1
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Gurung P, McGee JP, Dvorin JD. PfCAP-H is essential for assembly of condensin I complex and karyokinesis during asexual proliferation of Plasmodium falciparum. mBio 2024:e0285023. [PMID: 38564676 DOI: 10.1128/mbio.02850-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
Condensin I is a pentameric complex that regulates the mitotic chromosome assembly in eukaryotes. The kleisin subunit CAP-H of the condensin I complex acts as a linchpin to maintain the structural integrity and loading of this complex on mitotic chromosomes. This complex is present in all eukaryotes and has recently been identified in Plasmodium spp. However, how this complex is assembled and whether the kleisin subunit is critical for this complex in these parasites are yet to be explored. To examine the role of PfCAP-H during cell division within erythrocytes, we generated an inducible PfCAP-H knockout parasite. We find that PfCAP-H is dynamically expressed during mitosis with the peak expression at the metaphase plate. PfCAP-H interacts with PfCAP-G and is a non-SMC member of the condensin I complex. Notably, the absence of PfCAP-H does not alter the expression of PfCAP-G but affects its localization at the mitotic chromosomes. While mitotic spindle assembly is intact in PfCAP-H-deficient parasites, duplicated centrosomes remain clustered over the mass of unsegmented nuclei with failed karyokinesis. This failure leads to the formation of an abnormal nuclear mass, while cytokinesis occurs normally. Altogether, our data suggest that PfCAP-H plays a crucial role in maintaining the structural integrity of the condensin I complex on the mitotic chromosomes and is essential for the asexual development of malarial parasites. IMPORTANCE Mitosis is a fundamental process for Plasmodium parasites, which plays a vital role in their survival within two distinct hosts-human and Anopheles mosquitoes. Despite its great significance, our comprehension of mitosis and its regulation remains limited. In eukaryotes, mitosis is regulated by one of the pivotal complexes known as condensin complexes. The condensin complexes are responsible for chromosome condensation, ensuring the faithful distribution of genetic material to daughter cells. While condensin complexes have recently been identified in Plasmodium spp., our understanding of how this complex is assembled and its precise functions during the blood stage development of Plasmodium falciparum remains largely unexplored. In this study, we investigate the role of a central protein, PfCAP-H, during the blood stage development of P. falciparum. Our findings reveal that PfCAP-H is essential and plays a pivotal role in upholding the structure of condensin I and facilitating karyokinesis.
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Affiliation(s)
- Pratima Gurung
- Division of Infectious Diseases, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - James P McGee
- Division of Infectious Diseases, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Jeffrey D Dvorin
- Division of Infectious Diseases, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
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2
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Ando R, Shimozono S, Ago H, Takagi M, Sugiyama M, Kurokawa H, Hirano M, Niino Y, Ueno G, Ishidate F, Fujiwara T, Okada Y, Yamamoto M, Miyawaki A. StayGold variants for molecular fusion and membrane-targeting applications. Nat Methods 2024; 21:648-656. [PMID: 38036853 PMCID: PMC11009113 DOI: 10.1038/s41592-023-02085-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/12/2023] [Indexed: 12/02/2023]
Abstract
Although StayGold is a bright and highly photostable fluorescent protein, its propensity for obligate dimer formation may hinder applications in molecular fusion and membrane targeting. To attain monovalent as well as bright and photostable labeling, we engineered tandem dimers of StayGold to promote dispersibility. On the basis of the crystal structure of this fluorescent protein, we disrupted the dimerization to generate a monomeric variant that offers improved photostability and brightness compared to StayGold. We applied the new monovalent StayGold tools to live-cell imaging experiments using spinning-disk laser-scanning confocal microscopy or structured illumination microscopy. We achieved cell-wide, high-spatiotemporal resolution and sustained imaging of dynamic subcellular events, including the targeting of endogenous condensin I to mitotic chromosomes, the movement of the Golgi apparatus and its membranous derivatives along microtubule networks, the distribution of cortical filamentous actin and the remolding of cristae membranes within mobile mitochondria.
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Affiliation(s)
- Ryoko Ando
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako-city, Japan
- Biotechnological Optics Research Team, RIKEN Center for Advanced Photonics, Wako-city, Japan
- Department of Optical Biomedical Science, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Satoshi Shimozono
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako-city, Japan
| | - Hideo Ago
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Japan
| | - Masatoshi Takagi
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research (CPR), Saitama, Japan
| | - Mayu Sugiyama
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako-city, Japan
| | - Hiroshi Kurokawa
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako-city, Japan
| | - Masahiko Hirano
- Biotechnological Optics Research Team, RIKEN Center for Advanced Photonics, Wako-city, Japan
| | - Yusuke Niino
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako-city, Japan
| | - Go Ueno
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Japan
| | - Fumiyoshi Ishidate
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Takahiro Fujiwara
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yasushi Okada
- Laboratory for Cell Polarity Regulation, RIKEN Center for Biosystems Dynamics Research, Suita, Japan
- Department of Cell Biology, Department of Physics, UBI and WPI-IRCN, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Masaki Yamamoto
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Japan
| | - Atsushi Miyawaki
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako-city, Japan.
- Biotechnological Optics Research Team, RIKEN Center for Advanced Photonics, Wako-city, Japan.
- Laboratory of Bioresponse Analysis, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
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3
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Cao R, Tian H, Tian Y, Fu X. A Hierarchical Mechanotransduction System: From Macro to Micro. Adv Sci (Weinh) 2024; 11:e2302327. [PMID: 38145330 PMCID: PMC10953595 DOI: 10.1002/advs.202302327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 10/27/2023] [Indexed: 12/26/2023]
Abstract
Mechanotransduction is a strictly regulated process whereby mechanical stimuli, including mechanical forces and properties, are sensed and translated into biochemical signals. Increasing data demonstrate that mechanotransduction is crucial for regulating macroscopic and microscopic dynamics and functionalities. However, the actions and mechanisms of mechanotransduction across multiple hierarchies, from molecules, subcellular structures, cells, tissues/organs, to the whole-body level, have not been yet comprehensively documented. Herein, the biological roles and operational mechanisms of mechanotransduction from macro to micro are revisited, with a focus on the orchestrations across diverse hierarchies. The implications, applications, and challenges of mechanotransduction in human diseases are also summarized and discussed. Together, this knowledge from a hierarchical perspective has the potential to refresh insights into mechanotransduction regulation and disease pathogenesis and therapy, and ultimately revolutionize the prevention, diagnosis, and treatment of human diseases.
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Affiliation(s)
- Rong Cao
- Department of Endocrinology and MetabolismCenter for Diabetes Metabolism ResearchState Key Laboratory of Biotherapy and Cancer CenterWest China Medical SchoolWest China HospitalSichuan University and Collaborative Innovation CenterChengduSichuan610041China
| | - Huimin Tian
- Department of Endocrinology and MetabolismCenter for Diabetes Metabolism ResearchState Key Laboratory of Biotherapy and Cancer CenterWest China Medical SchoolWest China HospitalSichuan University and Collaborative Innovation CenterChengduSichuan610041China
| | - Yan Tian
- Department of Endocrinology and MetabolismCenter for Diabetes Metabolism ResearchState Key Laboratory of Biotherapy and Cancer CenterWest China Medical SchoolWest China HospitalSichuan University and Collaborative Innovation CenterChengduSichuan610041China
| | - Xianghui Fu
- Department of Endocrinology and MetabolismCenter for Diabetes Metabolism ResearchState Key Laboratory of Biotherapy and Cancer CenterWest China Medical SchoolWest China HospitalSichuan University and Collaborative Innovation CenterChengduSichuan610041China
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4
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Gurung P, McGee JP, Dvorin JD. PfCAP-H is essential for assembly of condensin I complex and karyokinesis during asexual proliferation of Plasmodium falciparum. bioRxiv 2024:2024.02.26.582160. [PMID: 38464281 PMCID: PMC10925219 DOI: 10.1101/2024.02.26.582160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Condensin I is a pentameric complex that regulates the mitotic chromosome assembly in eukaryotes. The kleisin subunit CAP-H of the condensin I complex acts as a linchpin to maintain the structural integrity and loading of this complex on mitotic chromosomes. This complex is present in all eukaryotes and has recently been identified in Plasmodium spp. However, how this complex is assembled and whether the kleisin subunit is critical for this complex in these parasites is yet to be explored. To examine the role of PfCAP-H during cell division within erythrocytes, we generated an inducible PfCAP-H knockout parasite. We find that PfCAP-H is dynamically expressed during mitosis with the peak expression at the metaphase plate. PfCAP-H interacts with PfCAP-G and is a non-SMC member of the condensin I complex. Notably, the absence of PfCAP-H does not alter the expression of PfCAP-G but affects its localization at the mitotic chromosomes. While mitotic spindle assembly is intact in PfCAP-H deficient parasites, duplicated centrosomes remain clustered over the mass of unsegmented nuclei with failed karyokinesis. This failure leads to the formation of an abnormal nuclear mass, while cytokinesis occurs normally. Altogether, our data suggest that PfCAP-H plays a crucial role in maintaining the structural integrity of the condensin I complex on the mitotic chromosomes and is essential for the asexual development of malarial parasites.
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Affiliation(s)
- Pratima Gurung
- Division of Infectious Diseases, Boston Children’s Hospital, Boston, M.A
- Department of Pediatrics, Harvard Medical School, Boston, M.A
| | - James P. McGee
- Division of Infectious Diseases, Boston Children’s Hospital, Boston, M.A
| | - Jeffrey D. Dvorin
- Division of Infectious Diseases, Boston Children’s Hospital, Boston, M.A
- Department of Pediatrics, Harvard Medical School, Boston, M.A
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5
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Iida S, Ide S, Tamura S, Tani T, Goto T, Shribak M, Maeshima K. Orientation-Independent-DIC imaging reveals that a transient rise in depletion force contributes to mitotic chromosome condensation. bioRxiv 2024:2023.11.11.566679. [PMID: 37986866 PMCID: PMC10659371 DOI: 10.1101/2023.11.11.566679] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Genomic information must be faithfully transmitted into two daughter cells during mitosis. To ensure the transmission process, interphase chromatin is further condensed into mitotic chromosomes. Although protein factors like condensins and topoisomerase IIα are involved in the assembly of mitotic chromosomes, the physical bases of the condensation process remain unclear. Depletion force/macromolecular crowding, an effective attractive force that arises between large structures in crowded environments around chromosomes, may contribute to the condensation process. To approach this issue, we investigated the "chromosome milieu" during mitosis of living human cells using orientation-independent-differential interference contrast (OI-DIC) module combined with a confocal laser scanning microscope, which is capable of precisely mapping optical path differences and estimating molecular densities. We found that the molecular density surrounding chromosomes increased with the progression from prometaphase to anaphase, concurring with chromosome condensation. However, the molecular density went down in telophase, when chromosome decondensation began. Changes in the molecular density around chromosomes by hypotonic or hypertonic treatment consistently altered the condensation levels of chromosomes. In vitro, native chromatin was converted into liquid droplets of chromatin in the presence of cations and a macromolecular crowder. Additional crowder made the chromatin droplets stiffer and more solid-like, with further condensation. These results suggest that a transient rise in depletion force, likely triggered by the relocation of macromolecules (proteins, RNAs and others) via nuclear envelope breakdown and also by a subsequent decrease in cell-volumes, contributes to mitotic chromosome condensation, shedding light on a new aspect of the condensation mechanism in living human cells.
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Affiliation(s)
- Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Tomomi Tani
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Osaka 563-8577, Japan
| | - Tatsuhiko Goto
- Research Center for Global Agromedicine and Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Michael Shribak
- Marine Biological Laboratory, 7 MBL St, Woods Hole, MA 02543, USA
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
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6
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Yoshida MM, Kinoshita K, Shintomi K, Aizawa Y, Hirano T. Regulation of condensin II by self-suppression and release mechanisms. Mol Biol Cell 2024; 35:ar21. [PMID: 38088875 PMCID: PMC10881152 DOI: 10.1091/mbc.e23-10-0392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 01/14/2024] Open
Abstract
In vertebrates, two distinct condensin complexes, condensin I and condensin II, cooperate to drive mitotic chromosome assembly. It remains largely unknown how the two complexes differentially contribute to this process at a mechanistic level. We have previously dissected the role of individual subunits of condensin II by introducing recombinant complexes into Xenopus egg extracts. Here we extend these efforts by introducing a modified functional assay using extracts depleted of topoisomerase IIα (topo IIα), which allows us to further elucidate the functional similarities and differences between condensin I and condensin II. The intrinsically disordered C-terminal region of the CAP-D3 subunit (the D3 C-tail) is a major target of Cdk1 phosphorylation, and phosphorylation-deficient mutations in this region impair condensin II functions. We also identify a unique helical structure in CAP-D3 (the D3 HEAT docker) that is predicted to directly interact with CAP-G2. Deletion of the D3 HEAT docker, along with the D3 C-tail, enhances the ability of condensin II to assemble mitotic chromosomes. Taken together, we propose a self-suppression mechanism unique to condensin II that is released by mitotic phosphorylation. Evolutionary implications of our findings are also discussed.
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Affiliation(s)
- Makoto M. Yoshida
- Chromosome Dynamics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | | | - Keishi Shintomi
- Chromosome Dynamics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Yuuki Aizawa
- Chromosome Dynamics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Tatsuya Hirano
- Chromosome Dynamics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
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7
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Zhang L, Hu C, Xu Z, Li H, Ye B, Li X, Czajkowsky DM, Shao Z. Quantitative catalogue of mammalian mitotic chromosome-associated RNAs. Sci Data 2024; 11:43. [PMID: 38184632 PMCID: PMC10771512 DOI: 10.1038/s41597-023-02884-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/27/2023] [Indexed: 01/08/2024] Open
Abstract
The faithful transmission of a cell's identity and functionality to its daughters during mitosis requires the proper assembly of mitotic chromosomes from interphase chromatin in a process that involves significant changes in the genome-bound material, including the RNA. However, our understanding of the RNA that is associated with the mitotic chromosome is presently limited. Here, we present complete and quantitative characterizations of the full-length mitotic chromosome-associated RNAs (mCARs) for 3 human cell lines, a monkey cell line, and a mouse cell line derived from high-depth RNA sequencing (3 replicates, 47 M mapped read pairs for each replicate). Overall, we identify, on average, more than 20,400 mCAR species per cell-type (including isoforms), more than 5,200 of which are enriched on the chromosome. Notably, overall, more than 2,700 of these mCARs were previously unknown, which thus also expands the annotated genome of these species. We anticipate that these datasets will provide an essential resource for future studies to better understand the functioning of mCARs on the mitotic chromosome and in the cell.
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Affiliation(s)
- Le Zhang
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chuansheng Hu
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zeqian Xu
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hua Li
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bishan Ye
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xinhui Li
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Daniel M Czajkowsky
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Zhifeng Shao
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
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8
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Zhang Y, Cao J, Lu M, Kardol P, Wang J, Fan G, Kong D. The origin of bi-dimensionality in plant root traits. Trends Ecol Evol 2024; 39:78-88. [PMID: 37777374 DOI: 10.1016/j.tree.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 10/02/2023]
Abstract
Plant roots show extraordinary diversity in form and function in heterogeneous environments. Mounting evidence has shown global bi-dimensionality in root traits, the root economics spectrum (RES), and an orthogonal dimension describing mycorrhizal collaboration; however, the origin of the bi-dimensionality remains unresolved. Here, we propose that bi-dimensionality arises from the cylindrical geometry of roots, allometry between root cortex and stele, and independence between root cell wall thickness and cell number. Root geometry and mycorrhizal collaboration may both underlie the bi-dimensionality. Further, we emphasize why plant roots should be cylindrical rather than flat. Finally, we highlight the need to integrate organ-, cellular-, and molecular-level processes driving the bi-dimensionality in plant roots to fully understand plant diversity and functions.
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Affiliation(s)
- Yue Zhang
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Jingjing Cao
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | | | - Paul Kardol
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Umeå, 75007, Sweden; Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, 90183, Sweden
| | - Junjian Wang
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Guoqiang Fan
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Deliang Kong
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China.
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9
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Wang UTT, Tian X, Liou YH, Lee SP, Hu HT, Lu CH, Lin PT, Cheng YJ, Chen P, Chen BC. Protein and lipid expansion microscopy with trypsin and tyramide signal amplification for 3D imaging. Sci Rep 2023; 13:21922. [PMID: 38081848 PMCID: PMC10713663 DOI: 10.1038/s41598-023-48959-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Expansion microscopy, whereby the relative positions of biomolecules are physically increased via hydrogel expansion, can be used to reveal ultrafine structures of cells under a conventional microscope. Despite its utility for achieving super-resolution imaging, expansion microscopy suffers a major drawback, namely reduced fluorescence signals caused by excessive proteolysis and swelling effects. This caveat results in a lower photon budget and disfavors fluorescence imaging over a large field of view that can cover an entire expanded cell, especially in 3D. In addition, the complex procedures and specialized reagents of expansion microscopy hinder its popularization. Here, we modify expansion microscopy by deploying trypsin digestion to reduce protein loss and tyramide signal amplification to enhance fluorescence signal for point-scanning-based imaging. We name our new methodology TT-ExM to indicate dual trypsin and tyramide treatments. TT-ExM may be applied for both antibody and lipid staining. TT-ExM displayed enhanced protein retention for endoplasmic reticulum and mitochondrial markers in COS-7 cell cultures. Importantly, TT-ExM-based lipid staining clearly revealed the complex 3D membrane structures in entire expanded cells. Through combined lipid and DNA staining, our TT-ExM methodology highlighted mitochondria by revealing their DNA and membrane structures in cytoplasm, as well as the lipid-rich structures formed via phase separation in nuclei at interphase. We also observed lipid-rich chromosome matrices in the mitotic cells. These high-quality 3D images demonstrate the practicality of TT-ExM. Thus, readily available reagents can be deployed in TT-ExM to significantly enhance fluorescence signals and generate high-quality and ultrafine-resolution images under confocal microscopy.
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Affiliation(s)
- Ueh-Ting Tim Wang
- Affiliated Senior High School of National Taiwan Normal University, Taipei, 106348, Taiwan
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Xuejiao Tian
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica and National Tsing Hua University, Taipei, 11529, Taiwan
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Yae-Huei Liou
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Sue-Ping Lee
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Hsiao-Tang Hu
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chieh-Han Lu
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
- Institute and Undergraduate Program of Electro-Optical Engineering, National Taiwan Normal University, Taipei, 116, Taiwan
| | - Po-Ting Lin
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Ya-Jen Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
- Neuroscience Program, NPAS, Academia Sinica, Taipei, 11529, Taiwan, ROC
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan.
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10
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Jadav N, Velamoor S, Huang D, Cassin L, Hazelton N, Eruera AR, Burga LN, Bostina M. Beyond the surface: Investigation of tumorsphere morphology using volume electron microscopy. J Struct Biol 2023; 215:108035. [PMID: 37805154 DOI: 10.1016/j.jsb.2023.108035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
The advent of volume electron microscopy (vEM) has provided unprecedented insights into cellular and subcellular organization, revolutionizing our understanding of cancer biology. This study presents a previously unexplored comparative analysis of the ultrastructural disparities between cancer cells cultured as monolayers and tumorspheres. By integrating a robust workflow that incorporates high-pressure freezing followed by freeze substitution (HPF/FS), serial block face scanning electron microscopy (SBF-SEM), manual and deep learning-based segmentation, and statistical analysis, we have successfully generated three-dimensional (3D) reconstructions of monolayer and tumorsphere cells, including their subcellular organelles. Our findings reveal a significant degree of variation in cellular morphology in tumorspheres. We observed the increased prevalence of nuclear envelope invaginations in tumorsphere cells compared to monolayers. Furthermore, we detected a diverse range of mitochondrial morphologies exclusively in tumorsphere cells, as well as intricate cellular interconnectivity within the tumorsphere architecture. These remarkable ultrastructural differences emphasize the use of tumorspheres as a superior model for cancer research due to their relevance to in vivo conditions. Our results strongly advocate for the utilization of tumorsphere cells in cancer research studies, enhancing the precision and relevance of experimental outcomes, and ultimately accelerating therapeutic advancements.
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Affiliation(s)
- Nickhil Jadav
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Sailakshmi Velamoor
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Daniel Huang
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Léna Cassin
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Niki Hazelton
- Otago Micro and Nano Imaging (OMNI) Electron Microscopy Suite, University of Otago, Dunedin, New Zealand
| | - Alice-Roza Eruera
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Laura N Burga
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Mihnea Bostina
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand; Otago Micro and Nano Imaging (OMNI) Electron Microscopy Suite, University of Otago, Dunedin, New Zealand.
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11
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Chien E, Michael WM. Transcriptional repression during spermatogenesis in C. elegans requires TOP-2, condensin II, and the MET-2 H3K9 methyltransferase. MicroPubl Biol 2023; 2023:10.17912/micropub.biology.000933. [PMID: 37692088 PMCID: PMC10483280 DOI: 10.17912/micropub.biology.000933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 08/07/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023]
Abstract
In C. elegans RNA polymerase II (RNAPII) transcription is globally repressed as oocytes prepare for meiosis. Recent work has identified the transcriptional repressors responsible for genome silencing in oocytes, and they are topoisomerase II ( TOP-2 ), condensin II, the H3K9 methyltransferase SET-25 and MET-2 , and the PIE-1 protein. Here, we focus on TOP-2 , condensin II, and MET-2 and ask if they play a similar role during spermatogenesis. We report that spermatocytes undergo transcriptional repression, as inferred by a deactivation of RNAPII, and this requires TOP-2 , the CAPG-2 subunit of condensin II, and the histone methyltransferase MET-2 .
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Affiliation(s)
- Emilie Chien
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States
| | - W. Matthew Michael
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States
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12
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Batty P, Langer CCH, Takács Z, Tang W, Blaukopf C, Peters J, Gerlich DW. Cohesin-mediated DNA loop extrusion resolves sister chromatids in G2 phase. EMBO J 2023; 42:e113475. [PMID: 37357575 PMCID: PMC10425840 DOI: 10.15252/embj.2023113475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/26/2023] [Accepted: 06/14/2023] [Indexed: 06/27/2023] Open
Abstract
Genetic information is stored in linear DNA molecules, which are highly folded inside cells. DNA replication along the folded template path yields two sister chromatids that initially occupy the same nuclear region in an intertwined arrangement. Dividing cells must disentangle and condense the sister chromatids into separate bodies such that a microtubule-based spindle can move them to opposite poles. While the spindle-mediated transport of sister chromatids has been studied in detail, the chromosome-intrinsic mechanics presegregating sister chromatids have remained elusive. Here, we show that human sister chromatids resolve extensively already during interphase, in a process dependent on the loop-extruding activity of cohesin, but not that of condensins. Increasing cohesin's looping capability increases sister DNA resolution in interphase nuclei to an extent normally seen only during mitosis, despite the presence of abundant arm cohesion. That cohesin can resolve sister chromatids so extensively in the absence of mitosis-specific activities indicates that DNA loop extrusion is a generic mechanism for segregating replicated genomes, shared across different Structural Maintenance of Chromosomes (SMC) protein complexes in all kingdoms of life.
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Affiliation(s)
- Paul Batty
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Christoph CH Langer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
| | - Zsuzsanna Takács
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
| | - Claudia Blaukopf
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
| | - Jan‐Michael Peters
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
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13
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Spicer MFD, Gerlich DW. The material properties of mitotic chromosomes. Curr Opin Struct Biol 2023; 81:102617. [PMID: 37279615 PMCID: PMC10448380 DOI: 10.1016/j.sbi.2023.102617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/28/2023] [Accepted: 05/04/2023] [Indexed: 06/08/2023]
Abstract
Chromosomes transform during the cell cycle, allowing transcription and replication during interphase and chromosome segregation during mitosis. Morphological changes are thought to be driven by the combined effects of DNA loop extrusion and a chromatin solubility phase transition. By extruding the chromatin fibre into loops, condensins enrich at an axial core and provide resistance to spindle pulling forces. Mitotic chromosomes are further compacted by deacetylation of histone tails, rendering chromatin insoluble and resistant to penetration by microtubules. Regulation of surface properties by Ki-67 allows independent chromosome movement in early mitosis and clustering during mitotic exit. Recent progress has provided insight into how the extraordinary material properties of chromatin emerge from these activities, and how these properties facilitate faithful chromosome segregation.
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Affiliation(s)
- Maximilian F D Spicer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030, Vienna, Austria. https://twitter.com/Spicer__Max
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030, Vienna, Austria.
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14
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Lee HM, Hong SJ, Gill R, Caldairou B, Wang I, Zhang JG, Deleo F, Schrader D, Bartolomei F, Guye M, Cho KH, Barba C, Sisodiya S, Jackson G, Hogan RE, Wong-Kisiel L, Cascino GD, Schulze-Bonhage A, Lopes-Cendes I, Cendes F, Guerrini R, Bernhardt B, Bernasconi N, Bernasconi A. Multimodal mapping of regional brain vulnerability to focal cortical dysplasia. Brain 2023; 146:3404-3415. [PMID: 36852571 PMCID: PMC10393418 DOI: 10.1093/brain/awad060] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/17/2023] [Accepted: 02/02/2023] [Indexed: 03/01/2023] Open
Abstract
Focal cortical dysplasia (FCD) type II is a highly epileptogenic developmental malformation and a common cause of surgically treated drug-resistant epilepsy. While clinical observations suggest frequent occurrence in the frontal lobe, mechanisms for such propensity remain unexplored. Here, we hypothesized that cortex-wide spatial associations of FCD distribution with cortical cytoarchitecture, gene expression and organizational axes may offer complementary insights into processes that predispose given cortical regions to harbour FCD. We mapped the cortex-wide MRI distribution of FCDs in 337 patients collected from 13 sites worldwide. We then determined its associations with (i) cytoarchitectural features using histological atlases by Von Economo and Koskinas and BigBrain; (ii) whole-brain gene expression and spatiotemporal dynamics from prenatal to adulthood stages using the Allen Human Brain Atlas and PsychENCODE BrainSpan; and (iii) macroscale developmental axes of cortical organization. FCD lesions were preferentially located in the prefrontal and fronto-limbic cortices typified by low neuron density, large soma and thick grey matter. Transcriptomic associations with FCD distribution uncovered a prenatal component related to neuroglial proliferation and differentiation, likely accounting for the dysplastic makeup, and a postnatal component related to synaptogenesis and circuit organization, possibly contributing to circuit-level hyperexcitability. FCD distribution showed a strong association with the anterior region of the antero-posterior axis derived from heritability analysis of interregional structural covariance of cortical thickness, but not with structural and functional hierarchical axes. Reliability of all results was confirmed through resampling techniques. Multimodal associations with cytoarchitecture, gene expression and axes of cortical organization indicate that prenatal neurogenesis and postnatal synaptogenesis may be key points of developmental vulnerability of the frontal lobe to FCD. Concordant with a causal role of atypical neuroglial proliferation and growth, our results indicate that FCD-vulnerable cortices display properties indicative of earlier termination of neurogenesis and initiation of cell growth. They also suggest a potential contribution of aberrant postnatal synaptogenesis and circuit development to FCD epileptogenicity.
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Affiliation(s)
- Hyo M Lee
- Neuroimaging of Epilepsy Laboratory, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Seok-Jun Hong
- Neuroimaging of Epilepsy Laboratory, Montreal Neurological Institute, McGill University, Montreal, Canada
- Center for Neuroscience Imaging, Research Institute for Basic Science, Department of Global Biomedical Engineering, SungKyunKwan University, Suwon, KoreaSuwon, Korea
| | - Ravnoor Gill
- Neuroimaging of Epilepsy Laboratory, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Benoit Caldairou
- Neuroimaging of Epilepsy Laboratory, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Irene Wang
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jian-guo Zhang
- Department of Functional Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Francesco Deleo
- Epilepsy Unit, Fondazione IRCCS Istituto Neurologico C. Besta, Milano, Italy
| | - Dewi Schrader
- Department of Pediatrics, British Columbia Children’s Hospital, Vancouver, Canada
| | - Fabrice Bartolomei
- Aix Marseille Univ, INSERM, INS, Institut de Neurosciences des Systèmes, Marseille, 13005, France
| | - Maxime Guye
- Aix Marseille University, CNRS, CRMBM UMR 7339, Marseille, France
| | - Kyoo Ho Cho
- Department of Neurology, Yonsei University College of Medicine, Seoul, Korea
| | - Carmen Barba
- Meyer Children's Hospital IRCCS, Florence, Italy
- University of Florence, 50121 Florence, Italy
| | - Sanjay Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK
| | - Graeme Jackson
- The Florey Institute of Neuroscience and Mental Health and The University of Melbourne, Victoria, Australia
| | - R Edward Hogan
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | | | | | | | - Iscia Lopes-Cendes
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP) and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas SP, Brazil
| | - Fernando Cendes
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas SP, Brazil
| | - Renzo Guerrini
- Meyer Children's Hospital IRCCS, Florence, Italy
- University of Florence, 50121 Florence, Italy
| | - Boris Bernhardt
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Neda Bernasconi
- Neuroimaging of Epilepsy Laboratory, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Andrea Bernasconi
- Neuroimaging of Epilepsy Laboratory, Montreal Neurological Institute, McGill University, Montreal, Canada
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15
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Kabirova E, Nurislamov A, Shadskiy A, Smirnov A, Popov A, Salnikov P, Battulin N, Fishman V. Function and Evolution of the Loop Extrusion Machinery in Animals. Int J Mol Sci 2023; 24:ijms24055017. [PMID: 36902449 PMCID: PMC10003631 DOI: 10.3390/ijms24055017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/25/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Structural maintenance of chromosomes (SMC) complexes are essential proteins found in genomes of all cellular organisms. Essential functions of these proteins, such as mitotic chromosome formation and sister chromatid cohesion, were discovered a long time ago. Recent advances in chromatin biology showed that SMC proteins are involved in many other genomic processes, acting as active motors extruding DNA, which leads to the formation of chromatin loops. Some loops formed by SMC proteins are highly cell type and developmental stage specific, such as SMC-mediated DNA loops required for VDJ recombination in B-cell progenitors, or dosage compensation in Caenorhabditis elegans and X-chromosome inactivation in mice. In this review, we focus on the extrusion-based mechanisms that are common for multiple cell types and species. We will first describe an anatomy of SMC complexes and their accessory proteins. Next, we provide biochemical details of the extrusion process. We follow this by the sections describing the role of SMC complexes in gene regulation, DNA repair, and chromatin topology.
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Affiliation(s)
- Evelyn Kabirova
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Artem Nurislamov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Artem Shadskiy
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexander Smirnov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Andrey Popov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Pavel Salnikov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Nariman Battulin
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Veniamin Fishman
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Artificial Intelligence Research Institute (AIRI), 121108 Moscow, Russia
- Correspondence:
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16
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Tkemaladze J. Reduction, proliferation, and differentiation defects of stem cells over time: a consequence of selective accumulation of old centrioles in the stem cells? Mol Biol Rep 2023; 50:2751-2761. [PMID: 36583780 DOI: 10.1007/s11033-022-08203-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND All molecules, structures, cells in organisms are subjected to destruction during the process of vital activities. In the organisms of most multicellular animals and humans, the regeneration process always takes place: destruction of old cells and their replacement with the new. The replacement of cells happens even if the cells are in perfect condition. The sooner the organism destroys the cells that emerged a certain time ago and replaces them with the new (i.e., the higher is the regeneration tempo), the younger the organism is. DISCUSSION Stem cells are progenitor cells of the substituting young cells. Asymmetric division of a mother stem cell gives rise to one, analogous to the mother, daughter cell, and to a second daughter cell that takes the path of further differentiation. Despite such asymmetric divisions, the pool of stem cells diminishes in its quantity over time. Moreover, intervals between stem cell divisions increase. The combination of these two processes causes the decline of regeneration tempo and aging of the organism. CONCLUSION During asymmetric stem cell divisions daughter cells, with preserved potency of the stem cell, selectively conserve mother (old) centrioles. In contrast with molecules of nuclear DNA, reparations do not take place in centrioles. Hypothetically, old centrioles are more subjected to destruction than other structures of a cell-which makes centrioles potentially the main structure of aging.
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Affiliation(s)
- Jaba Tkemaladze
- Free University of Tbilisi, 240 David Aghmashenebeli Alley, 0159, Tbilisi, Georgia.
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17
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Yuki R, Ikeda Y, Yasutake R, Saito Y, Nakayama Y. SH2D4A promotes centrosome maturation to support spindle microtubule formation and mitotic progression. Sci Rep 2023; 13:2067. [PMID: 36739326 PMCID: PMC9899277 DOI: 10.1038/s41598-023-29362-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/02/2023] [Indexed: 02/06/2023] Open
Abstract
Mitotic progression requires the precise formation of spindle microtubules based on mature centrosomes. During the G2/M transition, centrosome maturation progresses, and associated microtubules bundle to form mitotic spindle fibers and capture the chromosomes for alignment at the cell equator. Mitotic kinases-induced phosphorylation signaling is necessary for these processes. Here, we identified SH2 domain-containing protein 4A (SH2D4A/PPP1R38) as a new mitotic regulator. SH2D4A knockdown delays mitotic progression. The time-lapse imaging analysis showed that SH2D4A specifically contributes to the alignment of chromosomes. The cold treatment assay and microtubule regrowth assay indicated that SH2D4A promotes microtubule nucleation to support kinetochore-microtubule attachment. This may be due to the centrosome maturation by SH2D4A via centrosomal recruitment of pericentriolar material (PCM) such as cep192, γ-tubulin, and PLK1. SH2D4A was found to be a negative regulator of PP1 phosphatase. Consistently, treatment with a PP1 inhibitor rescues SH2D4A-knockdown-induced phenotypes, including the microtubule nucleation and centrosomal recruitment of active PLK1. These results suggest that SH2D4A is involved in PCM recruitment to centrosomes and centrosome maturation through attenuation of PP1 phosphatases, accelerating the spindle formation and supporting mitotic progression.
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Affiliation(s)
- Ryuzaburo Yuki
- Department of Biochemistry & Molecular Biology, Kyoto Pharmaceutical University, 5 Misasagi-Nakauchi-cho, Yamashina-ku, Kyoto, 607-8414, Japan.
| | - Yuki Ikeda
- Department of Biochemistry & Molecular Biology, Kyoto Pharmaceutical University, 5 Misasagi-Nakauchi-cho, Yamashina-ku, Kyoto, 607-8414, Japan
| | - Ryuji Yasutake
- Department of Biochemistry & Molecular Biology, Kyoto Pharmaceutical University, 5 Misasagi-Nakauchi-cho, Yamashina-ku, Kyoto, 607-8414, Japan
| | - Youhei Saito
- Department of Biochemistry & Molecular Biology, Kyoto Pharmaceutical University, 5 Misasagi-Nakauchi-cho, Yamashina-ku, Kyoto, 607-8414, Japan
| | - Yuji Nakayama
- Department of Biochemistry & Molecular Biology, Kyoto Pharmaceutical University, 5 Misasagi-Nakauchi-cho, Yamashina-ku, Kyoto, 607-8414, Japan.
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18
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Soujanya M, Bihani A, Hajirnis N, Pathak RU, Mishra RK. Nuclear architecture and the structural basis of mitotic memory. Chromosome Res 2023; 31:8. [PMID: 36725757 DOI: 10.1007/s10577-023-09714-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/13/2022] [Accepted: 12/19/2022] [Indexed: 02/03/2023]
Abstract
The nucleus is a complex organelle that hosts the genome and is essential for vital processes like DNA replication, DNA repair, transcription, and splicing. The genome is non-randomly organized in the three-dimensional space of the nucleus. This functional sub-compartmentalization was thought to be organized on the framework of nuclear matrix (NuMat), a non-chromatin scaffold that functions as a substratum for various molecular processes of the nucleus. More recently, nuclear bodies or membrane-less subcompartments of the nucleus are thought to arise due to phase separation of chromatin, RNA, and proteins. The nuclear architecture is an amalgamation of the relative organization of chromatin, epigenetic landscape, the nuclear bodies, and the nucleoskeleton in the three-dimensional space of the nucleus. During mitosis, the nucleus undergoes drastic changes in morphology to the degree that it ceases to exist as such; various nuclear components, including the envelope that defines the nucleus, disintegrate, and the chromatin acquires mitosis-specific epigenetic marks and condenses to form chromosome. Upon mitotic exit, chromosomes are decondensed, re-establish hierarchical genome organization, and regain epigenetic and transcriptional status similar to that of the mother cell. How this mitotic memory is inherited during cell division remains a puzzle. NuMat components that are a part of the mitotic chromosome in the form of mitotic chromosome scaffold (MiCS) could potentially be the seeds that guide the relative re-establishment of the epigenome, chromosome territories, and the nuclear bodies. Here, we synthesize the advances towards understanding cellular memory of nuclear architecture across mitosis and propose a hypothesis that a subset of NuMat proteome essential for nucleation of various nuclear bodies are retained in MiCS to serve as seeds of mitotic memory, thus ensuring the daughter cells re-establish the complex status of nuclear architecture similar to that of the mother cells, thereby maintaining the pre-mitotic transcriptional status.
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Affiliation(s)
- Mamilla Soujanya
- CSIR - Centre for Cellular & Molecular Biology, Hyderabad, India
- AcSIR - Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Ashish Bihani
- CSIR - Centre for Cellular & Molecular Biology, Hyderabad, India
| | - Nikhil Hajirnis
- CSIR - Centre for Cellular & Molecular Biology, Hyderabad, India
- Department of Anatomy and Neurobiology, University of Maryland, Baltimore, USA
| | - Rashmi U Pathak
- CSIR - Centre for Cellular & Molecular Biology, Hyderabad, India
| | - Rakesh K Mishra
- CSIR - Centre for Cellular & Molecular Biology, Hyderabad, India.
- AcSIR - Academy of Scientific and Innovative Research, Ghaziabad, India.
- TIGS - Tata Institute for Genetics and Society, Bangalore, India.
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19
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Cao YF, Xie L, Tong BB, Chu MY, Shi WQ, Li X, He JZ, Wang SH, Wu ZY, Deng DX, Zheng YQ, Li ZM, Xu XE, Liao LD, Cheng YW, Li LY, Xu LY, Li EM. Targeting USP10 induces degradation of oncogenic ANLN in esophageal squamous cell carcinoma. Cell Death Differ 2023; 30:527-543. [PMID: 36526897 PMCID: PMC9950447 DOI: 10.1038/s41418-022-01104-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/17/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Anillin (ANLN) is a mitosis-related protein that promotes contractile ring formation and cytokinesis, but its cell cycle-dependent degradation mechanisms in cancer cells remain unclear. Here, we show that high expression of ANLN promotes cytokinesis and proliferation in esophageal squamous cell carcinoma (ESCC) cells and is associated with poor prognosis in ESCC patients. Furthermore, the findings of the study showed that the deubiquitinating enzyme USP10 interacts with ANLN and positively regulates ANLN protein levels. USP10 removes the K11- and K63-linked ubiquitin chains of ANLN through its deubiquitinase activity and prevents ANLN ubiquitin-mediated degradation. Importantly, USP10 promotes contractile ring assembly at the cytokinetic furrow as well as cytokinesis by stabilizing ANLN. Interestingly, USP10 and the E3 ubiquitin ligase APC/C co-activator Cdh1 formed a functional complex with ANLN in a non-competitive manner to balance ANLN protein levels. In addition, the macrolide compound FW-04-806 (F806), a natural compound with potential for treating ESCC, inhibited the mitosis of ESCC cells by targeting USP10 and promoting ANLN degradation. F806 selectively targeted USP10 and inhibited its catalytic activity but did not affect the binding of Cdh1 to ANLN and alters the balance of the USP10-Cdh1-ANLN complex. Additionally, USP10 expression was positively correlated with ANLN level and poor prognosis of ESCC patients. Overall, targeting the USP10-ANLN axis can effectively inhibit ESCC cell-cycle progression.
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Affiliation(s)
- Yu-Fei Cao
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Lei Xie
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Bei-Bei Tong
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Man-Yu Chu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong, PR China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Wen-Qi Shi
- Clinical Research Center, Shantou Central Hospital, Shantou, Guangdong, PR China
| | - Xiang Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong, PR China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Jian-Zhong He
- Department of Pathology, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, PR China
| | - Shao-Hong Wang
- Clinical Research Center, Shantou Central Hospital, Shantou, Guangdong, PR China
| | - Zhi-Yong Wu
- Clinical Research Center, Shantou Central Hospital, Shantou, Guangdong, PR China
| | - Dan-Xia Deng
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong, PR China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Ya-Qi Zheng
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong, PR China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Zhi-Mao Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong, PR China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Xiu-E Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong, PR China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Lian-Di Liao
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong, PR China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Yin-Wei Cheng
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong, PR China
- Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Li-Yan Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong, PR China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Li-Yan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong, PR China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong, PR China
- Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, PR China
| | - En-Min Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong, PR China
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20
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Rocha H, Simões PA, Budrewicz J, Lara-Gonzalez P, Carvalho AX, Dumont J, Desai A, Gassmann R. Nuclear-enriched protein phosphatase 4 ensures outer kinetochore assembly prior to nuclear dissolution. J Cell Biol 2023; 222:213846. [PMID: 36719399 PMCID: PMC9930252 DOI: 10.1083/jcb.202208154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/15/2022] [Accepted: 01/05/2023] [Indexed: 02/01/2023] Open
Abstract
A landmark event in the transition from interphase to mitosis in metazoans is nuclear envelope breakdown (NEBD). Important mitotic events occur prior to NEBD, including condensation of replicated chromosomes and assembly of kinetochores to rapidly engage spindle microtubules. Here, we show that nuclear-enriched protein phosphatase 4 (PP4) ensures robust assembly of the microtubule-coupling outer kinetochore prior to NEBD. In the absence of PP4, chromosomes exhibit extended monopolar orientation after NEBD and subsequently mis-segregate. A secondary consequence of diminished outer kinetochore assembly is defective sister chromatid resolution. After NEBD, a cytoplasmic activity compensates for PP4 loss, leading to outer kinetochore assembly and recovery of chromosomes from monopolar orientation to significant bi-orientation. The Ndc80-Ska microtubule-binding module of the outer kinetochore is required for this recovery. PP4 associates with the inner kinetochore protein CENP-C; however, disrupting the PP4-CENP-C interaction does not perturb chromosome segregation. These results establish that PP4-dependent outer kinetochore assembly prior to NEBD is critical for timely and proper engagement of chromosomes with spindle microtubules.
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Affiliation(s)
- Helder Rocha
- https://ror.org/05qpmg879Instituto de Investigação e Inovação em Saúde – i3S, Universidade do Porto, Porto, Portugal,Instituto de Biologia Molecular e Celular – IBMC, Universidade do Porto, Porto, Portugal
| | - Patrícia A. Simões
- https://ror.org/05qpmg879Instituto de Investigação e Inovação em Saúde – i3S, Universidade do Porto, Porto, Portugal,Instituto de Biologia Molecular e Celular – IBMC, Universidade do Porto, Porto, Portugal
| | - Jacqueline Budrewicz
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA, USA,Division of Biological Sciences, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Pablo Lara-Gonzalez
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA, USA,Division of Biological Sciences, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ana Xavier Carvalho
- https://ror.org/05qpmg879Instituto de Investigação e Inovação em Saúde – i3S, Universidade do Porto, Porto, Portugal,Instituto de Biologia Molecular e Celular – IBMC, Universidade do Porto, Porto, Portugal
| | - Julien Dumont
- https://ror.org/02c5gc203Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Arshad Desai
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA, USA,Division of Biological Sciences, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Reto Gassmann
- https://ror.org/05qpmg879Instituto de Investigação e Inovação em Saúde – i3S, Universidade do Porto, Porto, Portugal,Instituto de Biologia Molecular e Celular – IBMC, Universidade do Porto, Porto, Portugal
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21
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Pandey P, Khan F, Upadhyay TK, Sharangi AB. Deciphering the Immunomodulatory Role of Cyclin-Dependent Kinase 4/6 Inhibitors in the Tumor Microenvironment. Int J Mol Sci 2023; 24:ijms24032236. [PMID: 36768557 PMCID: PMC9916547 DOI: 10.3390/ijms24032236] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
Cancer is characterized by persistent cell proliferation driven by aberrant cell cycle regulation and stimulation of cyclin-dependent kinases (CDKs). A very intriguing and potential approach for the development of antitumor medicines is the suppression of CDKs that lead to induction of apoptosis and cell cycle arrest. The shift of the cell cycle from the G0/G1 phase to the S phase, which is characterized by active transcription and synthesis, depends on the development of the cyclin D-CDK4/6 complex. A precise balance between anticancer activity and general toxicity is demonstrated by CDK inhibitors, which can specifically block CDK4/6 and control the cell cycle by reducing the G1 to S phase transition. CDK4/6 inhibitors have recently been reported to exhibit significant cell growth inhibition via modulating the tumour microenvironment in cancerous cells. One significant new understanding is that these inhibitors serve important functions in the interaction among tumour cells and the host immune system in addition to being cytostatic. Herein, we discuss the biological significance of CDK4/6 inhibitors in cancer therapeutics, as well as their biological impact on T cells and other important immune cells. Furthermore, we explore the integration of preclinical findings of these pharmaceuticals' ability to enhance antitumor immunity.
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Affiliation(s)
- Pratibha Pandey
- Department of Biotechnology, Noida Institute of Engineering and Technology, 19, Knowledge Park-II, Institutional Area, Greater Noida 201306, India
| | - Fahad Khan
- Department of Biotechnology, Noida Institute of Engineering and Technology, 19, Knowledge Park-II, Institutional Area, Greater Noida 201306, India
- Correspondence:
| | - Tarun Kumar Upadhyay
- Department of Biotechnology, Parul Institute of Applied Sciences and Centre of Research for Development, Parul University, Vadodara 391760, India
| | - Amit Baran Sharangi
- Department of Plantation Spices Medicinal and Aromatic Crops, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur 741252, India
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22
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Roh S, Lee T, Cheong DY, Kim Y, Oh S, Lee G. Direct observation of surface charge and stiffness of human metaphase chromosomes. Nanoscale Adv 2023; 5:368-377. [PMID: 36756276 PMCID: PMC9846444 DOI: 10.1039/d2na00620k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/17/2022] [Indexed: 06/18/2023]
Abstract
Metaphase chromosomes in which both polynucleotides and proteins are condensed with hierarchies are closely related to life phenomena such as cell division, cancer development, and cellular senescence. Nevertheless, their nature is rarely revealed, owing to their structural complexity and technical limitations in analytical methods. In this study, we used surface potential and nanomechanics mapping technology based on atomic force microscopy to measure the surface charge and intrinsic stiffness of metaphase chromosomes. We found that extra materials covering the chromosomes after the extraction process were positively charged. With the covering materials, the chromosomes were positively charged (ca. 44.9 ± 16.48 mV) and showed uniform stiffness (ca. 6.23 ± 1.98 MPa). In contrast, after getting rid of the extra materials through treatment with RNase and protease, the chromosomes were strongly negatively charged (ca. -197.4 ± 77.87 mV) and showed relatively non-uniform and augmented stiffness (ca. 36.87 ± 17.56 MPa). The results suggested undulating but compact coordination of condensed chromosomes. Additionally, excessive treatment with RNase and protease could destroy the chromosomal structure, providing an exceptional opportunity for multiscale stiffness mapping of polynucleotides, nucleosomes, chromatin fibers, and chromosomes in a single image. Our approach offers a new horizon in terms of an analytical technique for studying chromosome-related diseases.
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Affiliation(s)
- Seokbeom Roh
- Department of Biotechnology and Bioinformatics, Korea University Sejong 30019 Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University Sejong 30019 Korea
| | - Taeha Lee
- Department of Biotechnology and Bioinformatics, Korea University Sejong 30019 Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University Sejong 30019 Korea
| | - Da Yeon Cheong
- Department of Biotechnology and Bioinformatics, Korea University Sejong 30019 Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University Sejong 30019 Korea
| | - Yeonjin Kim
- Department of Biotechnology and Bioinformatics, Korea University Sejong 30019 Korea
| | - Soohwan Oh
- College of Pharmacy, Korea University Sejong 30019 Korea
| | - Gyudo Lee
- Department of Biotechnology and Bioinformatics, Korea University Sejong 30019 Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University Sejong 30019 Korea
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23
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van der Zanden SY, Jongsma MLM, Neefjes ACM, Berlin I, Neefjes J. Maintaining soluble protein homeostasis between nuclear and cytoplasmic compartments across mitosis. Trends Cell Biol 2023; 33:18-29. [PMID: 35778326 DOI: 10.1016/j.tcb.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/23/2022] [Accepted: 06/06/2022] [Indexed: 12/27/2022]
Abstract
The nuclear envelope (NE) is central to the architecture of eukaryotic cells, both as a physical barrier separating the nucleus from the cytoplasm and as gatekeeper of selective transport between them. However, in open mitosis, the NE fragments to allow for spindle formation and segregation of chromosomes, resulting in intermixing of nuclear and cytoplasmic soluble fractions. Recent studies have shed new light on the mechanisms driving reinstatement of soluble proteome homeostasis following NE reformation in daughter cells. Here, we provide an overview of how mitotic cells confront this challenge to ensure continuity of basic cellular functions across generations and elaborate on the implications for the proteasome - a macromolecular machine that functions in both cytoplasmic and nuclear compartments.
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Affiliation(s)
- Sabina Y van der Zanden
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands
| | - Marlieke L M Jongsma
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands
| | - Anna C M Neefjes
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands
| | - Ilana Berlin
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands.
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands.
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24
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Wang L, Dong X, Wu Y, Zhou Q, Xu R, Ren L, Zhang C, Tao M, Luo K, Zeng Y, Liu S. Proteomics-based molecular and functional characteristic profiling of muscle tissue in Triploid crucian carp. Mol Omics 2022; 18:967-976. [PMID: 36349986 DOI: 10.1039/d2mo00215a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Triploid crucian carp (TCC) is a kind of artificially bred fish with huge economic value to China. It has several excellent characteristics, such as fast growth, strong disease resistance and delicious taste. However, as a regionally specific fish, the underlying molecular mechanisms of these characteristics are largely unknown. In this study, we performed quantitative proteomics on the muscle tissues of TCC and its parents, allotetraploid (♂), red crucian carp (♀) and common carp. Combined with multiple bioinformatic analysis, we found that the taste of TCC can be mainly attributed to umami amino acid-enriched proteins such as PURBA, PVALBI and ATP5F1B, and that its rapid growth can be mainly ascribed to the high expression and regulation of metabolism-related proteins such as NDUFS1, ENO1A and CS. These play significant roles in substrate and energy metabolism, as well as in bias transformation. Subsequently, we identified several proteins, including MDH1AA, GOT1 and DLAT, that may serve as potential regulators of innate immunity by regulating the biosynthesis and transformation of significant antibiotics and antimicrobial peptides. In conclusion, this study can serve as a significant reference for similar investigations and shed light on the molecular and biological functions of individual proteins in TCC muscle tissue.
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Affiliation(s)
- Lingxiang Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China. .,National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Xiaoping Dong
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China. .,National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Yun Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China. .,National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Qian Zhou
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Rongfang Xu
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China.
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China.
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China.
| | - Kaikun Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China.
| | - Yong Zeng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China. .,National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China.
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25
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Randall RS, Jourdain C, Nowicka A, Kaduchová K, Kubová M, Ayoub MA, Schubert V, Tatout C, Colas I, Kalyanikrishna, Desset S, Mermet S, Boulaflous-Stevens A, Kubalová I, Mandáková T, Heckmann S, Lysak MA, Panatta M, Santoro R, Schubert D, Pecinka A, Routh D, Baroux C. Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes. Nucleus 2022; 13:277-299. [PMID: 36447428 PMCID: PMC9754023 DOI: 10.1080/19491034.2022.2144013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Nucleus, chromatin, and chromosome organization studies heavily rely on fluorescence microscopy imaging to elucidate the distribution and abundance of structural and regulatory components. Three-dimensional (3D) image stacks are a source of quantitative data on signal intensity level and distribution and on the type and shape of distribution patterns in space. Their analysis can lead to novel insights that are otherwise missed in qualitative-only analyses. Quantitative image analysis requires specific software and workflows for image rendering, processing, segmentation, setting measurement points and reference frames and exporting target data before further numerical processing and plotting. These tasks often call for the development of customized computational scripts and require an expertise that is not broadly available to the community of experimental biologists. Yet, the increasing accessibility of high- and super-resolution imaging methods fuels the demand for user-friendly image analysis workflows. Here, we provide a compendium of strategies developed by participants of a training school from the COST action INDEPTH to analyze the spatial distribution of nuclear and chromosomal signals from 3D image stacks, acquired by diffraction-limited confocal microscopy and super-resolution microscopy methods (SIM and STED). While the examples make use of one specific commercial software package, the workflows can easily be adapted to concurrent commercial and open-source software. The aim is to encourage biologists lacking custom-script-based expertise to venture into quantitative image analysis and to better exploit the discovery potential of their images.Abbreviations: 3D FISH: three-dimensional fluorescence in situ hybridization; 3D: three-dimensional; ASY1: ASYNAPTIC 1; CC: chromocenters; CO: Crossover; DAPI: 4',6-diamidino-2-phenylindole; DMC1: DNA MEIOTIC RECOMBINASE 1; DSB: Double-Strand Break; FISH: fluorescence in situ hybridization; GFP: GREEN FLUORESCENT PROTEIN; HEI10: HUMAN ENHANCER OF INVASION 10; NCO: Non-Crossover; NE: Nuclear Envelope; Oligo-FISH: oligonucleotide fluorescence in situ hybridization; RNPII: RNA Polymerase II; SC: Synaptonemal Complex; SIM: structured illumination microscopy; ZMM (ZIP: MSH4: MSH5 and MER3 proteins); ZYP1: ZIPPER-LIKE PROTEIN 1.
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Affiliation(s)
- Ricardo S Randall
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | | | - Anna Nowicka
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany, v. v. i. (IEB), Olomouc, Czech Republic
| | - Kateřina Kaduchová
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany, v. v. i. (IEB), Olomouc, Czech Republic
| | - Michaela Kubová
- Central European Institute of Technology (CEITEC) and Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Mohammad A. Ayoub
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466Seeland, Germany
| | - Christophe Tatout
- Institut Génétique, Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, 63001Clermont-Ferrand, France
| | - Isabelle Colas
- The James Hutton Institute, Errol Road, Invergowrie, DD2 5DA, Scotland UK
| | | | - Sophie Desset
- Institut Génétique, Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, 63001Clermont-Ferrand, France
| | - Sarah Mermet
- Institut Génétique, Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, 63001Clermont-Ferrand, France
| | - Aurélia Boulaflous-Stevens
- Institut Génétique, Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, 63001Clermont-Ferrand, France
| | - Ivona Kubalová
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466Seeland, Germany
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC) and Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466Seeland, Germany
| | - Martin A. Lysak
- Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Martina Panatta
- Department of Molecular Mechanisms of Disease, DMMD, University of Zürich, Zürich, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease, DMMD, University of Zürich, Zürich, Switzerland
| | | | - Ales Pecinka
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany, v. v. i. (IEB), Olomouc, Czech Republic
| | - Devin Routh
- Service and Support for Science IT (S3IT), Universität Zürich, Zürich, Switzerland
| | - Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland,CONTACT Célia Baroux Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
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26
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Archambault V, Li J, Emond-Fraser V, Larouche M. Dephosphorylation in nuclear reassembly after mitosis. Front Cell Dev Biol 2022; 10:1012768. [PMID: 36268509 PMCID: PMC9576876 DOI: 10.3389/fcell.2022.1012768] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
In most animal cell types, the interphase nucleus is largely disassembled during mitotic entry. The nuclear envelope breaks down and chromosomes are compacted into separated masses. Chromatin organization is also mostly lost and kinetochores assemble on centromeres. Mitotic protein kinases play several roles in inducing these transformations by phosphorylating multiple effector proteins. In many of these events, the mechanistic consequences of phosphorylation have been characterized. In comparison, how the nucleus reassembles at the end of mitosis is less well understood in mechanistic terms. In recent years, much progress has been made in deciphering how dephosphorylation of several effector proteins promotes nuclear envelope reassembly, chromosome decondensation, kinetochore disassembly and interphase chromatin organization. The precise roles of protein phosphatases in this process, in particular of the PP1 and PP2A groups, are emerging. Moreover, how these enzymes are temporally and spatially regulated to ensure that nuclear reassembly progresses in a coordinated manner has been partly uncovered. This review provides a global view of nuclear reassembly with a focus on the roles of dephosphorylation events. It also identifies important open questions and proposes hypotheses.
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Affiliation(s)
- Vincent Archambault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
- *Correspondence: Vincent Archambault,
| | - Jingjing Li
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Virginie Emond-Fraser
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Myreille Larouche
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
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27
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Yoshida MM, Kinoshita K, Aizawa Y, Tane S, Yamashita D, Shintomi K, Hirano T. Molecular dissection of condensin II-mediated chromosome assembly using in vitro assays. eLife 2022; 11:78984. [PMID: 35983835 PMCID: PMC9433093 DOI: 10.7554/elife.78984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 08/11/2022] [Indexed: 11/18/2022] Open
Abstract
In vertebrates, condensin I and condensin II cooperate to assemble rod-shaped chromosomes during mitosis. Although the mechanism of action and regulation of condensin I have been studied extensively, our corresponding knowledge of condensin II remains very limited. By introducing recombinant condensin II complexes into Xenopus egg extracts, we dissect the roles of its individual subunits in chromosome assembly. We find that one of two HEAT subunits, CAP-D3, plays a crucial role in condensin II-mediated assembly of chromosome axes, whereas the other HEAT subunit, CAP-G2, has a very strong negative impact on this process. The structural maintenance of chromosomes ATPase and the basic amino acid clusters of the kleisin subunit CAP-H2 are essential for this process. Deletion of the C-terminal tail of CAP-D3 increases the ability of condensin II to assemble chromosomes and further exposes a hidden function of CAP-G2 in the lateral compaction of chromosomes. Taken together, our results uncover a multilayered regulatory mechanism unique to condensin II, and provide profound implications for the evolution of condensin II.
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Affiliation(s)
| | | | - Yuuki Aizawa
- Chromosome Dynamics Laboratory, RIKEN, Wako, Japan
| | - Shoji Tane
- Chromosome Dynamics Laboratory, RIKEN, Wako, Japan
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28
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Huang F, Chen L, Guo W, Huang T, Cai Y, Yang F. Identification of Human Cell Cycle Phase Markers Based on Single-Cell RNA-Seq Data by Using Machine Learning Methods. BioMed Research International 2022; 2022:1-19. [PMID: 36004205 PMCID: PMC9393965 DOI: 10.1155/2022/2516653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 12/17/2022]
Abstract
The cell cycle is composed of a series of ordered, highly regulated processes through which a cell grows and duplicates its genome and eventually divides into two daughter cells. According to the complex changes in cell structure and biosynthesis, the cell cycle is divided into four phases: gap 1 (G1), DNA synthesis (S), gap 2 (G2), and mitosis (M). Determining which cell cycle phases a cell is in is critical to the research of cancer development and pharmacy for targeting cell cycle. However, current detection methods have the following problems: (1) they are complicated and time consuming to perform, and (2) they cannot detect the cell cycle on a large scale. Rapid developments in single-cell technology have made dissecting cells on a large scale possible with unprecedented resolution. In the present research, we construct efficient classifiers and identify essential gene biomarkers based on single-cell RNA sequencing data through Boruta and three feature ranking algorithms (e.g., mRMR, MCFS, and SHAP by LightGBM) by utilizing four advanced classification algorithms. Meanwhile, we mine a series of classification rules that can distinguish different cell cycle phases. Collectively, we have provided a novel method for determining the cell cycle and identified new potential cell cycle-related genes, thereby contributing to the understanding of the processes that regulate the cell cycle.
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29
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Schneider MWG, Gibson BA, Otsuka S, Spicer MFD, Petrovic M, Blaukopf C, Langer CCH, Batty P, Nagaraju T, Doolittle LK, Rosen MK, Gerlich DW. A mitotic chromatin phase transition prevents perforation by microtubules. Nature 2022. [PMID: 35922507 DOI: 10.1038/s41586-022-05027-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 06/27/2022] [Indexed: 12/20/2022]
Abstract
Dividing eukaryotic cells package extremely long chromosomal DNA molecules into discrete bodies to enable microtubule-mediated transport of one genome copy to each of the newly forming daughter cells1–3. Assembly of mitotic chromosomes involves DNA looping by condensin4–8 and chromatin compaction by global histone deacetylation9–13. Although condensin confers mechanical resistance to spindle pulling forces14–16, it is not known how histone deacetylation affects material properties and, as a consequence, segregation mechanics of mitotic chromosomes. Here we show how global histone deacetylation at the onset of mitosis induces a chromatin-intrinsic phase transition that endows chromosomes with the physical characteristics necessary for their precise movement during cell division. Deacetylation-mediated compaction of chromatin forms a structure dense in negative charge and allows mitotic chromosomes to resist perforation by microtubules as they are pushed to the metaphase plate. By contrast, hyperacetylated mitotic chromosomes lack a defined surface boundary, are frequently perforated by microtubules and are prone to missegregation. Our study highlights the different contributions of DNA loop formation and chromatin phase separation to genome segregation in dividing cells. Histone deacetylation at the onset of mitosis induces a chromatin-intrinsic phase transition that endows chromosomes with the physical characteristics necessary for their precise movement during cell division.
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Liu L, Chen H, Chen X, Yao C, Shen W, Jia C. KNTC1 as a putative tumor oncogene in pancreatic cancer. J Cancer Res Clin Oncol 2022:10.1007/s00432-022-04146-3. [DOI: 10.1007/s00432-022-04146-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/13/2022] [Indexed: 12/09/2022]
Abstract
Abstract
Purpose
Recent studies have demonstrated that kinetochore-associated protein 1 (KNTC1) plays a significant role in the carcinogenesis of numerous types of cancer. This study aimed to explore the role and possible mechanisms of KNTC1 in the development of pancreatic cancer.
Methods and results
We analyzed differentially expressed genes by RNA sequencing in three paired pancreatic cancer and para-cancerous tissue samples and found that the expression of KNTC1 was significantly upregulated in pancreatic cancer. A Cancer and Tumor Gene Map pan-analysis showed that high expression of KNTC1 was related to poor prognosis in 9499 tumor samples. With immunohistochemical staining, we found that the high expression of KNTC1 in pancreatic cancer was related to pathological grade and clinical prognosis. Similarly, RT-PCR results indicated that the expression of KNTC1 was higher in three groups of pancreatic cancer cell lines (BxPC-3, PANC-1, and SW1990) than in normal pancreatic ductal cells. We introduced lentivirus-mediated shRNA targeting KNTC1 into PANC-1 and SW1990 cells and found that KNTC1 knockdown significantly decreased cell growth and increased cell apoptosis compared to the control group cells. Bioinformatic analysis of the cell expression profile revealed that differential genes were mainly enriched in the cell cycle, mitosis, and STAT3 signaling pathways, and co-immunoprecipitation confirmed an interaction between KNTC1 and cell division cycle associated 8.
Conclusions
KNTC1 could be linked to the pathophysiology of pancreatic cancer and may be an early diagnostic marker of cervical precancerous lesions.
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Moreno-Andrés D, Bhattacharyya A, Scheufen A, Stegmaier J. LiveCellMiner: A new tool to analyze mitotic progression. PLoS One 2022; 17:e0270923. [PMID: 35797385 PMCID: PMC9262191 DOI: 10.1371/journal.pone.0270923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
Live-cell imaging has become state of the art to accurately identify the nature of mitotic and cell cycle defects. Low- and high-throughput microscopy setups have yield huge data amounts of cells recorded in different experimental and pathological conditions. Tailored semi-automated and automated image analysis approaches allow the analysis of high-content screening data sets, saving time and avoiding bias. However, they were mostly designed for very specific experimental setups, which restricts their flexibility and usability. The general need for dedicated experiment-specific user-annotated training sets and experiment-specific user-defined segmentation parameters remains a major bottleneck for fully automating the analysis process. In this work we present LiveCellMiner, a highly flexible open-source software tool to automatically extract, analyze and visualize both aggregated and time-resolved image features with potential biological relevance. The software tool allows analysis across high-content data sets obtained in different platforms, in a quantitative and unbiased manner. As proof of principle application, we analyze here the dynamic chromatin and tubulin cytoskeleton features in human cells passing through mitosis highlighting the versatile and flexible potential of this tool set.
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Affiliation(s)
- Daniel Moreno-Andrés
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
- * E-mail: (DMA), (JS)
| | - Anuk Bhattacharyya
- Institute of Imaging and Computer Vision, RWTH Aachen University, Aachen, Germany
| | - Anja Scheufen
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Johannes Stegmaier
- Institute of Imaging and Computer Vision, RWTH Aachen University, Aachen, Germany
- * E-mail: (DMA), (JS)
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Matsuo K. Photopharmacological Tools for Mitotic Cell Division. YAKUGAKU ZASSHI 2022; 142:513-519. [DOI: 10.1248/yakushi.21-00203-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Kazuya Matsuo
- Research Institute for Electronic Science, Hokkaido University
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Mitter M, Takacs Z, Köcher T, Micura R, Langer CCH, Gerlich DW. Sister chromatid-sensitive Hi-C to map the conformation of replicated genomes. Nat Protoc 2022. [PMID: 35478248 DOI: 10.1038/s41596-022-00687-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 01/19/2022] [Indexed: 12/23/2022]
Abstract
Chromosome conformation capture (Hi-C) techniques map the 3D organization of entire genomes. How sister chromatids fold in replicated chromosomes, however, cannot be determined with conventional Hi-C because of the identical DNA sequences of sister chromatids. Here, we present a protocol for sister chromatid-sensitive Hi-C (scsHi-C) that enables the distinction of DNA contacts within individual sister chromatids (cis sister contacts) from those between sister chromatids (trans sister contacts), thereby allowing investigation of the organization of replicated genomes. scsHi-C is based on live-cell labeling of nascent DNA by the synthetic nucleoside 4-thio-thymidine (4sT), which incorporates into a distinct DNA strand on each sister chromatid because of semi-conservative DNA replication. After purification of genomic DNA and in situ Hi-C library preparation, 4sT is chemically converted into 5-methyl-cytosine in the presence of OsO4/NH4Cl to introduce T-to-C signature point mutations on 4sT-labeled DNA. The Hi-C library is then sequenced, and ligated fragments are assigned to sister chromatids on the basis of strand orientation and the presence of signature mutations. The ensemble of scsHi-C contacts thereby represents genome-wide contact probabilities within and across sister chromatids. scsHi-C can be completed in 2 weeks, has been successfully applied in HeLa cells and can potentially be established for any cell type that allows proper cell cycle synchronization and incorporation of sufficient amounts of 4sT. The genome-wide maps of replicated chromosomes detected by scsHi-C enable investigation of the molecular mechanisms shaping sister chromatid topologies and the relevance of sister chromatid conformation in crucial processes like DNA repair, mitotic chromosome formation and potentially other biological processes.
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Choi EH, Yoon S, Koh YE, Hong TK, Do JT, Lee BK, Hahn Y, Kim KP. Meiosis-specific cohesin complexes display essential and distinct roles in mitotic embryonic stem cell chromosomes. Genome Biol 2022; 23:70. [PMID: 35241136 PMCID: PMC8892811 DOI: 10.1186/s13059-022-02632-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/14/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Cohesin is a chromosome-associated SMC-kleisin complex that mediates sister chromatid cohesion, recombination, and most chromosomal processes during mitosis and meiosis. However, it remains unclear whether meiosis-specific cohesin complexes are functionally active in mitotic chromosomes. RESULTS Through high-resolution 3D-structured illumination microscopy (3D-SIM) and functional analyses, we report multiple biological processes associated with the meiosis-specific cohesin components, α-kleisin REC8 and STAG3, and the distinct loss of function of meiotic cohesin during the cell cycle of embryonic stem cells (ESCs). First, we show that STAG3 is required for the efficient localization of REC8 to the nucleus by interacting with REC8. REC8-STAG3-containing cohesin regulates topological properties of chromosomes and maintains sister chromatid cohesion. Second, REC8-cohesin has additional sister chromatid cohesion roles in concert with mitotic RAD21-cohesin on ESC chromosomes. SIM imaging of REC8 and RAD21 co-staining revealed that the two types of α-kleisin subunits exhibited distinct loading patterns along ESC chromosomes. Third, knockdown of REC8 or RAD21-cohesin not only leads to higher rates of premature sister chromatid separation and delayed replication fork progression, which can cause proliferation and developmental defects, but also enhances chromosome compaction by hyperloading of retinoblastoma protein-condensin complexes from the prophase onward. CONCLUSIONS Our findings indicate that the delicate balance between mitotic and meiotic cohesins may regulate ESC-specific chromosomal organization and the mitotic program.
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Affiliation(s)
- Eui-Hwan Choi
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, South Korea
| | - Seobin Yoon
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, South Korea
| | - Young Eun Koh
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, South Korea
| | - Tae Kyung Hong
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, South Korea
| | - Jeong Tae Do
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, South Korea
| | - Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University of Albany-State University of New York, Rensselaer, NY, USA
| | - Yoonsoo Hahn
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, South Korea
| | - Keun P Kim
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, South Korea.
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Abstract
Proteomics has revealed that the ~20,000 human genes engender a far greater number of proteins, or proteoforms, that are diversified in large part by post-translational modifications (PTMs). How such PTMs affect protein structure and function is an active area of research but remains technically challenging to assess on a proteome-wide scale. Here, we describe a chemical proteomic method to quantitatively relate serine/threonine phosphorylation to changes in the reactivity of cysteine residues, a parameter that can affect the potential for cysteines to be post-translationally modified or engaged by covalent drugs. Leveraging the extensive high-stoichiometry phosphorylation occurring in mitotic cells, we discover numerous cysteines that exhibit phosphorylation-dependent changes in reactivity on diverse proteins enriched in cell cycle regulatory pathways. The discovery of bidirectional changes in cysteine reactivity often occurring in proximity to serine/threonine phosphorylation events points to the broad impact of phosphorylation on the chemical reactivity of proteins and the future potential to create small-molecule probes that differentially target proteoforms with PTMs.
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Affiliation(s)
- Esther K Kemper
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Yuanjin Zhang
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Melissa M Dix
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Benjamin F Cravatt
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
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Brändle F, Frühbauer B, Jagannathan M. Principles and functions of pericentromeric satellite DNA clustering into chromocenters. Semin Cell Dev Biol 2022; 128:26-39. [PMID: 35144860 DOI: 10.1016/j.semcdb.2022.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 12/29/2022]
Abstract
Simple non-coding tandem repeats known as satellite DNA are observed widely across eukaryotes. These repeats occupy vast regions at the centromere and pericentromere of chromosomes but their contribution to cellular function has remained incompletely understood. Here, we review the literature on pericentromeric satellite DNA and discuss its organization and functions across eukaryotic species. We specifically focus on chromocenters, DNA-dense nuclear foci that contain clustered pericentromeric satellite DNA repeats from multiple chromosomes. We first discuss chromocenter formation and the roles that epigenetic modifications, satellite DNA transcripts and sequence-specific satellite DNA-binding play in this process. We then review the newly emerging functions of chromocenters in genome encapsulation, the maintenance of cell fate and speciation. We specifically highlight how the rapid divergence of satellite DNA repeats impacts reproductive isolation between closely related species. Together, we underline the importance of this so-called 'junk DNA' in fundamental biological processes.
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Affiliation(s)
- Franziska Brändle
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland
| | - Benjamin Frühbauer
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland
| | - Madhav Jagannathan
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland.
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Shankar R, Lettman MM, Whisler W, Frankel EB, Audhya A. The ESCRT machinery directs quality control over inner nuclear membrane architecture. Cell Rep 2022; 38:110263. [PMID: 35045304 PMCID: PMC8801257 DOI: 10.1016/j.celrep.2021.110263] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 11/21/2021] [Accepted: 12/21/2021] [Indexed: 11/20/2022] Open
Abstract
The late-acting endosomal sorting complex required for transport (ESCRT) machinery has been implicated in facilitating the resealing of the nuclear envelope (NE) after mitosis, enabling compartmentalization of the genome away from the cytoplasm. Here, we leverage the stereotypic first division of the C. elegans embryo to identify additional functions of the ESCRT machinery in maintaining the structure of the inner nuclear membrane. Specifically, impaired ESCRT function results in a defect in the pruning of inner nuclear membrane invaginations, which arise normally during NE reformation and expansion. Additionally, in combination with a hypomorphic mutation that interferes with assembly of the underlying nuclear lamina, inhibition of ESCRT function significantly perturbs NE architecture and increases chromosome segregation defects, resulting in penetrant embryonic lethality. Our findings highlight links between ESCRT-mediated inner nuclear membrane remodeling, maintenance of nuclear envelope morphology, and the preservation of the genome during early development. In this study, Shankar et al. demonstrate that defects in ESCRT machinery functions impair pruning of inner nuclear membrane invaginations that form normally after mitotic exit as the nuclear envelope undergoes expansion. These findings highlight a critical role for the ESCRT machinery in the maintenance of inner nuclear membrane morphology.
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Affiliation(s)
- Raakhee Shankar
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Molly M Lettman
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - William Whisler
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Elisa B Frankel
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.
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Tane S, Shintomi K, Kinoshita K, Tsubota Y, Yoshida MM, Nishiyama T, Hirano T. Cell cycle-specific loading of condensin I is regulated by the N-terminal tail of its kleisin subunit. eLife 2022; 11:84694. [PMID: 36511239 PMCID: PMC9797191 DOI: 10.7554/elife.84694] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Condensin I is a pentameric protein complex that plays an essential role in mitotic chromosome assembly in eukaryotic cells. Although it has been shown that condensin I loading is mitosis specific, it remains poorly understood how the robust cell cycle regulation of condensin I is achieved. Here, we set up a panel of in vitro assays to demonstrate that cell cycle-specific loading of condensin I is regulated by the N-terminal tail (N-tail) of its kleisin subunit CAP-H. Deletion of the N-tail accelerates condensin I loading and chromosome assembly in Xenopus egg mitotic extracts. Phosphorylation-deficient and phosphorylation-mimetic mutations in the CAP-H N-tail decelerate and accelerate condensin I loading, respectively. Remarkably, deletion of the N-tail enables condensin I to assemble mitotic chromosome-like structures even in interphase extracts. Together with other extract-free functional assays in vitro, our results uncover one of the multilayered mechanisms that ensure cell cycle-specific loading of condensin I onto chromosomes.
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Affiliation(s)
- Shoji Tane
- Chromosome Dynamics Laboratory, RIKENWakoJapan
| | | | | | - Yuko Tsubota
- Division of Biological Sciences, Graduate School of Science, Nagoya UniversityNagoyaJapan
| | | | - Tomoko Nishiyama
- Division of Biological Sciences, Graduate School of Science, Nagoya UniversityNagoyaJapan
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Gönenc II, Wolff A, Schmidt J, Zibat A, Müller C, Cyganek L, Argyriou L, Räschle M, Yigit G, Wollnik B. OUP accepted manuscript. Hum Mol Genet 2022; 31:2185-2193. [PMID: 35099000 PMCID: PMC9262399 DOI: 10.1093/hmg/ddab373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/02/2021] [Accepted: 12/27/2021] [Indexed: 11/12/2022] Open
Abstract
Bloom syndrome (BS) is an autosomal recessive disease clinically characterized by primary microcephaly, growth deficiency, immunodeficiency and predisposition to cancer. It is mainly caused by biallelic loss-of-function mutations in the BLM gene, which encodes the BLM helicase, acting in DNA replication and repair processes. Here, we describe the gene expression profiles of three BS fibroblast cell lines harboring causative, biallelic truncating mutations obtained by single-cell (sc) transcriptome analysis. We compared the scRNA transcription profiles from three BS patient cell lines to two age-matched wild-type controls and observed specific deregulation of gene sets related to the molecular processes characteristically affected in BS, such as mitosis, chromosome segregation, cell cycle regulation and genomic instability. We also found specific upregulation of genes of the Fanconi anemia pathway, in particular FANCM, FANCD2 and FANCI, which encode known interaction partners of BLM. The significant deregulation of genes associated with inherited forms of primary microcephaly observed in our study might explain in part the molecular pathogenesis of microcephaly in BS, one of the main clinical characteristics in patients. Finally, our data provide first evidence of a novel link between BLM dysfunction and transcriptional changes in condensin complex I and II genes. Overall, our study provides novel insights into gene expression profiles in BS on an sc level, linking specific genes and pathways to BLM dysfunction.
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Affiliation(s)
| | | | - Julia Schmidt
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Arne Zibat
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Christian Müller
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Lukas Cyganek
- Stem Cell Unit, Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, 37075 Göttingen, Germany
| | - Loukas Argyriou
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Markus Räschle
- Department of Molecular Genetics, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Gökhan Yigit
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, 37075 Göttingen, Germany
| | - Bernd Wollnik
- To whom correspondence should be addressed at: Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073 Göttingen, Germany. Tel: +49 5513960606; Fax: +49 5513969303;
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Parker MW, Kao JA, Huang A, Berger JM, Botchan MR. Molecular determinants of phase separation for Drosophila DNA replication licensing factors. eLife 2021; 10:e70535. [PMID: 34951585 PMCID: PMC8813052 DOI: 10.7554/elife.70535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 12/23/2021] [Indexed: 12/02/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) of intrinsically disordered regions (IDRs) in proteins can drive the formation of membraneless compartments in cells. Phase-separated structures enrich for specific partner proteins and exclude others. Previously, we showed that the IDRs of metazoan DNA replication initiators drive DNA-dependent phase separation in vitro and chromosome binding in vivo, and that initiator condensates selectively recruit replication-specific partner proteins (Parker et al., 2019). How initiator IDRs facilitate LLPS and maintain compositional specificity is unknown. Here, using Drosophila melanogaster (Dm) Cdt1 as a model initiation factor, we show that phase separation results from a synergy between electrostatic DNA-bridging interactions and hydrophobic inter-IDR contacts. Both sets of interactions depend on sequence composition (but not sequence order), are resistant to 1,6-hexanediol, and do not depend on aromaticity. These findings demonstrate that distinct sets of interactions drive condensate formation and specificity across different phase-separating systems and advance efforts to predict IDR LLPS propensity and partner selection a priori.
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Affiliation(s)
- Matthew W Parker
- Department of Biophysics, University of Texas Southwestern Medical CenterDallasUnited States
| | - Jonchee A Kao
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Alvin Huang
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of MedicineBaltimoreUnited States
| | - Michael R Botchan
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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Li JN, Wang MY, Chen YT, Kuo YL, Chen PS. Expression of SnoRNA U50A Is Associated with Better Prognosis and Prolonged Mitosis in Breast Cancer. Cancers (Basel) 2021; 13:cancers13246304. [PMID: 34944924 PMCID: PMC8699759 DOI: 10.3390/cancers13246304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/22/2021] [Accepted: 11/26/2021] [Indexed: 11/24/2022] Open
Abstract
Simple Summary SnoRNAs are essential for fundamental cellular processes. However, emerging evidence shows that snoRNAs play regulatory roles during cancer progression. The snoRNA U50A (U50A) is a newly-identified putative tumor suppressor, but its clinical and mechanistic impacts in breast cancer remain elusive. In this study, we quantified the copy number of U50A in breast cancer patient tissues and found that a higher level of U50A expression is correlated with better overall survival in breast cancer patients. By utilizing transcriptomic analysis, we demonstrated that U50A prolongs mitosis and reduces colony-forming ability through downregulating mitosis-related genes. Consistent with these in vitro results, breast cancer tissues expressing higher U50A significantly exhibited accumulated mitotic tumor cells and were associated with reduced tumor size. Altogether, this is the first study showing the clinical, cellular, and regulatory impacts of snoRNA U50A in human breast cancer. Abstract Small nucleolar RNAs (snoRNAs) are small noncoding RNAs generally recognized as housekeeping genes. Genomic analysis has shown that snoRNA U50A (U50A) is a candidate tumor suppressor gene deleted in less than 10% of breast cancer patients. To date, the pathological roles of U50A in cancer, including its clinical significance and its regulatory impact at the molecular level, are not well-defined. Here, we quantified the copy number of U50A in human breast cancer tissues. Our results showed that the U50A expression level is correlated with better prognosis in breast cancer patients. Utilizing RNA-sequencing for transcriptomic analysis, we revealed that U50A downregulates mitosis-related genes leading to arrested cancer cell mitosis and suppressed colony-forming ability. Moreover, in support of the impacts of U50A in prolonging mitosis and inhibiting clonogenic activity, breast cancer tissues with higher U50A expression exhibit accumulated mitotic tumor cells. In conclusion, based on the evidence from U50A-downregulated mitosis-related genes, prolonged mitosis, repressed colony-forming ability, and clinical analyses, we demonstrated molecular insights into the pathological impact of snoRNA U50A in human breast cancer.
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Affiliation(s)
- Jie-Ning Li
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan;
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan;
| | - Ming-Yang Wang
- Department of Surgery, National Taiwan University Hospital, Taipei 100, Taiwan;
| | - Yi-Ting Chen
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan;
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Yao-Lung Kuo
- Department of Surgery, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Breast Medical Center, National Cheng Kung University Hospital, Tainan 701, Taiwan
- Correspondence: (Y.-L.K.); or (P.-S.C.); Tel.: +886-6-2353535 (ext. 5224) (Y.-L.K.); +886-6-2353535 (ext. 6233) (P.-S.C.); Fax: +886-6-2368549 (Y.-L.K.); +886-6-2363956 (P.-S.C.)
| | - Pai-Sheng Chen
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan;
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan;
- Correspondence: (Y.-L.K.); or (P.-S.C.); Tel.: +886-6-2353535 (ext. 5224) (Y.-L.K.); +886-6-2353535 (ext. 6233) (P.-S.C.); Fax: +886-6-2368549 (Y.-L.K.); +886-6-2363956 (P.-S.C.)
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Sung D, Lim C, Takagi M, Jung C, Lee H, Cho DH, Shin JY, Ahn K, Hwang J, Nam D, Kohmura Y, Ishikawa T, Noh DY, Imamoto N, Jeon JH, Song C. Stochastic chromatin packing of 3D mitotic chromosomes revealed by coherent X-rays. Proc Natl Acad Sci U S A 2021; 118:e2109921118. [PMID: 34750262 DOI: 10.1073/pnas.2109921118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 11/18/2022] Open
Abstract
DNA molecules are atomic-scale information storage molecules that promote reliable information transfer via fault-free repetitions of replications and transcriptions. Remarkable accuracy of compacting a few-meters-long DNA into a micrometer-scale object, and the reverse, makes the chromosome one of the most intriguing structures from both physical and biological viewpoints. However, its three-dimensional (3D) structure remains elusive with challenges in observing native structures of specimens at tens-of-nanometers resolution. Here, using cryogenic coherent X-ray diffraction imaging, we succeeded in obtaining nanoscale 3D structures of metaphase chromosomes that exhibited a random distribution of electron density without characteristics of high-order folding structures. Scaling analysis of the chromosomes, compared with a model structure having the same density profile as the experimental results, has discovered the fractal nature of density distributions. Quantitative 3D density maps, corroborated by molecular dynamics simulations, reveal that internal structures of chromosomes conform to diffusion-limited aggregation behavior, which indicates that 3D chromatin packing occurs via stochastic processes.
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43
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Vernizzi L, Lehner CF. Bivalent individualization during chromosome territory formation in Drosophila spermatocytes by controlled condensin II protein activity and additional force generators. PLoS Genet 2021; 17:e1009870. [PMID: 34669718 PMCID: PMC8559962 DOI: 10.1371/journal.pgen.1009870] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/01/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
Reduction of genome ploidy from diploid to haploid necessitates stable pairing of homologous chromosomes into bivalents before the start of the first meiotic division. Importantly, this chromosome pairing must avoid interlocking of non-homologous chromosomes. In spermatocytes of Drosophila melanogaster, where homolog pairing does not involve synaptonemal complex formation and crossovers, associations between non-homologous chromosomes are broken up by chromosome territory formation in early spermatocytes. Extensive non-homologous associations arise from the coalescence of the large blocks of pericentromeric heterochromatin into a chromocenter and from centromere clustering. Nevertheless, during territory formation, bivalents are moved apart into spatially separate subnuclear regions. The condensin II subunits, Cap-D3 and Cap-H2, have been implicated, but the remarkable separation of bivalents during interphase might require more than just condensin II. For further characterization of this process, we have applied time-lapse imaging using fluorescent markers of centromeres, telomeres and DNA satellites in pericentromeric heterochromatin. We describe the dynamics of the disruption of centromere clusters and the chromocenter in normal spermatocytes. Mutations in Cap-D3 and Cap-H2 abolish chromocenter disruption, resulting in excessive chromosome missegregation during M I. Chromocenter persistence in the mutants is not mediated by the special system, which conjoins homologs in compensation for the absence of crossovers in Drosophila spermatocytes. However, overexpression of Cap-H2 precluded conjunction between autosomal homologs, resulting in random segregation of univalents. Interestingly, Cap-D3 and Cap-H2 mutant spermatocytes displayed conspicuous stretching of the chromocenter, as well as occasional chromocenter disruption, suggesting that territory formation might involve forces unrelated to condensin II. While the molecular basis of these forces remains to be clarified, they are not destroyed by inhibitors of F actin and microtubules. Our results indicate that condensin II activity promotes chromosome territory formation in co-operation with additional force generators and that careful co-ordination with alternative homolog conjunction is crucial.
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Affiliation(s)
- Luisa Vernizzi
- Department of Molecular Life Science (DMLS), University of Zurich, Zurich, Switzerland
| | - Christian F. Lehner
- Department of Molecular Life Science (DMLS), University of Zurich, Zurich, Switzerland
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Salehi N, Karimi-Jafari MH, Totonchi M, Amiri-Yekta A. Integration and gene co-expression network analysis of scRNA-seq transcriptomes reveal heterogeneity and key functional genes in human spermatogenesis. Sci Rep 2021; 11:19089. [PMID: 34580317 DOI: 10.1038/s41598-021-98267-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/27/2021] [Indexed: 02/07/2023] Open
Abstract
Spermatogenesis is a complex process of cellular division and differentiation that begins with spermatogonia stem cells and leads to functional spermatozoa production. However, many of the molecular mechanisms underlying this process remain unclear. Single-cell RNA sequencing (scRNA-seq) is used to sequence the entire transcriptome at the single-cell level to assess cell-to-cell variability. In this study, more than 33,000 testicular cells from different scRNA-seq datasets with normal spermatogenesis were integrated to identify single-cell heterogeneity on a more comprehensive scale. Clustering, cell type assignments, differential expressed genes and pseudotime analysis characterized 5 spermatogonia, 4 spermatocyte, and 4 spermatid cell types during the spermatogenesis process. The UTF1 and ID4 genes were introduced as the most specific markers that can differentiate two undifferentiated spermatogonia stem cell sub-cellules. The C7orf61 and TNP can differentiate two round spermatid sub-cellules. The topological analysis of the weighted gene co-expression network along with the integrated scRNA-seq data revealed some bridge genes between spermatogenesis's main stages such as DNAJC5B, C1orf194, HSP90AB1, BST2, EEF1A1, CRISP2, PTMS, NFKBIA, CDKN3, and HLA-DRA. The importance of these key genes is confirmed by their role in male infertility in previous studies. It can be stated that, this integrated scRNA-seq of spermatogenic cells offers novel insights into cell-to-cell heterogeneity and suggests a list of key players with a pivotal role in male infertility from the fertile spermatogenesis datasets. These key functional genes can be introduced as candidates for filtering and prioritizing genotype-to-phenotype association in male infertility.
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45
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Abstract
Condensation and faithful separation of the genome are crucial for the cellular life cycle. During chromosome segregation, mechanical forces generated by the mitotic spindle pull apart the sister chromatids. The mechanical nature of this process has motivated a lot of research interest into the mechanical properties of mitotic chromosomes. Although their fundamental mechanical characteristics are known, it still remains unclear how these characteristics emerge from the structure of the mitotic chromosome. Recent advances in genomics, computational and super-resolution microscopy techniques have greatly promoted our understanding of the chromosomal structure and have motivated us to review the mechanical characteristics of chromosomes in light of the current structural insights. In this review, we will first introduce the current understanding of the chromosomal structure, before reviewing characteristic mechanical properties such as the Young's modulus and the bending modulus of mitotic chromosomes. Then we will address the approaches used to relate mechanical properties to the structure of chromosomes and we will also discuss how mechanical characterization can aid in elucidating their structure. Finally, future challenges, recent developments and emergent questions in this research field will be discussed.
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46
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Abstract
cGAS, an innate immune sensor of cellular stress, recognizes double-stranded DNA mislocalized in the cytosol upon infection, mitochondrial stress, DNA damage, or malignancy. Early models suggested that cytosolic localization of cGAS prevents autoreactivity to nuclear and mitochondrial self-DNA, but this paradigm has shifted in light of recent findings of cGAS as a predominantly nuclear protein tightly bound to chromatin. This has raised the question how nuclear cGAS is kept inactive while being surrounded by chromatin, and what function nuclear localization of cGAS may serve in the first place? Cryo-EM structures have revealed that cGAS interacts with nucleosomes, the minimal units of chromatin, mainly via histones H2A/H2B, and that these protein-protein interactions block cGAS from DNA binding and thus prevent autoreactivity. Here, we discuss the biological implications of nuclear cGAS and its interaction with chromatin, including various mechanisms for nuclear cGAS inhibition, release of chromatin-bound cGAS, regulation of different cGAS pools in the cell, and chromatin structure/chromatin protein effects on cGAS activation leading to cGAS-induced autoimmunity.
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Affiliation(s)
- Carina C de Oliveira Mann
- Gene CenterLudwig‐Maximilians‐UniversitätMunichGermany
- Department of BiochemistryLudwig‐Maximilians‐UniversitätMunichGermany
| | - Karl‐Peter Hopfner
- Gene CenterLudwig‐Maximilians‐UniversitätMunichGermany
- Department of BiochemistryLudwig‐Maximilians‐UniversitätMunichGermany
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47
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Koide H, Kodera N, Bisht S, Takada S, Terakawa T. Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy. PLoS Comput Biol 2021; 17:e1009265. [PMID: 34329301 PMCID: PMC8357123 DOI: 10.1371/journal.pcbi.1009265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/11/2021] [Accepted: 07/10/2021] [Indexed: 11/19/2022] Open
Abstract
The condensin protein complex compacts chromatin during mitosis using its DNA-loop extrusion activity. Previous studies proposed scrunching and loop-capture models as molecular mechanisms for the loop extrusion process, both of which assume the binding of double-strand (ds) DNA to the hinge domain formed at the interface of the condensin subunits Smc2 and Smc4. However, how the hinge domain contacts dsDNA has remained unknown. Here, we conducted atomic force microscopy imaging of the budding yeast condensin holo-complex and used this data as basis for coarse-grained molecular dynamics simulations to model the hinge structure in a transient open conformation. We then simulated the dsDNA binding to open and closed hinge conformations, predicting that dsDNA binds to the outside surface when closed and to the outside and inside surfaces when open. Our simulations also suggested that the hinge can close around dsDNA bound to the inside surface. Based on these simulation results, we speculate that the conformational change of the hinge domain might be essential for the dsDNA binding regulation and play roles in condensin-mediated DNA-loop extrusion.
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Affiliation(s)
- Hiroki Koide
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Noriyuki Kodera
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Shveta Bisht
- Cell Biology and Biophysics Unit, Structural and Computational Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Tsuyoshi Terakawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
- PREST, Japan Science and Technology Agency (JST), Kawaguchi, Japan
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Strom AR, Biggs RJ, Banigan EJ, Wang X, Chiu K, Herman C, Collado J, Yue F, Ritland Politz JC, Tait LJ, Scalzo D, Telling A, Groudine M, Brangwynne CP, Marko JF, Stephens AD. HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics. eLife 2021; 10:e63972. [PMID: 34106828 PMCID: PMC8233041 DOI: 10.7554/elife.63972] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 06/08/2021] [Indexed: 12/14/2022] Open
Abstract
Chromatin, which consists of DNA and associated proteins, contains genetic information and is a mechanical component of the nucleus. Heterochromatic histone methylation controls nucleus and chromosome stiffness, but the contribution of heterochromatin protein HP1α (CBX5) is unknown. We used a novel HP1α auxin-inducible degron human cell line to rapidly degrade HP1α. Degradation did not alter transcription, local chromatin compaction, or histone methylation, but did decrease chromatin stiffness. Single-nucleus micromanipulation reveals that HP1α is essential to chromatin-based mechanics and maintains nuclear morphology, separate from histone methylation. Further experiments with dimerization-deficient HP1αI165E indicate that chromatin crosslinking via HP1α dimerization is critical, while polymer simulations demonstrate the importance of chromatin-chromatin crosslinkers in mechanics. In mitotic chromosomes, HP1α similarly bolsters stiffness while aiding in mitotic alignment and faithful segregation. HP1α is therefore a critical chromatin-crosslinking protein that provides mechanical strength to chromosomes and the nucleus throughout the cell cycle and supports cellular functions.
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Affiliation(s)
- Amy R Strom
- Howard Hughes Medical Institute, Department of Chemical and Biological Engineering, Princeton UniversityPrincetonUnited States
| | - Ronald J Biggs
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Edward J Banigan
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Xiaotao Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - Katherine Chiu
- Biology Department, University of Massachusetts AmherstAmherstUnited States
| | - Cameron Herman
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Jimena Collado
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | | | - Leah J Tait
- The Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - David Scalzo
- The Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Agnes Telling
- The Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Mark Groudine
- The Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Clifford P Brangwynne
- Howard Hughes Medical Institute, Department of Chemical and Biological Engineering, Princeton UniversityPrincetonUnited States
| | - John F Marko
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
- Department of Physics and Astronomy, Northwestern UniversityEvanstonUnited States
| | - Andrew D Stephens
- Biology Department, University of Massachusetts AmherstAmherstUnited States
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49
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Abstract
Unlike bacteria, mammalian cells need to complete DNA replication before segregating their chromosomes for the maintenance of genome integrity. Thus, cells have evolved efficient pathways to restore stalled and/or collapsed replication forks during S-phase, and when necessary, also to delay cell cycle progression to ensure replication completion. However, strong evidence shows that cells can proceed to mitosis with incompletely replicated DNA when under mild replication stress (RS) conditions. Consequently, the incompletely replicated genomic gaps form, predominantly at common fragile site regions, where the converging fork-like DNA structures accumulate. These branched structures pose a severe threat to the faithful disjunction of chromosomes as they physically interlink the partially duplicated sister chromatids. In this review, we provide an overview discussing how cells respond and deal with the under-replicated DNA structures that escape from the S/G2 surveillance system. We also focus on recent research of a mitotic break-induced replication pathway (also known as mitotic DNA repair synthesis), which has been proposed to operate during prophase in an attempt to finish DNA synthesis at the under-replicated genomic regions. Finally, we discuss recent data on how mild RS may cause chromosome instability and mutations that accelerate cancer genome evolution.
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Affiliation(s)
- Camelia Mocanu
- Chromosome Dynamics and Stability Group, Genome Damage and Stability Centre, University of Sussex, Brighton BN1 7BG, UK
| | - Kok-Lung Chan
- Chromosome Dynamics and Stability Group, Genome Damage and Stability Centre, University of Sussex, Brighton BN1 7BG, UK
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50
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Sajid A, Lalani EN, Chen B, Hashimoto T, Griffin DK, Bhartiya A, Thompson G, Robinson IK, Yusuf M. Ultra-Structural Imaging Provides 3D Organization of 46 Chromosomes of a Human Lymphocyte Prophase Nucleus. Int J Mol Sci 2021; 22:ijms22115987. [PMID: 34206020 PMCID: PMC8198510 DOI: 10.3390/ijms22115987] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 11/18/2022] Open
Abstract
Three dimensional (3D) ultra-structural imaging is an important tool for unraveling the organizational structure of individual chromosomes at various stages of the cell cycle. Performing hitherto uninvestigated ultra-structural analysis of the human genome at prophase, we used serial block-face scanning electron microscopy (SBFSEM) to understand chromosomal architectural organization within 3D nuclear space. Acquired images allowed us to segment, reconstruct, and extract quantitative 3D structural information about the prophase nucleus and the preserved, intact individual chromosomes within it. Our data demonstrate that each chromosome can be identified with its homolog and classified into respective cytogenetic groups. Thereby, we present the first 3D karyotype built from the compact axial structure seen on the core of all prophase chromosomes. The chromosomes display parallel-aligned sister chromatids with familiar chromosome morphologies with no crossovers. Furthermore, the spatial positions of all 46 chromosomes revealed a pattern showing a gene density-based correlation and a neighborhood map of individual chromosomes based on their relative spatial positioning. A comprehensive picture of 3D chromosomal organization at the nanometer level in a single human lymphocyte cell is presented.
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Affiliation(s)
- Atiqa Sajid
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi 74800, Pakistan; (A.S.); (E.-N.L.)
| | - El-Nasir Lalani
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi 74800, Pakistan; (A.S.); (E.-N.L.)
| | - Bo Chen
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; (B.C.); (A.B.); (I.K.R.)
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China
- Key Laboratory of Performance Evolution and Control for Engineering Structures of the Ministry of Education, Tongji University, Shanghai 200092, China
| | - Teruo Hashimoto
- Department of Materials, University of Manchester, Oxford Road, Manchester M13 9PL, UK; (T.H.); (G.T.)
| | | | - Archana Bhartiya
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; (B.C.); (A.B.); (I.K.R.)
| | - George Thompson
- Department of Materials, University of Manchester, Oxford Road, Manchester M13 9PL, UK; (T.H.); (G.T.)
| | - Ian K. Robinson
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; (B.C.); (A.B.); (I.K.R.)
- Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Mohammed Yusuf
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi 74800, Pakistan; (A.S.); (E.-N.L.)
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; (B.C.); (A.B.); (I.K.R.)
- Correspondence:
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