1
|
Cheng H, Zhang N, Pati D. Cohesin subunit RAD21: From biology to disease. Gene 2020; 758:144966. [PMID: 32687945 PMCID: PMC7949736 DOI: 10.1016/j.gene.2020.144966] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 02/06/2023]
Abstract
RAD21 (also known as KIAA0078, NXP1, HR21, Mcd1, Scc1, and hereafter called RAD21), an essential gene, encodes a DNA double-strand break (DSB) repair protein that is evolutionarily conserved in all eukaryotes from budding yeast to humans. RAD21 protein is a structural component of the highly conserved cohesin complex consisting of RAD21, SMC1a, SMC3, and SCC3 [STAG1 (SA1) and STAG2 (SA2) in metazoans] proteins, involved in sister chromatid cohesion. This function is essential for proper chromosome segregation, post-replicative DNA repair, and prevention of inappropriate recombination between repetitive regions. In interphase, cohesin also functions in the control of gene expression by binding to numerous sites within the genome. In addition to playing roles in the normal cell cycle and DNA DSB repair, RAD21 is also linked to the apoptotic pathways. Germline heterozygous or homozygous missense mutations in RAD21 have been associated with human genetic disorders, including developmental diseases such as Cornelia de Lange syndrome (CdLS) and chronic intestinal pseudo-obstruction (CIPO) called Mungan syndrome, respectively, and collectively termed as cohesinopathies. Somatic mutations and amplification of the RAD21 have also been widely reported in both human solid and hematopoietic tumors. Considering the role of RAD21 in a broad range of cellular processes that are hot spots in neoplasm, it is not surprising that the deregulation of RAD21 has been increasingly evident in human cancers. Herein, we review the biology of RAD21 and the cellular processes that this important protein regulates and discuss the significance of RAD21 deregulation in cancer and cohesinopathies.
Collapse
Affiliation(s)
- Haizi Cheng
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, United States; Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Nenggang Zhang
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, United States; Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Debananda Pati
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, United States; Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States; Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States.
| |
Collapse
|
2
|
da Costa-Nunes JA, Capitão C, Kozak J, Costa-Nunes P, Ducasa GM, Pontes O, Angelis KJ. The AtRAD21.1 and AtRAD21.3 Arabidopsis cohesins play a synergistic role in somatic DNA double strand break damage repair. BMC PLANT BIOLOGY 2014; 14:353. [PMID: 25511710 PMCID: PMC4273318 DOI: 10.1186/s12870-014-0353-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 11/26/2014] [Indexed: 05/19/2023]
Abstract
BACKGROUND The RAD21 cohesin plays, besides its well-recognised role in chromatid cohesion, a role in DNA double strand break (dsb) repair. In Arabidopsis there are three RAD21 paralog genes (AtRAD21.1, AtRAD21.2 and AtRAD21.3), yet only AtRAD21.1 has been shown to be required for DNA dsb damage repair. Further investigation of the role of cohesins in DNA dsb repair was carried out and is here reported. RESULTS We show for the first time that not only AtRAD21.1 but also AtRAD21.3 play a role in somatic DNA dsb repair. Comet data shows that the lack of either cohesins induces a similar high basal level of DNA dsb in the nuclei and a slower DNA dsb repair kinetics in both cohesin mutants. The observed AtRAD21.3 transcriptional response to DNA dsb induction reinforces further the role of this cohesin in DNA dsb repair. The importance of AtRAD21.3 in DNA dsb damage repair, after exposure to DNA dsb damage inducing agents, is notorious and recognisably evident at the phenotypical level, particularly when the AtRAD21.1 gene is also disrupted. CONCLUSIONS Our data demonstrates that both Arabidopsis cohesin (AtRAD21.1 and AtRAD21.3) play a role in somatic DNA dsb repair. Furthermore, the phenotypical data from the atrad21.1 atrad21.3 double mutant indicates that these two cohesins function synergistically in DNA dsb repair. The implications of this data are discussed.
Collapse
Affiliation(s)
- José A da Costa-Nunes
- />Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa (UNL), Av. República, Apartado 127, 2781-901 Oeiras, Portugal
| | - Cláudio Capitão
- />Laboratório de Biotecnologia de Células Vegetais, ITQB, UNL, Av. República, Apartado 127, 2781-901 Oeiras, Portugal
- />Current address: Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Jaroslav Kozak
- />Molecular Farming Lab., Institute of Experimental Botany AS CR, Na Karlovce 1, 160 00 Praha 6, Czech Republic
| | - Pedro Costa-Nunes
- />Department of Biology, University of New Mexico, 235 Castetter Hall, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001 New Mexico USA
- />Current address: Nuclear Organization and Epigenetics Lab., Shanghai Center for Plant Stress Biology (PSC), No. 3888 Chenhua Road, Shanghai, 201602 P. R. China
| | - Gloria M Ducasa
- />Department of Biology, University of New Mexico, 235 Castetter Hall, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001 New Mexico USA
| | - Olga Pontes
- />Department of Biology, University of New Mexico, 235 Castetter Hall, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001 New Mexico USA
- />Current address: Nuclear Organization and Epigenetics Lab., Shanghai Center for Plant Stress Biology (PSC), No. 3888 Chenhua Road, Shanghai, 201602 P. R. China
| | - Karel J Angelis
- />Molecular Farming Lab., Institute of Experimental Botany AS CR, Na Karlovce 1, 160 00 Praha 6, Czech Republic
| |
Collapse
|
3
|
Guillou E, Ibarra A, Coulon V, Casado-Vela J, Rico D, Casal I, Schwob E, Losada A, Méndez J. Cohesin organizes chromatin loops at DNA replication factories. Genes Dev 2010; 24:2812-22. [PMID: 21159821 PMCID: PMC3003199 DOI: 10.1101/gad.608210] [Citation(s) in RCA: 170] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 10/22/2010] [Indexed: 12/23/2022]
Abstract
Genomic DNA is packed in chromatin fibers organized in higher-order structures within the interphase nucleus. One level of organization involves the formation of chromatin loops that may provide a favorable environment to processes such as DNA replication, transcription, and repair. However, little is known about the mechanistic basis of this structuration. Here we demonstrate that cohesin participates in the spatial organization of DNA replication factories in human cells. Cohesin is enriched at replication origins and interacts with prereplication complex proteins. Down-regulation of cohesin slows down S-phase progression by limiting the number of active origins and increasing the length of chromatin loops that correspond with replicon units. These results give a new dimension to the role of cohesin in the architectural organization of interphase chromatin, by showing its participation in DNA replication.
Collapse
Affiliation(s)
- Emmanuelle Guillou
- DNA Replication Group, Spanish National Cancer Research Centre (CNIO), E-28029 Madrid, Spain
| | - Arkaitz Ibarra
- DNA Replication Group, Spanish National Cancer Research Centre (CNIO), E-28029 Madrid, Spain
| | - Vincent Coulon
- Institut de Génétique Moléculaire de Montpellier, CNRS-Université Montpellier 1 et 2, 34293 Montpellier, Cedex 5, France
| | - Juan Casado-Vela
- Protein Technology Unit, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), E-28029 Madrid, Spain
| | - Daniel Rico
- Structural Computational Biology Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), E-28029 Madrid, Spain
| | - Ignacio Casal
- Protein Technology Unit, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), E-28029 Madrid, Spain
| | - Etienne Schwob
- Institut de Génétique Moléculaire de Montpellier, CNRS-Université Montpellier 1 et 2, 34293 Montpellier, Cedex 5, France
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), E-28029 Madrid, Spain
| | - Juan Méndez
- DNA Replication Group, Spanish National Cancer Research Centre (CNIO), E-28029 Madrid, Spain
| |
Collapse
|
4
|
Albrethsen J, Knol JC, Jimenez CR. Unravelling the nuclear matrix proteome. J Proteomics 2008; 72:71-81. [PMID: 18957335 DOI: 10.1016/j.jprot.2008.09.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Revised: 09/29/2008] [Accepted: 09/30/2008] [Indexed: 12/28/2022]
Abstract
The nuclear matrix (NM) model posits the presence of a protein/RNA scaffold that spans the mammalian nucleus. The NM proteins are involved in basic nuclear function and are a promising source of protein biomarkers for cancer. Importantly, the NM proteome is operationally defined as the proteins from cells and tissue that are extracted following a specific biochemical protocol; in brief, the soluble proteins and lipids, cytoskeleton, and chromatin elements are removed in a sequential fashion, leaving behind the proteins that compose the NM. So far, the NM has not been sufficiently verified as a biological entity and only preliminary at the molecular level. Here, we argue for a combined effort of proteomics, immunodetection and microscopy to unravel the composition and structure of the NM.
Collapse
Affiliation(s)
- Jakob Albrethsen
- OncoProteomics Laboratory, CCA 1-60, Department Medical Oncology, VUmc-Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | | | | |
Collapse
|
5
|
da Costa-Nunes JA, Bhatt AM, O'Shea S, West CE, Bray CM, Grossniklaus U, Dickinson HG. Characterization of the three Arabidopsis thaliana RAD21 cohesins reveals differential responses to ionizing radiation. JOURNAL OF EXPERIMENTAL BOTANY 2006; 57:971-83. [PMID: 16488915 DOI: 10.1093/jxb/erj083] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The RAD21/REC8 gene family has been implicated in sister chromatid cohesion and DNA repair in several organisms. Unlike most eukaryotes, Arabidopsis thaliana has three RAD21 gene homologues, and their cloning and characterization are reported here. All three genes, AtRAD21.1, AtRAD21.2, and AtRAD21.3, are expressed in tissues rich in cells undergoing cell division, and AtRAD21.3 shows the highest relative level of expression. An increase in steady-state levels of AtRAD21.1 transcript was also observed, specifically after the induction of DNA damage. Phenotypic analysis of the atrad21.1 and atrad21.3 mutants revealed that neither of the single mutants was lethal, probably due to the redundancy in function of the AtRAD21 genes. However, AtRAD21.1 plays a critical role in recovery from DNA damage during seed imbibition, prior to germination, as atrad21.1 mutant seeds are hypersensitive to radiation damage.
Collapse
MESH Headings
- Arabidopsis/genetics
- Arabidopsis/physiology
- Arabidopsis/radiation effects
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Arabidopsis Proteins/physiology
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomal Proteins, Non-Histone/physiology
- Cloning, Molecular
- DNA Damage
- Flowers/anatomy & histology
- Flowers/physiology
- Flowers/radiation effects
- Gene Expression Regulation, Plant
- Genes, Plant
- Genes, Reporter
- Molecular Sequence Data
- Mutation
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Nuclear Proteins/physiology
- Phenotype
- RNA, Messenger/metabolism
- Radiation, Ionizing
- Seedlings/anatomy & histology
- Seedlings/physiology
- Seedlings/radiation effects
- Seeds/anatomy & histology
- Seeds/physiology
- Seeds/radiation effects
- Sequence Analysis, Protein
- Sequence Homology, Nucleic Acid
Collapse
Affiliation(s)
- J A da Costa-Nunes
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | | | | | | | | | | | | |
Collapse
|
6
|
Pedersen TX, Leethanakul C, Patel V, Mitola D, Lund LR, Danø K, Johnsen M, Gutkind JS, Bugge TH. Laser capture microdissection-based in vivo genomic profiling of wound keratinocytes identifies similarities and differences to squamous cell carcinoma. Oncogene 2003; 22:3964-76. [PMID: 12813470 DOI: 10.1038/sj.onc.1206614] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Keratinocytes undergo a dramatic phenotypic conversion during reepithelialization of skin wounds to become hyperproliferative, migratory, and invasive. This transient healing response phenotypically resembles malignant transformation of keratinocytes during squamous cell carcinoma progression. Here we present the first analysis of global changes in keratinocyte gene expression during skin wound healing in vivo, and compare these changes to changes in gene expression during malignant conversion of keratinized epithelium. Laser capture microdissection was used to isolate RNA from wound keratinocytes from incisional mouse skin wounds and adjacent normal skin keratinocytes. Changes in gene expression were determined by comparative cDNA array analyses, and the approach was validated by in situ hybridization. The analyses identified 48 candidate genes not previously associated with wound reepithelialization. Furthermore, the analyses revealed that the phenotypic resemblance of wound keratinocytes to squamous cell carcinoma is mimicked at the level of gene expression, but notable differences between the two tissue-remodeling processes were also observed. The combination of laser capture microdissection and cDNA array analysis provides a powerful new tool to unravel the complex changes in gene expression that underlie physiological and pathological remodeling of keratinized epithelium.
Collapse
Affiliation(s)
- Tanja Xenia Pedersen
- Proteases and Tissue Remodeling Unit, Oral & Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, 30 Convent Drive, Room 211, Bethesda, MD 20892, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Kimura Y, Sakai F, Nakano O, Kisaki O, Sugimoto H, Sawamura T, Sadano H, Osumi T. The newly identified human nuclear protein NXP-2 possesses three distinct domains, the nuclear matrix-binding, RNA-binding, and coiled-coil domains. J Biol Chem 2002; 277:20611-7. [PMID: 11927593 DOI: 10.1074/jbc.m201440200] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Using a monoclonal antibody that recognizes a nuclear matrix protein, we selected a cDNA clone from a lambdagt11 human placenta cDNA library. This cDNA encoded a 939-amino acid protein designated nuclear matrix protein NXP-2. Northern blot analysis indicated that NXP-2 was expressed in various tissues at different levels. Forcibly expressed green fluorescent protein-tagged NXP-2 as well as endogenous NXP-2 was localized in the nucleus and distributed to the nuclear matrix. NXP-2 was released from the nuclear matrix when RNase A was included in the buffer for nuclear matrix preparation. Mapping of functional domains was carried out using green fluorescent protein-tagged truncated mutants of NXP-2. The region of amino acids 326-353 was responsible for nuclear matrix binding and contained a cluster of hydrophobic amino acids that was similar to the nuclear matrix targeting signal of acute myeloleukemia protein. The central region (amino acids 500-591) was demonstrated to be required for RNA binding by Northwestern analysis, although NXP-2 lacked a known RNA binding motif. The region of amino acid residues 682-876 was predicted to have a coiled-coil structure. The RNA-binding, nuclear matrix-binding, and coiled-coil domains are structurally separated, suggesting that NXP-2 plays important roles in diverse nuclear functions, including RNA metabolism and maintenance of nuclear architecture.
Collapse
Affiliation(s)
- Yukio Kimura
- Department of Life Science, Graduate School and Faculty of Science, Himeji Institute of Technology, Kamigori, Hyogo 678-1201, Japan
| | | | | | | | | | | | | | | |
Collapse
|
8
|
Dong F, Cai X, Makaroff CA. Cloning and characterization of two Arabidopsis genes that belong to the RAD21/REC8 family of chromosome cohesin proteins. Gene 2001; 271:99-108. [PMID: 11410371 DOI: 10.1016/s0378-1119(01)00499-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Sister chromatid cohesion is required for proper chromosome segregation during cell division. One group of proteins that is essential for sister chromatid cohesion during mitosis and meiosis is the RAD21/REC8 family of cohesin proteins. Two cohesin proteins are found in yeast; one that functions mainly in mitosis while the other participates in meiosis. In contrast, only one cohesin gene appears to be present in Drosophila. In previous studies we identified an Arabidopsis cohesin protein that is required for meiosis. In this report we describe the isolation and characterization of two additional Arabidopsis cohesin genes. The structure of the genes suggests that they arose via a gene duplication event followed by extensive sequence evolution. Transcripts for the two genes are present throughout the plant and are highest in regions of active cell division, suggesting that the proteins may participate in chromosome cohesion during mitosis.
Collapse
Affiliation(s)
- F Dong
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | | | | |
Collapse
|
9
|
Sook Kim M, Hyen Baek J, Bae MK, Kim KW. Human rad21 gene, hHR21(SP), is downregulated by hypoxia in human tumor cells. Biochem Biophys Res Commun 2001; 281:1106-12. [PMID: 11243849 DOI: 10.1006/bbrc.2001.4488] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To identify genes differentially expressed under normoxic (21% O(2)) or hypoxic (1% O(2)) conditions, we used the technique of mRNA differential display using total RNA extracted from Chang human liver cells. Among downregulated genes by hypoxia, we focused on hHR21(SP) (human homologue of rad21 S. pombe) that is involved in DNA double-strand break repair. Northern blot analysis revealed that mRNA expression of hHR21(SP) was inhibited by hypoxia in various tumor cell lines, such as HepG2, SKHep1, MCF7, and HT1080 cells. We also found that hypoglycemia and heat shock significantly decreased the hHR21(SP) level, indicating that a DNA double-strand break repair gene, hHR21(SP) might be regulated by environmental stresses. In addition, wortmannin, a DNA-dependent protein kinase (DNA-PK) inhibitor, decreased the level of hHR21(SP) mRNA, indicating that DNA-PK might be involved in the regulation of hHR21(SP). These results propose a new understanding of hHR21(SP) regulations in human tumor cells.
Collapse
Affiliation(s)
- M Sook Kim
- Department of Molecular Biology, Pusan National University, Pusan, 609-735, Korea
| | | | | | | |
Collapse
|