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Teng Z, Yang L, Zhang Q, Chen Y, Wang X, Zheng Y, Tian A, Tian D, Lin Z, Deng WM, Liu H. Topoisomerase I is an evolutionarily conserved key regulator for satellite DNA transcription. Nat Commun 2024; 15:5151. [PMID: 38886382 PMCID: PMC11183047 DOI: 10.1038/s41467-024-49567-5] [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: 03/26/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024] Open
Abstract
RNA Polymerase (RNAP) II transcription on non-coding repetitive satellite DNAs plays an important role in chromosome segregation, but a little is known about the regulation of satellite transcription. We here show that Topoisomerase I (TopI), not TopII, promotes the transcription of α-satellite DNAs, the main type of satellite DNAs on human centromeres. Mechanistically, TopI localizes to centromeres, binds RNAP II and facilitates RNAP II elongation. Interestingly, in response to DNA double-stranded breaks (DSBs), α-satellite transcription is dramatically stimulated in a DNA damage checkpoint-independent but TopI-dependent manner, and these DSB-induced α-satellite RNAs form into strong speckles in the nucleus. Remarkably, TopI-dependent satellite transcription also exists in mouse 3T3 and Drosophila S2 cells and in Drosophila larval imaginal wing discs and tumor tissues. Altogether, our findings herein reveal an evolutionally conserved mechanism with TopI as a key player for the regulation of satellite transcription at both cellular and animal levels.
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Affiliation(s)
- Zhen Teng
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Lu Yang
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Qian Zhang
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Yujue Chen
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Xianfeng Wang
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Yiran Zheng
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Aiguo Tian
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
- Tulane Aging Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Di Tian
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Zhen Lin
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Wu-Min Deng
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Hong Liu
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA.
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
- Tulane Aging Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
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2
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Teng Z, Yang L, Zhang Q, Chen Y, Wang X, Zheng Y, Tian A, Tian D, Lin Z, Deng WM, Liu H. Topoisomerase I is an Evolutionarily Conserved Key Regulator for Satellite DNA Transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592391. [PMID: 38746280 PMCID: PMC11092777 DOI: 10.1101/2024.05.03.592391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Repetitive satellite DNAs, divergent in nucleic-acid sequence and size across eukaryotes, provide a physical site for centromere assembly to orchestrate chromosome segregation during the cell cycle. These non-coding DNAs are transcribed by RNA polymerase (RNAP) II and the transcription has been shown to play a role in chromosome segregation, but a little is known about the regulation of centromeric transcription, especially in higher organisms with tandemly-repeated-DNA-sequence centromeres. Using RNA interference knockdown, chemical inhibition and AID/IAA degradation, we show that Topoisomerase I (TopI), not TopII, promotes the transcription of α-satellite DNAs, the main type of satellite on centromeres in human cells. Mechanistically, TopI localizes to centromeres, binds RNAP II and facilitates RNAP II elongation on centromeres. Interestingly, in response to DNA double-stranded breaks (DSBs) induced by chemotherapy drugs or CRSPR/Cas9, α-satellite transcription is dramatically stimulated in a DNA damage checkpoint-independent but TopI-dependent manner. These DSB-induced α-satellite RNAs were predominantly derived from the α-satellite high-order repeats of human centromeres and forms into strong speckles in the nucleus. Remarkably, TopI-dependent satellite transcription also exists in mouse 3T3 and Drosophila S2 cells and in Drosophila larval imaginal wing discs and tumor tissues. Altogether, our findings herein reveal an evolutionally conserved mechanism with TopI as a key player for the regulation of satellite transcription at both cellular and animal levels.
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Affiliation(s)
- Zhen Teng
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
- Contribute equally
| | - Lu Yang
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
- Contribute equally
| | - Qian Zhang
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
- Contribute equally
| | - Yujue Chen
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Xianfeng Wang
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Yiran Zheng
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Aiguo Tian
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
- Tulane Aging Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Di Tian
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Zhen Lin
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Wu-Min Deng
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Hong Liu
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
- Tulane Aging Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
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3
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Benedetti F, Silvestri G, Denaro F, Finesso G, Contreras-Galindo R, Munawwar A, Williams S, Davis H, Bryant J, Wang Y, Radaelli E, Rathinam CV, Gallo RC, Zella D. Mycoplasma DnaK expression increases cancer development in vivo upon DNA damage. Proc Natl Acad Sci U S A 2024; 121:e2320859121. [PMID: 38412130 DOI: 10.1073/pnas.2320859121] [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: 11/27/2023] [Accepted: 01/24/2024] [Indexed: 02/29/2024] Open
Abstract
Well-controlled repair mechanisms are involved in the maintenance of genomic stability, and their failure can precipitate DNA abnormalities and elevate tumor risk. In addition, the tumor microenvironment, enriched with factors inducing oxidative stress and affecting cell cycle checkpoints, intensifies DNA damage when repair pathways falter. Recent research has unveiled associations between certain bacteria, including Mycoplasmas, and various cancers, and the causative mechanism(s) are under active investigation. We previously showed that Mycoplasma fermentans DnaK, an HSP70 family chaperone protein, hampers the activity of proteins like PARP1 and p53, crucial for genomic integrity. Moreover, our analysis of its interactome in human cancer cell lines revealed DnaK's engagement with several components of DNA-repair machinery. Finally, in vivo experiments performed in our laboratory using a DnaK knock-in mouse model generated by our group demonstrated that DnaK exposure led to increased DNA copy number variants, indicative of genomic instability. We present here evidence that expression of DnaK is linked to increased i) incidence of tumors in vivo upon exposure to urethane, a DNA damaging agent; ii) spontaneous DNA damage ex vivo; and iii) expression of proinflammatory cytokines ex vivo, variations in reactive oxygen species levels, and increased β-galactosidase activity across tissues. Moreover, DnaK was associated with increased centromeric instability. Overall, these findings highlight the significance of Mycoplasma DnaK in the etiology of cancer and other genetic disorders providing a promising target for prevention, diagnostics, and therapeutics.
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Affiliation(s)
- Francesca Benedetti
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Giovannino Silvestri
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Frank Denaro
- Department of Biology, Morgan State University, Baltimore, MD 21251
| | - Giovanni Finesso
- Comparative Pathology Core, Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Arshi Munawwar
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Sumiko Williams
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Biology, Morgan State University, Baltimore, MD 21251
| | - Harry Davis
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Joseph Bryant
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Yin Wang
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Surgery, School of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Enrico Radaelli
- Comparative Pathology Core, Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Chozha V Rathinam
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Robert C Gallo
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Davide Zella
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201
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4
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Gussakovsky D, Booy EP, Brown MJF, McKenna SA. Nuclear SRP9/SRP14 heterodimer transcriptionally regulates 7SL and BC200 RNA expression. RNA (NEW YORK, N.Y.) 2023; 29:1185-1200. [PMID: 37156570 PMCID: PMC10351891 DOI: 10.1261/rna.079649.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/21/2023] [Indexed: 05/10/2023]
Abstract
The SRP9/SRP14 heterodimer is a central component of signal recognition particle (SRP) RNA (7SL) processing and Alu retrotransposition. In this study, we sought to establish the role of nuclear SRP9/SRP14 in the transcriptional regulation of 7SL and BC200 RNA. 7SL and BC200 RNA steady-state levels, rate of decay, and transcriptional activity were evaluated under SRP9/SRP14 knockdown conditions. Immunofluorescent imaging, and subcellular fractionation of MCF-7 cells, revealed a distinct nuclear localization for SRP9/SRP14. The relationship between this localization and transcriptional activity at 7SL and BC200 genes was also examined. These findings demonstrate a novel nuclear function of SRP9/SRP14 establishing that this heterodimer transcriptionally regulates 7SL and BC200 RNA expression. We describe a model in which SRP9/SRP14 cotranscriptionally regulate 7SL and BC200 RNA expression. Our model is also a plausible pathway for regulating Alu RNA transcription and is consistent with the hypothesized roles of SRP9/SRP14 transporting 7SL RNA into the nucleolus for posttranscriptional processing, and trafficking of Alu RNA for retrotransposition.
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Affiliation(s)
- Daniel Gussakovsky
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Mira J F Brown
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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5
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Partscht P, Simon A, Chen NP, Erhardt S, Schiebel E. The HIPK2/CDC14B-MeCP2 axis enhances the spindle assembly checkpoint block by promoting cyclin B translation. SCIENCE ADVANCES 2023; 9:eadd6982. [PMID: 36662865 PMCID: PMC9858502 DOI: 10.1126/sciadv.add6982] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 12/16/2022] [Indexed: 05/12/2023]
Abstract
Mitotic perturbations activate the spindle assembly checkpoint (SAC) that keeps cells in prometaphase with high CDK1 activity. Prolonged mitotic arrest is eventually bypassed by gradual cyclin B decline followed by slippage of cells into G1 without chromosome segregation, a process that promotes cell transformation and drug resistance. Hitherto, the cyclin B1 decay is exclusively defined by mechanisms that involve its proteasomal degradation. Here, we report that hyperphosphorylated HIPK2 kinase accumulates in mitotic cells and phosphorylates the Rett syndrome protein MeCP2 at Ser92, a regulation that is counteracted by CDC14B phosphatase. MeCP2S92 phosphorylation leads to the enhanced translation of cyclin B1, which is important for cells with persistent SAC activation to counteract the proteolytic decline of cyclin B1 and therefore to suspend mitotic slippage. Hence, the HIPK2/CDC14B-MeCP2 axis functions as an enhancer of the SAC-induced mitotic block. Collectively, our study revises the prevailing view of how cells confer a sustainable SAC.
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Affiliation(s)
- Patrick Partscht
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg 69120, Germany
- Heidelberg Biosciences International Graduate School (HBIGS), Universität Heidelberg, Heidelberg, Germany
| | - Alexander Simon
- Heidelberg Biosciences International Graduate School (HBIGS), Universität Heidelberg, Heidelberg, Germany
- Zoological Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe 76131, Germany
| | - Nan-Peng Chen
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg 69120, Germany
| | - Sylvia Erhardt
- Zoological Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe 76131, Germany
| | - Elmar Schiebel
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg 69120, Germany
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6
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Centromere defects, chromosome instability, and cGAS-STING activation in systemic sclerosis. Nat Commun 2022; 13:7074. [PMID: 36400785 PMCID: PMC9674829 DOI: 10.1038/s41467-022-34775-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/04/2022] [Indexed: 11/21/2022] Open
Abstract
Centromere defects in Systemic Sclerosis (SSc) have remained unexplored despite the fact that many centromere proteins were discovered in patients with SSc. Here we report that lesion skin fibroblasts from SSc patients show marked alterations in centromeric DNA. SSc fibroblasts also show DNA damage, abnormal chromosome segregation, aneuploidy (only in diffuse cutaneous (dcSSc)) and micronuclei (in all types of SSc), some of which lose centromere identity while retaining centromere DNA sequences. Strikingly, we find cytoplasmic "leaking" of centromere proteins in limited cutaneous SSc (lcSSc) fibroblasts. Cytoplasmic centromere proteins co-localize with antigen presenting MHC Class II molecules, which correlate precisely with the presence of anti-centromere antibodies. CENPA expression and micronuclei formation correlate highly with activation of the cGAS-STING/IFN-β pathway as well as markers of reactive oxygen species (ROS) and fibrosis, ultimately suggesting a link between centromere alterations, chromosome instability, SSc autoimmunity, and fibrosis.
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7
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Xie B, Pu Y, Yang F, Chen W, Yue W, Ma J, Zhang N, Jiang Y, Wu J, Lin Y, Liang X, Wang C, Zou P, Li M. Proteomic Mapping and Targeting of Mitotic Pericentriolar Material in Tumors Bearing Centrosome Amplification. Cancer Res 2022; 82:2576-2592. [PMID: 35648393 DOI: 10.1158/0008-5472.can-22-0225] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/06/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022]
Abstract
Recent work has made it clear that pericentriolar material (PCM), the matrix of proteins surrounding centrioles, contributes to most functions of centrosomes. Given the occurrence of centrosome amplification in most solid tumors and the unconventional survival of these tumor cells, it is tempting to hypothesize that gel-like mitotic PCM would cluster extra centrosomes to defend against mitotic errors and increase tumor cell survival. However, because PCM lacks an encompassing membrane, is highly dynamic, and is physically connected to centrioles, few methods can decode the components of this microscale matrix. In this study, we took advantage of differential labeling between two sets of APEX2-centrosome reactions to design a strategy for acquiring the PCM proteome in living undisturbed cells without synchronization treatment, which identified 392 PCM proteins. Localization of ubiquitination promotion proteins away from PCM was a predominant mechanism to maintain the large size of PCM for centrosome clustering during mitosis in cancer cells. Depletion of PCM gene kinesin family member 20A (KIF20A) caused centrosome clustering failure and apoptosis in cancer cells in vitro and in vivo. Thus, our study suggests a strategy for targeting a wide range of tumors exhibiting centrosome amplification and provides a proteomic resource for future mining of PCM proteins. SIGNIFICANCE This study identifies the proteome of pericentriolar material and reveals therapeutic vulnerabilities in tumors bearing centrosome amplification.
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Affiliation(s)
- Bingteng Xie
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, P.R. China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, P.R. China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing, P.R. China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Peking University Third Hospital, Beijing, P.R. China
| | - Yang Pu
- State Key Laboratory of Medical Molecular Biology, Department of Physiology, Institute of Basic Medical Sciences and School of Basic Medicine, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Fan Yang
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, P.R. China
| | - Wei Chen
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, P.R. China
| | - Wei Yue
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, P.R. China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, P.R. China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing, P.R. China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Peking University Third Hospital, Beijing, P.R. China
| | - Jihong Ma
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, P.R. China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, P.R. China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing, P.R. China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Peking University Third Hospital, Beijing, P.R. China
| | - Na Zhang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, P.R. China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, P.R. China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing, P.R. China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Peking University Third Hospital, Beijing, P.R. China
| | - Yuening Jiang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, P.R. China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, P.R. China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing, P.R. China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Peking University Third Hospital, Beijing, P.R. China
| | - Jiegen Wu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P.R. China
| | - Yihan Lin
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P.R. China
| | - Xin Liang
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, P.R. China
| | - Chu Wang
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, P.R. China
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, P.R. China.,PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, P.R. China.,Chinese Institute for Brain Research (CIBR), Beijing, P.R. China
| | - Mo Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, P.R. China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, P.R. China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing, P.R. China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Peking University Third Hospital, Beijing, P.R. China
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8
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Winans S, Yu HJ, de Los Santos K, Wang GZ, KewalRamani VN, Goff SP. A point mutation in HIV-1 integrase redirects proviral integration into centromeric repeats. Nat Commun 2022; 13:1474. [PMID: 35304442 PMCID: PMC8933506 DOI: 10.1038/s41467-022-29097-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/24/2022] [Indexed: 11/25/2022] Open
Abstract
Retroviruses utilize the viral integrase (IN) protein to integrate a DNA copy of their genome into host chromosomal DNA. HIV-1 integration sites are highly biased towards actively transcribed genes, likely mediated by binding of the IN protein to specific host factors, particularly LEDGF, located at these gene regions. We here report a substantial redirection of integration site distribution induced by a single point mutation in HIV-1 IN. Viruses carrying the K258R IN mutation exhibit a high frequency of integrations into centromeric alpha satellite repeat sequences, as assessed by deep sequencing, a more than 10-fold increase over wild-type. Quantitative PCR and in situ immunofluorescence assays confirm this bias of the K258R mutant virus for integration into centromeric DNA. Immunoprecipitation studies identify host factors binding to IN that may account for the observed bias for integration into centromeres. Centromeric integration events are known to be enriched in the latent reservoir of infected memory T cells, as well as in elite controllers who limit viral replication without intervention. The K258R point mutation in HIV-1 IN is also present in databases of latent proviruses found in patients, and may reflect an unappreciated aspect of the establishment of viral latency. HIV-1 integration sites are biased towards actively transcribed genes, likely mediated by binding of the viral integrase (IN) protein to host factors. Here, Winans et al. show that the K258R point mutation in IN eredirects viral DNA integration to the centromeres of host chromosomes, which may affect HIV latency.
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Affiliation(s)
- Shelby Winans
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA.,Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA.,Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Hyun Jae Yu
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory, Frederick, MD, USA
| | - Kenia de Los Santos
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA.,Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA.,Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Gary Z Wang
- Department of Pathology, Columbia University Medical Center, New York, NY, USA
| | - Vineet N KewalRamani
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Stephen P Goff
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA. .,Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA. .,Howard Hughes Medical Institute, Columbia University, New York, NY, USA.
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9
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de Lima LG, Howe E, Singh VP, Potapova T, Li H, Xu B, Castle J, Crozier S, Harrison CJ, Clifford SC, Miga KH, Ryan SL, Gerton JL. PCR amplicons identify widespread copy number variation in human centromeric arrays and instability in cancer. CELL GENOMICS 2021; 1:100064. [PMID: 34993501 PMCID: PMC8730464 DOI: 10.1016/j.xgen.2021.100064] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 07/13/2021] [Accepted: 08/24/2021] [Indexed: 12/13/2022]
Abstract
Centromeric α-satellite repeats represent ~6% of the human genome, but their length and repetitive nature make sequencing and analysis of those regions challenging. However, centromeres are essential for the stable propagation of chromosomes, so tools are urgently needed to monitor centromere copy number and how it influences chromosome transmission and genome stability. We developed and benchmarked droplet digital PCR (ddPCR) assays that measure copy number for five human centromeric arrays. We applied them to characterize natural variation in centromeric array size, analyzing normal tissue from 37 individuals from China and 39 individuals from the US and UK. Each chromosome-specific array varies in size up to 10-fold across individuals and up to 50-fold across chromosomes, indicating a unique complement of arrays in each individual. We also used the ddPCR assays to analyze centromere copy number in 76 matched tumor-normal samples across four cancer types, representing the most-comprehensive quantitative analysis of centromeric array stability in cancer to date. In contrast to stable transmission in cultured cells, centromeric arrays show gain and loss events in each of the cancer types, suggesting centromeric α-satellite DNA represents a new category of genome instability in cancer. Our methodology for measuring human centromeric-array copy number will advance research on centromeres and genome integrity in normal and disease states.
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Affiliation(s)
| | - Edmund Howe
- The Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | - Tamara Potapova
- The Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Hua Li
- The Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Baoshan Xu
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Institute of Stomatological Research, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Jemma Castle
- Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Steve Crozier
- Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | | | | | - Karen H. Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Sarra L. Ryan
- Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Jennifer L. Gerton
- The Stowers Institute for Medical Research, Kansas City, MO, USA
- University of Kansas Medical Center, Kansas City, KS, USA
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10
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Racca C, Britton S, Hédouin S, Francastel C, Calsou P, Larminat F. BRCA1 prevents R-loop-associated centromeric instability. Cell Death Dis 2021; 12:896. [PMID: 34599155 PMCID: PMC8486751 DOI: 10.1038/s41419-021-04189-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/01/2021] [Accepted: 09/15/2021] [Indexed: 02/05/2023]
Abstract
Centromeres are defined by chromatin containing the histone H3 variant CENP-A assembled onto repetitive α-satellite sequences, which are actively transcribed throughout the cell cycle. Centromeres play an essential role in chromosome inheritance and genome stability through coordinating kinetochores assembly during mitosis. Structural and functional alterations of the centromeres cause aneuploidy and chromosome aberrations which can induce cell death. In human cells, the tumor suppressor BRCA1 associates with centromeric chromatin in the absence of exogenous damage. While we previously reported that BRCA1 contributes to proper centromere homeostasis, the mechanism underlying its centromeric function and recruitment was not fully understood. Here, we show that BRCA1 association with centromeric chromatin depends on the presence of R-loops, which are non-canonical three-stranded structures harboring a DNA:RNA hybrid and are frequently formed during transcription. Subsequently, BRCA1 counteracts the accumulation of R-loops at centromeric α-satellite repeats. Strikingly, BRCA1-deficient cells show impaired localization of CENP-A, higher transcription of centromeric RNA, increased breakage at centromeres and formation of acentric micronuclei, all these features being R-loop-dependent. Finally, BRCA1 depletion reveals a Rad52-dependent hyper-recombination process between centromeric satellite repeats, associated with centromere instability and missegregation. Altogether, our findings provide molecular insights into the key function of BRCA1 in maintaining centromere stability and identity.
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Affiliation(s)
- Carine Racca
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue contre le Cancer, 2018, Toulouse, France
| | - Sébastien Britton
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue contre le Cancer, 2018, Toulouse, France
| | - Sabrine Hédouin
- Université de Paris, Epigénétique et Destin Cellulaire, CNRS, Paris, F-75013, France.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Claire Francastel
- Université de Paris, Epigénétique et Destin Cellulaire, CNRS, Paris, F-75013, France
| | - Patrick Calsou
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue contre le Cancer, 2018, Toulouse, France
| | - Florence Larminat
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France. .,Equipe Labellisée Ligue contre le Cancer, 2018, Toulouse, France.
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11
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Ito N, Tsukamoto K, Taniguchi K, Takahashi K, Okamoto A, Aoki H, Otera‐Takahashi Y, Kitagawa M, Ogata‐Kawata H, Morita H, Hata K, Nakabayashi K. Isolation and characterization of fetal nucleated red blood cells from maternal blood as a target for single cell sequencing-based non-invasive genetic testing. Reprod Med Biol 2021; 20:352-360. [PMID: 34262404 PMCID: PMC8254165 DOI: 10.1002/rmb2.12392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/12/2021] [Accepted: 05/20/2021] [Indexed: 01/04/2023] Open
Abstract
PURPOSE Although non-invasive prenatal testing (NIPT) based on cell-free DNA (cfDNA) in maternal plasma has been prevailing worldwide, low levels of fetal DNA fraction may lead to false-negative results. Since fetal cells in maternal blood provide a pure source of fetal genomic DNA, we aimed to establish a workflow to isolate and sequence fetal nucleated red blood cells (fNRBCs) individually as a target for NIPT. METHODS Using male-bearing pregnancy cases, we isolated fNRBCs individually from maternal blood by FACS, and obtained their genomic sequence data through PCR screening with a Y-chromosome marker and whole-genome amplification (WGA)-based whole-genome sequencing. RESULTS The PCR and WGA efficiencies of fNRBC candidates were consistently lower than those of control cells. Sequencing data analyses revealed that although the majority of the fNRBC candidates were confirmed to be of fetal origin, many of the WGA-based genomic libraries from fNRBCs were considered to have been amplified from a portion of genomic DNA. CONCLUSIONS We established a workflow to isolate and sequence fNRBCs individually. However, our results demonstrated that, to make cell-based NIPT targeting fNRBCs feasible, cell isolation procedures need to be further refined such that the nuclei of fNRBCs are kept intact.
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Affiliation(s)
- Noriko Ito
- Department of Maternal‐Fetal BiologyNational Center for Child Health and DevelopmentTokyoJapan
- Department of Pharmacotherapeutics, Course of Medical and Dental SciencesNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Kazuhiro Tsukamoto
- Department of Pharmacotherapeutics, Course of Medical and Dental SciencesNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Kosuke Taniguchi
- Department of Maternal‐Fetal BiologyNational Center for Child Health and DevelopmentTokyoJapan
| | - Ken Takahashi
- Department of Maternal‐Fetal BiologyNational Center for Child Health and DevelopmentTokyoJapan
- Department of Obstetrics and GynecologyThe Jikei University School of MedicineTokyoJapan
| | - Aikou Okamoto
- Department of Obstetrics and GynecologyThe Jikei University School of MedicineTokyoJapan
| | | | | | | | - Hiroko Ogata‐Kawata
- Department of Maternal‐Fetal BiologyNational Center for Child Health and DevelopmentTokyoJapan
| | - Hideaki Morita
- Department of Allergy and Clinical ImmunologyNational Center for Child Health and DevelopmentTokyoJapan
| | - Kenichiro Hata
- Department of Maternal‐Fetal BiologyNational Center for Child Health and DevelopmentTokyoJapan
| | - Kazuhiko Nakabayashi
- Department of Maternal‐Fetal BiologyNational Center for Child Health and DevelopmentTokyoJapan
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12
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Hoffmann S, Izquierdo HM, Gamba R, Chardon F, Dumont M, Keizer V, Hervé S, McNulty SM, Sullivan BA, Manel N, Fachinetti D. A genetic memory initiates the epigenetic loop necessary to preserve centromere position. EMBO J 2020; 39:e105505. [PMID: 32945564 PMCID: PMC7560200 DOI: 10.15252/embj.2020105505] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 08/10/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
Centromeres are built on repetitive DNA sequences (CenDNA) and a specific chromatin enriched with the histone H3 variant CENP‐A, the epigenetic mark that identifies centromere position. Here, we interrogate the importance of CenDNA in centromere specification by developing a system to rapidly remove and reactivate CENP‐A (CENP‐AOFF/ON). Using this system, we define the temporal cascade of events necessary to maintain centromere position. We unveil that CENP‐B bound to CenDNA provides memory for maintenance on human centromeres by promoting de novo CENP‐A deposition. Indeed, lack of CENP‐B favors neocentromere formation under selective pressure. Occasionally, CENP‐B triggers centromere re‐activation initiated by CENP‐C, but not CENP‐A, recruitment at both ectopic and native centromeres. This is then sufficient to initiate the CENP‐A‐based epigenetic loop. Finally, we identify a population of CENP‐A‐negative, CENP‐B/C‐positive resting CD4+ T cells capable to re‐express and reassembles CENP‐A upon cell cycle entry, demonstrating the physiological importance of the genetic memory.
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Affiliation(s)
| | | | - Riccardo Gamba
- Institut Curie, CNRS, UMR 144, PSL Research University, Paris, France
| | - Florian Chardon
- Institut Curie, CNRS, UMR 144, PSL Research University, Paris, France
| | - Marie Dumont
- Institut Curie, CNRS, UMR 144, PSL Research University, Paris, France
| | - Veer Keizer
- Institut Curie, CNRS, UMR 144, PSL Research University, Paris, France
| | - Solène Hervé
- Institut Curie, CNRS, UMR 144, PSL Research University, Paris, France
| | - Shannon M McNulty
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Beth A Sullivan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Nicolas Manel
- Institut Curie, PSL Research University, INSERM U932, Paris, France
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13
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Saha AK, Contreras-Galindo R, Niknafs YS, Iyer M, Qin T, Padmanabhan K, Siddiqui J, Palande M, Wang C, Qian B, Ward E, Tang T, Tomlins SA, Gitlin SD, Sartor MA, Omenn GS, Chinnaiyan AM, Markovitz DM. The role of the histone H3 variant CENPA in prostate cancer. J Biol Chem 2020; 295:8537-8549. [PMID: 32371391 PMCID: PMC7307189 DOI: 10.1074/jbc.ra119.010080] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 04/14/2020] [Indexed: 01/26/2023] Open
Abstract
Overexpression of centromeric proteins has been identified in a number of human malignancies, but the functional and mechanistic contributions of these proteins to disease progression have not been characterized. The centromeric histone H3 variant centromere protein A (CENPA) is an epigenetic mark that determines centromere identity. Here, using an array of approaches, including RNA-sequencing and ChIP-sequencing analyses, immunohistochemistry-based tissue microarrays, and various cell biology assays, we demonstrate that CENPA is highly overexpressed in prostate cancer in both tissue and cell lines and that the level of CENPA expression correlates with the disease stage in a large cohort of patients. Gain-of-function and loss-of-function experiments confirmed that CENPA promotes prostate cancer cell line growth. The results from the integrated sequencing experiments suggested a previously unidentified function of CENPA as a transcriptional regulator that modulates expression of critical proliferation, cell-cycle, and centromere/kinetochore genes. Taken together, our findings show that CENPA overexpression is crucial to prostate cancer growth.
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Affiliation(s)
- Anjan K Saha
- Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan, USA.,Program in Cancer Biology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Yashar S Niknafs
- Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan, USA.,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Matthew Iyer
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Karthik Padmanabhan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Javed Siddiqui
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Monica Palande
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Claire Wang
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Brian Qian
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Elizabeth Ward
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Tara Tang
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Scott D Gitlin
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Gilbert S Omenn
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Arul M Chinnaiyan
- Program in Cancer Biology, University of Michigan, Ann Arbor, Michigan, USA.,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - David M Markovitz
- Program in Cancer Biology, University of Michigan, Ann Arbor, Michigan, USA .,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA.,Program in Immunology, University of Michigan, Ann Arbor, Michigan, USA
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14
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Gamba R, Fachinetti D. From evolution to function: Two sides of the same CENP-B coin? Exp Cell Res 2020; 390:111959. [DOI: 10.1016/j.yexcr.2020.111959] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/07/2020] [Accepted: 03/12/2020] [Indexed: 10/24/2022]
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15
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Sullivan LL, Sullivan BA. Genomic and functional variation of human centromeres. Exp Cell Res 2020; 389:111896. [PMID: 32035947 DOI: 10.1016/j.yexcr.2020.111896] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/29/2020] [Accepted: 02/05/2020] [Indexed: 10/25/2022]
Abstract
Centromeres are central to chromosome segregation and genome stability, and thus their molecular foundations are important for understanding their function and the ways in which they go awry. Human centromeres typically form at large megabase-sized arrays of alpha satellite DNA for which there is little genomic understanding due to its repetitive nature. Consequently, it has been difficult to achieve genome assemblies at centromeres using traditional next generation sequencing approaches, so that centromeres represent gaps in the current human genome assembly. The role of alpha satellite DNA has been debated since centromeres can form, albeit rarely, on non-alpha satellite DNA. Conversely, the simple presence of alpha satellite DNA is not sufficient for centromere function since chromosomes with multiple alpha satellite arrays only exhibit a single location of centromere assembly. Here, we discuss the organization of human centromeres as well as genomic and functional variation in human centromere location, and current understanding of the genomic and epigenetic mechanisms that underlie centromere flexibility in humans.
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Affiliation(s)
| | - Beth A Sullivan
- Department of Molecular Genetics and Microbiology, USA; Division of Human Genetics, Duke University School of Medicine, Durham, NC, 27710, USA.
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16
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Dumont M, Gamba R, Gestraud P, Klaasen S, Worrall JT, De Vries SG, Boudreau V, Salinas-Luypaert C, Maddox PS, Lens SM, Kops GJ, McClelland SE, Miga KH, Fachinetti D. Human chromosome-specific aneuploidy is influenced by DNA-dependent centromeric features. EMBO J 2019; 39:e102924. [PMID: 31750958 DOI: 10.15252/embj.2019102924] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/21/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022] Open
Abstract
Intrinsic genomic features of individual chromosomes can contribute to chromosome-specific aneuploidy. Centromeres are key elements for the maintenance of chromosome segregation fidelity via a specialized chromatin marked by CENP-A wrapped by repetitive DNA. These long stretches of repetitive DNA vary in length among human chromosomes. Using CENP-A genetic inactivation in human cells, we directly interrogate if differences in the centromere length reflect the heterogeneity of centromeric DNA-dependent features and whether this, in turn, affects the genesis of chromosome-specific aneuploidy. Using three distinct approaches, we show that mis-segregation rates vary among different chromosomes under conditions that compromise centromere function. Whole-genome sequencing and centromere mapping combined with cytogenetic analysis, small molecule inhibitors, and genetic manipulation revealed that inter-chromosomal heterogeneity of centromeric features, but not centromere length, influences chromosome segregation fidelity. We conclude that faithful chromosome segregation for most of human chromosomes is biased in favor of centromeres with high abundance of DNA-dependent centromeric components. These inter-chromosomal differences in centromere features can translate into non-random aneuploidy, a hallmark of cancer and genetic diseases.
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Affiliation(s)
- Marie Dumont
- Institut Curie, PSL Research University, CNRS, UMR144, Paris, France
| | - Riccardo Gamba
- Institut Curie, PSL Research University, CNRS, UMR144, Paris, France
| | - Pierre Gestraud
- Institut Curie, PSL Research University, CNRS, UMR144, Paris, France.,PSL Research University, Institut Curie Research Center, INSERM U900, Paris, France.,MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Sjoerd Klaasen
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, The Netherlands
| | - Joseph T Worrall
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Sippe G De Vries
- Oncode Institute, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Vincent Boudreau
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | | | - Paul S Maddox
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Susanne Ma Lens
- Oncode Institute, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Geert Jpl Kops
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, The Netherlands
| | | | - Karen H Miga
- Center for Biomolecular Science & Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
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17
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Scelfo A, Fachinetti D. Keeping the Centromere under Control: A Promising Role for DNA Methylation. Cells 2019; 8:cells8080912. [PMID: 31426433 PMCID: PMC6721688 DOI: 10.3390/cells8080912] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 08/06/2019] [Accepted: 08/15/2019] [Indexed: 01/22/2023] Open
Abstract
In order to maintain cell and organism homeostasis, the genetic material has to be faithfully and equally inherited through cell divisions while preserving its integrity. Centromeres play an essential task in this process; they are special sites on chromosomes where kinetochores form on repetitive DNA sequences to enable accurate chromosome segregation. Recent evidence suggests that centromeric DNA sequences, and epigenetic regulation of centromeres, have important roles in centromere physiology. In particular, DNA methylation is abundant at the centromere, and aberrant DNA methylation, observed in certain tumors, has been correlated to aneuploidy and genomic instability. In this review, we evaluate past and current insights on the relationship between centromere function and the DNA methylation pattern of its underlying sequences.
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Affiliation(s)
- Andrea Scelfo
- Institut Curie, PSL Research University, CNRS, UMR144, 26 rue d'Ulm, 75005 Paris, France.
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, CNRS, UMR144, 26 rue d'Ulm, 75005 Paris, France.
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18
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Abstract
Centromere genomics remain poorly characterized in cancer, due to technologic limitations in sequencing and bioinformatics methodologies that make high-resolution delineation of centromeric loci difficult to achieve. We here leverage a highly specific and targeted rapid PCR methodology to quantitatively assess the genomic landscape of centromeres in cancer cell lines and primary tissue. PCR-based profiling of centromeres revealed widespread heterogeneity of centromeric and pericentromeric sequences in cancer cells and tissues as compared to healthy counterparts. Quantitative reductions in centromeric core and pericentromeric markers (α-satellite units and HERV-K copies) were observed in neoplastic samples as compared to healthy counterparts. Subsequent phylogenetic analysis of a pericentromeric endogenous retrovirus amplified by PCR revealed possible gene conversion events occurring at numerous pericentromeric loci in the setting of malignancy. Our findings collectively represent a more comprehensive evaluation of centromere genetics in the setting of malignancy, providing valuable insight into the evolution and reshuffling of centromeric sequences in cancer development and progression.
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19
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Therapeutic application of the CRISPR system: current issues and new prospects. Hum Genet 2019; 138:563-590. [DOI: 10.1007/s00439-019-02028-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 05/13/2019] [Indexed: 12/23/2022]
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20
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Kaplan MH, Kaminski M, Estes JM, Gitlin SD, Zahn J, Elder JT, Tejasvi T, Gensterblum E, Sawalha AH, McGowan JP, Dosik MH, Direskeneli H, Direskeneli GS, Adebamowo SN, Adebamowo CA, Sajadi M, Contreras-Galindo R. Structural variation of centromeric endogenous retroviruses in human populations and their impact on cutaneous T-cell lymphoma, Sézary syndrome, and HIV infection. BMC Med Genomics 2019; 12:58. [PMID: 31046767 PMCID: PMC6498702 DOI: 10.1186/s12920-019-0505-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 04/15/2019] [Indexed: 12/16/2022] Open
Abstract
Background Human Endogenous Retroviruses type K HML-2 (HK2) are integrated into 117 or more areas of human chromosomal arms while two newly discovered HK2 proviruses, K111 and K222, spread extensively in pericentromeric regions, are the first retroviruses discovered in these areas of our genome. Methods We use PCR and sequencing analysis to characterize pericentromeric K111 proviruses in DNA from individuals of diverse ethnicities and patients with different diseases. Results We found that the 5′ LTR-gag region of K111 proviruses is missing in certain individuals, creating pericentromeric instability. K111 deletion (−/− K111) is seen in about 15% of Caucasian, Asian, and Middle Eastern populations; it is missing in 2.36% of African individuals, suggesting that the −/− K111 genotype originated out of Africa. As we identified the −/−K111 genotype in Cutaneous T-cell lymphoma (CTCL) cell lines, we studied whether the −/−K111 genotype is associated with CTCL. We found a significant increase in the frequency of detection of the −/−K111 genotype in Caucasian patients with severe CTCL and/or Sézary syndrome (n = 35, 37.14%), compared to healthy controls (n = 160, 15.6%) [p = 0.011]. The −/−K111 genotype was also found to vary in HIV-1 infection. Although Caucasian healthy individuals have a similar frequency of detection of the −/− K111 genotype, Caucasian HIV Long-Term Non-Progressors (LTNPs) and/or elite controllers, have significantly higher detection of the −/−K111 genotype (30.55%; n = 36) than patients who rapidly progress to AIDS (8.5%; n = 47) [p = 0.0097]. Conclusion Our data indicate that pericentromeric instability is associated with more severe CTCL and/or Sézary syndrome in Caucasians, and appears to allow T-cells to survive lysis by HIV infection. These findings also provide new understanding of human evolution, as the −/−K111 genotype appears to have arisen out of Africa and is distributed unevenly throughout the world, possibly affecting the severity of HIV in different geographic areas. Electronic supplementary material The online version of this article (10.1186/s12920-019-0505-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mark H Kaplan
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Mark Kaminski
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Judith M Estes
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Scott D Gitlin
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.,Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, 48105, USA
| | - Joseph Zahn
- Division of Dermatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - James T Elder
- Division of Dermatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.,Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, 48105, USA
| | - Trilokraj Tejasvi
- Division of Dermatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.,Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, 48105, USA
| | - Elizabeth Gensterblum
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Amr H Sawalha
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Joseph Patrick McGowan
- Division of Infectious Diseases, The Feinstein Institute for Medical research, Manhasset, NY, 11030, USA
| | | | - Haner Direskeneli
- Division of Rheumatology, School of Medicine, Marmara University, Istanbul, Turkey
| | | | - Sally N Adebamowo
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Clement A Adebamowo
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Mohammad Sajadi
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Rafael Contreras-Galindo
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA. .,Hormel Institute, University of Minnesota, Austin, MN, 55912, USA.
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