1
|
Bui M, Baek S, Bentahar RS, Melters DP, Dalal Y. Native and tagged CENP-A histones are functionally inequivalent. Epigenetics Chromatin 2024; 17:19. [PMID: 38825690 PMCID: PMC11145777 DOI: 10.1186/s13072-024-00543-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/22/2024] [Indexed: 06/04/2024] Open
Abstract
BACKGROUND Over the past several decades, the use of biochemical and fluorescent tags has elucidated mechanistic and cytological processes that would otherwise be impossible. The challenging nature of certain nuclear proteins includes low abundancy, poor antibody recognition, and transient dynamics. One approach to get around those issues is the addition of a peptide or larger protein tag to the target protein to improve enrichment, purification, and visualization. However, many of these studies were done under the assumption that tagged proteins can fully recapitulate native protein function. RESULTS We report that when C-terminally TAP-tagged CENP-A histone variant is introduced, it undergoes altered kinetochore protein binding, differs in post-translational modifications (PTMs), utilizes histone chaperones that differ from that of native CENP-A, and can partially displace native CENP-A in human cells. Additionally, these tagged CENP-A-containing nucleosomes have reduced centromeric incorporation at early G1 phase and poorly associates with linker histone H1.5 compared to native CENP-A nucleosomes. CONCLUSIONS These data suggest expressing tagged versions of histone variant CENP-A may result in unexpected utilization of non-native pathways, thereby altering the biological function of the histone variant.
Collapse
Affiliation(s)
- Minh Bui
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, 41 Medlars Drive, Bldg 41/Rm B1300, Bethesda, MD, 20892, USA.
| | - Songjoon Baek
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, 41 Medlars Drive, Bldg 41/Rm B1300, Bethesda, MD, 20892, USA
| | - Reda S Bentahar
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, 41 Medlars Drive, Bldg 41/Rm B1300, Bethesda, MD, 20892, USA
| | - Daniël P Melters
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, 41 Medlars Drive, Bldg 41/Rm B1300, Bethesda, MD, 20892, USA
| | - Yamini Dalal
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, 41 Medlars Drive, Bldg 41/Rm B1300, Bethesda, MD, 20892, USA.
| |
Collapse
|
2
|
Zhu M, Liang H, Zhang Z, Jiang H, Pu J, Hang X, Zhou Q, Xiang J, He X. Distinct mononuclear diploid cardiac subpopulation with minimal cell-cell communications persists in embryonic and adult mammalian heart. Front Med 2023; 17:939-956. [PMID: 37294383 DOI: 10.1007/s11684-023-0987-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 01/31/2023] [Indexed: 06/10/2023]
Abstract
A small proportion of mononuclear diploid cardiomyocytes (MNDCMs), with regeneration potential, could persist in adult mammalian heart. However, the heterogeneity of MNDCMs and changes during development remains to be illuminated. To this end, 12 645 cardiac cells were generated from embryonic day 17.5 and postnatal days 2 and 8 mice by single-cell RNA sequencing. Three cardiac developmental paths were identified: two switching to cardiomyocytes (CM) maturation with close CM-fibroblast (FB) communications and one maintaining MNDCM status with least CM-FB communications. Proliferative MNDCMs having interactions with macrophages and non-proliferative MNDCMs (non-pMNDCMs) with minimal cell-cell communications were identified in the third path. The non-pMNDCMs possessed distinct properties: the lowest mitochondrial metabolisms, the highest glycolysis, and high expression of Myl4 and Tnni1. Single-nucleus RNA sequencing and immunohistochemical staining further proved that the Myl4+Tnni1+ MNDCMs persisted in embryonic and adult hearts. These MNDCMs were mapped to the heart by integrating the spatial and single-cell transcriptomic data. In conclusion, a novel non-pMNDCM subpopulation with minimal cell-cell communications was unveiled, highlighting the importance of microenvironment contribution to CM fate during maturation. These findings could improve the understanding of MNDCM heterogeneity and cardiac development, thus providing new clues for approaches to effective cardiac regeneration.
Collapse
Affiliation(s)
- Miaomiao Zhu
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Huamin Liang
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zhe Zhang
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
| | - Hao Jiang
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jingwen Pu
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaoyi Hang
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qian Zhou
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jiacheng Xiang
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ximiao He
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China.
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China.
| |
Collapse
|
3
|
Seal RL, Denny P, Bruford EA, Gribkova AK, Landsman D, Marzluff WF, McAndrews M, Panchenko AR, Shaytan AK, Talbert PB. A standardized nomenclature for mammalian histone genes. Epigenetics Chromatin 2022; 15:34. [PMID: 36180920 PMCID: PMC9526256 DOI: 10.1186/s13072-022-00467-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/21/2022] [Indexed: 11/10/2022] Open
Abstract
Histones have a long history of research in a wide range of species, leaving a legacy of complex nomenclature in the literature. Community-led discussions at the EMBO Workshop on Histone Variants in 2011 resulted in agreement amongst experts on a revised systematic protein nomenclature for histones, which is based on a combination of phylogenetic classification and historical symbol usage. Human and mouse histone gene symbols previously followed a genome-centric system that was not applicable across all vertebrate species and did not reflect the systematic histone protein nomenclature. This prompted a collaboration between histone experts, the Human Genome Organization (HUGO) Gene Nomenclature Committee (HGNC) and Mouse Genomic Nomenclature Committee (MGNC) to revise human and mouse histone gene nomenclature aiming, where possible, to follow the new protein nomenclature whilst conforming to the guidelines for vertebrate gene naming. The updated nomenclature has also been applied to orthologous histone genes in chimpanzee, rhesus macaque, dog, cat, pig, horse and cattle, and can serve as a framework for naming other vertebrate histone genes in the future.
Collapse
Affiliation(s)
- Ruth L Seal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
- Department of Haematology, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0PT, UK.
| | - Paul Denny
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Elspeth A Bruford
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
- Department of Haematology, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0PT, UK
| | - Anna K Gribkova
- Department of Biology, Lomonosov Moscow State University, 119234, Moscow, Russia
| | - David Landsman
- Intramural Research Program, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA
| | - William F Marzluff
- Integrated Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Monica McAndrews
- Mouse Genome Informatics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Alexey K Shaytan
- Department of Biology, Lomonosov Moscow State University, 119234, Moscow, Russia
| | - Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA, 98109, USA
| |
Collapse
|
4
|
Amatori S, Tavolaro S, Gambardella S, Fanelli M. The dark side of histones: genomic organization and role of oncohistones in cancer. Clin Epigenetics 2021; 13:71. [PMID: 33827674 PMCID: PMC8025322 DOI: 10.1186/s13148-021-01057-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/22/2021] [Indexed: 02/07/2023] Open
Abstract
Background The oncogenic role of histone mutations is one of the most relevant discovery in cancer epigenetics. Recurrent mutations targeting histone genes have been described in pediatric brain tumors, chondroblastoma, giant cell tumor of bone and other tumor types. The demonstration that mutant histones can be oncogenic and drive the tumorigenesis in pediatric tumors, led to the coining of the term “oncohistones.” The first identified histone mutations were localized at or near residues normally targeted by post-translational modifications (PTMs) in the histone N-terminal tails and suggested a possible interference with histone PTMs regulation and reading. Main body In this review, we describe the peculiar organization of the multiple genes that encode histone proteins, and the latter advances in both the identification and the biological role of histone mutations in cancer. Recent works show that recurrent somatic mutations target both N-terminal tails and globular histone fold domain in diverse tumor types. Oncohistones are often dominant-negative and occur at higher frequencies in tumors affecting children and adolescents. Notably, in many cases the mutations target selectively only some of the genes coding the same histone protein and are frequently associated with specific tumor types or, as documented for histone variant H3.3 in pediatric glioma, with peculiar tumors arising from specific anatomic locations. Conclusion The overview of the most recent advances suggests that the oncogenic potential of histone mutations can be exerted, together with the alteration of histone PTMs, through the destabilization of nucleosome and DNA–nucleosome interactions, as well as through the disruption of higher-order chromatin structure. However, further studies are necessary to fully elucidate the mechanism of action of oncohistones, as well as to evaluate their possible application to cancer classification, prognosis and to the identification of new therapies.
Collapse
Affiliation(s)
- Stefano Amatori
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino Carlo Bo, Via Arco d'Augusto 2, 61032, Fano, PU, Italy.
| | - Simona Tavolaro
- Fredis Associazione, Via Edoardo Jenner 30, 00151, Rome, Italy
| | - Stefano Gambardella
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino Carlo Bo, Via Arco d'Augusto 2, 61032, Fano, PU, Italy.,IRCCS Neuromed, Via Atinense 18, 86077, Pozzilli, IS, Italy
| | - Mirco Fanelli
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino Carlo Bo, Via Arco d'Augusto 2, 61032, Fano, PU, Italy.
| |
Collapse
|
5
|
Hemerich D, Pei J, Harakalova M, van Setten J, Boymans S, Boukens BJ, Efimov IR, Michels M, van der Velden J, Vink A, Cheng C, van der Harst P, Moore JH, Mokry M, Tragante V, Asselbergs FW. Integrative Functional Annotation of 52 Genetic Loci Influencing Myocardial Mass Identifies Candidate Regulatory Variants and Target Genes. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2020; 12:e002328. [PMID: 30681347 DOI: 10.1161/circgen.118.002328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Regulatory elements may be involved in the mechanisms by which 52 loci influence myocardial mass, reflected by abnormal amplitude and duration of the QRS complex on the ECG. Functional annotation thus far did not take into account how these elements are affected in disease context. METHODS We generated maps of regulatory elements on hypertrophic cardiomyopathy patients (ChIP-seq N=14 and RNA-seq N=11) and nondiseased hearts (ChIP-seq N=4 and RNA-seq N=11). We tested enrichment of QRS-associated loci on elements differentially acetylated and directly regulating differentially expressed genes between hypertrophic cardiomyopathy patients and controls. We further performed functional annotation on QRS-associated loci using these maps of differentially active regulatory elements. RESULTS Regions differentially affected in disease showed a stronger enrichment ( P=8.6×10-5) for QRS-associated variants than those not showing differential activity ( P=0.01). Promoters of genes differentially regulated between hypertrophic cardiomyopathy patients and controls showed more enrichment ( P=0.001) than differentially acetylated enhancers ( P=0.8) and super-enhancers ( P=0.025). We also identified 74 potential causal variants overlapping these differential regulatory elements. Eighteen of the genes mapped confirmed previous findings, now also pinpointing the potentially affected regulatory elements and candidate causal variants. Fourteen new genes were also mapped. CONCLUSIONS Our results suggest differentially active regulatory elements between hypertrophic cardiomyopathy patients and controls can offer more insights into the mechanisms of QRS-associated loci than elements not affected by disease.
Collapse
Affiliation(s)
- Daiane Hemerich
- Department of Cardiology (D.H., M.H., J.v.S., V.T., F.W.A.), UMC Utrecht, Utrecht University, The Netherlands.,CAPES Foundation, Ministry of Education of Brazil, Brasília (D.H.)
| | - Jiayi Pei
- CAPES Foundation, Ministry of Education of Brazil, Brasília (D.H.).,Department of Nephrology and Hypertension (J.P., C.C.), UMC Utrecht
| | - Magdalena Harakalova
- Department of Cardiology (D.H., M.H., J.v.S., V.T., F.W.A.), UMC Utrecht, Utrecht University, The Netherlands
| | - Jessica van Setten
- Department of Cardiology (D.H., M.H., J.v.S., V.T., F.W.A.), UMC Utrecht, Utrecht University, The Netherlands
| | - Sander Boymans
- Department of Genetics, Center for Molecular Medicine, Cancer Genomics Netherlands (S.B.), UMC Utrecht
| | - Bas J Boukens
- Department of Medical Biology, Academic Medical Center, Amsterdam, The Netherlands (B.J.B.)
| | - Igor R Efimov
- Department of Biomedical Engineering, The George Washington University, Washington, DC (I.R.E.)
| | - Michelle Michels
- Department of Cardiology, Erasmus MC, Rotterdam, The Netherlands (M. Michels)
| | - Jolanda van der Velden
- Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Center (J.v.d.V.)
| | - Aryan Vink
- Department of Pathology (A.V.), UMC Utrecht, Utrecht University, The Netherlands
| | - Caroline Cheng
- Department of Nephrology and Hypertension (J.P., C.C.), UMC Utrecht
| | | | - Jason H Moore
- Department of Biostatistics and Epidemiology, Institute for Biomedical Informatics, University of Pennsylvania, PA (J.H.M.)
| | - Michal Mokry
- Department of Pediatrics, Wilhelmina Children's Hospital, Utrecht (M. Mokry.)
| | - Vinicius Tragante
- Department of Cardiology (D.H., M.H., J.v.S., V.T., F.W.A.), UMC Utrecht, Utrecht University, The Netherlands
| | - Folkert W Asselbergs
- Department of Cardiology (D.H., M.H., J.v.S., V.T., F.W.A.), UMC Utrecht, Utrecht University, The Netherlands.,Durrer Center for Cardiogenetic Research, ICINNetherlands Heart Institute, Utrecht (F.W.A.).,Institute of Cardiovascular Science, Faculty of Population Health Sciences (F.W.A.), University College London, United Kingdom.,Health Data Research UK London, Institute of Health Informatics F.W.A.), University College London, United Kingdom
| |
Collapse
|
6
|
Jin X, Hapsari ND, Lee S, Jo K. DNA binding fluorescent proteins as single-molecule probes. Analyst 2020; 145:4079-4095. [DOI: 10.1039/d0an00218f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA binding fluorescent proteins are useful probes for a broad range of biological applications.
Collapse
Affiliation(s)
- Xuelin Jin
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Natalia Diyah Hapsari
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
- Chemistry Education Program
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| |
Collapse
|
7
|
Abendroth C, Hofmeister A, Hake SB, Kamweru PK, Miess E, Dornblut C, Küffner I, Deng W, Leonhardt H, Orthaus S, Hoischen C, Diekmann S. The CENP-T C-terminus is exclusively proximal to H3.1 and not to H3.2 or H3.3. Int J Mol Sci 2015; 16:5839-63. [PMID: 25775162 PMCID: PMC4394509 DOI: 10.3390/ijms16035839] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 02/18/2015] [Accepted: 02/18/2015] [Indexed: 12/17/2022] Open
Abstract
The kinetochore proteins assemble onto centromeric chromatin and regulate DNA segregation during cell division. The inner kinetochore proteins bind centromeres while most outer kinetochore proteins assemble at centromeres during mitosis, connecting the complex to microtubules. The centromere-kinetochore complex contains specific nucleosomes and nucleosomal particles. CENP-A replaces canonical H3 in centromeric nucleosomes, defining centromeric chromatin. Next to CENP-A, the CCAN multi-protein complex settles which contains CENP-T/W/S/X. These four proteins are described to form a nucleosomal particle at centromeres. We had found the CENP-T C-terminus and the CENP-S termini next to histone H3.1 but not to CENP-A, suggesting that the Constitutive Centromere-Associated Network (CCAN) bridges a CENP-A- and a H3-containing nucleosome. Here, we show by in vivo FRET that this proximity between CENP-T and H3 is specific for H3.1 but neither for the H3.1 mutants H3.1(C96A) and H3.1(C110A) nor for H3.2 or H3.3. We also found CENP-M next to H3.1 but not to these H3.1 mutants. Consistently, we detected CENP-M next to CENP-S. These data elucidate the local molecular neighborhood of CCAN proteins next to a H3.1-containing centromeric nucleosome. They also indicate an exclusive position of H3.1 clearly distinct from H3.2, thus documenting a local, and potentially also functional, difference between H3.1 and H3.2.
Collapse
Affiliation(s)
- Christian Abendroth
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Antje Hofmeister
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Sandra B Hake
- Department of Molecular Biology, Center for Integrated Protein Science Munich (CIPSM), Adolf-Butenandt-Institute, Ludwig-Maximilians-Universität Munich, Schillerstr. 44, D-80336 Munich, Germany.
| | - Paul K Kamweru
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Elke Miess
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Carsten Dornblut
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Isabell Küffner
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Wen Deng
- Department of Biology II, Center for Integrated Protein Science, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, D-82152 Munich, Germany.
| | - Heinrich Leonhardt
- Department of Biology II, Center for Integrated Protein Science, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, D-82152 Munich, Germany.
| | | | - Christian Hoischen
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Stephan Diekmann
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| |
Collapse
|
8
|
Henze R, Huwald J, Mostajo N, Dittrich P, Ibrahim B. Structural analysis of in silico mutant experiments of human inner-kinetochore structure. Biosystems 2014; 127:47-59. [PMID: 25451768 DOI: 10.1016/j.biosystems.2014.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 08/20/2014] [Accepted: 11/04/2014] [Indexed: 12/31/2022]
Abstract
Large multi-molecular complexes like the kinetochore are lacking of suitable methods to determine their spatial structure. Here, we use and evaluate a novel modeling approach that combines rule-bases reaction network models with spatial molecular geometries. In particular, we introduce a method that allows to study in silico the influence of single interactions (e.g. bonds) on the spatial organization of large multi-molecular complexes and apply this method to an extended model of the human inner-kinetochore. Our computational analysis method encompasses determination of bond frequency, geometrical distances, statistical moments, and inter-dependencies between bonds using mutual information. For the analysis we have extend our previously reported human inner-kinetochore model by adding 13 new protein interactions and three protein geometry details. The model is validated by comparing the results of in silico with reported in vitro single protein deletion experiments. Our studies revealed that most simulations mimic the in vitro behavior of the kinetochore complex as expected. To identify the most important bonds in this model, we have created 39 mutants in silico by selectively disabling single protein interactions. In a total of 11,800 simulation runs we have compared the resulting structures to the wild-type. In particular, this allowed us to identify the interaction Cenp-W-H3 and Cenp-S-Cenp-X as having the strongest influence on the inner-kinetochore's structure. We conclude that our approach can become a useful tool for the in silico dynamical study of large, multi-molecular complexes.
Collapse
Affiliation(s)
- Richard Henze
- Bio Systems Analysis Group, Institute of Computer Science, Jena Centre for Bioinformatics and Friedrich Schiller University Jena, 07743 Jena, Germany.
| | - Jan Huwald
- Bio Systems Analysis Group, Institute of Computer Science, Jena Centre for Bioinformatics and Friedrich Schiller University Jena, 07743 Jena, Germany.
| | - Nelly Mostajo
- Bio Systems Analysis Group, Institute of Computer Science, Jena Centre for Bioinformatics and Friedrich Schiller University Jena, 07743 Jena, Germany.
| | - Peter Dittrich
- Bio Systems Analysis Group, Institute of Computer Science, Jena Centre for Bioinformatics and Friedrich Schiller University Jena, 07743 Jena, Germany.
| | - Bashar Ibrahim
- Bio Systems Analysis Group, Institute of Computer Science, Jena Centre for Bioinformatics and Friedrich Schiller University Jena, 07743 Jena, Germany; Umm Al-Qura University, 1109 Makkah Al-Mukarramah, Saudi Arabia; Al-Qunfudah Center for Scientific Research (QCSR), 21912 Al-Qunfudah, Saudi Arabia.
| |
Collapse
|
9
|
Tan T, Chen Z, Lei Y, Zhu Y, Liang Q. A regulatory effect of INMAP on centromere proteins: antisense INMAP induces CENP-B variation and centromeric halo. PLoS One 2014; 9:e91937. [PMID: 24633075 PMCID: PMC3954832 DOI: 10.1371/journal.pone.0091937] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 02/18/2014] [Indexed: 11/19/2022] Open
Abstract
CENP-B is a highly conserved protein that facilitates the assembly of specific centromere structures both in interphase nuclei and on mitotic chromosomes. INMAP is a conserved protein that localizes at nucleus in interphase cells and at mitotic apparatus in mitotic cells. Our previous results showed that INMAP over-expression leads to spindle defects, mitotic arrest and formation of polycentrosomal and multinuclear cells, indicating that INMAP may modulate the function of (a) key protein(s) in mitotic apparatus. In this study, we demonstrate that INMAP interacts with CENP-B and promotes cleavage of the N-terminal DNA binding domain from CENP-B. The cleaved CENP-B cannot associate with centromeres and thus lose its centromere-related functions. Consistent with these results, CENP-B in INMAP knockdown cells becomes more diffused around kinetochores. Although INMAP knockdown cells do not exhibit gross defects in mitotic spindle formation, these cells go through mitosis, especially prophase and metaphase, with different relative timing, indicating subtle abnormality. These results identify INMAP as a model regulator of CENP-B and support the notion that INMAP regulates mitosis through modulating CENP-B-mediated centromere organization.
Collapse
Affiliation(s)
- Tan Tan
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Zhe Chen
- Beijing Key Laboratory of Gene Resource and Molecular Development / Beijing Key Laboratory of Gene Engineering Drugs & Biological Technology, Beijing Normal University, Beijing, China
| | - Yan Lei
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yan Zhu
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Qianjin Liang
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
- Beijing Key Laboratory of Gene Resource and Molecular Development / Beijing Key Laboratory of Gene Engineering Drugs & Biological Technology, Beijing Normal University, Beijing, China
- * E-mail:
| |
Collapse
|
10
|
Biomolecular dynamics and binding studies in the living cell. Phys Life Rev 2014; 11:1-30. [DOI: 10.1016/j.plrev.2013.11.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 11/20/2013] [Indexed: 11/22/2022]
|
11
|
Ibrahim B, Henze R, Gruenert G, Egbert M, Huwald J, Dittrich P. Spatial rule-based modeling: a method and its application to the human mitotic kinetochore. Cells 2013; 2:506-44. [PMID: 24709796 PMCID: PMC3972674 DOI: 10.3390/cells2030506] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/05/2013] [Accepted: 06/25/2013] [Indexed: 12/23/2022] Open
Abstract
A common problem in the analysis of biological systems is the combinatorial explosion that emerges from the complexity of multi-protein assemblies. Conventional formalisms, like differential equations, Boolean networks and Bayesian networks, are unsuitable for dealing with the combinatorial explosion, because they are designed for a restricted state space with fixed dimensionality. To overcome this problem, the rule-based modeling language, BioNetGen, and the spatial extension, SRSim, have been developed. Here, we describe how to apply rule-based modeling to integrate experimental data from different sources into a single spatial simulation model and how to analyze the output of that model. The starting point for this approach can be a combination of molecular interaction data, reaction network data, proximities, binding and diffusion kinetics and molecular geometries at different levels of detail. We describe the technique and then use it to construct a model of the human mitotic inner and outer kinetochore, including the spindle assembly checkpoint signaling pathway. This allows us to demonstrate the utility of the procedure, show how a novel perspective for understanding such complex systems becomes accessible and elaborate on challenges that arise in the formulation, simulation and analysis of spatial rule-based models.
Collapse
Affiliation(s)
- Bashar Ibrahim
- Bio Systems Analysis Group, Institute of Computer Science, Jena Centre for Bioinformatics and Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, D-0007743 Jena, Germany.
| | - Richard Henze
- Bio Systems Analysis Group, Institute of Computer Science, Jena Centre for Bioinformatics and Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, D-0007743 Jena, Germany.
| | - Gerd Gruenert
- Bio Systems Analysis Group, Institute of Computer Science, Jena Centre for Bioinformatics and Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, D-0007743 Jena, Germany.
| | - Matthew Egbert
- Bio Systems Analysis Group, Institute of Computer Science, Jena Centre for Bioinformatics and Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, D-0007743 Jena, Germany.
| | - Jan Huwald
- Bio Systems Analysis Group, Institute of Computer Science, Jena Centre for Bioinformatics and Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, D-0007743 Jena, Germany.
| | - Peter Dittrich
- Bio Systems Analysis Group, Institute of Computer Science, Jena Centre for Bioinformatics and Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, D-0007743 Jena, Germany.
| |
Collapse
|
12
|
Tschernyschkow S, Herda S, Gruenert G, Döring V, Görlich D, Hofmeister A, Hoischen C, Dittrich P, Diekmann S, Ibrahim B. Rule-based modeling and simulations of the inner kinetochore structure. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 113:33-45. [PMID: 23562479 DOI: 10.1016/j.pbiomolbio.2013.03.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Combinatorial complexity is a central problem when modeling biochemical reaction networks, since the association of a few components can give rise to a large variation of protein complexes. Available classical modeling approaches are often insufficient for the analysis of very large and complex networks in detail. Recently, we developed a new rule-based modeling approach that facilitates the analysis of spatial and combinatorially complex problems. Here, we explore for the first time how this approach can be applied to a specific biological system, the human kinetochore, which is a multi-protein complex involving over 100 proteins. RESULTS Applying our freely available SRSim software to a large data set on kinetochore proteins in human cells, we construct a spatial rule-based simulation model of the human inner kinetochore. The model generates an estimation of the probability distribution of the inner kinetochore 3D architecture and we show how to analyze this distribution using information theory. In our model, the formation of a bridge between CenpA and an H3 containing nucleosome only occurs efficiently for higher protein concentration realized during S-phase but may be not in G1. Above a certain nucleosome distance the protein bridge barely formed pointing towards the importance of chromatin structure for kinetochore complex formation. We define a metric for the distance between structures that allow us to identify structural clusters. Using this modeling technique, we explore different hypothetical chromatin layouts. CONCLUSIONS Applying a rule-based network analysis to the spatial kinetochore complex geometry allowed us to integrate experimental data on kinetochore proteins, suggesting a 3D model of the human inner kinetochore architecture that is governed by a combinatorial algebraic reaction network. This reaction network can serve as bridge between multiple scales of modeling. Our approach can be applied to other systems beyond kinetochores.
Collapse
Affiliation(s)
- Sergej Tschernyschkow
- Bio Systems Analysis Group, Institute of Computer Science, Jena Centre for Bioinformatics and Friedrich Schiller University, Jena, Germany.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Eskat A, Deng W, Hofmeister A, Rudolphi S, Emmerth S, Hellwig D, Ulbricht T, Döring V, Bancroft JM, McAinsh AD, Cardoso MC, Meraldi P, Hoischen C, Leonhardt H, Diekmann S. Step-wise assembly, maturation and dynamic behavior of the human CENP-P/O/R/Q/U kinetochore sub-complex. PLoS One 2012; 7:e44717. [PMID: 23028590 PMCID: PMC3445539 DOI: 10.1371/journal.pone.0044717] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 08/06/2012] [Indexed: 11/18/2022] Open
Abstract
Kinetochores are multi-protein megadalton assemblies that are required for attachment of microtubules to centromeres and, in turn, the segregation of chromosomes in mitosis. Kinetochore assembly is a cell cycle regulated multi-step process. The initial step occurs during interphase and involves loading of the 15-subunit constitutive centromere associated complex (CCAN), which contains a 5-subunit (CENP-P/O/R/Q/U) sub-complex. Here we show using a fluorescent three-hybrid (F3H) assay and fluorescence resonance energy transfer (FRET) in living mammalian cells that CENP-P/O/R/Q/U subunits exist in a tightly packed arrangement that involves multifold protein-protein interactions. This sub-complex is, however, not pre-assembled in the cytoplasm, but rather assembled on kinetochores through the step-wise recruitment of CENP-O/P heterodimers and the CENP-P, -O, -R, -Q and -U single protein units. SNAP-tag experiments and immuno-staining indicate that these loading events occur during S-phase in a manner similar to the nucleosome binding components of the CCAN, CENP-T/W/N. Furthermore, CENP-P/O/R/Q/U binding to the CCAN is largely mediated through interactions with the CENP-N binding protein CENP-L as well as CENP-K. Once assembled, CENP-P/O/R/Q/U exchanges slowly with the free nucleoplasmic pool indicating a low off-rate for individual CENP-P/O/R/Q/U subunits. Surprisingly, we then find that during late S-phase, following the kinetochore-binding step, both CENP-Q and -U but not -R undergo oligomerization. We propose that CENP-P/O/R/Q/U self-assembles on kinetochores with varying stoichiometry and undergoes a pre-mitotic maturation step that could be important for kinetochores switching into the correct conformation necessary for microtubule-attachment.
Collapse
Affiliation(s)
| | - Wen Deng
- Department of Biology II, Center for Integrated Protein Science, Ludwig Maximilians University Munich, Planegg-Martinsried, Munich, Germany
| | | | | | | | | | | | | | - James M. Bancroft
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Andrew D. McAinsh
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | | | | | | | - Heinrich Leonhardt
- Department of Biology II, Center for Integrated Protein Science, Ludwig Maximilians University Munich, Planegg-Martinsried, Munich, Germany
| | | |
Collapse
|
14
|
Bui M, Dimitriadis EK, Hoischen C, An E, Quénet D, Giebe S, Nita-Lazar A, Diekmann S, Dalal Y. Cell-cycle-dependent structural transitions in the human CENP-A nucleosome in vivo. Cell 2012; 150:317-26. [PMID: 22817894 PMCID: PMC3592566 DOI: 10.1016/j.cell.2012.05.035] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 12/19/2011] [Accepted: 05/18/2012] [Indexed: 12/21/2022]
Abstract
In eukaryotes, DNA is packaged into chromatin by canonical histone proteins. The specialized histone H3 variant CENP-A provides an epigenetic and structural basis for chromosome segregation by replacing H3 at centromeres. Unlike exclusively octameric canonical H3 nucleosomes, CENP-A nucleosomes have been shown to exist as octamers, hexamers, and tetramers. An intriguing possibility reconciling these observations is that CENP-A nucleosomes cycle between octamers and tetramers in vivo. We tested this hypothesis by tracking CENP-A nucleosomal components, structure, chromatin folding, and covalent modifications across the human cell cycle. We report that CENP-A nucleosomes alter from tetramers to octamers before replication and revert to tetramers after replication. These structural transitions are accompanied by reversible chaperone binding, chromatin fiber folding changes, and previously undescribed modifications within the histone fold domains of CENP-A and H4. Our results reveal a cyclical nature to CENP-A nucleosome structure and have implications for the maintenance of epigenetic memory after centromere replication.
Collapse
Affiliation(s)
- Minh Bui
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Emilios K. Dimitriadis
- Laboratory of Biomedical Engineering and Physical Sciences, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD 20892, USA
| | | | - Eunkyung An
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Delphine Quénet
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | - Aleksandra Nita-Lazar
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | | | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| |
Collapse
|
15
|
Hellwig D, Emmerth S, Ulbricht T, Döring V, Hoischen C, Martin R, Samora CP, McAinsh AD, Carroll CW, Straight AF, Meraldi P, Diekmann S. Dynamics of CENP-N kinetochore binding during the cell cycle. J Cell Sci 2011; 124:3871-83. [PMID: 22100916 DOI: 10.1242/jcs.088625] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Accurate chromosome segregation requires the assembly of kinetochores, multiprotein complexes that assemble on the centromere of each sister chromatid. A key step in this process involves binding of the constitutive centromere-associated network (CCAN) to CENP-A, the histone H3 variant that constitutes centromeric nucleosomes. This network is proposed to operate as a persistent structural scaffold for assembly of the outer kinetochore during mitosis. Here, we show by fluorescence resonance energy transfer (FRET) that the N-terminus of CENP-N lies in close proximity to the N-terminus of CENP-A in vivo, consistent with in vitro data showing direct binding of CENP-N to CENP-A. Furthermore, we demonstrate in living cells that CENP-N is bound to kinetochores during S phase and G2, but is largely absent from kinetochores during mitosis and G1. By measuring the dynamics of kinetochore binding, we reveal that CENP-N undergoes rapid exchange in G1 until the middle of S phase when it becomes stably associated with kinetochores. The majority of CENP-N is loaded during S phase and dissociates again during G2. We propose a model in which CENP-N functions as a fidelity factor during centromeric replication and reveal that the CCAN network is considerably more dynamic than previously appreciated.
Collapse
Affiliation(s)
- Daniela Hellwig
- Molecular Biology, FLI, Beutenbergstrasse 11, 07745 Jena, Germany
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Driving chromosome segregation: lessons from the human and Drosophila centromere–kinetochore machinery. Biochem Soc Trans 2010; 38:1667-75. [DOI: 10.1042/bst0381667] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The kinetochore is a complex molecular machine that serves as the interface between sister chromatids and the mitotic spindle. The kinetochore assembles at a particular chromosomal locus, the centromere, which is essential to maintain genomic stability during cell division. The kinetochore is a macromolecular puzzle of subcomplexes assembled in a hierarchical manner and fulfils three main functions: microtubule attachment, chromosome and sister chromatid movement, and regulation of mitotic progression though the spindle assembly checkpoint. In the present paper we compare recent results on the assembly, organization and function of the kinetochore in human and Drosophila cells and conclude that, although essential functions are highly conserved, there are important differences that might help define what is a minimal chromosome segregation machinery.
Collapse
|
17
|
Antiproliferative effect of Aurora kinase targeting in mesothelioma. Lung Cancer 2010; 70:271-9. [PMID: 20371132 DOI: 10.1016/j.lungcan.2010.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2009] [Revised: 02/14/2010] [Accepted: 03/09/2010] [Indexed: 01/14/2023]
Abstract
The Aurora proteins are a small family of serine/threonine kinase that function in various stages of mitosis. Current interest in Aurora kinase relates to its role in tumours, and its potential as a therapeutic target. In this work we studied the expression of Aurora kinases A and B and related genes in human mesothelioma tissues and in five mesothelioma cell lines. Moreover, we analyzed the effects of ZM447439 (ZM), an Aurora kinase inhibitor, on cellular growth. Results evidenced an over-expression of Aurora kinase A and related genes in human mesothelioma tissues and an over-expression of Aurora kinases A and B in all cell lines. Moreover, we demonstrated that ZM447439 was able to inhibit cell growth in all cell lines and that this inhibition was due to a specific effect as demonstrated by the reduction in the level of Histone H3 phosphorylation. Our findings support a role of Aurora kinase in mesothelioma and the possibility of using Aurora kinase inhibitors in therapeutic modalities.
Collapse
|
18
|
Down the rabbit hole of centromere assembly and dynamics. Curr Opin Cell Biol 2010; 22:392-402. [PMID: 20303726 DOI: 10.1016/j.ceb.2010.02.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 02/15/2010] [Accepted: 02/24/2010] [Indexed: 12/19/2022]
Abstract
The centromere is perhaps the most iconic feature on a eukaryotic chromosome. An amateur enthusiast equipped with a light microscope can easily identify the center of each metacentric chromosome, marking the spot responsible for accurate genome segregation. This review will highlight findings that provide novel insights into how centromeres are assembled and disassembled, the role centromeric proteins play in repair, epigenetic features uniquely found at the centromere, and the three dimensional organization of centromeres caught in the act of mitosis. These advances have unveiled a veritable wonderland of non-canonical features that drive centromere function.
Collapse
|
19
|
Kwaaitaal M, Keinath NF, Pajonk S, Biskup C, Panstruga R. Combined bimolecular fluorescence complementation and Forster resonance energy transfer reveals ternary SNARE complex formation in living plant cells. PLANT PHYSIOLOGY 2010; 152:1135-47. [PMID: 20071602 PMCID: PMC2832253 DOI: 10.1104/pp.109.151142] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Accepted: 01/08/2010] [Indexed: 05/18/2023]
Abstract
Various fluorophore-based microscopic methods, comprising Förster resonance energy transfer (FRET) and bimolecular fluorescence complementation (BiFC), are suitable to study pairwise interactions of proteins in living cells. The analysis of interactions between more than two protein partners using these methods, however, remains difficult. In this study, we report the successful application of combined BiFC-FRET-fluorescence lifetime imaging microscopy and BiFC-FRET-acceptor photobleaching measurements to visualize the formation of ternary soluble N-ethylmaleimide-sensitive factor attachment receptor complexes in leaf epidermal cells. This method expands the repertoire of techniques to study protein-protein interactions in living plant cells by a procedure capable of visualizing simultaneously interactions between three fluorophore-tagged polypeptide partners.
Collapse
|
20
|
Ibraheem A, Campbell RE. Designs and applications of fluorescent protein-based biosensors. Curr Opin Chem Biol 2009; 14:30-6. [PMID: 19913453 DOI: 10.1016/j.cbpa.2009.09.033] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 09/23/2009] [Indexed: 10/20/2022]
Abstract
Genetically encoded biosensors allow the noninvasive imaging of specific biochemical or biorecognition processes with the preservation of subcellular spatial and temporal information. Aequorea green fluorescent protein (FP) and its engineered variants are a critical component of genetically encoded biosensors, as they serve to provide a 'read-out' of the biorecognition event under investigation. The family of FP-based biosensors includes a diverse array of designs that utilize various photophysical characteristics of the FPs. In this review, we will discuss these designs and their read-outs through reviewing some of the recent works in this area.
Collapse
Affiliation(s)
- Andreas Ibraheem
- University of Alberta, Department of Chemistry, Edmonton, Alberta, Canada T6G2G2
| | | |
Collapse
|
21
|
Acceptor-photobleaching FRET analysis of core kinetochore and NAC proteins in living human cells. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 38:781-91. [PMID: 19533115 DOI: 10.1007/s00249-009-0498-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Revised: 05/20/2009] [Accepted: 05/21/2009] [Indexed: 01/18/2023]
Abstract
Faithful chromatin segregation is mediated and controlled by the kinetochore protein network which assembles at centromeres. In this study, the neighbourhood relations of inner kinetochore and nucleosome-associated complex (NAC) proteins were analysed in living human interphase cells by acceptor photobleaching FRET. The data indicate that CENP-U is in close vicinity to CENP-I as well as to CENP-B and that CENP-M is close to CENP-T.
Collapse
|
22
|
Abstract
Centromeres are the discrete sites of spindle microtubule attachment on chromosomes during mitosis and meiosis in all eukaryotes. These highly specialized chromatin structures typically occupy the same site for thousands of generations, yet the mechanism by which centromeres are established, maintained, and function remain a mystery. In metazoans, centromeric DNA sequence has proven not to be the key determinant of centromeric identity; therefore, centromeres are thought to be epigenetically specified by their specialized chromatin structure. In all eukaryotes, the centromere-specific histone H3 variant CenH3 replaces canonical H3 within nucleosomes at centric chromatin. This specialized nucleosome is the building block upon which all other centromere-associated proteins depend. This review highlights exciting new findings that have resulted in a paradigm shift in our understanding of CenH3 assembly into centromeric chromatin, CenH3 nucleosomal structure, CenH3 chromatin folding, the contribution of these factors to centromeric identity, and finally, the intimate role cell-cycle-regulated transcription and pericentric heterochromatin play in the maintenance and integrity of centromeres.
Collapse
Affiliation(s)
- Yamini Dalal
- Chromatin Structure and Epigenetic Mechanisms Unit, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
23
|
Orthaus S, Klement K, Happel N, Hoischen C, Diekmann S. Linker histone H1 is present in centromeric chromatin of living human cells next to inner kinetochore proteins. Nucleic Acids Res 2009; 37:3391-406. [PMID: 19336418 PMCID: PMC2691837 DOI: 10.1093/nar/gkp199] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Revised: 03/09/2009] [Accepted: 03/10/2009] [Indexed: 01/04/2023] Open
Abstract
The vertebrate kinetochore complex assembles at the centromere on alpha-satellite DNA. In humans, alpha-satellite DNA has a repeat length of 171 bp slightly longer than the DNA in the chromatosome containing the linker histone H1. The centromere-binding protein CENP-B binds specifically to alpha-satellite DNA with properties of a centromeric-linker histone. Here, we analysed if linker histone H1 is present at or excluded from centromeric chromatin by CENP-B. By immunostaining we detected the presence, but no enrichment or depletion of five different H1 subtypes at centromeric chromatin. The binding dynamics of H1 at centromeric sites were similar to that at other locations in the genome. These dynamics did not change in CENP-B depleted cells, suggesting that CENP-B and H1 co-exist in centromeric chromatin with no or little functional overlap. By bimolecular fluorescence complementation (BiFC) and Förster resonance energy transfer (FRET), we revealed that the linker histone H1 subtypes H1 degrees and H1.2 bind to centromeric chromatin in interphase nuclei in direct neighbourhood to inner kinetochore proteins.
Collapse
Affiliation(s)
- S. Orthaus
- Leibniz-Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena and Department of Molecular Biology, Institute for Biochemistry and Molecular Cell Biology, University Goettingen, Humboldtallee 23, D-37073 Goettingen, Germany
| | - K. Klement
- Leibniz-Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena and Department of Molecular Biology, Institute for Biochemistry and Molecular Cell Biology, University Goettingen, Humboldtallee 23, D-37073 Goettingen, Germany
| | - N. Happel
- Leibniz-Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena and Department of Molecular Biology, Institute for Biochemistry and Molecular Cell Biology, University Goettingen, Humboldtallee 23, D-37073 Goettingen, Germany
| | - C. Hoischen
- Leibniz-Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena and Department of Molecular Biology, Institute for Biochemistry and Molecular Cell Biology, University Goettingen, Humboldtallee 23, D-37073 Goettingen, Germany
| | - S. Diekmann
- Leibniz-Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena and Department of Molecular Biology, Institute for Biochemistry and Molecular Cell Biology, University Goettingen, Humboldtallee 23, D-37073 Goettingen, Germany
| |
Collapse
|
24
|
Marshall OJ, Marshall AT, Choo KHA. Three-dimensional localization of CENP-A suggests a complex higher order structure of centromeric chromatin. ACTA ACUST UNITED AC 2009; 183:1193-202. [PMID: 19114591 PMCID: PMC2606971 DOI: 10.1083/jcb.200804078] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The histone H3 variant centromere protein A (CENP-A) is central to centromere formation throughout eukaryotes. A long-standing question in centromere biology has been the organization of CENP-A at the centromere and its implications for the structure of centromeric chromatin. In this study, we describe the three-dimensional localization of CENP-A at the inner kinetochore plate through serial-section transmission electron microscopy of human mitotic chromosomes. At the kinetochores of normal centromeres and at a neocentromere, CENP-A occupies a compact domain at the inner kinetochore plate, stretching across two thirds of the length of the constriction but encompassing only one third of the constriction width and height. Within this domain, evidence of substructure is apparent. Combined with previous chromatin immunoprecipitation results (Saffery, R., H. Sumer, S. Hassan, L.H. Wong, J.M. Craig, K. Todokoro, M. Anderson, A. Stafford, and K.H.A. Choo. 2003. Mol. Cell. 12:509–516; Chueh, A.C., L.H. Wong, N. Wong, and K.H.A. Choo. 2005. Hum. Mol. Genet. 14:85–93), our data suggest that centromeric chromatin is arranged in a coiled 30-nm fiber that is itself coiled or folded to form a higher order structure.
Collapse
Affiliation(s)
- Owen J Marshall
- Chromosome and Chromatin Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | | | | |
Collapse
|
25
|
Gonçalves Dos Santos Silva A, Sarkar R, Harizanova J, Guffei A, Mowat M, Garini Y, Mai S. Centromeres in cell division, evolution, nuclear organization and disease. J Cell Biochem 2008; 104:2040-58. [PMID: 18425771 DOI: 10.1002/jcb.21766] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
As the spindle fiber attachment region of the chromosome, the centromere has been investigated in a variety of contexts. Here, we will review current knowledge about this unique chromosomal region and its relevance for proper cell division, speciation, and disease. Understanding the three-dimensional organization of centromeres in normal and tumor cells is just beginning to emerge. Multidisciplinary research will allow for new insights into its normal and aberrant nuclear organization and may allow for new therapeutic interventions that target events linked to centromere function and cell division.
Collapse
|
26
|
Hellwig D, Münch S, Orthaus S, Hoischen C, Hemmerich P, Diekmann S. Live-cell imaging reveals sustained centromere binding of CENP-T via CENP-A and CENP-B. JOURNAL OF BIOPHOTONICS 2008; 1:245-254. [PMID: 19412974 DOI: 10.1002/jbio.200810014] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
At the centromere, a network of proteins, the kinetochore, assembles in order to grant correct chromatin segregation. In this study the dynamics and molecular interactions of the inner kinetochore protein CENP-T were analyzed employing a variety of fluorescence microscopy techniques in living human cells. Acceptor-bleaching FRET indicates that CENP-T directly associates with CENP-A and CENP-B. CENP-T exchange into centromeres is restricted to the S-phase of the cell cycle as revealed by FRAP, suggesting a coreplicational loading mechanism, as we have recently also demonstrated for CENP-I. These properties make CENP-T one of the basic inner kinetochore proteins with most further proteins binding downstream, suggesting a fundamental role of CENP-T in kinetochore function.
Collapse
Affiliation(s)
- Daniela Hellwig
- Leibniz-Institute for Age Research - Fritz Lipmann Institute, Dept. of Molecular Biology, Beutenbergstr. 11, D-07745 Jena, Germany
| | | | | | | | | | | |
Collapse
|
27
|
Hemmerich P, Weidtkamp-Peters S, Hoischen C, Schmiedeberg L, Erliandri I, Diekmann S. Dynamics of inner kinetochore assembly and maintenance in living cells. ACTA ACUST UNITED AC 2008; 180:1101-14. [PMID: 18347072 PMCID: PMC2290840 DOI: 10.1083/jcb.200710052] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
To investigate the dynamics of centromere organization, we have assessed the exchange rates of inner centromere proteins (CENPs) by quantitative microscopy throughout the cell cycle in human cells. CENP-A and CENP-I are stable centromere components that are incorporated into centromeres via a “loading-only” mechanism in G1 and S phase, respectively. A subfraction of CENP-H also stays stably bound to centromeres. In contrast, CENP-B, CENP-C, and some CENP-H and hMis12 exhibit distinct and cell cycle–specific centromere binding stabilities, with residence times ranging from seconds to hours. CENP-C and CENP-H are immobilized at centromeres specifically during replication. In mitosis, all inner CENPs become completely immobilized. CENPs are highly mobile throughout bulk chromatin, which is consistent with a binding-diffusion behavior as the mechanism to scan for vacant high-affinity binding sites at centromeres. Our data reveal a wide range of cell cycle–specific assembly plasticity of the centromere that provides both stability through sustained binding of some components and flexibility through dynamic exchange of other components.
Collapse
Affiliation(s)
- Peter Hemmerich
- Leibniz Institute for Age Research, Fritz Lipmann Institute, 07745 Jena, Germany. phemmer@fl i-leibniz.de
| | | | | | | | | | | |
Collapse
|