THE JOURNAL OF IMMUNOLOGY 2021; 207:1990-2004. [PMID: 34507949 DOI: 10.4049/jimmunol.2100362] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/11/2021] [Indexed: 11/19/2022]
Abstract
In type 1 diabetes (T1D) autoreactive CD8 T cells infiltrate pancreatic islets and destroy insulin-producing β cells. Progression to T1D onset is a chronic process, which suggests that the effector activity of β-cell autoreactive CD8 T cells needs to be maintained throughout the course of disease development. The mechanism that sustains diabetogenic CD8 T cell effectors during the course of T1D progression has not been completely defined. Here we used single-cell RNA sequencing to gain further insight into the phenotypic complexity of islet-infiltrating CD8 T cells in NOD mice. We identified two functionally distinct subsets of activated CD8 T cells, CD44highTCF1+CXCR6- and CD44highTCF1-CXCR6+, in islets of prediabetic NOD mice. Compared with CD44highTCF1+CXCR6- CD8 T cells, the CD44highTCF1-CXCR6+ subset expressed higher levels of inhibitory and cytotoxic molecules and was more prone to apoptosis. Adoptive cell transfer experiments revealed that CD44highTCF1+CXCR6- CD8 T cells, through continuous generation of the CD44highTCF1-CXCR6+ subset, were more capable than the latter population to promote insulitis and the development of T1D. We further showed that direct IL-27 signaling in CD8 T cells promoted the generation of terminal effectors from the CD44highTCF1+CXCR6- population. These results indicate that islet CD44highTCF1+CXCR6- CD8 T cells are a progenitor-like subset with self-renewing capacity, and, under an IL-27-controlled mechanism, they differentiate into the CD44highTCF1-CXCR6+ terminal effector population. Our study provides new insight into the sustainability of the CD8 T cell response in the pathogenesis of T1D.
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Affiliation(s)
- Ashley E Ciecko
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
| | - David M Schauder
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI.,Versiti Blood Research Institute, Milwaukee, WI
| | - Bardees Foda
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI.,Max McGee National Research Center for Juvenile Diabetes, Medical College of Wisconsin, Milwaukee, WI.,Department of Molecular Genetics and Enzymology, National Research Center, Dokki, Egypt
| | - Galina Petrova
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Moujtaba Y Kasmani
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI.,Versiti Blood Research Institute, Milwaukee, WI
| | | | - Chien-Wei Lin
- Division of Biostatistics, Institute for Health and Society, Medical College of Wisconsin, Milwaukee, WI; and
| | - William R Drobyski
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI.,Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Weiguo Cui
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI.,Versiti Blood Research Institute, Milwaukee, WI
| | - Yi-Guang Chen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI; .,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI.,Max McGee National Research Center for Juvenile Diabetes, Medical College of Wisconsin, Milwaukee, WI
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18
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Tallan A, Stanton BZ. Inducible Protein Degradation to Understand Genome Architecture. Biochemistry 2021; 60:2387-2396. [PMID: 34292716 DOI: 10.1021/acs.biochem.1c00306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We review exciting recent advances in protein degradation, with a focus on chromatin structure. In our analysis of the literature, we highlight studies of kinetic control of protein stability for cohesin, condensin, ATP-dependent chromatin remodeling, and pioneer transcription factors. With new connections emerging between chromatin remodeling and genome structure, we anticipate exciting developments at the intersection of these topics to be revealed in the coming years. Moreover, we pay special attention to the 20-year anniversary of PROTACs, with an overview of E3 ligase/target pairings and central questions that might lead to the next generation of PROTACs with an expanded scope and generality. While steady-state experimental measurements with constitutive genome editing are impactful, we highlight complementary approaches for rapid kinetic protein degradation to uncover early targeting functions and to understand the central determinants of genome structure-function relationships.
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Affiliation(s)
- Alexi Tallan
- Abigail Wexner Research Institute, Nationwide Children's Hospital, Center for Childhood Cancer and Blood Diseases, 700 Children's Drive, Columbus, Ohio 43205, United States.,Molecular, Cellular, and Developmental Biology Program, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Benjamin Z Stanton
- Abigail Wexner Research Institute, Nationwide Children's Hospital, Center for Childhood Cancer and Blood Diseases, 700 Children's Drive, Columbus, Ohio 43205, United States.,Molecular, Cellular, and Developmental Biology Program, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States.,Department of Pediatrics, The Ohio State University College of Medicine, 370 West 9th Avenue, Columbus, Ohio 43210, United States.,Department of Biological Chemistry and Pharmacology, The Ohio State University College of Medicine, 370 West 9th Avenue, Columbus, Ohio 43210, United States
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19
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Davidson IF, Peters JM. Genome folding through loop extrusion by SMC complexes. Nat Rev Mol Cell Biol 2021; 22:445-464. [PMID: 33767413 DOI: 10.1038/s41580-021-00349-7] [Citation(s) in RCA: 186] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 02/02/2023]
Abstract
Genomic DNA is folded into loops and topologically associating domains (TADs), which serve important structural and regulatory roles. It has been proposed that these genomic structures are formed by a loop extrusion process, which is mediated by structural maintenance of chromosomes (SMC) protein complexes. Recent single-molecule studies have shown that the SMC complexes condensin and cohesin are indeed able to extrude DNA into loops. In this Review, we discuss how the loop extrusion hypothesis can explain key features of genome architecture; cellular functions of loop extrusion, such as separation of replicated DNA molecules, facilitation of enhancer-promoter interactions and immunoglobulin gene recombination; and what is known about the mechanism of loop extrusion and its regulation, for example, by chromatin boundaries that depend on the DNA binding protein CTCF. We also discuss how the loop extrusion hypothesis has led to a paradigm shift in our understanding of both genome architecture and the functions of SMC complexes.
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Affiliation(s)
- Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
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20
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Pathania A, Liu W, Matityahu A, Irudayaraj J, Onn I. Chromosome loading of cohesin depends on conserved residues in Scc3. Curr Genet 2021; 67:447-459. [PMID: 33404730 DOI: 10.1007/s00294-020-01150-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/12/2020] [Accepted: 12/15/2020] [Indexed: 10/22/2022]
Abstract
Cohesin is essential for sister chromatid cohesion, which ensures equal segregation of the chromatids to daughter cells. However, the molecular mechanism by which cohesin mediates this function is elusive. Scc3, one of the four core subunits of cohesin, is vital to cohesin activity. However, the mechanism by which Scc3 contributes to the activity and identity of its functional domains is not fully understood. Here, we describe an in-frame five-amino acid insertion mutation after glutamic acid 704 (scc3-E704ins) in yeast Scc3, located in the middle of the second armadillo repeat. Mutated cohesin-scc3-E704ins complexes are unable to establish cohesion. Detailed molecular and genetic analyses revealed that the mutated cohesin has reduced affinity to the Scc2 loader. This inhibits its enrichment at centromeres and chromosomal arms. Mutant complexes show a slow diffusion rate in live cells suggesting that they induce a major conformational change in the complex. The analysis of systematic mutations in the insertion region of Scc3 revealed two conserved aspartic acid residues that are essential for the activity. The study offers a better understanding of the contribution of Scc3 to cohesin activity and the mechanism by which cohesin tethers the sister chromatids during the cell cycle.
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Affiliation(s)
- Anjali Pathania
- The Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold St, P.O. Box 1589, 1311502, Safed, Israel
| | - Wenjie Liu
- Micro and Nanotechnology Laboratory, Department of Bioengineering, Beckman Institute, Carl Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carle Foundation Hospital, Mills Breast Cancer Institute, Urbana, IL, USA
| | - Avi Matityahu
- The Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold St, P.O. Box 1589, 1311502, Safed, Israel
| | - Joseph Irudayaraj
- Micro and Nanotechnology Laboratory, Department of Bioengineering, Beckman Institute, Carl Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carle Foundation Hospital, Mills Breast Cancer Institute, Urbana, IL, USA
| | - Itay Onn
- The Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold St, P.O. Box 1589, 1311502, Safed, Israel.
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21
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Paulson JR, Hudson DF, Cisneros-Soberanis F, Earnshaw WC. Mitotic chromosomes. Semin Cell Dev Biol 2021; 117:7-29. [PMID: 33836947 PMCID: PMC8406421 DOI: 10.1016/j.semcdb.2021.03.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 01/25/2023]
Abstract
Our understanding of the structure and function of mitotic chromosomes has come a long way since these iconic objects were first recognized more than 140 years ago, though many details remain to be elucidated. In this chapter, we start with the early history of chromosome studies and then describe the path that led to our current understanding of the formation and structure of mitotic chromosomes. We also discuss some of the remaining questions. It is now well established that each mitotic chromatid consists of a central organizing region containing a so-called "chromosome scaffold" from which loops of DNA project radially. Only a few key non-histone proteins and protein complexes are required to form the chromosome: topoisomerase IIα, cohesin, condensin I and condensin II, and the chromokinesin KIF4A. These proteins are concentrated along the axis of the chromatid. Condensins I and II are primarily responsible for shaping the chromosome and the scaffold, and they produce the loops of DNA by an ATP-dependent process known as loop extrusion. Modelling of Hi-C data suggests that condensin II adopts a spiral staircase arrangement with an extruded loop extending out from each step in a roughly helical pattern. Condensin I then forms loops nested within these larger condensin II loops, thereby giving rise to the final compaction of the mitotic chromosome in a process that requires Topo IIα.
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Affiliation(s)
- James R Paulson
- Department of Chemistry, University of Wisconsin Oshkosh, 800 Algoma Boulevard, Oshkosh, WI 54901, USA.
| | - Damien F Hudson
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Fernanda Cisneros-Soberanis
- Wellcome Trust Centre for Cell Biology, ICB, University of Edinburgh, Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, ICB, University of Edinburgh, Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK.
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22
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Matityahu A, Onn I. Hit the brakes - a new perspective on the loop extrusion mechanism of cohesin and other SMC complexes. J Cell Sci 2021; 134:jcs247577. [PMID: 33419949 DOI: 10.1242/jcs.247577] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The three-dimensional structure of chromatin is determined by the action of protein complexes of the structural maintenance of chromosome (SMC) family. Eukaryotic cells contain three SMC complexes, cohesin, condensin, and a complex of Smc5 and Smc6. Initially, cohesin was linked to sister chromatid cohesion, the process that ensures the fidelity of chromosome segregation in mitosis. In recent years, a second function in the organization of interphase chromatin into topologically associated domains has been determined, and loop extrusion has emerged as the leading mechanism of this process. Interestingly, fundamental mechanistic differences exist between mitotic tethering and loop extrusion. As distinct molecular switches that aim to suppress loop extrusion in different biological contexts have been identified, we hypothesize here that loop extrusion is the default biochemical activity of cohesin and that its suppression shifts cohesin into a tethering mode. With this model, we aim to provide an explanation for how loop extrusion and tethering can coexist in a single cohesin complex and also apply it to the other eukaryotic SMC complexes, describing both similarities and differences between them. Finally, we present model-derived molecular predictions that can be tested experimentally, thus offering a new perspective on the mechanisms by which SMC complexes shape the higher-order structure of chromatin.
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Affiliation(s)
- Avi Matityahu
- 8 Henrietta Szold St., The Azrieli Faculty of Medicine, Bar-Ilan University, P.O. Box 1589 Safed, Israel
| | - Itay Onn
- 8 Henrietta Szold St., The Azrieli Faculty of Medicine, Bar-Ilan University, P.O. Box 1589 Safed, Israel
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23
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Zuilkoski CM, Skibbens RV. PCNA antagonizes cohesin-dependent roles in genomic stability. PLoS One 2020; 15:e0235103. [PMID: 33075068 PMCID: PMC7571713 DOI: 10.1371/journal.pone.0235103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 10/04/2020] [Indexed: 12/23/2022] Open
Abstract
PCNA sliding clamp binds factors through which histone deposition, chromatin remodeling, and DNA repair are coupled to DNA replication. PCNA also directly binds Eco1/Ctf7 acetyltransferase, which in turn activates cohesins and establishes cohesion between nascent sister chromatids. While increased recruitment thus explains the mechanism through which elevated levels of chromatin-bound PCNA rescue eco1 mutant cell growth, the mechanism through which PCNA instead worsens cohesin mutant cell growth remains unknown. Possibilities include that elevated levels of long-lived chromatin-bound PCNA reduce either cohesin deposition onto DNA or cohesin acetylation. Instead, our results reveal that PCNA increases the levels of both chromatin-bound cohesin and cohesin acetylation. Beyond sister chromatid cohesion, PCNA also plays a critical role in genomic stability such that high levels of chromatin-bound PCNA elevate genotoxic sensitivities and recombination rates. At a relatively modest increase of chromatin-bound PCNA, however, fork stability and progression appear normal in wildtype cells. Our results reveal that even a moderate increase of PCNA indeed sensitizes cohesin mutant cells to DNA damaging agents and in a process that involves the DNA damage response kinase Mec1(ATR), but not Tel1(ATM). These and other findings suggest that PCNA mis-regulation results in genome instabilities that normally are resolved by cohesin. Elevating levels of chromatin-bound PCNA may thus help target cohesinopathic cells linked that are linked to cancer.
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Affiliation(s)
- Caitlin M. Zuilkoski
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Robert V. Skibbens
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
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24
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Tao H, Lambert JP, Yung TM, Zhu M, Hahn NA, Li D, Lau K, Sturgeon K, Puviindran V, Zhang X, Gong W, Chen XX, Anderson G, Garry DJ, Henkelman RM, Sun Y, Iulianella A, Kawakami Y, Gingras AC, Hui CC, Hopyan S. IRX3/5 regulate mitotic chromatid segregation and limb bud shape. Development 2020; 147:dev.180042. [PMID: 32907847 DOI: 10.1242/dev.180042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/25/2020] [Indexed: 01/19/2023]
Abstract
Pattern formation is influenced by transcriptional regulation as well as by morphogenetic mechanisms that shape organ primordia, although factors that link these processes remain under-appreciated. Here we show that, apart from their established transcriptional roles in pattern formation, IRX3/5 help to shape the limb bud primordium by promoting the separation and intercalation of dividing mesodermal cells. Surprisingly, IRX3/5 are required for appropriate cell cycle progression and chromatid segregation during mitosis, possibly in a nontranscriptional manner. IRX3/5 associate with, promote the abundance of, and share overlapping functions with co-regulators of cell division such as the cohesin subunits SMC1, SMC3, NIPBL and CUX1. The findings imply that IRX3/5 coordinate early limb bud morphogenesis with skeletal pattern formation.
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Affiliation(s)
- Hirotaka Tao
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Jean-Philippe Lambert
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Theodora M Yung
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Min Zhu
- Department of Mechanical and Industrial Engineering, University of Toronto, ON M5S 3G8, Canada
| | - Noah A Hahn
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Danyi Li
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kimberly Lau
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Kendra Sturgeon
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Vijitha Puviindran
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Xiaoyun Zhang
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Wuming Gong
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Xiao Xiao Chen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Gregory Anderson
- Mouse Imaging Centre, Hospital for Sick Children, Toronto Centre for Phenogenomics, Department of Medical Biophysics, University of Toronto, Toronto, ON M5T 3H7, Canada
| | - Daniel J Garry
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - R Mark Henkelman
- Mouse Imaging Centre, Hospital for Sick Children, Toronto Centre for Phenogenomics, Department of Medical Biophysics, University of Toronto, Toronto, ON M5T 3H7, Canada
| | - Yu Sun
- Department of Mechanical and Industrial Engineering, University of Toronto, ON M5S 3G8, Canada
| | - Angelo Iulianella
- Department of Medical Neuroscience, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Chi-Chung Hui
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sevan Hopyan
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Division of Orthopaedic Surgery, Hospital for Sick Children and University of Toronto, Toronto M5G 1X8, Canada
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25
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Arruda NL, Carico ZM, Justice M, Liu YF, Zhou J, Stefan HC, Dowen JM. Distinct and overlapping roles of STAG1 and STAG2 in cohesin localization and gene expression in embryonic stem cells. Epigenetics Chromatin 2020; 13:32. [PMID: 32778134 PMCID: PMC7418333 DOI: 10.1186/s13072-020-00353-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/28/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The three-dimensional organization of the genome in the nucleus plays an integral role in many biological processes, including gene expression. The genome is folded into DNA loops that bring together distal regulatory elements and genes. Cohesin, a ring-shaped protein complex, is a major player in the formation of DNA loops. Cohesin is composed of a core trimer and one of two variant STAG subunits, STAG1 or STAG2. It is not understood whether variant STAG proteins give rise to cohesin complexes with distinct functions. Recent studies have begun to characterize the roles of STAG1 and STAG2, with partially contradictory results. RESULTS Here, we generate stable single-knockout embryonic stem cell lines to investigate the individual contributions of STAG1 and STAG2 in regulating cohesin chromosomal localization and function. We report both overlapping roles for STAG1 and STAG2 in cohesin localization and somewhat distinct roles in gene expression. STAG1 and STAG2 occupy the same sites across the genome, yet do not exist together in a higher order complex. Despite their shared localization, STAG1 and STAG2 have both distinct and redundant effects on gene expression. Loss of both STAG1 and STAG2 causes widespread transcriptome dysregulation, altered cohesin DNA occupancy, and reduced cell proliferation. CONCLUSIONS Together, this work reveals the requirement of at least one STAG protein for proper cohesin function. STAG1 and STAG2 have independent roles in cohesin localization and both overlapping and distinct roles in gene expression. The roles of STAG1 and STAG2 in mouse embryonic stem cells may be somewhat different than in other cell types, due to their relative expression levels. These results advance our understanding of the link between mammalian genome organization and gene expression during development and disease contexts.
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Affiliation(s)
- Nicole L Arruda
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Zachary M Carico
- Cancer Epigenetics Training Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Megan Justice
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Ying Frances Liu
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Junjie Zhou
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Holden C Stefan
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jill M Dowen
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Cancer Epigenetics Training Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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26
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van der Lelij P, Newman JA, Lieb S, Jude J, Katis V, Hoffmann T, Hinterndorfer M, Bader G, Kraut N, Pearson MA, Peters JM, Zuber J, Gileadi O, Petronczki M. STAG1 vulnerabilities for exploiting cohesin synthetic lethality in STAG2-deficient cancers. Life Sci Alliance 2020; 3:e202000725. [PMID: 32467316 PMCID: PMC7266993 DOI: 10.26508/lsa.202000725] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 12/16/2022] Open
Abstract
The cohesin subunit STAG2 has emerged as a recurrently inactivated tumor suppressor in human cancers. Using candidate approaches, recent studies have revealed a synthetic lethal interaction between STAG2 and its paralog STAG1 To systematically probe genetic vulnerabilities in the absence of STAG2, we have performed genome-wide CRISPR screens in isogenic cell lines and identified STAG1 as the most prominent and selective dependency of STAG2-deficient cells. Using an inducible degron system, we show that chemical genetic degradation of STAG1 protein results in the loss of sister chromatid cohesion and rapid cell death in STAG2-deficient cells, while sparing STAG2-wild-type cells. Biochemical assays and X-ray crystallography identify STAG1 regions that interact with the RAD21 subunit of the cohesin complex. STAG1 mutations that abrogate this interaction selectively compromise the viability of STAG2-deficient cells. Our work highlights the degradation of STAG1 and inhibition of its interaction with RAD21 as promising therapeutic strategies. These findings lay the groundwork for the development of STAG1-directed small molecules to exploit synthetic lethality in STAG2-mutated tumors.
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Grants
- Wellcome Trust
- 106169/ZZ14/Z Wellcome Trust
- European Research Council
- Human Frontier Science Program
- Wellcome
- Innovative Medicines Initiative (European Union-EU/European Federation of Pharmaceutical Industries and Associations-EFPIA)
- European Community’s Seventh Framework Programme
- Austrian Science Fund, FWF
- AbbVie, Bayer Pharma AG, Boehringer Ingelheim, Canada Foundation for Innovation, Eshelman Institute for Innovation, Genome Canada
- Janssen, Merck KGaA Darmstadt Germany, MSD, Novartis Pharma AG, Ontario Ministry of Economic Development and Innovation, Pfizer, São Paulo Research Foundation-FAPESP, Takeda
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Affiliation(s)
- Petra van der Lelij
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Joseph A Newman
- Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Simone Lieb
- Boehringer Ingelheim Regional Center Vienna (RCV) GmbH & Co KG, Vienna, Austria
| | - Julian Jude
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Vittorio Katis
- Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Thomas Hoffmann
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Matthias Hinterndorfer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Gerd Bader
- Boehringer Ingelheim Regional Center Vienna (RCV) GmbH & Co KG, Vienna, Austria
| | - Norbert Kraut
- Boehringer Ingelheim Regional Center Vienna (RCV) GmbH & Co KG, Vienna, Austria
| | - Mark A Pearson
- Boehringer Ingelheim Regional Center Vienna (RCV) GmbH & Co KG, Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Medical University of Vienna, VBC, Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Medical University of Vienna, VBC, Vienna, Austria
| | - Opher Gileadi
- Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Mark Petronczki
- Boehringer Ingelheim Regional Center Vienna (RCV) GmbH & Co KG, Vienna, Austria
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27
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Li M, Gan J, Sun Y, Xu Z, Yang J, Sun Y, Li C. Architectural proteins for the formation and maintenance of the 3D genome. SCIENCE CHINA. LIFE SCIENCES 2020; 63:795-810. [PMID: 32249389 DOI: 10.1007/s11427-019-1613-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 12/26/2019] [Indexed: 12/20/2022]
Abstract
Eukaryotic genomes are densely packaged into hierarchical three-dimensional (3D) structures that contain information about gene regulation and many other biological processes. With the development of imaging and sequencing-based technologies, 3D genome studies have revealed that the high-order chromatin structure is composed of hierarchical levels, including chromosome territories, A/B compartments, topologically associated domains, and chromatin loops. However, how this chromatin architecture is formed and maintained is not completely clear. In this review, we introduce experimental methods to investigate the 3D genome, review major architectural proteins that regulate 3D chromatin organization in mammalian cells, such as CTCF (CCCTC-binding factor), cohesin, lamins, and transcription factors, and discuss relevant mechanisms such as phase separation.
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Affiliation(s)
- Mengfan Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies; School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jingbo Gan
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies; School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yuao Sun
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies; School of Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Membrane Biology, School of Life Sciences; Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Zihan Xu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies; School of Life Sciences, Peking University, Beijing, 100871, China
| | - Junsheng Yang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies; School of Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Membrane Biology, School of Life Sciences; Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, School of Life Sciences; Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China.
| | - Cheng Li
- Center for Statistical Science, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China.
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28
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Golfier S, Quail T, Kimura H, Brugués J. Cohesin and condensin extrude DNA loops in a cell cycle-dependent manner. eLife 2020; 9:e53885. [PMID: 32396063 PMCID: PMC7316503 DOI: 10.7554/elife.53885] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/11/2020] [Indexed: 12/14/2022] Open
Abstract
Loop extrusion by structural maintenance of chromosomes (SMC) complexes has been proposed as a mechanism to organize chromatin in interphase and metaphase. However, the requirements for chromatin organization in these cell cycle phases are different, and it is unknown whether loop extrusion dynamics and the complexes that extrude DNA also differ. Here, we used Xenopus egg extracts to reconstitute and image loop extrusion of single DNA molecules during the cell cycle. We show that loops form in both metaphase and interphase, but with distinct dynamic properties. Condensin extrudes DNA loops non-symmetrically in metaphase, whereas cohesin extrudes loops symmetrically in interphase. Our data show that loop extrusion is a general mechanism underlying DNA organization, with dynamic and structural properties that are biochemically regulated during the cell cycle.
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Affiliation(s)
- Stefan Golfier
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
- Centre for Systems Biology DresdenDresdenGermany
- Cluster of Excellence Physics of Life, TU DresdenDresdenGermany
| | - Thomas Quail
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
- Centre for Systems Biology DresdenDresdenGermany
- Cluster of Excellence Physics of Life, TU DresdenDresdenGermany
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of TechnologyYokohamaJapan
| | - Jan Brugués
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
- Centre for Systems Biology DresdenDresdenGermany
- Cluster of Excellence Physics of Life, TU DresdenDresdenGermany
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29
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Benedict B, van Schie JJM, Oostra AB, Balk JA, Wolthuis RMF, Riele HT, de Lange J. WAPL-Dependent Repair of Damaged DNA Replication Forks Underlies Oncogene-Induced Loss of Sister Chromatid Cohesion. Dev Cell 2020; 52:683-698.e7. [PMID: 32084359 DOI: 10.1016/j.devcel.2020.01.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 11/19/2019] [Accepted: 01/22/2020] [Indexed: 12/22/2022]
Abstract
Premature loss of sister chromatid cohesion at metaphase is a diagnostic marker for different cohesinopathies. Here, we report that metaphase spreads of many cancer cell lines also show premature loss of sister chromatid cohesion. Cohesion loss occurs independently of mutations in cohesion factors including SA2, a cohesin subunit frequently inactivated in cancer. In untransformed cells, induction of DNA replication stress by activation of oncogenes or inhibition of DNA replication is sufficient to trigger sister chromatid cohesion loss. Importantly, cell growth under conditions of replication stress requires the cohesin remover WAPL. WAPL promotes rapid RAD51-dependent repair and restart of broken replication forks. We propose that active removal of cohesin allows cancer cells to overcome DNA replication stress. This leads to oncogene-induced cohesion loss from newly synthesized sister chromatids that may contribute to genomic instability and likely represents a targetable cancer cell vulnerability.
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Affiliation(s)
- Bente Benedict
- Netherlands Cancer Institute, Division of Tumor Biology and Immunology, Amsterdam, the Netherlands
| | - Janne J M van Schie
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Anneke B Oostra
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Jesper A Balk
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Rob M F Wolthuis
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands.
| | - Hein Te Riele
- Netherlands Cancer Institute, Division of Tumor Biology and Immunology, Amsterdam, the Netherlands.
| | - Job de Lange
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands.
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30
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Wutz G, Ladurner R, St Hilaire BG, Stocsits RR, Nagasaka K, Pignard B, Sanborn A, Tang W, Várnai C, Ivanov MP, Schoenfelder S, van der Lelij P, Huang X, Dürnberger G, Roitinger E, Mechtler K, Davidson IF, Fraser P, Lieberman-Aiden E, Peters JM. ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesin STAG1 from WAPL. eLife 2020; 9:e52091. [PMID: 32065581 PMCID: PMC7054000 DOI: 10.7554/elife.52091] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 02/10/2020] [Indexed: 12/19/2022] Open
Abstract
Eukaryotic genomes are folded into loops. It is thought that these are formed by cohesin complexes via extrusion, either until loop expansion is arrested by CTCF or until cohesin is removed from DNA by WAPL. Although WAPL limits cohesin's chromatin residence time to minutes, it has been reported that some loops exist for hours. How these loops can persist is unknown. We show that during G1-phase, mammalian cells contain acetylated cohesinSTAG1 which binds chromatin for hours, whereas cohesinSTAG2 binds chromatin for minutes. Our results indicate that CTCF and the acetyltransferase ESCO1 protect a subset of cohesinSTAG1 complexes from WAPL, thereby enable formation of long and presumably long-lived loops, and that ESCO1, like CTCF, contributes to boundary formation in chromatin looping. Our data are consistent with a model of nested loop extrusion, in which acetylated cohesinSTAG1 forms stable loops between CTCF sites, demarcating the boundaries of more transient cohesinSTAG2 extrusion activity.
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Affiliation(s)
- Gordana Wutz
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Rene Ladurner
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Brian Glenn St Hilaire
- The Center for Genome Architecture, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Center for Theoretical Biological Physics, Rice UniversityHoustonUnited States
| | - Roman R Stocsits
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Kota Nagasaka
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Benoit Pignard
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Adrian Sanborn
- The Center for Genome Architecture, Baylor College of MedicineHoustonUnited States
- Department of Computer Science, Stanford UniversityStanfordUnited States
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Csilla Várnai
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research CampusCambridgeUnited Kingdom
- Centre for Computational Biology, University of BirminghamBirminghamUnited Kingdom
| | - Miroslav P Ivanov
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Stefan Schoenfelder
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research CampusCambridgeUnited Kingdom
| | - Petra van der Lelij
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Xingfan Huang
- The Center for Genome Architecture, Baylor College of MedicineHoustonUnited States
- Departments of Computer Science and Computational and Applied Mathematics, Rice UniversityHoustonUnited States
- Departments of Computer Science and Genome Sciences, University of WashingtonSeattleUnited States
| | - Gerhard Dürnberger
- Institute of Molecular Biotechnology, Vienna Biocenter (VBC)ViennaAustria
| | | | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology, Vienna Biocenter (VBC)ViennaAustria
| | - Iain Finley Davidson
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research CampusCambridgeUnited Kingdom
- Department of Biological Science, Florida State UniversityTallahasseeUnited States
| | - Erez Lieberman-Aiden
- The Center for Genome Architecture, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Center for Theoretical Biological Physics, Rice UniversityHoustonUnited States
- Departments of Computer Science and Computational and Applied Mathematics, Rice UniversityHoustonUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
- Shanghai Institute for Advanced Immunochemical Studies, Shanghai Tech UniversityShanghaiChina
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
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31
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Li D, Mosbruger T, Verma D, Swaminathan S. Complex Interactions between Cohesin and CTCF in Regulation of Kaposi's Sarcoma-Associated Herpesvirus Lytic Transcription. J Virol 2020; 94:e01279-19. [PMID: 31666380 PMCID: PMC6955261 DOI: 10.1128/jvi.01279-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/18/2019] [Indexed: 12/18/2022] Open
Abstract
CTCF and the cohesin complex modify chromatin by binding to DNA and interacting with each other and with other cellular proteins. Both proteins regulate transcription by a variety of local effects on transcription and by long-range topological effects. CTCF and cohesin also bind to herpesvirus genomes at specific sites and regulate viral transcription during latent and lytic cycles of replication. Kaposi's sarcoma-associated herpesvirus (KSHV) transcription is regulated by CTCF and cohesin, with both proteins previously reported to act as restrictive factors for lytic cycle transcription and virion production. In this study, we examined the interdependence of CTCF and cohesin binding to the KSHV genome. Chromatin immunoprecipitation sequencing (ChIP-seq) analyses revealed that cohesin binding to the KSHV genome is highly CTCF dependent, whereas CTCF binding does not require cohesin. Furthermore, depletion of CTCF leads to the almost complete dissociation of cohesin from sites at which they colocalize. Thus, previous studies that examined the effects of CTCF depletion actually represent the concomitant depletion of both CTCF and cohesin components. Analysis of the effects of single and combined depletion indicates that CTCF primarily activates KSHV lytic transcription, whereas cohesin has primarily inhibitory effects. Furthermore, CTCF or cohesin depletion was found to have regulatory effects on cellular gene expression relevant for the control of viral infection, with both proteins potentially facilitating the expression of multiple genes important in the innate immune response to viruses. Thus, CTCF and cohesin have both positive and negative effects on KSHV lytic replication as well as effects on the host cell that enhance antiviral defenses.IMPORTANCE Kaposi's sarcoma-associated herpesvirus (KSHV) is causally linked to Kaposi's sarcoma and several lymphoproliferative diseases. KSHV, like other herpesviruses, intermittently reactivates from latency and enters a lytic cycle in which numerous lytic mRNAs and proteins are produced, culminating in infectious virion production. These lytic proteins may also contribute to tumorigenesis. Reactivation from latency is controlled by processes that restrict or activate the transcription of KSHV lytic genes. KSHV gene expression is modulated by binding of the host cell proteins CTCF and cohesin complex to the KSHV genome. These proteins bind to and modulate the conformation of chromatin, thereby regulating transcription. We have analyzed the interdependence of binding of CTCF and cohesin and demonstrate that while CTCF is required for cohesin binding to KSHV, they have very distinct effects, with cohesin primarily restricting KSHV lytic transcription. Furthermore, we show that cohesin and CTCF also exert effects on the host cell that promote antiviral defenses.
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Affiliation(s)
- Dajiang Li
- Division of Infectious Diseases, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Tim Mosbruger
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Dinesh Verma
- Division of Infectious Diseases, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Sankar Swaminathan
- Division of Infectious Diseases, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah, USA
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El Beaino M, Liu J, Wasylishen AR, Pourebrahim R, Migut A, Bessellieu BJ, Huang K, Lin PP. Loss of Stag2 cooperates with EWS-FLI1 to transform murine Mesenchymal stem cells. BMC Cancer 2020; 20:3. [PMID: 31898537 PMCID: PMC6941350 DOI: 10.1186/s12885-019-6465-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 12/15/2019] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Ewing sarcoma is a malignancy of primitive cells, possibly of mesenchymal origin. It is probable that genetic perturbations other than EWS-FLI1 cooperate with it to produce the tumor. Sequencing studies identified STAG2 mutations in approximately 15% of cases in humans. In the present study, we hypothesize that loss of Stag2 cooperates with EWS-FLI1 in generating sarcomas derived from murine mesenchymal stem cells (MSCs). METHODS Mice bearing an inducible EWS-FLI1 transgene were crossed to p53-/- mice in pure C57/Bl6 background. MSCs were derived from the bone marrow of the mice. EWS-FLI1 induction and Stag2 knockdown were achieved in vitro by adenovirus-Cre and shRNA-bearing pGIPZ lentiviral infection, respectively. The cells were then treated with ionizing radiation to 10 Gy. Anchorage independent growth in vitro was assessed by soft agar assays. Cellular migration and invasion were evaluated by transwell assays. Cells were injected with Matrigel intramuscularly into C57/Bl6 mice to test for tumor formation. RESULTS Primary murine MSCs with the genotype EWS-FLI1 p53-/- were resistant to transformation and did not form tumors in syngeneic mice without irradiation. Stag2 inhibition increased the efficiency and speed of sarcoma formation significantly in irradiated EWS-FLI1 p53-/- MSCs. The efficiency of tumor formation was 91% for cells in mice injected with Stag2-repressed cells and 22% for mice receiving cells without Stag2 inhibition (p < .001). Stag2 knockdown reduced survival of mice in Kaplan-Meier analysis (p < .001). It also increased MSC migration and invasion in vitro but did not affect proliferation rate or aneuploidy. CONCLUSION Loss of Stag2 has a synergistic effect with EWS-FLI1 in the production of sarcomas from murine MSCs, but the mechanism may not relate to increased proliferation or chromosomal instability. Primary murine MSCs are resistant to transformation, and the combination of p53 null mutation, EWS-FLI1, and Stag2 inhibition does not confer immediate conversion of MSCs to sarcomas. Irradiation is necessary in this model, suggesting that perturbations of other genes beside Stag2 and p53 are likely to be essential in the development of EWS-FLI1-driven sarcomas from MSCs.
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Affiliation(s)
- Marc El Beaino
- Department of Orthopaedic Oncology - Unit 1448, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Jiayong Liu
- Department of Bone and Soft Tissue Tumor, Peking University Cancer Hospital & Institute, 52 Fu-Cheng Road, Hai-Dian District, Beijing, 100142, China
| | - Amanda R Wasylishen
- Department of Genetics - Unit 1010, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Rasoul Pourebrahim
- Department of Leukemia - Unit 428, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Agata Migut
- Department of Orthopaedic Oncology - Unit 1448, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Bryan J Bessellieu
- Department of Orthopaedic Oncology - Unit 1448, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Ke Huang
- Department of Orthopaedic Oncology - Unit 1448, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Patrick P Lin
- Department of Orthopaedic Oncology - Unit 1448, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.
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Davidson IF, Bauer B, Goetz D, Tang W, Wutz G, Peters JM. DNA loop extrusion by human cohesin. Science 2019; 366:1338-1345. [PMID: 31753851 DOI: 10.1126/science.aaz3418] [Citation(s) in RCA: 422] [Impact Index Per Article: 84.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/06/2019] [Indexed: 01/03/2023]
Abstract
Eukaryotic genomes are folded into loops and topologically associating domains, which contribute to chromatin structure, gene regulation, and gene recombination. These structures depend on cohesin, a ring-shaped DNA-entrapping adenosine triphosphatase (ATPase) complex that has been proposed to form loops by extrusion. Such an activity has been observed for condensin, which forms loops in mitosis, but not for cohesin. Using biochemical reconstitution, we found that single human cohesin complexes form DNA loops symmetrically at rates up to 2.1 kilo-base pairs per second. Loop formation and maintenance depend on cohesin's ATPase activity and on NIPBL-MAU2, but not on topological entrapment of DNA by cohesin. During loop formation, cohesin and NIPBL-MAU2 reside at the base of loops, which indicates that they generate loops by extrusion. Our results show that cohesin and NIPBL-MAU2 form an active holoenzyme that interacts with DNA either pseudo-topologically or non-topologically to extrude genomic interphase DNA into loops.
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Affiliation(s)
- Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Benedikt Bauer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Daniela Goetz
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Gordana Wutz
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria.
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Abramo K, Valton AL, Venev SV, Ozadam H, Fox AN, Dekker J. A chromosome folding intermediate at the condensin-to-cohesin transition during telophase. Nat Cell Biol 2019; 21:1393-1402. [PMID: 31685986 PMCID: PMC6858582 DOI: 10.1038/s41556-019-0406-2] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/19/2019] [Indexed: 01/09/2023]
Abstract
Chromosome folding is modulated as cells progress through the cell cycle. During mitosis, condensins fold chromosomes into helical loop arrays. In interphase, the cohesin complex generates loops and topologically associating domains (TADs), while a separate process of compartmentalization drives segregation of active and inactive chromatin. We used synchronized cell cultures to determine how the mitotic chromosome conformation transforms into the interphase state. Using high-throughput chromosome conformation capture (Hi-C) analysis, chromatin binding assays and immunofluorescence, we show that, by telophase, condensin-mediated loops are lost and a transient folding intermediate is formed that is devoid of most loops. By cytokinesis, cohesin-mediated CTCF-CTCF loops and the positions of TADs emerge. Compartment boundaries are also established early, but long-range compartmentalization is a slow process and proceeds for hours after cells enter G1. Our results reveal the kinetics and order of events by which the interphase chromosome state is formed and identify telophase as a critical transition between condensin- and cohesin-driven chromosome folding.
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Affiliation(s)
- Kristin Abramo
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anne-Laure Valton
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sergey V Venev
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Hakan Ozadam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - A Nicole Fox
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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Galander S, Barton RE, Kelly DA, Marston AL. Spo13 prevents premature cohesin cleavage during meiosis. Wellcome Open Res 2019; 4:29. [PMID: 30906881 PMCID: PMC6426077 DOI: 10.12688/wellcomeopenres.15066.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2019] [Indexed: 01/21/2024] Open
Abstract
Background: Meiosis produces gametes through two successive nuclear divisions, meiosis I and meiosis II. In contrast to mitosis and meiosis II, where sister chromatids are segregated, during meiosis I, homologous chromosomes are segregated. This requires the monopolar attachment of sister kinetochores and the loss of cohesion from chromosome arms, but not centromeres, during meiosis I. The establishment of both sister kinetochore mono-orientation and cohesion protection rely on the budding yeast meiosis I-specific Spo13 protein, the functional homolog of fission yeast Moa1 and mouse MEIKIN. Methods: Here we investigate the effects of loss of SPO13 on cohesion during meiosis I using a live-cell imaging approach. Results: Unlike wild type, cells lacking SPO13 fail to maintain the meiosis-specific cohesin subunit, Rec8, at centromeres and segregate sister chromatids to opposite poles during anaphase I. We show that the cohesin-destabilizing factor, Wpl1, is not primarily responsible for the loss of cohesion during meiosis I. Instead, premature loss of centromeric cohesin during anaphase I in spo13 Δ cells relies on separase-dependent cohesin cleavage. Further, cohesin loss in spo13 Δ anaphase I cells is blocked by forcibly tethering the regulatory subunit of protein phosphatase 2A, Rts1, to Rec8. Conclusions: Our findings indicate that separase-dependent cleavage of phosphorylated Rec8 causes premature cohesin loss in spo13 Δ cells.
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Affiliation(s)
- Stefan Galander
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Rachael E. Barton
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - David A. Kelly
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Adèle L. Marston
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
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36
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Galander S, Barton RE, Kelly DA, Marston AL. Spo13 prevents premature cohesin cleavage during meiosis. Wellcome Open Res 2019; 4:29. [PMID: 30906881 PMCID: PMC6426077 DOI: 10.12688/wellcomeopenres.15066.2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2019] [Indexed: 01/11/2023] Open
Abstract
Background: Meiosis produces gametes through two successive nuclear divisions, meiosis I and meiosis II. In contrast to mitosis and meiosis II, where sister chromatids are segregated, during meiosis I, homologous chromosomes are segregated. This requires the monopolar attachment of sister kinetochores and the loss of cohesion from chromosome arms, but not centromeres, during meiosis I. The establishment of both sister kinetochore mono-orientation and cohesion protection rely on the budding yeast meiosis I-specific Spo13 protein, the functional homolog of fission yeast Moa1 and mouse MEIKIN. Methods: Here we investigate the effects of loss of
SPO13 on cohesion during meiosis I using a live-cell imaging approach. Results: Unlike wild type, cells lacking
SPO13 fail to maintain the meiosis-specific cohesin subunit, Rec8, at centromeres and segregate sister chromatids to opposite poles during anaphase I. We show that the cohesin-destabilizing factor, Wpl1, is not primarily responsible for the loss of cohesion during meiosis I. Instead, premature loss of centromeric cohesin during anaphase I in
spo13Δ cells relies on separase-dependent cohesin cleavage. Further, cohesin loss in
spo13Δ anaphase I cells is blocked by forcibly tethering the regulatory subunit of protein phosphatase 2A, Rts1, to Rec8. Conclusions: Our findings indicate that separase-dependent cleavage of phosphorylated Rec8 causes premature cohesin loss in
spo13Δ cells.
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Affiliation(s)
- Stefan Galander
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Rachael E Barton
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - David A Kelly
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Adèle L Marston
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
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37
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Folco HD, McCue A, Balachandran V, Grewal SIS. Cohesin Impedes Heterochromatin Assembly in Fission Yeast Cells Lacking Pds5. Genetics 2019; 213:127-141. [PMID: 31278118 PMCID: PMC6727797 DOI: 10.1534/genetics.119.302256] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/24/2019] [Indexed: 01/05/2023] Open
Abstract
The fission yeast Schizosaccharomyces pombe is a powerful genetic model system for uncovering fundamental principles of heterochromatin assembly and epigenetic inheritance of chromatin states. Heterochromatin defined by histone H3 lysine 9 methylation and HP1 proteins coats large chromosomal domains at centromeres, telomeres, and the mating-type (mat) locus. Although genetic and biochemical studies have provided valuable insights into heterochromatin assembly, many key mechanistic details remain unclear. Here, we use a sensitized reporter system at the mat locus to screen for factors affecting heterochromatic silencing. In addition to known components of heterochromatin assembly pathways, our screen identified eight new factors including the cohesin-associated protein Pds5. We find that Pds5 enriched throughout heterochromatin domains is required for proper maintenance of heterochromatin. This function of Pds5 requires its associated Eso1 acetyltransferase, which is implicated in the acetylation of cohesin. Indeed, introducing an acetylation-mimicking mutation in a cohesin subunit suppresses defects in heterochromatin assembly in pds5∆ and eso1∆ cells. Our results show that in cells lacking Pds5, cohesin interferes with heterochromatin assembly. Supporting this, eliminating cohesin from the mat locus in the pds5∆ mutant restores both heterochromatin assembly and gene silencing. These analyses highlight an unexpected requirement for Pds5 in ensuring proper coordination between cohesin and heterochromatin factors to effectively maintain gene silencing.
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Affiliation(s)
- H Diego Folco
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Andrea McCue
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
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38
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Cattoglio C, Pustova I, Walther N, Ho JJ, Hantsche-Grininger M, Inouye CJ, Hossain MJ, Dailey GM, Ellenberg J, Darzacq X, Tjian R, Hansen AS. Determining cellular CTCF and cohesin abundances to constrain 3D genome models. eLife 2019; 8:e40164. [PMID: 31205001 PMCID: PMC6579579 DOI: 10.7554/elife.40164] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 03/28/2019] [Indexed: 01/02/2023] Open
Abstract
Achieving a quantitative and predictive understanding of 3D genome architecture remains a major challenge, as it requires quantitative measurements of the key proteins involved. Here, we report the quantification of CTCF and cohesin, two causal regulators of topologically associating domains (TADs) in mammalian cells. Extending our previous imaging studies (Hansen et al., 2017), we estimate bounds on the density of putatively DNA loop-extruding cohesin complexes and CTCF binding site occupancy. Furthermore, co-immunoprecipitation studies of an endogenously tagged subunit (Rad21) suggest the presence of cohesin dimers and/or oligomers. Finally, based on our cell lines with accurately measured protein abundances, we report a method to conveniently determine the number of molecules of any Halo-tagged protein in the cell. We anticipate that our results and the established tool for measuring cellular protein abundances will advance a more quantitative understanding of 3D genome organization, and facilitate protein quantification, key to comprehend diverse biological processes.
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Affiliation(s)
- Claudia Cattoglio
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical InstituteBerkeleyUnited States
| | - Iryna Pustova
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical InstituteBerkeleyUnited States
| | - Nike Walther
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Jaclyn J Ho
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical InstituteBerkeleyUnited States
| | | | - Carla J Inouye
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical InstituteBerkeleyUnited States
| | - M Julius Hossain
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Gina M Dailey
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
| | - Jan Ellenberg
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical InstituteBerkeleyUnited States
| | - Anders S Hansen
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical InstituteBerkeleyUnited States
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Holzmann J, Politi AZ, Nagasaka K, Hantsche-Grininger M, Walther N, Koch B, Fuchs J, Dürnberger G, Tang W, Ladurner R, Stocsits RR, Busslinger GA, Novák B, Mechtler K, Davidson IF, Ellenberg J, Peters JM. Absolute quantification of cohesin, CTCF and their regulators in human cells. eLife 2019; 8:e46269. [PMID: 31204999 PMCID: PMC6606026 DOI: 10.7554/elife.46269] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 06/13/2019] [Indexed: 12/15/2022] Open
Abstract
The organisation of mammalian genomes into loops and topologically associating domains (TADs) contributes to chromatin structure, gene expression and recombination. TADs and many loops are formed by cohesin and positioned by CTCF. In proliferating cells, cohesin also mediates sister chromatid cohesion, which is essential for chromosome segregation. Current models of chromatin folding and cohesion are based on assumptions of how many cohesin and CTCF molecules organise the genome. Here we have measured absolute copy numbers and dynamics of cohesin, CTCF, NIPBL, WAPL and sororin by mass spectrometry, fluorescence-correlation spectroscopy and fluorescence recovery after photobleaching in HeLa cells. In G1-phase, there are ~250,000 nuclear cohesin complexes, of which ~ 160,000 are chromatin-bound. Comparison with chromatin immunoprecipitation-sequencing data implies that some genomic cohesin and CTCF enrichment sites are unoccupied in single cells at any one time. We discuss the implications of these findings for how cohesin can contribute to genome organisation and cohesion.
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Affiliation(s)
- Johann Holzmann
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
- Gregor Mendel Institute, Austrian Academy of SciencesVienna Biocenter (VBC)ViennaAustria
| | - Antonio Z Politi
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Kota Nagasaka
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
| | | | - Nike Walther
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Birgit Koch
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Johannes Fuchs
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
- Gregor Mendel Institute, Austrian Academy of SciencesVienna Biocenter (VBC)ViennaAustria
| | - Gerhard Dürnberger
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
- Gregor Mendel Institute, Austrian Academy of SciencesVienna Biocenter (VBC)ViennaAustria
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
| | - Rene Ladurner
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
| | - Roman R Stocsits
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
| | - Georg A Busslinger
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
| | - Béla Novák
- Department of BiochemistryUniversity of OxfordOxfordUnited Kingdom
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
- Gregor Mendel Institute, Austrian Academy of SciencesVienna Biocenter (VBC)ViennaAustria
| | - Iain Finley Davidson
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
| | - Jan Ellenberg
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
- Medical University of ViennaViennaAustria
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Kim JS, He X, Liu J, Duan Z, Kim T, Gerard J, Kim B, Pillai MM, Lane WS, Noble WS, Budnik B, Waldman T. Systematic proteomics of endogenous human cohesin reveals an interaction with diverse splicing factors and RNA-binding proteins required for mitotic progression. J Biol Chem 2019; 294:8760-8772. [PMID: 31010829 PMCID: PMC6552432 DOI: 10.1074/jbc.ra119.007832] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/18/2019] [Indexed: 12/23/2022] Open
Abstract
The cohesin complex regulates sister chromatid cohesion, chromosome organization, gene expression, and DNA repair. Cohesin is a ring complex composed of four core subunits and seven regulatory subunits. In an effort to comprehensively identify additional cohesin-interacting proteins, we used gene editing to introduce a dual epitope tag into the endogenous allele of each of 11 known components of cohesin in cultured human cells, and we performed MS analyses on dual-affinity purifications. In addition to reciprocally identifying all known components of cohesin, we found that cohesin interacts with a panoply of splicing factors and RNA-binding proteins (RBPs). These included diverse components of the U4/U6.U5 tri-small nuclear ribonucleoprotein complex and several splicing factors that are commonly mutated in cancer. The interaction between cohesin and splicing factors/RBPs was RNA- and DNA-independent, occurred in chromatin, was enhanced during mitosis, and required RAD21. Furthermore, cohesin-interacting splicing factors and RBPs followed the cohesin cycle and prophase pathway of cell cycle-regulated interactions with chromatin. Depletion of cohesin-interacting splicing factors and RBPs resulted in aberrant mitotic progression. These results provide a comprehensive view of the endogenous human cohesin interactome and identify splicing factors and RBPs as functionally significant cohesin-interacting proteins.
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Affiliation(s)
- Jung-Sik Kim
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Xiaoyuan He
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Jie Liu
- the Department of Genome Sciences
| | - Zhijun Duan
- Institute for Stem Cell and Regenerative Medicine, and
- Division of Hematology, University of Washington, Seattle, Washington 98195
| | - Taeyeon Kim
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Julia Gerard
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Brian Kim
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Manoj M Pillai
- the Section of Hematology, Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, and
| | - William S Lane
- the Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts 02138
| | | | - Bogdan Budnik
- the Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts 02138
| | - Todd Waldman
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057,
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41
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Mirkovic M, Oliveira RA. Centromeric Cohesin: Molecular Glue and Much More. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019; 56:485-513. [PMID: 28840250 DOI: 10.1007/978-3-319-58592-5_20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sister chromatid cohesion, mediated by the cohesin complex, is a prerequisite for faithful chromosome segregation during mitosis. Premature release of sister chromatid cohesion leads to random segregation of the genetic material and consequent aneuploidy. Multiple regulatory mechanisms ensure proper timing for cohesion establishment, concomitant with DNA replication, and cohesion release during the subsequent mitosis. Here we summarize the most important phases of the cohesin cycle and the coordination of cohesion release with the progression through mitosis. We further discuss recent evidence that has revealed additional functions for centromeric localization of cohesin in the fidelity of mitosis in metazoans. Beyond its well-established role as "molecular glue", centromeric cohesin complexes are now emerging as a scaffold for multiple fundamental processes during mitosis, including the formation of correct chromosome and kinetochore architecture, force balance with the mitotic spindle, and the association with key molecules that regulate mitotic fidelity, particularly at the chromosomal inner centromere. Centromeric chromatin may be thus seen as a dynamic place where cohesin ensures mitotic fidelity by multiple means.
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Affiliation(s)
- Mihailo Mirkovic
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 2780-156, Oeiras, Portugal
| | - Raquel A Oliveira
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 2780-156, Oeiras, Portugal.
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42
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Perez S, Gevor M, Davidovich A, Kaspi A, Yamin K, Domovich T, Meirson T, Matityahu A, Brody Y, Stemmer SM, El-Osta A, Haviv I, Onn I, Gal-Tanamy M. Dysregulation of the cohesin subunit RAD21 by Hepatitis C virus mediates host-virus interactions. Nucleic Acids Res 2019; 47:2455-2471. [PMID: 30698808 PMCID: PMC6412124 DOI: 10.1093/nar/gkz052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 12/30/2018] [Accepted: 01/24/2019] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) infection is the leading cause of chronic hepatitis, which often results in liver fibrosis, cirrhosis and hepatocellular carcinoma (HCC). HCV possesses an RNA genome and its replication is confined to the cytoplasm. Yet, infection with HCV leads to global changes in gene expression, and chromosomal instability (CIN) in the host cell. The mechanisms by which the cytoplasmic virus affects these nuclear processes are elusive. Here, we show that HCV modulates the function of the Structural Maintenance of Chromosome (SMC) protein complex, cohesin, which tethers remote regions of chromatin. We demonstrate that infection of hepatoma cells with HCV leads to up regulation of the expression of the RAD21 cohesin subunit and changes cohesin residency on the chromatin. These changes regulate the expression of genes associated with virus-induced pathways. Furthermore, siRNA downregulation of viral-induced RAD21 reduces HCV infection. During mitosis, HCV infection induces hypercondensation of chromosomes and the appearance of multi-centrosomes. We provide evidence that the underlying mechanism involves the viral NS3/4 protease and the cohesin regulator, WAPL. Altogether, our results provide the first evidence that HCV induces changes in gene expression and chromosome structure of infected cells by modulating cohesin.
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Affiliation(s)
- Shira Perez
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Cancer Personalized Medicine and Diagnostic Genomics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Michael Gevor
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Ateret Davidovich
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Antony Kaspi
- Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, Australia
| | - Katreena Yamin
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Tom Domovich
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Tomer Meirson
- Cell Migration and Invasion Laboratory, Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Avi Matityahu
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Yehuda Brody
- The Broad institute of Harvard and MIT, Cambridge, MA, USA
| | - Salomon M Stemmer
- Davidoff Center, Rabin Medical Center, Beilinson Campus, Petach Tikva, and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, Australia
- Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR
| | - Izhak Haviv
- Cancer Personalized Medicine and Diagnostic Genomics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Itay Onn
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Meital Gal-Tanamy
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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43
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Rankin S. Reconstituting Nuclear and Chromosome Dynamics Using Xenopus Extracts. Cold Spring Harb Protoc 2019; 2019:pdb.top097105. [PMID: 30150319 DOI: 10.1101/pdb.top097105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Extracts prepared from the eggs of frogs, particularly Xenopus species, have provided critical material for seminal studies of nuclear and chromosome dynamics over several decades. Their usefulness for these types of analyses lies in several important characteristics: stockpiled nuclear components, absence of endogenous DNA, and intact and functioning signaling networks. These factors have allowed detailed molecular analyses of many aspects of chromosome biology, including DNA replication, checkpoint signaling, epigenetic control, and chromosome condensation, cohesion, and segregation. In this introduction, the preparation and application of Xenopus egg extracts for the study of chromosomes and chromatin are described in detail.
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Affiliation(s)
- Susannah Rankin
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104; .,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104
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44
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Carvajal-Maldonado D, Byrum AK, Jackson J, Wessel S, Lemaçon D, Guitton-Sert L, Quinet A, Tirman S, Graziano S, Masson JY, Cortez D, Gonzalo S, Mosammaparast N, Vindigni A. Perturbing cohesin dynamics drives MRE11 nuclease-dependent replication fork slowing. Nucleic Acids Res 2019; 47:1294-1310. [PMID: 29917110 PMCID: PMC6379725 DOI: 10.1093/nar/gky519] [Citation(s) in RCA: 28] [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: 01/26/2018] [Revised: 05/22/2018] [Accepted: 05/25/2018] [Indexed: 12/14/2022] Open
Abstract
Pds5 is required for sister chromatid cohesion, and somewhat paradoxically, to remove cohesin from chromosomes. We found that Pds5 plays a critical role during DNA replication that is distinct from its previously known functions. Loss of Pds5 hinders replication fork progression in unperturbed human and mouse cells. Inhibition of MRE11 nuclease activity restores fork progression, suggesting that Pds5 protects forks from MRE11-activity. Loss of Pds5 also leads to double-strand breaks, which are again reduced by MRE11 inhibition. The replication function of Pds5 is independent of its previously reported interaction with BRCA2. Unlike Pds5, BRCA2 protects forks from nucleolytic degradation only in the presence of genotoxic stress. Moreover, our iPOND analysis shows that the loading of Pds5 and other cohesion factors on replication forks is not affected by the BRCA2 status. Pds5 role in DNA replication is shared by the other cohesin-removal factor Wapl, but not by the cohesin complex component Rad21. Interestingly, depletion of Rad21 in a Pds5-deficient background rescues the phenotype observed upon Pds5 depletion alone. These findings support a model where loss of either component of the cohesin releasin complex perturbs cohesin dynamics on replication forks, hindering fork progression and promoting MRE11-dependent fork slowing.
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Affiliation(s)
- Denisse Carvajal-Maldonado
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Andrea K Byrum
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jessica Jackson
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Sarah Wessel
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Delphine Lemaçon
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Laure Guitton-Sert
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Axis, 9 McMahon, Québec City, QC G1R 2J6, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Annabel Quinet
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Stephanie Tirman
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Simona Graziano
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Axis, 9 McMahon, Québec City, QC G1R 2J6, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Susana Gonzalo
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alessandro Vindigni
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
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45
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Liang C, Zhang Z, Chen Q, Yan H, Zhang M, Xiang X, Yi Q, Pan X, Cheng H, Wang F. A positive feedback mechanism ensures proper assembly of the functional inner centromere during mitosis in human cells. J Biol Chem 2019; 294:1437-1450. [PMID: 30498087 PMCID: PMC6364785 DOI: 10.1074/jbc.ra118.006046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/27/2018] [Indexed: 01/25/2023] Open
Abstract
The inner centromere region of a mitotic chromosome critically regulates sister chromatid cohesion and kinetochore-microtubule attachments. However, the molecular mechanism underlying inner centromere assembly remains elusive. Here, using CRISPR/Cas9-based gene editing in HeLa cells, we disrupted the interaction of Shugoshin 1 (Sgo1) with histone H2A phosphorylated on Thr-120 (H2ApT120) to selectively release Sgo1 from mitotic centromeres. Interestingly, cells expressing the H2ApT120-binding defective mutant of Sgo1 have an elevated rate of chromosome missegregation accompanied by weakened centromeric cohesion and decreased centromere accumulation of the chromosomal passenger complex (CPC), an integral part of the inner centromere and a key player in the correction of erroneous kinetochore-microtubule attachments. When artificially tethered to centromeres, a Sgo1 mutant defective in binding protein phosphatase 2A (PP2A) is not able to support proper centromeric cohesion and CPC accumulation, indicating that the Sgo1-PP2A interaction is essential for the integrity of mitotic centromeres. We further provide evidence indicating that Sgo1 protects centromeric cohesin to create a binding site for the histone H3-associated protein kinase Haspin, which not only inhibits the cohesin release factor Wapl and thereby strengthens centromeric cohesion but also phosphorylates histone H3 at Thr-3 to position CPC at inner centromeres. Taken together, our findings reveal a positive feedback-based mechanism that ensures proper assembly of the functional inner centromere during mitosis. They further suggest a causal link between centromeric cohesion defects and chromosomal instability in cancer cells.
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Affiliation(s)
- Cai Liang
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Zhenlei Zhang
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Qinfu Chen
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Haiyan Yan
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Miao Zhang
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xingfeng Xiang
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Qi Yi
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xuan Pan
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Hankun Cheng
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Fangwei Wang
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China.
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46
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Hong S, Joo JH, Yun H, Kim K. The nature of meiotic chromosome dynamics and recombination in budding yeast. J Microbiol 2019; 57:221-231. [PMID: 30671743 DOI: 10.1007/s12275-019-8541-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/24/2018] [Accepted: 10/26/2018] [Indexed: 12/28/2022]
Abstract
During meiosis, crossing over allows for the exchange of genes between homologous chromosomes, enabling their segregation and leading to genetic variation in the resulting gametes. Spo11, a topoisomerase-like protein expressed in eukaryotes, and diverse accessory factors induce programmed double-strand breaks (DSBs) to initiate meiotic recombination during the early phase of meiosis after DNA replication. DSBs are further repaired via meiosis-specific homologous recombination. Studies on budding yeast have provided insights into meiosis and genetic recombination and have improved our understanding of higher eukaryotic systems. Cohesin, a chromosome-associated multiprotein complex, mediates sister chromatid cohesion (SCC), and is conserved from yeast to humans. Diverse cohesin subunits in budding yeast have been identified in DNA metabolic pathways, such as DNA replication, chromosome segregation, recombination, DNA repair, and gene regulation. During cell cycle, SCC is established by multiple cohesin subunits, which physically bind sister chromatids together and modulate proteins that involve in the capturing and separation of sister chromatids. Cohesin components include at least four core subunits that establish and maintain SCC: two structural maintenance chromosome subunits (Smc1 and Smc3), an α-kleisin subunit (Mcd1/Scc1 during mitosis and Rec8 during meiosis), and Scc3/Irr1 (SA1 and SA2). In addition, the cohesin-associated factors Pds5 and Rad61 regulate structural modifications and cell cyclespecific dynamics of chromatin to ensure accurate chromosome segregation. In this review, we discuss SCC and the recombination pathway, as well as the relationship between the two processes in budding yeast, and we suggest a possible conserved mechanism for meiotic chromosome dynamics from yeast to humans.
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Affiliation(s)
- Soogil Hong
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jeong Hwan Joo
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyeseon Yun
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Keunpil Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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47
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Litwin I, Pilarczyk E, Wysocki R. The Emerging Role of Cohesin in the DNA Damage Response. Genes (Basel) 2018; 9:genes9120581. [PMID: 30487431 PMCID: PMC6316000 DOI: 10.3390/genes9120581] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 12/23/2022] Open
Abstract
Faithful transmission of genetic material is crucial for all organisms since changes in genetic information may result in genomic instability that causes developmental disorders and cancers. Thus, understanding the mechanisms that preserve genome integrity is of fundamental importance. Cohesin is a multiprotein complex whose canonical function is to hold sister chromatids together from S-phase until the onset of anaphase to ensure the equal division of chromosomes. However, recent research points to a crucial function of cohesin in the DNA damage response (DDR). In this review, we summarize recent advances in the understanding of cohesin function in DNA damage signaling and repair. First, we focus on cohesin architecture and molecular mechanisms that govern sister chromatid cohesion. Next, we briefly characterize the main DDR pathways. Finally, we describe mechanisms that determine cohesin accumulation at DNA damage sites and discuss possible roles of cohesin in DDR.
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Affiliation(s)
- Ireneusz Litwin
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland.
| | - Ewa Pilarczyk
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland.
| | - Robert Wysocki
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland.
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48
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Sapkota H, Wasiak E, Daum JR, Gorbsky GJ. Multiple determinants and consequences of cohesion fatigue in mammalian cells. Mol Biol Cell 2018; 29:1811-1824. [PMID: 29846129 PMCID: PMC6085821 DOI: 10.1091/mbc.e18-05-0315] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 12/12/2022] Open
Abstract
Cells delayed in metaphase with intact mitotic spindles undergo cohesion fatigue, where sister chromatids separate asynchronously, while cells remain in mitosis. Cohesion fatigue requires release of sister chromatid cohesion. However, the pathways that breach sister chromatid cohesion during cohesion fatigue remain unknown. Using moderate-salt buffers to remove loosely bound chromatin cohesin, we show that "cohesive" cohesin is not released during chromatid separation during cohesion fatigue. Using a regulated protein heterodimerization system to lock different cohesin ring interfaces at specific times in mitosis, we show that the Wapl-mediated pathway of cohesin release is not required for cohesion fatigue. By manipulating microtubule stability and cohesin complex integrity in cell lines with varying sensitivity to cohesion fatigue, we show that rates of cohesion fatigue reflect a dynamic balance between spindle pulling forces and resistance to separation by interchromatid cohesion. Finally, while massive separation of chromatids in cohesion fatigue likely produces inviable cell progeny, we find that short metaphase delays, leading to partial chromatid separation, predispose cells to chromosome missegregation. Thus, complete separation of one or a few chromosomes and/or partial separation of sister chromatids may be an unrecognized but common source of chromosome instability that perpetuates the evolution of malignant cells in cancer.
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Affiliation(s)
- Hem Sapkota
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Emilia Wasiak
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - John R. Daum
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Gary J. Gorbsky
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
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49
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Shah VJ, Maddika S. CRL7 SMU1 E3 ligase complex-driven H2B ubiquitylation functions in sister chromatid cohesion by regulating SMC1 expression. J Cell Sci 2018; 131:jcs.213868. [PMID: 29507117 DOI: 10.1242/jcs.213868] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/26/2018] [Indexed: 12/26/2022] Open
Abstract
Cullin-RING-type E3 ligases (CRLs) control a broad range of biological processes by ubiquitylating numerous cellular substrates. However, the role of CRL E3 ligases in chromatid cohesion is unknown. In this study, we identified a new CRL-type E3 ligase (designated as CRL7SMU1 complex) that has an essential role in the maintenance of chromatid cohesion. We demonstrate that SMU1, DDB1, CUL7 and RNF40 are integral components of this complex. SMU1, by acting as a substrate recognition module, binds to H2B and mediates monoubiquitylation at the lysine (K) residue K120 through CRL7SMU1 E3 ligase complex. Depletion of CRL7SMU1 leads to loss of H2B ubiquitylation at the SMC1a locus and, thus, subsequently compromised SMC1a expression in cells. Knockdown of CRL7SMU1 components or loss of H2B ubiquitylation leads to defective sister chromatid cohesion, which is rescued by restoration of SMC1a expression. Together, our results unveil an important role of CRL7SMU1 E3 ligase in promoting H2B ubiquitylation for maintenance of sister chromatid cohesion during mitosis.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Varun Jayeshkumar Shah
- Laboratory of Cell Death & Cell Survival, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India-500 039.,Graduate studies, Manipal Academy of Higher Education, Manipal, India-576 104
| | - Subbareddy Maddika
- Laboratory of Cell Death & Cell Survival, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India-500 039
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50
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Litwin I, Wysocki R. New insights into cohesin loading. Curr Genet 2018; 64:53-61. [PMID: 28631016 DOI: 10.1007/s00294-017-0723-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 01/13/2023]
Abstract
Cohesin is a conserved, ring-shaped protein complex that encircles sister chromatids and ensures correct chromosome segregation during mitosis and meiosis. It also plays a crucial role in the regulation of gene expression, DNA condensation, and DNA repair through both non-homologous end joining and homologous recombination. Cohesins are spatiotemporally regulated by the Scc2-Scc4 complex which facilitates cohesin loading onto chromatin at specific chromosomal sites. Over the last few years, much attention has been paid to cohesin and cohesin loader as it became clear that even minor disruptions of these complexes may lead to developmental disorders and cancers. Here we summarize recent developments in the structure of Scc2-Scc4 complex, cohesin loading process, and mediators that determine the Scc2-Scc4 binding patterns to chromatin.
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Affiliation(s)
- Ireneusz Litwin
- Institute of Experimental Biology, University of Wroclaw, 50-328, Wroclaw, Poland.
| | - Robert Wysocki
- Institute of Experimental Biology, University of Wroclaw, 50-328, Wroclaw, Poland
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