51
|
Murayama Y, Samora CP, Kurokawa Y, Iwasaki H, Uhlmann F. Establishment of DNA-DNA Interactions by the Cohesin Ring. Cell 2018; 172:465-477.e15. [PMID: 29358048 PMCID: PMC5786502 DOI: 10.1016/j.cell.2017.12.021] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 10/12/2017] [Accepted: 12/16/2017] [Indexed: 01/14/2023]
Abstract
The ring-shaped structural maintenance of chromosome (SMC) complexes are multi-subunit ATPases that topologically encircle DNA. SMC rings make vital contributions to numerous chromosomal functions, including mitotic chromosome condensation, sister chromatid cohesion, DNA repair, and transcriptional regulation. They are thought to do so by establishing interactions between more than one DNA. Here, we demonstrate DNA-DNA tethering by the purified fission yeast cohesin complex. DNA-bound cohesin efficiently and topologically captures a second DNA, but only if that is single-stranded DNA (ssDNA). Like initial double-stranded DNA (dsDNA) embrace, second ssDNA capture is ATP-dependent, and it strictly requires the cohesin loader complex. Second-ssDNA capture is relatively labile but is converted into stable dsDNA-dsDNA cohesion through DNA synthesis. Our study illustrates second-DNA capture by an SMC complex and provides a molecular model for the establishment of sister chromatid cohesion.
Collapse
Affiliation(s)
- Yasuto Murayama
- Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
| | - Catarina P Samora
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Yumiko Kurokawa
- Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Hiroshi Iwasaki
- Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Frank Uhlmann
- Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan; Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| |
Collapse
|
52
|
Zawadzka K, Zawadzki P, Baker R, Rajasekar KV, Wagner F, Sherratt DJ, Arciszewska LK. MukB ATPases are regulated independently by the N- and C-terminal domains of MukF kleisin. eLife 2018; 7:31522. [PMID: 29323635 PMCID: PMC5812716 DOI: 10.7554/elife.31522] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/10/2018] [Indexed: 12/21/2022] Open
Abstract
The Escherichia coli SMC complex, MukBEF, acts in chromosome segregation. MukBEF shares the distinctive architecture of other SMC complexes, with one prominent difference; unlike other kleisins, MukF forms dimers through its N-terminal domain. We show that a 4-helix bundle adjacent to the MukF dimerisation domain interacts functionally with the MukB coiled-coiled ‘neck’ adjacent to the ATPase head. We propose that this interaction leads to an asymmetric tripartite complex, as in other SMC complexes. Since MukF dimerisation is preserved during this interaction, MukF directs the formation of dimer of dimer MukBEF complexes, observed previously in vivo. The MukF N- and C-terminal domains stimulate MukB ATPase independently and additively. We demonstrate that impairment of the MukF interaction with MukB in vivo leads to ATP hydrolysis-dependent release of MukBEF complexes from chromosomes. Most DNA in a cell is arranged in structures called chromosomes. From bacteria to humans, chromosomes have to be compacted and highly organized to allow the cells to maintain and use their genetic information. In all organisms, large ring-shaped protein complexes play a crucial role in managing chromosomes. They transport and organize DNA thanks to reactions whose precise mechanism remains unknown. In bacteria, MukB and a type of kleisin called MukF are two examples of molecules involved in chromosome management. Two MukBs join at one end to form a hinge; at the other end, each MukB protein has a neck and a head. The two heads are linked by the kleisin to form a large protein ring, which can open to capture DNA. The MukB heads can trigger a biochemical reaction that creates the energy essential to trap and release DNA during DNA transport. Here, Zawadzka et al. study how the different components of the MukB-kleisin complex interact with each other to undergo the biochemical reactions that lead to DNA transport. The experiments show that the kleisin joins two MukB heads by attaching the base of one to the neck of the other, asymmetrically closing the ring. The separate interactions of different regions of the kleisin to the head and neck of MukB independently activate the two MukB heads, thereby controlling essential steps in the reactions with DNA. Two MukB-kleisin ring complexes are joined to each other because of a tight interaction between the two kleisin molecules. This leads Zawadzka et al. to suggest that DNA is sequentially grabbed and released from these two rings during DNA transport, similar to how a climbing rope is attached and released through carabiners. Cells cannot survive or be healthy without their chromosomes being accurately managed. It is still unclear how molecules such as MukBs and kleinsins drive this process. A better picture of their structure and interactions is an essential first step to understand these mechanisms.
Collapse
Affiliation(s)
- Katarzyna Zawadzka
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Pawel Zawadzki
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Rachel Baker
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Florence Wagner
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - David J Sherratt
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | |
Collapse
|
53
|
Murayama Y. DNA entry, exit and second DNA capture by cohesin: insights from biochemical experiments. Nucleus 2018; 9:492-502. [PMID: 30205748 PMCID: PMC6244732 DOI: 10.1080/19491034.2018.1516486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/28/2018] [Accepted: 08/16/2018] [Indexed: 12/23/2022] Open
Abstract
Cohesin is a ring-shaped, multi-subunit ATPase assembly that is fundamental to the spatiotemporal organization of chromosomes. The ring establishes a variety of chromosomal structures including sister chromatid cohesion and chromatin loops. At the core of the ring is a pair of highly conserved SMC (Structural Maintenance of Chromosomes) proteins, which are closed by the flexible kleisin subunit. In common with other essential SMC complexes including condensin and the SMC5-6 complex, cohesin encircles DNA inside its cavity, with the aid of HEAT (Huntingtin, elongation factor 3, protein phosphatase 2A and TOR) repeat auxiliary proteins. Through this topological embrace, cohesin is thought to establish a series of intra- and interchromosomal interactions by tethering more than one DNA molecule. Recent progress in biochemical reconstitution of cohesin provides molecular insights into how this ring complex topologically binds and mediates DNA-DNA interactions. Here, I review these studies and discuss how cohesin mediates such chromosome interactions.
Collapse
Affiliation(s)
- Yasuto Murayama
- Chromosome Biochemistry Laboratory, Center for Frontier Research, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| |
Collapse
|
54
|
Abstract
Structural maintenance of chromosome (SMC) protein complexes, including cohesin and condensin, are increasingly being recognized for their important role in cancer and development, making it critical that we understand how these evolutionarily conserved multi-subunit protein complexes associate with and organize the genome. We review adaptor proteins for SMC complexes and how these adaptors may capture SMC complexes following loop extrusion to provide a framework for chromosome organization.
Collapse
Affiliation(s)
- Kobe C. Yuen
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Oncology Biomarker Development, Genentech, Inc., South San Francisco, California, United States of America
| | - Jennifer L. Gerton
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, Kansas, United States of America
- University of Kansas Cancer Center, Kansas City, Kansas, United States of America
| |
Collapse
|
55
|
Scheinost JC, Gligoris TG. Structurally Guided In Vivo Crosslinking. Methods Mol Biol 2018; 1764:123-132. [PMID: 29605912 DOI: 10.1007/978-1-4939-7759-8_8] [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] [Indexed: 12/17/2023]
Abstract
The focus of modern molecular biology on protein structure and function has reached unparalleled levels. Whether interacting with nucleic acids or other proteins, protein contacts are the basis for fine-tuning all cellular processes. It is for this reason imperative that protein interactions are studied in ways that reflect actual events taking place inside living cells.Here, we describe in detail a method that combines the residue-level resolution provided by structural biology with physiological studies inside living cells, with the overall goal of explaining the contribution of protein-protein interactions in cellular processes. We use as a powerful example our experience with the DNA exit gate interface of the chromosomal cohesin complex, and we argue that this methodology may be followed to address similar questions within any protein complex and in various model systems.
Collapse
|
56
|
Marston AL, Wassmann K. Multiple Duties for Spindle Assembly Checkpoint Kinases in Meiosis. Front Cell Dev Biol 2017; 5:109. [PMID: 29322045 PMCID: PMC5733479 DOI: 10.3389/fcell.2017.00109] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 11/28/2017] [Indexed: 11/17/2022] Open
Abstract
Cell division in mitosis and meiosis is governed by evolutionary highly conserved protein kinases and phosphatases, controlling the timely execution of key events such as nuclear envelope breakdown, spindle assembly, chromosome attachment to the spindle and chromosome segregation, and cell cycle exit. In mitosis, the spindle assembly checkpoint (SAC) controls the proper attachment to and alignment of chromosomes on the spindle. The SAC detects errors and induces a cell cycle arrest in metaphase, preventing chromatid separation. Once all chromosomes are properly attached, the SAC-dependent arrest is relieved and chromatids separate evenly into daughter cells. The signaling cascade leading to checkpoint arrest depends on several protein kinases that are conserved from yeast to man. In meiosis, haploid cells containing new genetic combinations are generated from a diploid cell through two specialized cell divisions. Though apparently less robust, SAC control also exists in meiosis. Recently, it has emerged that SAC kinases have additional roles in executing accurate chromosome segregation during the meiotic divisions. Here, we summarize the main differences between mitotic and meiotic cell divisions, and explain why meiotic divisions pose special challenges for correct chromosome segregation. The less-known meiotic roles of the SAC kinases are described, with a focus on two model systems: yeast and mouse oocytes. The meiotic roles of the canonical checkpoint kinases Bub1, Mps1, the pseudokinase BubR1 (Mad3), and Aurora B and C (Ipl1) will be discussed. Insights into the molecular signaling pathways that bring about the special chromosome segregation pattern during meiosis will help us understand why human oocytes are so frequently aneuploid.
Collapse
Affiliation(s)
- Adele L Marston
- Wellcome Centre for Cell Biology, Institute for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Katja Wassmann
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris Seine, UMR7622, Paris, France.,Centre National de la Recherche Scientifique, Institut de Biologie Paris Seine, UMR7622 Developmental Biology Lab, Paris, France
| |
Collapse
|
57
|
Eeftens J, Dekker C. Catching DNA with hoops—biophysical approaches to clarify the mechanism of SMC proteins. Nat Struct Mol Biol 2017; 24:1012-1020. [DOI: 10.1038/nsmb.3507] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/18/2017] [Indexed: 12/11/2022]
|
58
|
Liu Y, Su H, Liu Y, Zhang J, Dong Q, Birchler JA, Han F. Cohesion and centromere activity are required for phosphorylation of histone H3 in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:1121-1131. [PMID: 29032586 DOI: 10.1111/tpj.13748] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/03/2017] [Accepted: 10/10/2017] [Indexed: 05/03/2023]
Abstract
Haspin-mediated phosphorylation of histone H3 at threonine 3 (H3T3ph) promotes proper deposition of Aurora B at the inner centromere to ensure faithful chromosome segregation in metazoans. However, the function of H3T3ph remains relatively unexplored in plants. Here, we show that in maize (Zea mays L.) mitotic cells, H3T3ph is concentrated at pericentromeric and centromeric regions. Additional weak H3T3ph signals occur between cohered sister chromatids at prometaphase. Immunostaining on dicentric chromosomes reveals that an inactive centromere cannot maintain H3T3ph at metaphase, indicating that a functional centromere is required for H3T3 phosphorylation. H3T3ph locates at a newly formed centromeric region that lacks detectable CentC sequences and strongly reduced CRM and ZmBs repeat sequences at metaphase II. These results suggest that centromeric localization of H3T3ph is not dependent on centromeric sequences. In maize meiocytes, H3T3 phosphorylation occurs at the late diakinesis and extends to the entire chromosome at metaphase I, but is exclusively limited to the centromere at metaphase II. The H3T3ph signals are absent in the afd1 (absence of first division) and sgo1 (shugoshin) mutants during meiosis II when the sister chromatids exhibit random distribution. Further, we show that H3T3ph is mainly located at the pericentromere during meiotic prophase II but is restricted to the inner centromere at metaphase II. We propose that this relocation of H3T3ph depends on tension at the centromere and is required to promote bi-orientation of sister chromatids.
Collapse
Affiliation(s)
- Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Handong Su
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yalin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qianhua Dong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211-7400, USA
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| |
Collapse
|
59
|
Sarlós K, Biebricher A, Petermann EJG, Wuite GJL, Hickson ID. Knotty Problems during Mitosis: Mechanistic Insight into the Processing of Ultrafine DNA Bridges in Anaphase. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 82:187-195. [PMID: 29167280 DOI: 10.1101/sqb.2017.82.033647] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
To survive and proliferate, cells have to faithfully segregate their newly replicated genomic DNA to the two daughter cells. However, the sister chromatids of mitotic chromosomes are frequently interlinked by so-called ultrafine DNA bridges (UFBs) that are visible in the anaphase of mitosis. UFBs can only be detected by the proteins bound to them and not by staining with conventional DNA dyes. These DNA bridges are presumed to represent entangled sister chromatids and hence pose a threat to faithful segregation. A failure to accurately unlink UFB DNA results in chromosome segregation errors and binucleation. This, in turn, compromises genome integrity, which is a hallmark of cancer. UFBs are actively removed during anaphase, and most known UFB-associated proteins are enzymes involved in DNA repair in interphase. However, little is known about the mitotic activities of these enzymes or the exact DNA structures present on UFBs. We focus on the biology of UFBs, with special emphasis on their underlying DNA structure and the decatenation machineries that process UFBs.
Collapse
Affiliation(s)
- Kata Sarlós
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Andreas Biebricher
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Erwin J G Petermann
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
| |
Collapse
|
60
|
Zhang J, Han F. Centromere pairing precedes meiotic chromosome pairing in plants. SCIENCE CHINA. LIFE SCIENCES 2017; 60:1197-1202. [PMID: 28755295 DOI: 10.1007/s11427-017-9109-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/02/2017] [Indexed: 10/19/2022]
Abstract
Meiosis is a specialized eukaryotic cell division, in which diploid cells undergo a single round of DNA replication and two rounds of nuclear division to produce haploid gametes. In most eukaryotes, the core events of meiotic prophase I are chromosomal pairing, synapsis and recombination. To ensure accurate chromosomal segregation, homologs have to identify and align along each other at the onset of meiosis. Although much progress has been made in elucidating meiotic processes, information on the mechanisms underlying chromosome pairing is limited in contrast to the meiotic recombination and synapsis events. Recent research in many organisms indicated that centromere interactions during early meiotic prophase facilitate homologous chromosome pairing, and functional centromere is a prerequisite for centromere pairing such as in maize. Here, we summarize the recent achievements of chromosome pairing research on plants and other organisms, and outline centromere interactions, nuclear chromosome orientation, and meiotic cohesin, as main determinants of chromosome pairing in early meiotic prophase.
Collapse
Affiliation(s)
- Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
61
|
Zhang W, Yeung CHL, Wu L, Yuen KWY. E3 ubiquitin ligase Bre1 couples sister chromatid cohesion establishment to DNA replication in Saccharomyces cerevisiae. eLife 2017; 6:28231. [PMID: 29058668 PMCID: PMC5699866 DOI: 10.7554/elife.28231] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 10/22/2017] [Indexed: 12/12/2022] Open
Abstract
Bre1, a conserved E3 ubiquitin ligase in Saccharomyces cerevisiae, together with its interacting partner Lge1, are responsible for histone H2B monoubiquitination, which regulates transcription, DNA replication, and DNA damage response and repair, ensuring the structural integrity of the genome. Deletion of BRE1 or LGE1 also results in whole chromosome instability. We discovered a novel role for Bre1, Lge1 and H2Bub1 in chromosome segregation and sister chromatid cohesion. Bre1’s function in G1 and S phases contributes to cohesion establishment, but it is not required for cohesion maintenance in G2 phase. Bre1 is dispensable for the loading of cohesin complex to chromatin in G1, but regulates the localization of replication factor Mcm10 and cohesion establishment factors Ctf4, Ctf18 and Eco1 to early replication origins in G1 and S phases, and promotes cohesin subunit Smc3 acetylation for cohesion stabilization. H2Bub1 epigenetically marks the origins, potentially signaling the coupling of DNA replication and cohesion establishment. Most of the DNA in a cell is stored in structures called chromosomes. During every cell cycle, each cell needs to replicate its chromosomes, hold the two chromosome copies (also known as “sister chromatids”) together before cell division, and distribute them equally to the two new cells. Each step must be executed accurately otherwise the new cells will have extra or missing chromosomes – a condition that is seen in many cancer cells and that can cause embryos to die. Since these processes are so essential to life, they are highly similar in a range of species, from single-celled organisms such as yeast to multicellular organisms like humans. However, it was not clear when and how sister chromatids first join together, or how this process is linked to DNA replication. The DNA in the sister chromatids is wrapped around proteins called histones to form a structure known as chromatin. An enzyme called Bre1 plays roles in gene transcription and DNA replication and repair by adding ubiquitin molecules to a histone called H2B. Now, by using genetic, molecular and cell biological approaches to study baker and brewer yeast cells, Zhang et al. show that the activity of Bre1 helps to hold sister chromatids together. Specifically, Bre1 recruits proteins to the chromatin before and during DNA replication, which help to initiate replication and to establish cohesion between the sister chromatids. The ubiquitin molecule attached to H2B by Bre1 is also essential for establishing cohesion, acting as a mark that helps to link the two processes. In the future it will be worthwhile to investigate whether genetic mutations that prevent sister chromatids adhering to each other is a major cause of the chromosome abnormalities seen in cancer cells. This knowledge may be useful for diagnosing cancers. Drugs that prevent the activity of Bre1 and other proteins involved in holding together sister chromatids could also be developed as potential cancer treatments that kill cancer cells by causing instability in their number of chromosomes.
Collapse
Affiliation(s)
- Wei Zhang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | | | - Liwen Wu
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Karen Wing Yee Yuen
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| |
Collapse
|
62
|
Zhang W, Yeung CHL, Wu L, Yuen KWY. E3 ubiquitin ligase Bre1 couples sister chromatid cohesion establishment to DNA replication in Saccharomyces cerevisiae. eLife 2017; 6:28231. [PMID: 29058668 DOI: 10.7554/elife.28231.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 10/22/2017] [Indexed: 05/25/2023] Open
Abstract
Bre1, a conserved E3 ubiquitin ligase in Saccharomyces cerevisiae, together with its interacting partner Lge1, are responsible for histone H2B monoubiquitination, which regulates transcription, DNA replication, and DNA damage response and repair, ensuring the structural integrity of the genome. Deletion of BRE1 or LGE1 also results in whole chromosome instability. We discovered a novel role for Bre1, Lge1 and H2Bub1 in chromosome segregation and sister chromatid cohesion. Bre1's function in G1 and S phases contributes to cohesion establishment, but it is not required for cohesion maintenance in G2 phase. Bre1 is dispensable for the loading of cohesin complex to chromatin in G1, but regulates the localization of replication factor Mcm10 and cohesion establishment factors Ctf4, Ctf18 and Eco1 to early replication origins in G1 and S phases, and promotes cohesin subunit Smc3 acetylation for cohesion stabilization. H2Bub1 epigenetically marks the origins, potentially signaling the coupling of DNA replication and cohesion establishment.
Collapse
Affiliation(s)
- Wei Zhang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | | | - Liwen Wu
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Karen Wing Yee Yuen
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| |
Collapse
|
63
|
Fazio G, Bettini LR, Rigamonti S, Meta D, Biondi A, Cazzaniga G, Selicorni A, Massa V. Impairment of Retinoic Acid Signaling in Cornelia de Lange Syndrome Fibroblasts. Birth Defects Res 2017; 109:1268-1276. [PMID: 28752682 DOI: 10.1002/bdr2.1070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 05/12/2017] [Accepted: 05/24/2017] [Indexed: 12/16/2023]
Abstract
BACKGROUND Cornelia de Lange syndrome (CdLS) is a rare genetic disorder affecting the neurodevelopment, gastrointestinal, musculoskeletal systems. CdLS is caused by mutations within NIPBL, SMC1A, SMC3, RAD21, and HDAC8 genes. These genes codify for the "cohesin complex" playing a role in chromatid adhesion, DNA repair and gene expression regulation. The aim of this study was to investigate retinoic acid (RA) signaling pathway, a master developmental regulator, in CdLS cells. METHODS Skin biopsies from CdLS patients and healthy controls were cultured and derived primary fibroblast cells were treated with RA or dimethyl sulfoxide (vehicle). After RA treatment, cells were harvested and RNA was isolated for quantitative real-time polymerase chain reaction experiments. RESULTS We analyzed several components of RA metabolism in a human cell line of kidney fibroblasts (293T), in addition to fibroblasts collected from both NIPBL-mutated patients and healthy donors, with or without RA treatment. In all cases, ADH and RALDH1 gene expression was not affected by RA treatment, while CRABP1 was induced. CRABP2 was dramatically upregulated upon RA treatment in healthy donors but not in CdLS patients cells. CONCLUSION We investigated if CdLS alterations are associated to perturbation of RA signaling. Cells derived from CdLS patients do not respond to RA signaling as efficiently as healthy controls. RA pathway alterations suggest a possible underlying mechanism for several cellular and developmental abnormalities associated with cohesin function. Birth Defects Research 109:1268-1276, 2017. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Grazia Fazio
- Centro Ricerca M. Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Laura Rachele Bettini
- Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Silvia Rigamonti
- Università degli Studi di Milano, Dipartimento di Scienze della Salute, Milan, Italy
| | - Dorela Meta
- Centro Ricerca M. Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
- Istituto Auxologico Italiano, Cusano Milanino, Italy
| | - Andrea Biondi
- Centro Ricerca M. Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
- Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Giovanni Cazzaniga
- Centro Ricerca M. Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Angelo Selicorni
- Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
- Department of Pediatrics, Presidio S. Fermo, ASST Lariana, Como, Italy
| | - Valentina Massa
- Università degli Studi di Milano, Dipartimento di Scienze della Salute, Milan, Italy
| |
Collapse
|
64
|
Lin SJ, O'Connell MJ. DNA Topoisomerase II modulates acetyl-regulation of cohesin-mediated chromosome dynamics. Curr Genet 2017; 63:923-930. [PMID: 28382430 PMCID: PMC5628089 DOI: 10.1007/s00294-017-0691-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 03/29/2017] [Accepted: 03/30/2017] [Indexed: 10/19/2022]
Abstract
Cohesin is one of three multi-protein structural maintenance of chromosome (SMC) complexes that regulate eukaryotic chromosome dynamics. It forms a ring-shaped structure that embraces sister chromatids through interphase to promote their pairing. In preparation for mitosis, most cohesin is stripped from the chromosome arms in prophase by a poorly defined process that is associated with cohesin phosphorylation. In the fission yeast Schizosaccharomyces pombe this prophase pathway is dependent on the cohesin-related Smc5/6 complex, and this requirement is heightened in Smc5/6 hypomorphs by DNA damage, replication stress and Topoisomerase II (Top2) dysfunction. Cohesin interacts with chromosomes immediately upon mitotic exit and becomes cohesive coincident with DNA replication. Cohesiveness is promoted by acetylation of the Smc3 subunit by an acetyltransferase, known as Eso1 in the S. pombe, which counteracts the anti-cohesive function(s) of the cohesin regulators Pds5 and Wpl1. We recently showed that Eso1 and Smc5/6 antagonize each other, and concurrent inactivation restores sister chromatid separation following genotoxic stress. Here, we have investigated the relationship between Top2 and Eso1 in successful completion of mitosis. We observe that partial inactivation of both results in a synthetic lethal mitotic block, but this is not overcome by deleting pds5 or wpl1. However, analysis of both acetyl-blocking and mimetic mutations in Smc3 indicates that the cycling of cohesin acetyl-regulation is more important than acetyl-status per se, highlighting the non-linear nature of the cohesin cycle.
Collapse
Affiliation(s)
- Su-Jiun Lin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA
| | - Matthew J O'Connell
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA.
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
65
|
Brackley CA, Johnson J, Michieletto D, Morozov AN, Nicodemi M, Cook PR, Marenduzzo D. Nonequilibrium Chromosome Looping via Molecular Slip Links. PHYSICAL REVIEW LETTERS 2017; 119:138101. [PMID: 29341686 DOI: 10.1103/physrevlett.119.138101] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Indexed: 06/07/2023]
Abstract
We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of molecules like cohesin, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred "loading site." This emergent collective behavior favors the extrusion of loops which are much larger than the ones formed by single slip links.
Collapse
Affiliation(s)
- C A Brackley
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - J Johnson
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - D Michieletto
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - A N Morozov
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - M Nicodemi
- Dipartimento di Fisica, Universita' di Napoli Federico II, INFN Napoli, CNR, SPIN, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - P R Cook
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - D Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| |
Collapse
|
66
|
Hinshaw SM, Makrantoni V, Harrison SC, Marston AL. The Kinetochore Receptor for the Cohesin Loading Complex. Cell 2017; 171:72-84.e13. [PMID: 28938124 PMCID: PMC5610175 DOI: 10.1016/j.cell.2017.08.017] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 05/03/2017] [Accepted: 08/09/2017] [Indexed: 12/29/2022]
Abstract
The ring-shaped cohesin complex brings together distant DNA domains to maintain, express, and segregate the genome. Establishing specific chromosomal linkages depends on cohesin recruitment to defined loci. One such locus is the budding yeast centromere, which is a paradigm for targeted cohesin loading. The kinetochore, a multiprotein complex that connects centromeres to microtubules, drives the recruitment of high levels of cohesin to link sister chromatids together. We have exploited this system to determine the mechanism of specific cohesin recruitment. We show that phosphorylation of the Ctf19 kinetochore protein by a conserved kinase, DDK, provides a binding site for the Scc2/4 cohesin loading complex, thereby directing cohesin loading to centromeres. A similar mechanism targets cohesin to chromosomes in vertebrates. These findings represent a complete molecular description of targeted cohesin loading, a phenomenon with wide-ranging importance in chromosome segregation and, in multicellular organisms, transcription regulation.
Collapse
Affiliation(s)
- Stephen M Hinshaw
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Vasso Makrantoni
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Stephen C Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Adèle L Marston
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
| |
Collapse
|
67
|
Norton HK, Phillips-Cremins JE. Crossed wires: 3D genome misfolding in human disease. J Cell Biol 2017; 216:3441-3452. [PMID: 28855250 PMCID: PMC5674879 DOI: 10.1083/jcb.201611001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 06/09/2017] [Accepted: 08/16/2017] [Indexed: 12/13/2022] Open
Abstract
Norton and Phillips-Cremins review the 3D architecture of the genome and discuss links between chromatin misfolding and human diseases. Mammalian genomes are folded into unique topological structures that undergo precise spatiotemporal restructuring during healthy development. Here, we highlight recent advances in our understanding of how the genome folds inside the 3D nucleus and how these folding patterns are miswired during the onset and progression of mammalian disease states. We discuss potential mechanisms underlying the link among genome misfolding, genome dysregulation, and aberrant cellular phenotypes. We also discuss cases in which the endogenous 3D genome configurations in healthy cells might be particularly susceptible to mutation or translocation. Together, these data support an emerging model in which genome folding and misfolding is critically linked to the onset and progression of a broad range of human diseases.
Collapse
Affiliation(s)
- Heidi K Norton
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
| | - Jennifer E Phillips-Cremins
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA .,Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| |
Collapse
|
68
|
Fujita Y, Yamashita T. Spatial organization of genome architecture in neuronal development and disease. Neurochem Int 2017; 119:49-56. [PMID: 28757389 DOI: 10.1016/j.neuint.2017.06.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 06/19/2017] [Accepted: 06/26/2017] [Indexed: 01/19/2023]
Abstract
Although mammalian genomes encode genetic information in their linear sequences, their fundamental function with regard to gene expression depends on the higher-order structure of chromosomes. Current techniques for the evaluation of chromosomal structure have revealed that genomes are arranged at several hierarchical levels in three-dimensional space. The spatial organization of genomes involves the formation of chromatin loops that bypass a wide range of genomic distances, providing a connection between enhancers and chromosomal domains. Furthermore, they form chromatin domains that are arranged into chromosome territories in the three-dimensional space of the cell nucleus. Recent studies have shown that the spatial organization of the genome is essential for normal brain development and function. Activity-dependent alterations in the spatial organization of the genome can regulate transcriptional activity related to neuronal plasticity. Disruptions in the higher-order chromatin architecture have been implicated in neuropsychiatric disorders, such as cognitive dysfunction and anxiety. Here, we discuss the growing interest in the role of genome organization in brain development and neurological disorders.
Collapse
Affiliation(s)
- Yuki Fujita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Toshihide Yamashita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Frontier Biosciences, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
69
|
Cheng JM, Liu YX. Age-Related Loss of Cohesion: Causes and Effects. Int J Mol Sci 2017; 18:E1578. [PMID: 28737671 PMCID: PMC5536066 DOI: 10.3390/ijms18071578] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 12/25/2022] Open
Abstract
Aneuploidy is a leading genetic cause of birth defects and lower implantation rates in humans. Most errors in chromosome number originate from oocytes. Aneuploidy in oocytes increases with advanced maternal age. Recent studies support the hypothesis that cohesion deterioration with advanced maternal age represents a leading cause of age-related aneuploidy. Cohesin generates cohesion, and is established only during the premeiotic S phase of fetal development without any replenishment throughout a female's period of fertility. Cohesion holds sister chromatids together until meiosis resumes at puberty, and then chromosome segregation requires the release of sister chromatid cohesion from chromosome arms and centromeres at anaphase I and anaphase II, respectively. The time of cohesion cleavage plays an important role in correct chromosome segregation. This review focuses specifically on the causes and effects of age-related cohesion deterioration in female meiosis.
Collapse
Affiliation(s)
- Jin-Mei Cheng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong 226001, China.
| | - Yi-Xun Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|
70
|
Maternal age-dependent APC/C-mediated decrease in securin causes premature sister chromatid separation in meiosis II. Nat Commun 2017; 8:15346. [PMID: 28516917 PMCID: PMC5454377 DOI: 10.1038/ncomms15346] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 03/21/2017] [Indexed: 12/27/2022] Open
Abstract
Sister chromatid attachment during meiosis II (MII) is maintained by securin-mediated inhibition of separase. In maternal ageing, oocytes show increased inter-sister kinetochore distance and premature sister chromatid separation (PSCS), suggesting aberrant separase activity. Here, we find that MII oocytes from aged mice have less securin than oocytes from young mice and that this reduction is mediated by increased destruction by the anaphase promoting complex/cyclosome (APC/C) during meiosis I (MI) exit. Inhibition of the spindle assembly checkpoint (SAC) kinase, Mps1, during MI exit in young oocytes replicates this phenotype. Further, over-expression of securin or Mps1 protects against the age-related increase in inter-sister kinetochore distance and PSCS. These findings show that maternal ageing compromises the oocyte SAC–APC/C axis leading to a decrease in securin that ultimately causes sister chromatid cohesion loss. Manipulating this axis and/or increasing securin may provide novel therapeutic approaches to alleviating the risk of oocyte aneuploidy in maternal ageing. Sister chromatid cohesion during meiosis II (MII), maintained by securin-mediated inhibition of separase, is reduced in aged mouse oocytes. Here the authors show that, in MII oocytes, securin levels are reduced by increased destruction by the anaphase promoting complex/cyclosome.
Collapse
|
71
|
Jonak K, Zagoriy I, Oz T, Graf P, Rojas J, Mengoli V, Zachariae W. APC/C-Cdc20 mediates deprotection of centromeric cohesin at meiosis II in yeast. Cell Cycle 2017; 16:1145-1152. [PMID: 28514186 DOI: 10.1080/15384101.2017.1320628] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Cells undergoing meiosis produce haploid gametes through one round of DNA replication followed by 2 rounds of chromosome segregation. This requires that cohesin complexes, which establish sister chromatid cohesion during S phase, are removed in a stepwise manner. At meiosis I, the separase protease triggers the segregation of homologous chromosomes by cleaving cohesin's Rec8 subunit on chromosome arms. Cohesin persists at centromeres because the PP2A phosphatase, recruited by the shugoshin protein, dephosphorylates Rec8 and thereby protects it from cleavage. While chromatids disjoin upon cleavage of centromeric Rec8 at meiosis II, it was unclear how and when centromeric Rec8 is liberated from its protector PP2A. One proposal is that bipolar spindle forces separate PP2A from Rec8 as cells enter metaphase II. We show here that sister centromere biorientation is not sufficient to "deprotect" Rec8 at meiosis II in yeast. Instead, our data suggest that the ubiquitin-ligase APC/CCdc20 removes PP2A from centromeres by targeting for degradation the shugoshin Sgo1 and the kinase Mps1. This implies that Rec8 remains protected until entry into anaphase II when it is phosphorylated concurrently with the activation of separase. Here, we provide further support for this model and speculate on its relevance to mammalian oocytes.
Collapse
Affiliation(s)
- Katarzyna Jonak
- a Laboratory of Chromosome Biology , Max Planck Institute of Biochemistry , Martinsried , Germany
| | - Ievgeniia Zagoriy
- a Laboratory of Chromosome Biology , Max Planck Institute of Biochemistry , Martinsried , Germany
| | - Tugce Oz
- a Laboratory of Chromosome Biology , Max Planck Institute of Biochemistry , Martinsried , Germany
| | - Peter Graf
- a Laboratory of Chromosome Biology , Max Planck Institute of Biochemistry , Martinsried , Germany
| | - Julie Rojas
- a Laboratory of Chromosome Biology , Max Planck Institute of Biochemistry , Martinsried , Germany
| | - Valentina Mengoli
- a Laboratory of Chromosome Biology , Max Planck Institute of Biochemistry , Martinsried , Germany
| | - Wolfgang Zachariae
- a Laboratory of Chromosome Biology , Max Planck Institute of Biochemistry , Martinsried , Germany
| |
Collapse
|
72
|
Fujita Y, Masuda K, Bando M, Nakato R, Katou Y, Tanaka T, Nakayama M, Takao K, Miyakawa T, Tanaka T, Ago Y, Hashimoto H, Shirahige K, Yamashita T. Decreased cohesin in the brain leads to defective synapse development and anxiety-related behavior. J Exp Med 2017; 214:1431-1452. [PMID: 28408410 PMCID: PMC5413336 DOI: 10.1084/jem.20161517] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/14/2017] [Accepted: 03/03/2017] [Indexed: 11/21/2022] Open
Abstract
Abnormal epigenetic regulation can cause the nervous system to develop abnormally. Here, we sought to understand the mechanism by which this occurs by investigating the protein complex cohesin, which is considered to regulate gene expression and, when defective, is associated with higher-level brain dysfunction and the developmental disorder Cornelia de Lange syndrome (CdLS). We generated conditional Smc3-knockout mice and observed greater dendritic complexity and larger numbers of immature synapses in the cerebral cortex of Smc3+/- mice. Smc3+/- mice also exhibited more anxiety-related behavior, which is a symptom of CdLS. Further, a gene ontology analysis after RNA-sequencing suggested the enrichment of immune processes, particularly the response to interferons, in the Smc3+/- mice. Indeed, fewer synapses formed in their cortical neurons, and this phenotype was rescued by STAT1 knockdown. Thus, low levels of cohesin expression in the developing brain lead to changes in gene expression that in turn lead to a specific and abnormal neuronal and behavioral phenotype.
Collapse
Affiliation(s)
- Yuki Fujita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Koji Masuda
- Research Center for Epigenetic Disease, Institute for Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Masashige Bando
- Research Center for Epigenetic Disease, Institute for Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Ryuichiro Nakato
- Research Center for Epigenetic Disease, Institute for Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Yuki Katou
- Research Center for Epigenetic Disease, Institute for Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Takashi Tanaka
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Masahiro Nakayama
- Department of Pathology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka 594-1101, Japan
| | - Keizo Takao
- Life Science Research Center, University of Toyama, Toyama 930-0194, Japan
| | - Tsuyoshi Miyakawa
- Life Science Research Center, University of Toyama, Toyama 930-0194, Japan
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Aichi 470-1192, Japan
| | - Tatsunori Tanaka
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Yukio Ago
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Hitoshi Hashimoto
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
- Division of Bioscience, Institute for Datability Science, Osaka University, Osaka 565-0871, Japan
- iPS Cell-based Research Project on Brain Neuropharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
- Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Osaka 565-0871, Japan
| | - Katsuhiko Shirahige
- Research Center for Epigenetic Disease, Institute for Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Toshihide Yamashita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| |
Collapse
|
73
|
Goto Y, Yamagishi Y, Shintomi-Kawamura M, Abe M, Tanno Y, Watanabe Y. Pds5 Regulates Sister-Chromatid Cohesion and Chromosome Bi-orientation through a Conserved Protein Interaction Module. Curr Biol 2017; 27:1005-1012. [PMID: 28343969 DOI: 10.1016/j.cub.2017.02.066] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/06/2017] [Accepted: 02/28/2017] [Indexed: 11/24/2022]
Abstract
Sister-chromatid cohesion is established by the cohesin complex in S phase and persists until metaphase, when sister chromatids are captured by microtubules emanating from opposite poles [1]. The Aurora-B-containing chromosome passenger complex (CPC) plays a crucial role in achieving chromosome bi-orientation by correcting erroneous microtubule attachment [2]. The centromeric localization of the CPC relies largely on histone H3-T3 phosphorylation (H3-pT3), which is mediated by the mitotic histone kinase Haspin/Hrk1 [3-5]. Hrk1 localization to centromeres depends largely on the cohesin subunit Pds5 in fission yeast [5]; however, it is unknown how Pds5 regulates Hrk1 localization. Here we identify a conserved Hrk1-interacting motif (HIM) in Pds5 and a Pds5-interacting motif (PIM) in Hrk1 in fission yeast. Mutations in either motif result in the displacement of Hrk1 from centromeres. We also show that the mechanism of Pds5-dependent Hrk1 recruitment is conserved in human cells. Notably, the PIM in Haspin/Hrk1 is reminiscent of the YSR motif found in the mammalian cohesin destabilizer Wapl and stabilizer Sororin, both of which bind PDS5 [6-12]. Similarly, and through the same motifs, fission yeast Pds5 binds to Wpl1/Wapl and acetyltransferase Eso1/Eco1, in addition to Hrk1. Thus, we have identified a protein-protein interaction module in Pds5 that serves as a chromatin platform for regulating sister-chromatid cohesion and chromosome bi-orientation.
Collapse
Affiliation(s)
- Yuhei Goto
- Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Tokyo 113-0032, Japan; Graduate Program in Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Yayoi, Tokyo 113-0032, Japan
| | - Yuya Yamagishi
- Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Tokyo 113-0032, Japan
| | - Miyuki Shintomi-Kawamura
- Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Tokyo 113-0032, Japan; Graduate Program in Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Yayoi, Tokyo 113-0032, Japan
| | - Mayumi Abe
- Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Tokyo 113-0032, Japan; Graduate Program in Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Yayoi, Tokyo 113-0032, Japan
| | - Yuji Tanno
- Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Tokyo 113-0032, Japan
| | - Yoshinori Watanabe
- Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Tokyo 113-0032, Japan; Graduate Program in Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Yayoi, Tokyo 113-0032, Japan.
| |
Collapse
|
74
|
Barrington C, Finn R, Hadjur S. Cohesin biology meets the loop extrusion model. Chromosome Res 2017; 25:51-60. [PMID: 28210885 PMCID: PMC5346154 DOI: 10.1007/s10577-017-9550-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 12/26/2016] [Accepted: 01/09/2017] [Indexed: 12/05/2022]
Abstract
Extensive research has revealed that cohesin acts as a topological device, trapping chromosomal DNA within a large tripartite ring. In so doing, cohesin contributes to the formation of compact and organized genomes. How exactly the cohesin subunits interact, how it opens, closes, and translocates on chromatin, and how it actually tethers DNA strands together are still being elucidated. A comprehensive understanding of these questions will shed light on how cohesin performs its many functions, including its recently proposed role as a chromatid loop extruder. Here, we discuss this possibility in light of our understanding of the molecular properties of cohesin complexes.
Collapse
Affiliation(s)
- Christopher Barrington
- Research Department of Cancer Biology, Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Ronald Finn
- Research Department of Cancer Biology, Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Suzana Hadjur
- Research Department of Cancer Biology, Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
| |
Collapse
|
75
|
Alt A, Dang HQ, Wells OS, Polo LM, Smith MA, McGregor GA, Welte T, Lehmann AR, Pearl LH, Murray JM, Oliver AW. Specialized interfaces of Smc5/6 control hinge stability and DNA association. Nat Commun 2017; 8:14011. [PMID: 28134253 PMCID: PMC5290277 DOI: 10.1038/ncomms14011] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/21/2016] [Indexed: 01/09/2023] Open
Abstract
The Structural Maintenance of Chromosomes (SMC) complexes: cohesin, condensin and Smc5/6 are involved in the organization of higher-order chromosome structure-which is essential for accurate chromosome duplication and segregation. Each complex is scaffolded by a specific SMC protein dimer (heterodimer in eukaryotes) held together via their hinge domains. Here we show that the Smc5/6-hinge, like those of cohesin and condensin, also forms a toroidal structure but with distinctive subunit interfaces absent from the other SMC complexes; an unusual 'molecular latch' and a functional 'hub'. Defined mutations in these interfaces cause severe phenotypic effects with sensitivity to DNA-damaging agents in fission yeast and reduced viability in human cells. We show that the Smc5/6-hinge complex binds preferentially to ssDNA and that this interaction is affected by both 'latch' and 'hub' mutations, suggesting a key role for these unique features in controlling DNA association by the Smc5/6 complex.
Collapse
Affiliation(s)
- Aaron Alt
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, BN1 9RQ, UK
| | - Hung Q. Dang
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Owen S. Wells
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Luis M. Polo
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, BN1 9RQ, UK
| | - Matt A. Smith
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Grant A. McGregor
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Thomas Welte
- Dynamic Biosensors GmbH, Lochhamer Strasse, D-81252 Martinsreid/Planegg, Germany
| | - Alan R. Lehmann
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Laurence H. Pearl
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, BN1 9RQ, UK
| | - Johanne M. Murray
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Antony W. Oliver
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, BN1 9RQ, UK
| |
Collapse
|
76
|
Kumar R. Separase: Function Beyond Cohesion Cleavage and an Emerging Oncogene. J Cell Biochem 2017; 118:1283-1299. [PMID: 27966791 DOI: 10.1002/jcb.25835] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 12/12/2016] [Indexed: 12/22/2022]
Abstract
Proper and timely segregation of genetic endowment is necessary for survival and perpetuation of every species. Mis-segregation of chromosomes and resulting aneuploidy leads to genetic instability, which can jeopardize the survival of an individual or population as a whole. Abnormality with segregation of genetic contents has been associated with several medical consequences including cancer, sterility, mental retardation, spontaneous abortion, miscarriages, and other birth related defects. Separase, by irreversible cleavage of cohesin complex subunit, paves the way for metaphase/anaphase transition during the cell cycle. Both over or reduced expression and altered level of separase have been associated with several medical consequences including cancer, as a result separase now emerges as an important oncogene and potential molecular target for medical intervenes. Recently, separase is also found to be essential in separation and duplication of centrioles. Here, I review the role of separase in mitosis, meiosis, non-canonical roles of separase, separase regulation, as a regulator of centriole disengagement, nonproteolytic roles, diverse substrates, structural insights, and association of separase with cancer. At the ends, I proposed a model which showed that separase is active throughout the cell cycle and there is a mere increase in separase activity during metaphase contrary to the common believes that separase is inactive throughout cell cycle except for metaphase. J. Cell. Biochem. 118: 1283-1299, 2017. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Ravinder Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400 076, Maharashtra, India
| |
Collapse
|
77
|
Kowalec P, Fronk J, Kurlandzka A. The Irr1/Scc3 protein implicated in chromosome segregation in Saccharomyces cerevisiae has a dual nuclear-cytoplasmic localization. Cell Div 2017; 12:1. [PMID: 28077952 PMCID: PMC5223379 DOI: 10.1186/s13008-016-0027-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/15/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Correct chromosome segregation depends on the sister chromatid cohesion complex. The essential, evolutionarily conserved regulatory protein Irr1/Scc3, is responsible for the complex loading onto DNA and for its removal. We found that, unexpectedly, Irr1 is present not only in the nucleus but also in the cytoplasm. RESULTS We show that Irr1 protein is enriched in the cytoplasm upon arrest of yeast cells in G1 phase following nitrogen starvation, diauxic shift or α-factor action, and also during normal cell cycle. Despite the presence of numerous Crm1-dependent export signals, the cytoplasmic pool of Irr1 is not derived through export from the nucleus but instead is simply retained in the cytoplasm. Cytoplasmic Irr1 interacts with the Imi1 protein implicated in glutathione homeostasis and mitochondrial integrity. CONCLUSIONS Besides regulation of the sister chromatid cohesion complex in the nucleus Irr1 appears to have an additional role in the cytoplasm, possibly through interaction with the cytoplasmic protein Imi1.
Collapse
Affiliation(s)
- Piotr Kowalec
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Jan Fronk
- Department of Molecular Biology, Faculty of Biology, Institute of Biochemistry, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Anna Kurlandzka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| |
Collapse
|
78
|
Zhang M, Dai X, Sun Y, Lu Y, Zhou C, Miao Y, Wang Y, Xiong B. Stag3 regulates microtubule stability to maintain euploidy during mouse oocyte meiotic maturation. Oncotarget 2017; 8:1593-1602. [PMID: 27906670 PMCID: PMC5352080 DOI: 10.18632/oncotarget.13684] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 11/12/2016] [Indexed: 12/31/2022] Open
Abstract
Stag3, a meiosis-specific subunit of cohesin complex, has been demonstrated to function in both male and female reproductive systems in mammals. However, its roles during oocyte meiotic maturation have not been fully defined. In the present study, we report that Stag3 uniquely accumulates on the spindle apparatus and colocalizes with microtubule fibers during mouse oocyte meiotic maturation. Depletion of Stag3 by gene-targeting morpholino disrupts normal spindle assembly and chromosome alignment in oocytes. We also find that depletion of Stag3 reduces the acetylated level of tubulin and microtubule resistance to microtubule depolymerizing drug, suggesting that Stag3 is required for microtubule stability. Consistent with these observations, kinetochore-microtubule attachment, an important mechanism controlling chromosome alignment, is severely impaired in Stag3-depleted oocytes, resultantly causing the significantly increased incidence of aneuploid eggs. Collectively, our data reveal that Stag3 is a novel regulator of microtubule dynamics to ensure euploidy during moue oocyte meiotic maturation.
Collapse
Affiliation(s)
- Mianqun Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoxin Dai
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yalu Sun
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yajuan Lu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Changyin Zhou
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yilong Miao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Wang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Bo Xiong
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
79
|
Abstract
The kollerin complex, consisting of Scc2/Scc4 in yeast and Nipbl/Mau2 in vertebrates, is crucial for the chromatin-association of the cohesin complex and therefore for the critical functions of cohesin in cell division, transcriptional regulation and chromatin organisation. Despite the recent efforts to determine the genomic localization of the kollerin complex in different cell lines, major questions still remain unresolved, for instance where cohesin is actually loaded onto chromatin. Further, Nipbl seems to have also additional roles, for instance as transcription factor.This chapter summarizes our current knowledge on kollerin function and the recent studies on the genomic localization of Scc2, highlighting and critically discussing controversial data.
Collapse
Affiliation(s)
- Kerstin S Wendt
- Department of Cell Biology, Erasmus MC, Faculty Building, Room Ee1020, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
| |
Collapse
|
80
|
Fan J, Jin H, Yu HG. A Dual-Color Reporter Assay of Cohesin-Mediated Gene Regulation in Budding Yeast Meiosis. Methods Mol Biol 2017; 1515:141-149. [PMID: 27797078 PMCID: PMC5551346 DOI: 10.1007/978-1-4939-6545-8_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
In this chapter, we describe a quantitative fluorescence-based assay of gene expression using the ratio of the reporter green fluorescence protein (GFP) to the internal red fluorescence protein (RFP) control. With this dual-color heterologous reporter assay, we have revealed cohesin-regulated genes and discovered a cis-acting DNA element, the Ty1-LTR, which interacts with cohesin and regulates gene expression during yeast meiosis. The method described here provides an effective cytological approach for quantitative analysis of global gene expression in budding yeast meiosis.
Collapse
Affiliation(s)
- Jinbo Fan
- Department of Biological Science, The Florida State University, Tallahassee, FL, 32306-4370, USA
| | - Hui Jin
- Department of Biological Science, The Florida State University, Tallahassee, FL, 32306-4370, USA
| | - Hong-Guo Yu
- Department of Biological Science, The Florida State University, Tallahassee, FL, 32306-4370, USA.
| |
Collapse
|
81
|
Abstract
During the cell cycle, duplicated sister chromatids become physically connected during S phase through a process called sister-chromatid cohesion. Cohesion is terminated during the metaphase-to-anaphase transition to trigger sister-chromatid segregation. The establishment and dissolution of cohesion are highly regulated by the cohesin complex and its multitude of regulators. In particular, the cohesin regulator Wapl promotes the release of cohesin from chromosomes during both interphase and mitosis. Here, we describe in vitro protein binding assays between Wapl and a cohesin subcomplex, and cellular assays in human cells that probe the functions of Wapl in cohesin release.
Collapse
Affiliation(s)
- Ge Zheng
- Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390, USA
| | - Zhuqing Ouyang
- Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390, USA
| | - Hongtao Yu
- Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390, USA.
| |
Collapse
|
82
|
Murayama Y, Uhlmann F. An In Vitro Assay for Monitoring Topological DNA Entrapment by the Chromosomal Cohesin Complex. Methods Mol Biol 2017; 1515:23-35. [PMID: 27797071 DOI: 10.1007/978-1-4939-6545-8_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The cohesin complex is involved in a broad range of chromosomal biology, including DNA repair, gene transcription as well as sister chromatid cohesion. Cohesin is a large, ring-shaped protein complex and is thought to entrap DNA molecules inside of its ring. The unique DNA association is central to cohesin function and requires its ATPase and another heterodimer complex called the cohesin loader. Here we describe the biochemical reconstitution of topological cohesin loading onto DNA using the purified fission yeast cohesin proteins.
Collapse
Affiliation(s)
- Yasuto Murayama
- Institute of Innovative Research, Tokyo Institute of Technology, M6-11, 2-12-1, Ookayama, Megro, Tokyo, 152-8550, Japan.
| | - Frank Uhlmann
- The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, UK
| |
Collapse
|
83
|
Lin SJ, Tapia-Alveal C, Jabado OJ, Germain D, O'Connell MJ. An acetyltransferase-independent function of Eso1 regulates centromere cohesion. Mol Biol Cell 2016; 27:4002-4010. [PMID: 27798241 PMCID: PMC5156541 DOI: 10.1091/mbc.e16-08-0596] [Citation(s) in RCA: 4] [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: 08/16/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 12/21/2022] Open
Abstract
Eukaryotes contain three essential Structural Maintenance of Chromosomes (SMC) complexes: cohesin, condensin, and Smc5/6. Cohesin forms a ring-shaped structure that embraces sister chromatids to promote their cohesion. The cohesiveness of cohesin is promoted by acetylation of N-terminal lysines of the Smc3 subunit by the acetyltransferases Eco1 in Saccharomyces cerevisiae and the homologue, Eso1, in Schizosaccharomyces pombe. In both yeasts, these acetyltransferases are essential for cell viability. However, whereas nonacetylatable Smc3 mutants are lethal in S. cerevisiae, they are not in S. pombe We show that the lethality of a temperature-sensitive allele of eso1 (eso1-H17) is due to activation of the spindle assembly checkpoint (SAC) and is associated with premature centromere separation. The lack of cohesion at the centromeres does not correlate with Psm3 acetylation or cohesin levels at the centromeres, but is associated ith significantly reduced recruitment of the cohesin regulator Pds5. The SAC activation in this context is dependent on Smc5/6 function, which is required to remove cohesin from chromosome arms but not centromeres. The mitotic defects caused by Smc5/6 and Eso1 dysfunction are cosuppressed in double mutants. This identifies a novel function (or functions) for Eso1 and Smc5/6 at centromeres and extends the functional relationships between these SMC complexes.
Collapse
Affiliation(s)
- Su-Jiun Lin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Claudia Tapia-Alveal
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Omar J Jabado
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Doris Germain
- Department of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Matthew J O'Connell
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| |
Collapse
|
84
|
Abstract
Cohesin is a large ring-shaped protein complex, conserved from yeast to human, which participates in most DNA transactions that take place in the nucleus. It mediates sister chromatid cohesion, which is essential for chromosome segregation and homologous recombination (HR)-mediated DNA repair. Together with architectural proteins and transcriptional regulators, such as CTCF and Mediator, respectively, it contributes to genome organization at different scales and thereby affects transcription, DNA replication, and locus rearrangement. Although cohesin is essential for cell viability, partial loss of function can affect these processes differently in distinct cell types. Mutations in genes encoding cohesin subunits and regulators of the complex have been identified in several cancers. Understanding the functional significance of these alterations may have relevant implications for patient classification, risk prediction, and choice of treatment. Moreover, identification of vulnerabilities in cancer cells harboring cohesin mutations may provide new therapeutic opportunities and guide the design of personalized treatments.
Collapse
Affiliation(s)
- Magali De Koninck
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid E-28029, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid E-28029, Spain
| |
Collapse
|
85
|
Liu YT, Chang KM, Ma CH, Jayaram M. Replication-dependent and independent mechanisms for the chromosome-coupled persistence of a selfish genome. Nucleic Acids Res 2016; 44:8302-23. [PMID: 27492289 PMCID: PMC5041486 DOI: 10.1093/nar/gkw694] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 07/26/2016] [Accepted: 07/27/2016] [Indexed: 12/21/2022] Open
Abstract
The yeast 2-micron plasmid epitomizes the evolutionary optimization of selfish extra-chromosomal genomes for stable persistence without jeopardizing their hosts' fitness. Analyses of fluorescence-tagged single-copy reporter plasmids and/or the plasmid partitioning proteins in native and non-native hosts reveal chromosome-hitchhiking as the likely means for plasmid segregation. The contribution of the partitioning system to equal segregation is bipartite- replication-independent and replication-dependent. The former nearly eliminates 'mother bias' (preferential plasmid retention in the mother cell) according to binomial distribution, thus limiting equal segregation of a plasmid pair to 50%. The latter enhances equal segregation of plasmid sisters beyond this level, elevating the plasmid close to chromosome status. Host factors involved in plasmid partitioning can be functionally separated by their participation in the replication-independent and/or replication-dependent steps. In the hitchhiking model, random tethering of a pair of plasmids to chromosomes signifies the replication-independent component of segregation; the symmetric tethering of plasmid sisters to sister chromatids embodies the replication-dependent component. The 2-micron circle broadly resembles the episomes of certain mammalian viruses in its chromosome-associated propagation. This unifying feature among otherwise widely differing selfish genomes suggests their evolutionary convergence to the common logic of exploiting, albeit via distinct molecular mechanisms, host chromosome segregation machineries for self-preservation.
Collapse
Affiliation(s)
- Yen-Ting Liu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Keng-Ming Chang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Chien-Hui Ma
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Makkuni Jayaram
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
86
|
Ma W, Schubert V, Martis MM, Hause G, Liu Z, Shen Y, Conrad U, Shi W, Scholz U, Taudien S, Cheng Z, Houben A. The distribution of α-kleisin during meiosis in the holocentromeric plant Luzula elegans. Chromosome Res 2016; 24:393-405. [PMID: 27294972 DOI: 10.1007/s10577-016-9529-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 05/03/2016] [Accepted: 05/05/2016] [Indexed: 11/25/2022]
Abstract
Holocentric chromosomes occur in a number of independent eukaryotic lineages, and they form holokinetic kinetochores along the entire poleward chromatid surfaces. Due to this alternative chromosome structure, Luzula elegans sister chromatids segregate already in anaphase I followed by the segregation of the homologues in anaphase II. However, not yet known is the localization and dynamics of cohesin and the structure of the synaptonemal complex (SC) during meiosis. We show here that the α-kleisin subunit of cohesin localizes at the centromeres of both mitotic and meiotic metaphase chromosomes and that it, thus, may contribute to assemble the centromere in L. elegans. This localization and the formation of a tripartite SC structure indicate that the prophase I behaviour of L. elegans is similar as in monocentric species.
Collapse
Affiliation(s)
- Wei Ma
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Mihaela Maria Martis
- Institute of Bioinformatics and Systems Biology/Munich Information Center for Protein Sequences, Helmholtz Center Munich, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Division of Cell Biology, Department of Clinical and Experimental Medicine, Bioinformatics Infrastructure for Life Sciences, Linköping University, 558185, Linköping, Sweden
| | - Gerd Hause
- Biocenter, Microscopy Unit, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120, Halle, Germany
| | - Zhaojun Liu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Yi Shen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Udo Conrad
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Wenqing Shi
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Stefan Taudien
- Leibniz Institute on Aging-Fritz-Lipmann-Institut e.V. (FLI), Beutenbergstraße 11, 07745, Jena, Germany
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany.
| |
Collapse
|
87
|
Gligoris T, Löwe J. Structural Insights into Ring Formation of Cohesin and Related Smc Complexes. Trends Cell Biol 2016; 26:680-693. [PMID: 27134029 PMCID: PMC4989898 DOI: 10.1016/j.tcb.2016.04.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/30/2016] [Accepted: 04/05/2016] [Indexed: 12/14/2022]
Abstract
Cohesin facilitates sister chromatid cohesion through the formation of a large ring structure that encircles DNA. Its function relies on two structural maintenance of chromosomes (Smc) proteins, which are found in almost all organisms tested, from bacteria to humans. In accordance with their ubiquity, Smc complexes, such as cohesin, condensin, Smc5-6, and the dosage compensation complex, affect almost all processes of DNA homeostasis. Although their precise molecular mechanism remains enigmatic, here we provide an overview of the architecture of eukaryotic Smc complexes with a particular focus on cohesin, which has seen the most progress recently. Given the evident conservation of many structural features between Smc complexes, it is expected that architecture and topology will have a significant role when deciphering their precise molecular mechanisms.
Collapse
Affiliation(s)
- Thomas Gligoris
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| |
Collapse
|
88
|
Abstract
Ghirlando and Felsenfeld review recent major advances in understanding the multiple roles of CTCF in gene regulation and genome organization and especially in how such domains are generated and organized. The role of the zinc finger protein CTCF in organizing the genome within the nucleus is now well established. Widely separated sites on DNA, occupied by both CTCF and the cohesin complex, make physical contacts that create large loop domains. Additional contacts between loci within those domains, often also mediated by CTCF, tend to be favored over contacts between loci in different domains. A large number of studies during the past 2 years have addressed the questions: How are these loops generated? What are the effects of disrupting them? Are there rules governing large-scale genome organization? It now appears that the strongest and evolutionarily most conserved of these CTCF interactions have specific rules for the orientation of the paired CTCF sites, implying the existence of a nonequilibrium mechanism of generation. Recent experiments that invert, delete, or inactivate one of a mating CTCF pair result in major changes in patterns of organization and gene expression in the surrounding regions. What remain to be determined are the detailed molecular mechanisms for re-establishing loop domains and maintaining them after replication and mitosis. As recently published data show, some mechanisms may involve interactions with noncoding RNAs as well as protein cofactors. Many CTCF sites are also involved in other functions such as modulation of RNA splicing and specific regulation of gene expression, and the relationship between these activities and loop formation is another unanswered question that should keep investigators occupied for some time.
Collapse
Affiliation(s)
- Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Gary Felsenfeld
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| |
Collapse
|
89
|
Bhardwaj S, Schlackow M, Rabajdova M, Gullerova M. Transcription facilitates sister chromatid cohesion on chromosomal arms. Nucleic Acids Res 2016; 44:6676-92. [PMID: 27084937 PMCID: PMC5001582 DOI: 10.1093/nar/gkw252] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Cohesin is a multi-subunit protein complex essential for sister chromatid cohesion, gene expression and DNA damage repair. Although structurally well studied, the underlying determinant of cohesion establishment on chromosomal arms remains enigmatic. Here, we show two populations of functionally distinct cohesin on chromosomal arms using a combination of genomics and single-locus specific DNA-FISH analysis. Chromatin bound cohesin at the loading sites co-localizes with Pds5 and Eso1 resulting in stable cohesion. In contrast, cohesin independent of its loader is unable to maintain cohesion and associates with chromatin in a dynamic manner. Cohesive sites coincide with highly expressed genes and transcription inhibition leads to destabilization of cohesin on chromatin. Furthermore, induction of transcription results in de novo recruitment of cohesive cohesin. Our data suggest that transcription facilitates cohesin loading onto chromosomal arms and is a key determinant of cohesive sites in fission yeast.
Collapse
Affiliation(s)
- Shweta Bhardwaj
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | | | | | - Monika Gullerova
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| |
Collapse
|
90
|
Hill VK, Kim JS, Waldman T. Cohesin mutations in human cancer. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1866:1-11. [PMID: 27207471 PMCID: PMC4980180 DOI: 10.1016/j.bbcan.2016.05.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/12/2016] [Accepted: 05/14/2016] [Indexed: 12/19/2022]
Abstract
Cohesin is a highly-conserved protein complex that plays important roles in sister chromatid cohesion, chromatin structure, gene expression, and DNA repair. In humans, cohesin is a ubiquitously expressed, multi-subunit protein complex composed of core subunits SMC1A, SMC3, RAD21, STAG1/2 and regulatory subunits WAPL, PDS5A/B, CDCA5, NIPBL, and MAU2. Recent studies have demonstrated that genes encoding cohesin subunits are somatically mutated in a wide range of human cancers. STAG2 is the most commonly mutated subunit, and in a recent analysis was identified as one of only 12 genes that are significantly mutated in four or more cancer types. In this review we summarize the findings reported to date and comment on potential functional implications of cohesin mutation in the pathogenesis of human cancer.
Collapse
Affiliation(s)
- Victoria K Hill
- Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, 3970 Reservoir Road, NW, NRB E304, Washington, DC 20057, USA
| | - Jung-Sik Kim
- Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, 3970 Reservoir Road, NW, NRB E304, Washington, DC 20057, USA
| | - Todd Waldman
- Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, 3970 Reservoir Road, NW, NRB E304, Washington, DC 20057, USA
| |
Collapse
|
91
|
Abstract
Animal cells undergo dramatic changes in shape, mechanics and polarity as they progress through the different stages of cell division. These changes begin at mitotic entry, with cell-substrate adhesion remodelling, assembly of a cortical actomyosin network and osmotic swelling, which together enable cells to adopt a near spherical form even when growing in a crowded tissue environment. These shape changes, which probably aid spindle assembly and positioning, are then reversed at mitotic exit to restore the interphase cell morphology. Here, we discuss the dynamics, regulation and function of these processes, and how cell shape changes and sister chromatid segregation are coupled to ensure that the daughter cells generated through division receive their fair inheritance.
Collapse
|
92
|
Stigler J, Çamdere GÖ, Koshland DE, Greene EC. Single-Molecule Imaging Reveals a Collapsed Conformational State for DNA-Bound Cohesin. Cell Rep 2016; 15:988-998. [PMID: 27117417 PMCID: PMC4856582 DOI: 10.1016/j.celrep.2016.04.003] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 02/05/2016] [Accepted: 03/28/2016] [Indexed: 11/30/2022] Open
Abstract
Cohesin is essential for the hierarchical organization of the eukaryotic genome and plays key roles in many aspects of chromosome biology. The conformation of cohesin bound to DNA remains poorly defined, leaving crucial gaps in our understanding of how cohesin fulfills its biological functions. Here, we use single-molecule microscopy to directly observe the dynamic and functional characteristics of cohesin bound to DNA. We show that cohesin can undergo rapid one-dimensional (1D) diffusion along DNA, but individual nucleosomes, nucleosome arrays, and other protein obstacles significantly restrict its mobility. Furthermore, we demonstrate that DNA motor proteins can readily push cohesin along DNA, but they cannot pass through the interior of the cohesin ring. Together, our results reveal that DNA-bound cohesin has a central pore that is substantially smaller than anticipated. These findings have direct implications for understanding how cohesin and other SMC proteins interact with and distribute along chromatin.
Collapse
Affiliation(s)
- Johannes Stigler
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Gamze Ö Çamdere
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Douglas E Koshland
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| |
Collapse
|
93
|
Nagasaka K, Hossain MJ, Roberti MJ, Ellenberg J, Hirota T. Sister chromatid resolution is an intrinsic part of chromosome organization in prophase. Nat Cell Biol 2016; 18:692-9. [PMID: 27136266 DOI: 10.1038/ncb3353] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/01/2016] [Indexed: 12/19/2022]
Abstract
The formation of mitotic chromosomes requires both compaction of chromatin and the resolution of replicated sister chromatids. Compaction occurs during mitotic prophase and prometaphase, and in prophase relies on the activity of condensin II complexes. Exactly when and how sister chromatid resolution occurs has been largely unknown, as has its molecular requirements. Here, we established a method to visualize sister resolution by sequential replication labelling with two distinct nucleotide derivatives. Quantitative three-dimensional imaging then allowed us to measure the resolution of sister chromatids throughout mitosis by calculating their non-overlapping volume within the whole chromosome. Unexpectedly, we found that sister chromatid resolution starts already at the beginning of prophase, proceeds concomitantly with chromatin compaction and is largely completed by the end of prophase. Sister chromatid resolution was abolished by inhibition of topoisomerase IIα and by depleting or preventing mitotic activation of condensin II, whereas blocking cohesin dissociation from chromosomes had little effect. Mitotic sister chromatid resolution is thus an intrinsic part of mitotic chromosome formation in prophase that relies largely on DNA decatenation and shares the molecular requirement for condensin II with prophase compaction.
Collapse
Affiliation(s)
- Kota Nagasaka
- Cancer Institute of the Japanese Foundation for Cancer Research, Division of Experimental Pathology, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.,Tokyo Institute of Technology, Department of Biological Sciences, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - M Julius Hossain
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - M Julia Roberti
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jan Ellenberg
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Toru Hirota
- Cancer Institute of the Japanese Foundation for Cancer Research, Division of Experimental Pathology, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| |
Collapse
|
94
|
Gómez R, Felipe-Medina N, Ruiz-Torres M, Berenguer I, Viera A, Pérez S, Barbero JL, Llano E, Fukuda T, Alsheimer M, Pendás AM, Losada A, Suja JA. Sororin loads to the synaptonemal complex central region independently of meiotic cohesin complexes. EMBO Rep 2016; 17:695-707. [PMID: 26951638 PMCID: PMC5341523 DOI: 10.15252/embr.201541060] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 02/03/2016] [Accepted: 02/05/2016] [Indexed: 11/09/2022] Open
Abstract
The distribution and regulation of the cohesin complexes have been extensively studied during mitosis. However, the dynamics of their different regulators in vertebrate meiosis is largely unknown. In this work, we have analyzed the distribution of the regulatory factor Sororin during male mouse meiosis. Sororin is detected at the central region of the synaptonemal complex during prophase I, in contrast with the previously reported localization of other cohesin components in the lateral elements. This localization of Sororin depends on the transverse filaments protein SYCP1, but not on meiosis-specific cohesin subunits REC8 and SMC1β. By late prophase I, Sororin accumulates at centromeres and remains there up to anaphase II The phosphatase activity of PP2A seems to be required for this accumulation. We hypothesize that Sororin function at the central region of the synaptonemal complex could be independent on meiotic cohesin complexes. In addition, we suggest that Sororin participates in the regulation of centromeric cohesion during meiosis in collaboration with SGO2-PP2A.
Collapse
Affiliation(s)
- Rocío Gómez
- Unidad de Biología Celular, Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Natalia Felipe-Medina
- Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca) Campus Miguel de Unamuno, Salamanca, Spain
| | - Miguel Ruiz-Torres
- Chromosome Dynamics Group, Centro Nacional de Investigaciones Oncológicas CNIO, Madrid, Spain
| | - Inés Berenguer
- Unidad de Biología Celular, Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Alberto Viera
- Unidad de Biología Celular, Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Sara Pérez
- Unidad de Biología Celular, Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - José Luis Barbero
- Departamento de Biología Celular y Molecular, Centro de Investigaciones Biológicas CSIC, Madrid, Spain
| | - Elena Llano
- Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca) Campus Miguel de Unamuno, Salamanca, Spain
| | - Tomoyuki Fukuda
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Manfred Alsheimer
- Department of Cell and Developmental Biology, Biocenter University of Würzburg, Würzburg, Germany
| | - Alberto M Pendás
- Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca) Campus Miguel de Unamuno, Salamanca, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Centro Nacional de Investigaciones Oncológicas CNIO, Madrid, Spain
| | - José A Suja
- Unidad de Biología Celular, Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| |
Collapse
|
95
|
Blattner AC, Chaurasia S, McKee BD, Lehner CF. Separase Is Required for Homolog and Sister Disjunction during Drosophila melanogaster Male Meiosis, but Not for Biorientation of Sister Centromeres. PLoS Genet 2016; 12:e1005996. [PMID: 27120695 PMCID: PMC4847790 DOI: 10.1371/journal.pgen.1005996] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/28/2016] [Indexed: 12/25/2022] Open
Abstract
Spatially controlled release of sister chromatid cohesion during progression through the meiotic divisions is of paramount importance for error-free chromosome segregation during meiosis. Cohesion is mediated by the cohesin protein complex and cleavage of one of its subunits by the endoprotease separase removes cohesin first from chromosome arms during exit from meiosis I and later from the pericentromeric region during exit from meiosis II. At the onset of the meiotic divisions, cohesin has also been proposed to be present within the centromeric region for the unification of sister centromeres into a single functional entity, allowing bipolar orientation of paired homologs within the meiosis I spindle. Separase-mediated removal of centromeric cohesin during exit from meiosis I might explain sister centromere individualization which is essential for subsequent biorientation of sister centromeres during meiosis II. To characterize a potential involvement of separase in sister centromere individualization before meiosis II, we have studied meiosis in Drosophila melanogaster males where homologs are not paired in the canonical manner. Meiosis does not include meiotic recombination and synaptonemal complex formation in these males. Instead, an alternative homolog conjunction system keeps homologous chromosomes in pairs. Using independent strategies for spermatocyte-specific depletion of separase complex subunits in combination with time-lapse imaging, we demonstrate that separase is required for the inactivation of this alternative conjunction at anaphase I onset. Mutations that abolish alternative homolog conjunction therefore result in random segregation of univalents during meiosis I also after separase depletion. Interestingly, these univalents become bioriented during meiosis II, suggesting that sister centromere individualization before meiosis II does not require separase.
Collapse
Affiliation(s)
- Ariane C. Blattner
- Institute of Molecular Life Sciences (IMLS), University of Zurich, Zurich, Switzerland
| | - Soumya Chaurasia
- Institute of Molecular Life Sciences (IMLS), University of Zurich, Zurich, Switzerland
| | - Bruce D. McKee
- Department of Biochemistry, Cellular and Molecular Biology (BCMB), University of Tennessee, Knoxville, Tennessee, United States of America
| | - Christian F. Lehner
- Institute of Molecular Life Sciences (IMLS), University of Zurich, Zurich, Switzerland
| |
Collapse
|
96
|
Fazio G, Gaston-Massuet C, Bettini LR, Graziola F, Scagliotti V, Cereda A, Ferrari L, Mazzola M, Cazzaniga G, Giordano A, Cotelli F, Bellipanni G, Biondi A, Selicorni A, Pistocchi A, Massa V. CyclinD1 Down-Regulation and Increased Apoptosis Are Common Features of Cohesinopathies. J Cell Physiol 2016. [PMID: 26206533 DOI: 10.1002/jcp.25106] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Genetic variants within components of the cohesin complex (NIPBL, SMC1A, SMC3, RAD21, PDS5, ESCO2, HDAC8) are believed to be responsible for a spectrum of human syndromes known as "cohesinopathies" that includes Cornelia de Lange Syndrome (CdLS). CdLS is a multiple malformation syndrome affecting almost any organ and causing severe developmental delay. Cohesinopathies seem to be caused by dysregulation of specific developmental pathways downstream of mutations in cohesin components. However, it is still unclear how mutations in different components of the cohesin complex affect the output of gene regulation. In this study, zebrafish embryos and SMC1A-mutated patient-derived fibroblasts were used to analyze abnormalities induced by SMC1A loss of function. We show that the knockdown of smc1a in zebrafish impairs neural development, increases apoptosis, and specifically down-regulates Ccnd1 levels. The same down-regulation of cohesin targets is observed in SMC1A-mutated patient fibroblasts. Previously, we have demonstrated that haploinsufficiency of NIPBL produces similar effects in zebrafish and in patients fibroblasts indicating a possible common feature for neurological defects and mental retardation in cohesinopathies. Interestingly, expression analysis of Smc1a and Nipbl in developing mouse embryos reveals a specific pattern in the hindbrain, suggesting a role for cohesins in neural development in vertebrates.
Collapse
Affiliation(s)
- Grazia Fazio
- Centro Ricerca Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Carles Gaston-Massuet
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London Medical School, Queen Mary University of London, London, UK
| | - Laura Rachele Bettini
- Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Federica Graziola
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London Medical School, Queen Mary University of London, London, UK.,Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
| | - Valeria Scagliotti
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London Medical School, Queen Mary University of London, London, UK
| | - Anna Cereda
- Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Luca Ferrari
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milano, Italy
| | - Mara Mazzola
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Gianni Cazzaniga
- Centro Ricerca Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Antonio Giordano
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania.,Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, Pennsylvania
| | - Franco Cotelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Gianfranco Bellipanni
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania.,Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, Pennsylvania
| | - Andrea Biondi
- Centro Ricerca Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy.,Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Angelo Selicorni
- Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Anna Pistocchi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milano, Italy.,Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Valentina Massa
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
| |
Collapse
|
97
|
Eeftens JM, Katan AJ, Kschonsak M, Hassler M, de Wilde L, Dief EM, Haering CH, Dekker C. Condensin Smc2-Smc4 Dimers Are Flexible and Dynamic. Cell Rep 2016; 14:1813-8. [PMID: 26904946 PMCID: PMC4785793 DOI: 10.1016/j.celrep.2016.01.063] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/21/2015] [Accepted: 01/20/2016] [Indexed: 12/20/2022] Open
Abstract
Structural maintenance of chromosomes (SMC) protein complexes, including cohesin and condensin, play key roles in the regulation of higher-order chromosome organization. Even though SMC proteins are thought to mechanistically determine the function of the complexes, their native conformations and dynamics have remained unclear. Here, we probe the topology of Smc2-Smc4 dimers of the S. cerevisiae condensin complex with high-speed atomic force microscopy (AFM) in liquid. We show that the Smc2-Smc4 coiled coils are highly flexible polymers with a persistence length of only ∼ 4 nm. Moreover, we demonstrate that the SMC dimers can adopt various architectures that interconvert dynamically over time, and we find that the SMC head domains engage not only with each other, but also with the hinge domain situated at the other end of the ∼ 45-nm-long coiled coil. Our findings reveal structural properties that provide insights into the molecular mechanics of condensin complexes.
Collapse
Affiliation(s)
- Jorine M Eeftens
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft 2628 CJ, the Netherlands
| | - Allard J Katan
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft 2628 CJ, the Netherlands
| | - Marc Kschonsak
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Markus Hassler
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Liza de Wilde
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft 2628 CJ, the Netherlands
| | - Essam M Dief
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft 2628 CJ, the Netherlands
| | - Christian H Haering
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft 2628 CJ, the Netherlands.
| |
Collapse
|
98
|
Abstract
Condensins are large protein complexes that play a central role in chromosome organization and segregation in the three domains of life. They display highly characteristic, rod-shaped structures with SMC (structural maintenance of chromosomes) ATPases as their core subunits and organize large-scale chromosome structure through active mechanisms. Most eukaryotic species have two distinct condensin complexes whose balanced usage is adapted flexibly to different organisms and cell types. Studies of bacterial condensins provide deep insights into the fundamental mechanisms of chromosome segregation. This Review surveys both conserved features and rich variations of condensin-based chromosome organization and discusses their evolutionary implications.
Collapse
Affiliation(s)
- Tatsuya Hirano
- Chromosome Dynamics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| |
Collapse
|
99
|
The partitioning and copy number control systems of the selfish yeast plasmid: an optimized molecular design for stable persistence in host cells. Microbiol Spectr 2016; 2. [PMID: 25541598 DOI: 10.1128/microbiolspec.plas-0003-2013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The multi-copy 2 micron plasmid of Saccharomyces cerevisiae, a resident of the nucleus, is remarkable for its high chromosome-like stability. The plasmid does not appear to contribute to the fitness of the host, nor does it impose a significant metabolic burden on the host at its steady state copy number. The plasmid may be viewed as a highly optimized selfish DNA element whose genome design is devoted entirely towards efficient replication, equal segregation and copy number maintenance. A partitioning system comprised of two plasmid coded proteins, Rep1 and Rep2, and a partitioning locus STB is responsible for equal or nearly equal segregation of plasmid molecules to mother and daughter cells. Current evidence supports a model in which the Rep-STB system promotes the physical association of the plasmid with chromosomes and thus plasmid segregation by a hitchhiking mechanism. The Flp site-specific recombination system housed by the plasmid plays a critical role in maintaining steady state plasmid copy number. A decrease in plasmid population due to rare missegregation events is rectified by plasmid amplification via a recombination induced rolling circle replication mechanism. Appropriate plasmid amplification, without runaway increase in copy number, is ensured by positive and negative regulation of FLP gene expression by plasmid coded proteins and by the control of Flp level/activity through host mediated post-translational modification(s) of Flp. The Flp system has been successfully utilized to understand mechanisms of site-specific recombination, to bring about directed genetic alterations for addressing fundamental problems in biology, and as a tool in biotechnological applications.
Collapse
|
100
|
Murayama Y, Uhlmann F. DNA Entry into and Exit out of the Cohesin Ring by an Interlocking Gate Mechanism. Cell 2015; 163:1628-40. [PMID: 26687354 PMCID: PMC4701713 DOI: 10.1016/j.cell.2015.11.030] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/25/2015] [Accepted: 11/04/2015] [Indexed: 01/03/2023]
Abstract
Structural maintenance of chromosome (SMC) complexes are proteinaceous rings that embrace DNA to enable vital chromosomal functions. The ring is formed by two SMC subunits, closed at a pair of ATPase heads, whose interaction is reinforced by a kleisin subunit. Using biochemical analysis of fission-yeast cohesin, we find that a similar series of events facilitates both topological entrapment and release of DNA. DNA-sensing lysines trigger ATP hydrolysis to open the SMC head interface, whereas the Wapl subunit disengages kleisin, but only after ATP rebinds. This suggests an interlocking gate mechanism for DNA transport both into and out of the cohesin ring. The entry direction is facilitated by a cohesin loader that appears to fold cohesin to expose the DNA sensor. Our results provide a model for dynamic DNA binding by all members of the SMC family and explain how lysine acetylation of cohesin establishes enduring sister chromatid cohesion.
Collapse
Affiliation(s)
- Yasuto Murayama
- The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, UK.
| | - Frank Uhlmann
- The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, UK.
| |
Collapse
|