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Di Nardo M, Musio A. Cohesin - bridging the gap among gene transcription, genome stability, and human diseases. FEBS Lett 2024. [PMID: 38852996 DOI: 10.1002/1873-3468.14949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/15/2024] [Accepted: 05/08/2024] [Indexed: 06/11/2024]
Abstract
The intricate landscape of cellular processes governing gene transcription, chromatin organization, and genome stability is a fascinating field of study. A key player in maintaining this delicate equilibrium is the cohesin complex, a molecular machine with multifaceted roles. This review presents an in-depth exploration of these intricate connections and their significant impact on various human diseases.
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Affiliation(s)
- Maddalena Di Nardo
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Pisa, Italy
| | - Antonio Musio
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Pisa, Italy
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2
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Agarwal A, Korsak S, Choudhury A, Plewczynski D. The dynamic role of cohesin in maintaining human genome architecture. Bioessays 2023; 45:e2200240. [PMID: 37603403 DOI: 10.1002/bies.202200240] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023]
Abstract
Recent advances in genomic and imaging techniques have revealed the complex manner of organizing billions of base pairs of DNA necessary for maintaining their functionality and ensuring the proper expression of genetic information. The SMC proteins and cohesin complex primarily contribute to forming higher-order chromatin structures, such as chromosomal territories, compartments, topologically associating domains (TADs) and chromatin loops anchored by CCCTC-binding factor (CTCF) protein or other genome organizers. Cohesin plays a fundamental role in chromatin organization, gene expression and regulation. This review aims to describe the current understanding of the dynamic nature of the cohesin-DNA complex and its dependence on cohesin for genome maintenance. We discuss the current 3C technique and numerous bioinformatics pipelines used to comprehend structural genomics and epigenetics focusing on the analysis of Cohesin-centred interactions. We also incorporate our present comprehension of Loop Extrusion (LE) and insights from stochastic modelling.
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Affiliation(s)
- Abhishek Agarwal
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Sevastianos Korsak
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | | | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
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3
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Zhang J, Li L, Miao Y, Liu X, Sun H, Jiang M, Li X, Li Z, Liu C, Liu B, Xu X, Cao Q, Hou W, Chen C, Lou H. Symmetric control of sister chromatid cohesion establishment. Nucleic Acids Res 2023; 51:4760-4773. [PMID: 36912084 PMCID: PMC10250241 DOI: 10.1093/nar/gkad146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 02/13/2023] [Accepted: 02/19/2023] [Indexed: 03/14/2023] Open
Abstract
Besides entrapping sister chromatids, cohesin drives other high-order chromosomal structural dynamics like looping, compartmentalization and condensation. ESCO2 acetylates a subset of cohesin so that cohesion must be established and only be established between nascent sister chromatids. How this process is precisely achieved remains unknown. Here, we report that GSK3 family kinases provide higher hierarchical control through an ESCO2 regulator, CRL4MMS22L. GSK3s phosphorylate Thr105 in MMS22L, resulting in homo-dimerization of CRL4MMS22L and ESCO2 during S phase as evidenced by single-molecule spectroscopy and several biochemical approaches. A single phospho-mimicking mutation on MMS22L (T105D) is sufficient to mediate their dimerization and rescue the cohesion defects caused by GSK3 or MMS22L depletion, whereas non-phosphorylable T105A exerts dominant-negative effects even in wildtype cells. Through cell fractionation and time-course measurements, we show that GSK3s facilitate the timely chromatin association of MMS22L and ESCO2 and subsequently SMC3 acetylation. The necessity of ESCO2 dimerization implicates symmetric control of cohesion establishment in eukaryotes.
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Affiliation(s)
- Jiaxin Zhang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Guangdong Key Laboratory for Genome Stability & Disease Prevention, School of Basic Medical Sciences, Shenzhen University Medical School, South China Hospital, Shenzhen 518116. State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Lili Li
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Guangdong Key Laboratory for Genome Stability & Disease Prevention, School of Basic Medical Sciences, Shenzhen University Medical School, South China Hospital, Shenzhen 518116. State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yu Miao
- School of Life Sciences; Beijing Advanced Innovation Center for Structural Biology; Beijing Frontier Research Center of Biological Structure, Tsinghua University, Beijing 100084, China
| | - Xiaojing Liu
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Guangdong Key Laboratory for Genome Stability & Disease Prevention, School of Basic Medical Sciences, Shenzhen University Medical School, South China Hospital, Shenzhen 518116. State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Haitao Sun
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Guangdong Key Laboratory for Genome Stability & Disease Prevention, School of Basic Medical Sciences, Shenzhen University Medical School, South China Hospital, Shenzhen 518116. State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Meiqian Jiang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Guangdong Key Laboratory for Genome Stability & Disease Prevention, School of Basic Medical Sciences, Shenzhen University Medical School, South China Hospital, Shenzhen 518116. State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaoli Li
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Guangdong Key Laboratory for Genome Stability & Disease Prevention, School of Basic Medical Sciences, Shenzhen University Medical School, South China Hospital, Shenzhen 518116. State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhen Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Cong Liu
- Department of Paediatrics, SCU-CUHK Joint Laboratory for Reproductive Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), West China Second University Hospital, Sichuan University, 610041 Chengdu, China
| | - Baohua Liu
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Guangdong Key Laboratory for Genome Stability & Disease Prevention, School of Basic Medical Sciences, Shenzhen University Medical School, South China Hospital, Shenzhen 518116. State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Guangdong Key Laboratory for Genome Stability & Disease Prevention, School of Basic Medical Sciences, Shenzhen University Medical School, South China Hospital, Shenzhen 518116. State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qinhong Cao
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Guangdong Key Laboratory for Genome Stability & Disease Prevention, School of Basic Medical Sciences, Shenzhen University Medical School, South China Hospital, Shenzhen 518116. State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wenya Hou
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Guangdong Key Laboratory for Genome Stability & Disease Prevention, School of Basic Medical Sciences, Shenzhen University Medical School, South China Hospital, Shenzhen 518116. State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Shenzhen University General Hospital and School of Medicine, Guangdong Key Laboratory for Genome Stability & Disease Prevention, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen University, Shenzhen 518060, China
| | - Chunlai Chen
- School of Life Sciences; Beijing Advanced Innovation Center for Structural Biology; Beijing Frontier Research Center of Biological Structure, Tsinghua University, Beijing 100084, China
| | - Huiqiang Lou
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Guangdong Key Laboratory for Genome Stability & Disease Prevention, School of Basic Medical Sciences, Shenzhen University Medical School, South China Hospital, Shenzhen 518116. State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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4
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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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5
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Wen Y, Liu W, David B, Ren W, Irudayaraj J. Multifunctional Oxygenated Particles for Targeted Cancer Drug Delivery and Evaluation with Darkfield Hyperspectral Imaging. ACS OMEGA 2022; 7:41275-41283. [PMID: 36406533 PMCID: PMC9670270 DOI: 10.1021/acsomega.2c04953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
We propose a novel multifunctional nanocarrier system for targeted drug delivery for lung cancer theranostics. Oxygenated particles (OPs) synthesized with an oxygen-encapsulating carboxymethyl cellulose shell were used as a platform to deliver oxygen to the hypoxic tumor microenvironment. The OPs synthesized could also be conjugated with ligands (e.g., antibodies) to target cancer cells expressing the corresponding antigens to deliver a drug, doxorubicin. In vitro testing of functionalized OPs showed increased efficacy of doxorubicin against the proliferation of lung cancer cells. Both confocal fluorescence imaging and darkfield microscopy hyperspectral imaging validated the OP complex and its efficient targeting of specific cells to deliver the therapeutic. The nanocarrier platform developed can also serve as a diagnostic imaging reagent as demonstrated by darkfield microscopy. Results show that the theranostic OPs developed with multifunctional modalities enabled targeted drug delivery with improved efficacy and tracking of drug delivery vehicles by imaging.
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Affiliation(s)
- Yi Wen
- Department
of Bioengineering, College of Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, Illinois 61801, United States
- Department
of Comparative Biosciences, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wenjie Liu
- Department
of Bioengineering, College of Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, Illinois 61801, United States
| | - Benjamin David
- Department
of Bioengineering, College of Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wen Ren
- Department
of Bioengineering, College of Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, Illinois 61801, United States
| | - Joseph Irudayaraj
- Department
of Bioengineering, College of Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, Illinois 61801, United States
- Department
of Comparative Biosciences, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Cancer
Center at Illinois; Carl R. Woese Institute for Genomic Biology; Beckman
Institute; Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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6
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Matityahu A, Onn I. It's all in the numbers: Cohesin stoichiometry. Front Mol Biosci 2022; 9:1010894. [PMID: 36330215 PMCID: PMC9623059 DOI: 10.3389/fmolb.2022.1010894] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/05/2022] [Indexed: 01/09/2024] Open
Abstract
Cohesin, a structural maintenance of chromosome (SMC) complex, organizes chromatin into three-dimensional structures by threading chromatin into loops and stabilizing long-range chromatin interactions. Four subunits in a 1:1:1:1 ratio compose the cohesin core, which is regulated by auxiliary factors that interact with or modify the core subunits. An ongoing debate about cohesin's mechanism of action regards its stoichiometry. Namely, is cohesin activity mediated by a single complex or cooperation between several complexes that organize into dimers or oligomers? Several investigations that used various experimental approaches have tried to resolve this dispute. Some have convincingly demonstrated that the cohesin monomer is the active unit. However, others have revealed the formation of cohesin dimers and higher-order clusters on and off chromosomes. Elucidating the biological function of cohesin clusters and determining what regulates their formation are just two of the many new questions raised by these findings. We briefly review the history of the argument about cohesin stoichiometry and the central evidence for cohesin activity as a monomer vs. an oligomer. Finally, we discuss the possible biological significance of cohesin oligomerization and present open questions that remain to be answered.
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Affiliation(s)
| | - Itay Onn
- The Azrieli Faculty of Medicine, Bar-Ilan University, Ramat Gan, Safed, Israel
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7
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Fold-change of chromatin condensation in yeast is a conserved property. Sci Rep 2022; 12:17393. [PMID: 36253460 PMCID: PMC9576780 DOI: 10.1038/s41598-022-22340-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/13/2022] [Indexed: 01/10/2023] Open
Abstract
During mitosis, chromatin is condensed and organized into mitotic chromosomes. Condensation is critical for genome stability and dynamics, yet the degree of condensation is significantly different between multicellular and single-cell eukaryotes. What is less clear is whether there is a minimum degree of chromosome condensation in unicellular eukaryotes. Here, we exploited two-photon microscopy to analyze chromatin condensation in live and fixed cells, enabling studies of some organisms that are not readily amenable to genetic modification. This includes the yeasts Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces lactis, and Candida albicans, as well as a protist Trypanosoma brucei. We found that mitotic chromosomes in this range of species are condensed about 1.5-fold relative to interphase chromatin. In addition, we used two-photon microscopy to reveal that chromatin reorganization in interphase human hepatoma cells infected by the hepatitis C virus is decondensed compared to uninfected cells, which correlates with the previously reported viral-induced changes in chromatin dynamics. This work demonstrates the power of two-photon microscopy to analyze chromatin in a broad range of cell types and conditions, including non-model single-cell eukaryotes. We suggest that similar condensation levels are an evolutionarily conserved property in unicellular eukaryotes and important for proper chromosome segregation. Furthermore, this provides new insights into the process of chromatin condensation during mitosis in unicellular organisms as well as the response of human cells to viral infection.
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8
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Choudhary K, Itzkovich Z, Alonso-Perez E, Bishara H, Dunn B, Sherlock G, Kupiec M. S. cerevisiae Cells Can Grow without the Pds5 Cohesin Subunit. mBio 2022; 13:e0142022. [PMID: 35708277 PMCID: PMC9426526 DOI: 10.1128/mbio.01420-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/31/2022] [Indexed: 12/11/2022] Open
Abstract
During DNA replication, the newly created sister chromatids are held together until their separation at anaphase. The cohesin complex is in charge of creating and maintaining sister chromatid cohesion (SCC) in all eukaryotes. In Saccharomyces cerevisiae cells, cohesin is composed of two elongated proteins, Smc1 and Smc3, bridged by the kleisin Mcd1/Scc1. The latter also acts as a scaffold for three additional proteins, Scc3/Irr1, Wpl1/Rad61, and Pds5. Although the HEAT-repeat protein Pds5 is essential for cohesion, its precise function is still debated. Deletion of the ELG1 gene, encoding a PCNA unloader, can partially suppress the temperature-sensitive pds5-1 allele, but not a complete deletion of PDS5. We carried out a genetic screen for high-copy-number suppressors and another for spontaneously arising mutants, allowing the survival of a pds5Δ elg1Δ strain. Our results show that cells remain viable in the absence of Pds5 provided that there is both an elevation in the level of Mcd1 (which can be due to mutations in the CLN2 gene, encoding a G1 cyclin), and an increase in the level of SUMO-modified PCNA on chromatin (caused by lack of PCNA unloading in elg1Δ mutants). The elevated SUMO-PCNA levels increase the recruitment of the Srs2 helicase, which evicts Rad51 molecules from the moving fork, creating single-stranded DNA (ssDNA) regions that serve as sites for increased cohesin loading and SCC establishment. Thus, our results delineate a double role for Pds5 in protecting the cohesin ring and interacting with the DNA replication machinery. IMPORTANCE Sister chromatid cohesion is vital for faithful chromosome segregation, chromosome folding into loops, and gene expression. A multisubunit protein complex known as cohesin holds the sister chromatids from S phase until the anaphase stage. In this study, we explore the function of the essential cohesin subunit Pds5 in the regulation of sister chromatid cohesion. We performed two independent genetic screens to bypass the function of the Pds5 protein. We observe that Pds5 protein is a cohesin stabilizer, and elevating the levels of Mcd1 protein along with SUMO-PCNA accumulation on chromatin can compensate for the loss of the PDS5 gene. In addition, Pds5 plays a role in coordinating the DNA replication and sister chromatid cohesion establishment. This work elucidates the function of cohesin subunit Pds5, the G1 cyclin Cln2, and replication factors PCNA, Elg1, and Srs2 in the proper regulation of sister chromatid cohesion.
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Affiliation(s)
- Karan Choudhary
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Ziv Itzkovich
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Elisa Alonso-Perez
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Hend Bishara
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Barbara Dunn
- Departments of Genetics, Stanford University, Stanford, California, USA
| | - Gavin Sherlock
- Departments of Genetics, Stanford University, Stanford, California, USA
| | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
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9
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Buskirk S, Skibbens RV. G1-Cyclin2 (Cln2) promotes chromosome hypercondensation in eco1/ctf7 rad61 null cells during hyperthermic stress in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2022; 12:6613937. [PMID: 35736360 PMCID: PMC9339302 DOI: 10.1093/g3journal/jkac157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022]
Abstract
Eco1/Ctf7 is a highly conserved acetyltransferase that activates cohesin complexes and is critical for sister chromatid cohesion, chromosome condensation, DNA damage repair, nucleolar integrity, and gene transcription. Mutations in the human homolog of ECO1 (ESCO2/EFO2), or in genes that encode cohesin subunits, result in severe developmental abnormalities and intellectual disabilities referred to as Roberts syndrome and Cornelia de Lange syndrome, respectively. In yeast, deletion of ECO1 results in cell inviability. Codeletion of RAD61 (WAPL in humans), however, produces viable yeast cells. These eco1 rad61 double mutants, however, exhibit a severe temperature-sensitive growth defect, suggesting that Eco1 or cohesins respond to hyperthermic stress through a mechanism that occurs independent of Rad61. Here, we report that deletion of the G1 cyclin CLN2 rescues the temperature-sensitive lethality otherwise exhibited by eco1 rad61 mutant cells, such that the triple mutant cells exhibit robust growth over a broad range of temperatures. While Cln1, Cln2, and Cln3 are functionally redundant G1 cyclins, neither CLN1 nor CLN3 deletions rescue the temperature-sensitive growth defects otherwise exhibited by eco1 rad61 double mutants. We further provide evidence that CLN2 deletion rescues hyperthermic growth defects independent of START and impacts the state of chromosome condensation. These findings reveal novel roles for Cln2 that are unique among the G1 cyclin family and appear critical for cohesin regulation during hyperthermic stress.
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Affiliation(s)
- Sean Buskirk
- Department of Biology, West Chester University, West Chester, PA 19383, USA
| | - Robert V Skibbens
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
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10
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Liu W, Padhi A, Zhang X, Narendran J, Anastasio MA, Nain AS, Irudayaraj J. Dynamic Heterochromatin States in Anisotropic Nuclei of Cells on Aligned Nanofibers. ACS NANO 2022; 16:10754-10767. [PMID: 35803582 PMCID: PMC9332347 DOI: 10.1021/acsnano.2c02660] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The cancer cell nucleus deforms as it invades the interstitial spaces in tissues and the tumor microenvironment. While alteration of the chromatin structure in a deformed nucleus is expected and documented, the chromatin structure in the nuclei of cells on aligned matrices has not been elucidated. In this work we elucidate the spatiotemporal organization of heterochromatin in the elongated nuclei of cells on aligned nanofibers with stimulated emission depletion nanoscopy and fluorescence correlation spectroscopy. We show that the anisotropy of nuclei is sufficient to drive H3K9me3-heterochromatin alterations, with enhanced H3K9me3 nanocluster compaction and aggregation states that otherwise are indistinguishable from diffraction-limited microscopy. We interrogated the higher-order heterochromatin structures within major chromatin compartments in anisotropic nuclei and discovered a wider spatial dispersion of nanodomain clusters in the nucleoplasm and condensed larger nanoclusters near the periphery and pericentromeric heterochromatin. Upon examining the spatiotemporal dynamics of heterochromatin in anisotropic nuclei, we observed reduced mobility of the constitutive heterochromatin mark H3K9me3 and the associated heterochromatin protein 1 (HP1α) at the nucleoplasm and periphery regions, correlating with increased viscosity and changes in gene expression. Since heterochromatin remodeling is crucial to genome integrity, our results reveal an unconventional H3K9me3 heterochromatin distribution, providing cues to an altered chromatin state due to perturbations of the nuclei in aligned fiber configurations.
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Affiliation(s)
- Wenjie Liu
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, 1102 Everitt Lab, 1406 W. Green Street, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Cancer Center at Illinois,
Micro and Nanotechnology Laboratory, Beckman
Institute, Carl Woese Institute for Genomic Biology, Urbana, Illinois 61801, United States
| | - Abinash Padhi
- Department
of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Xiaohui Zhang
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, 1102 Everitt Lab, 1406 W. Green Street, Urbana, Illinois 61801, United States
| | - Jairaj Narendran
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, 1102 Everitt Lab, 1406 W. Green Street, Urbana, Illinois 61801, United States
| | - Mark A. Anastasio
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, 1102 Everitt Lab, 1406 W. Green Street, Urbana, Illinois 61801, United States
| | - Amrinder S. Nain
- Department
of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Joseph Irudayaraj
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, 1102 Everitt Lab, 1406 W. Green Street, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Cancer Center at Illinois,
Micro and Nanotechnology Laboratory, Beckman
Institute, Carl Woese Institute for Genomic Biology, Urbana, Illinois 61801, United States
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11
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Liu W, Mohan SP, Nagaraj NR, Sundar Jaganathan S, Wen Y, Ramasubramanyan S, Irudayaraj J. Epigenetic alterations associated with dexamethasone sodium phosphate through DNMT and TET in RPE cells. Mol Vis 2021; 27:643-655. [PMID: 34924744 PMCID: PMC8645185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 11/18/2021] [Indexed: 11/29/2022] Open
Abstract
PURPOSE To elucidate the mechanism behind epigenetic alteration associated with dexamethasone (DEX) sodium phosphate treatment. METHODS We performed enzyme-linked immunosorbent assay to quantify changes in global DNA methylation and hydroxymethylation, quantitative real-time PCR (qRT-PCR) of the DNA methylation- and hydroxymethylation-related gene, in vitro DNA methyltransferase (DNMT) enzymatic activity assays with purified DNMTs, and DNA hydroxymethylation pattern with super-resolution imaging. RESULTS We identified global DNA hypomethylation and hyper-hydroxymethylation upon DEX treatment, associated with aberrant mRNA expression levels of DNMT and ten-eleven translocation (TET) proteins. Additionally, DEX exposure could directly hinder DNMT activities. CONCLUSIONS We showed that DEX-induced epigenetic alterations are linked to aberrant DNMT and TET expression, potentially through an essential role of DNMT.
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Affiliation(s)
- Wenjie Liu
- Department of Bioengineering, Cancer Center at Illinois, Micro and Nanotechnology Laboratory. University of Illinois at Urbana-Champaign, Urbana, IL,Biomedical Research Center in Mills Breast Cancer Institute, Carles Foundation Hospital, Urbana, IL
| | - Sruthi Priya Mohan
- R.S. Mehta Jain Department of Biochemistry and Cell Biology, KBIRVO, Vision Research Foundation, Chennai, TN, India
| | | | - Shyam Sundar Jaganathan
- R.S. Mehta Jain Department of Biochemistry and Cell Biology, KBIRVO, Vision Research Foundation, Chennai, TN, India
| | - Yi Wen
- Department of Bioengineering, Cancer Center at Illinois, Micro and Nanotechnology Laboratory. University of Illinois at Urbana-Champaign, Urbana, IL,Biomedical Research Center in Mills Breast Cancer Institute, Carles Foundation Hospital, Urbana, IL
| | - Sharada Ramasubramanyan
- R.S. Mehta Jain Department of Biochemistry and Cell Biology, KBIRVO, Vision Research Foundation, Chennai, TN, India
| | - Joseph Irudayaraj
- Department of Bioengineering, Cancer Center at Illinois, Micro and Nanotechnology Laboratory. University of Illinois at Urbana-Champaign, Urbana, IL,Biomedical Research Center in Mills Breast Cancer Institute, Carles Foundation Hospital, Urbana, IL
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12
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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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13
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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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14
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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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15
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Zuilkoski CM, Skibbens RV. PCNA promotes context-specific sister chromatid cohesion establishment separate from that of chromatin condensation. Cell Cycle 2020; 19:2436-2450. [PMID: 32926661 PMCID: PMC7553509 DOI: 10.1080/15384101.2020.1804221] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/08/2020] [Accepted: 07/24/2020] [Indexed: 10/23/2022] Open
Abstract
Cellular genomes undergo various structural changes that include cis tethering (the tethering together of two loci within a single DNA molecule), which promotes chromosome condensation and transcriptional activation, and trans tethering (the tethering together of two DNA molecules), which promotes sister chromatid cohesion and DNA repair. The protein complex termed cohesin promotes both cis and trans forms of DNA tethering, but the extent to which these cohesin functions occur in temporally or spatially defined contexts remains largely unknown. Prior studies indicate that DNA polymerase sliding clamp PCNA recruits cohesin acetyltransferase Eco1, suggesting that sister chromatid cohesion is established in the context of the DNA replication fork. In support of this model, elevated levels of PCNA rescue the temperature growth and cohesion defects exhibited by eco1 mutant cells. Here, we test whether Eco1-dependent chromatin condensation is also promoted in the context of this DNA replication fork component. Our results reveal that overexpressed PCNA does not promote DNA condensation in eco1 mutant cells, even though Smc3 acetylation levels are increased. We further provide evidence that replication fork-associated E3 ligase impacts on Eco1 are more complex that previously described. In combination, the data suggests that Eco1 acetylates Smc3 and thus promotes sister chromatid cohesion in context of the DNA replication fork, whereas a distinct cohesin population participates in chromatin condensation outside the context of the DNA replication fork.
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Affiliation(s)
- Caitlin M. Zuilkoski
- Department of Biological Sciences, Lehigh University, 18015, Bethlehem, Pennsylvania, USA
| | - Robert V. Skibbens
- Department of Biological Sciences, Lehigh University, 18015, Bethlehem, Pennsylvania, USA
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16
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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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17
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Copper mediates mitochondrial biogenesis in retinal pigment epithelial cells. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165843. [PMID: 32454166 DOI: 10.1016/j.bbadis.2020.165843] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/29/2020] [Accepted: 05/19/2020] [Indexed: 11/22/2022]
Abstract
Age related macular degeneration (AMD) is a multifactorial disease with genetic, biochemical and environmental risk factors. We observed a significant increase in copper levels in choroid-RPE from donor eyeballs with AMD. Adult retinal pigment epithelial cells (ARPE19 cells) exposed to copper in-vitro showed a 2-fold increase in copper influx transporter CTR1 and copper uptake at 50 μM concentration. Further there was 2-fold increase in cytochrome C oxidase activity and a 2-fold increase in the mRNA expression of NRF 2 with copper treatment. There was a significant increase in mitochondrial biogenesis markers PGC1β and TFAM which was confirmed by mitochondrial mass and copy number. On the contrary, in AMD choroid-RPE, the CTR1 mRNA was found to be significantly down-regulated compared to its respective controls. SCO1 and PGC1β mRNA showed an increase in choroid-RPE. Our study proposes copper to play an important role in mitochondrial biogenesis in RPE cells.
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18
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Liu W, Irudayaraj J. Perfluorooctanoic acid (PFOA) exposure inhibits DNA methyltransferase activities and alters constitutive heterochromatin organization. Food Chem Toxicol 2020; 141:111358. [PMID: 32315686 DOI: 10.1016/j.fct.2020.111358] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 03/13/2020] [Accepted: 04/12/2020] [Indexed: 12/20/2022]
Abstract
Perfluorooctanoic acid (PFOA) is a persistent and widespread industry-made chemical. Emerging evidence indicates that PFOA exposure could be meditated through DNA methylation, yet, the molecular mechanisms governing the epigenetic states have not been well established. In this study, we investigated the epigenetic alterations and inhibitory mechanisms upon PFOA exposure by identifying changes related to DNA methyltransferase (DNMT) with fluorescence correlation spectroscopy and stimulated emission depletion nanoscopy in human breast epithelial cells (MCF7). PFOA exposure at 100 and 200 μM altered the mobility of DNMT3A and inhibited the enzymatic activity of DNMT, resulting in global DNA demethylation. Moreover, PFOA significantly altered the heterochromatin organization, as noted by the distribution profile of histone 3 lysine 9 tri-methylation (H3K9me3) at 200 and 400 μM exposure levels with super-resolution microscopy. An increased redistribution around the periphery of the nucleus was noted with a more diffused distribution beyond the 200 μM exposure. Overall, exposure of PFOA resulted in DNA demethylation accompanied by altered expression patterns of DNMT1 and DNMT3A. These findings provided new insights on the epigenetic alterations and revealed an altered heterochromatin packaging upon exposure to PFOA, implicating a mechanistic mode of action of DNA demethylation through direct impacts on DNMTs and increasing susceptibility to diseases such as cancer.
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Affiliation(s)
- Wenjie Liu
- Department of Bioengineering, Cancer Center at Illinois, Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Biomedical Research Center in Mills Breast Cancer Institute, Carles Foundation Hospital, Urbana, IL, 61801, USA
| | - Joseph Irudayaraj
- Department of Bioengineering, Cancer Center at Illinois, Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Biomedical Research Center in Mills Breast Cancer Institute, Carles Foundation Hospital, Urbana, IL, 61801, USA.
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