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Chong MK, Rosas-Salvans M, Tran V, Dumont S. Chromosome size-dependent polar ejection force impairs mammalian mitotic error correction. J Cell Biol 2024; 223:e202310010. [PMID: 38727808 PMCID: PMC11090132 DOI: 10.1083/jcb.202310010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 03/28/2024] [Accepted: 04/29/2024] [Indexed: 05/15/2024] Open
Abstract
Accurate chromosome segregation requires sister kinetochores to biorient, attaching to opposite spindle poles. To this end, the mammalian kinetochore destabilizes incorrect attachments and stabilizes correct ones, but how it discriminates between these is not yet clear. Here, we test the model that kinetochore tension is the stabilizing cue and ask how chromosome size impacts that model. We live image PtK2 cells, with just 14 chromosomes, widely ranging in size, and find that long chromosomes align at the metaphase plate later than short chromosomes. Enriching for errors and imaging error correction live, we show that long chromosomes exhibit a specific delay in correcting attachments. Using chromokinesin overexpression and laser ablation to perturb polar ejection forces, we find that chromosome size and force on arms determine alignment order. Thus, we propose a model where increased force on long chromosomes can falsely stabilize incorrect attachments, delaying their biorientation. As such, long chromosomes may require compensatory mechanisms for correcting errors to avoid chromosomal instability.
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Affiliation(s)
- Megan K. Chong
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Miquel Rosas-Salvans
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Vanna Tran
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Sophie Dumont
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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2
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Zych MG, Hatch EM. Small spaces, big problems: The abnormal nucleoplasm of micronuclei and its consequences. Curr Opin Struct Biol 2024; 87:102839. [PMID: 38763098 DOI: 10.1016/j.sbi.2024.102839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/29/2024] [Accepted: 04/26/2024] [Indexed: 05/21/2024]
Abstract
Micronuclei (MN) form from missegregated chromatin that recruits its own nuclear envelope during mitotic exit and are a common consequence of chromosomal instability. MN are unstable due to errors in nuclear envelope organization and frequently rupture, leading to loss of compartmentalization, loss of nuclear functions, and major changes in genome stability and gene expression. However, recent work found that, even prior to rupture, nuclear processes can be severely defective in MN, which may contribute to rupture-associated defects and have lasting consequences for chromatin structure and function. In this review we discuss work that highlights nuclear function defects in intact MN, including their mechanisms and consequences, and how biases in chromosome missegregation into MN may affect the penetrance of these defects. Illuminating the nuclear environment of MN demonstrates that MN formation alone has major consequences for both the genome and cell and provides new insight into how nuclear content is regulated.
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Affiliation(s)
- Molly G Zych
- Molecular and Cellular Biology PhD Program, University of Washington, Seattle, WA, USA; Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA. https://twitter.com/ZychMolly
| | - Emily M Hatch
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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3
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Parl FF. Analysis of CENP-B Boxes as Anchor of Kinetochores in Centromeres of Human Chromosomes. Bioinform Biol Insights 2024; 18:11779322241248913. [PMID: 38690324 PMCID: PMC11060027 DOI: 10.1177/11779322241248913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 04/04/2024] [Indexed: 05/02/2024] Open
Abstract
The kinetochore is a multiprotein structure that attaches at one end to DNA in the centromere and at the other end to microtubules in the mitotic spindle. By connecting centromere and spindle, the kinetochore controls the migration of chromosomes during cell division. The exact position where the kinetochore assembles on each centromere was uncertain because large sections of centromeric DNA had not been sequenced due to highly repetitive alpha-satellite arrays. Embedded in the arrays is a 17 bp consensus sequence, the so-called CENP-B box, which binds the CENP-B protein, the only protein that binds directly to centromeric DNA. Recently, the Telomere-to-Telomere Consortium published the complete centromeric DNA sequences of all chromosomes including their epigenetic modifications in the T2T-CHM13 map. I used data from the T2T-CHM13 map to locate the CENP-B boxes in the centromeres as anchor of kinetochores. Most of the CENP-B boxes in centromeric DNA are methylated with the exception of the so-called centromere dip region (CDR), where CENP-B protein dimers bind to adjacent unmethylated CENP-B boxes and interact with CENP-A and CENP-C proteins to assemble the kinetochore. The centromeres of all chromosomes combined have a size of 407 Mb of which the kinetochores account for 5.0 Mb or 1.2%. There is no correlation between centromere and kinetochore size (P = .77). While the number of CENP-B boxes varies 4-fold between chromosomes, their density (number/Kb) varies less than 2-fold with a mean of 2.61 ± 0.33. The narrow range ensures a uniform pull of the spindle on the centromeres. I illustrate the findings in a model of the human kinetochore anchored at unmethylated CENP-B boxes in the CDR and present circos plots of chromosomes to show the location of kinetochores in their respective centromeres.
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Affiliation(s)
- Fritz F Parl
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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4
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Lynch AR, Bradford S, Zhou AS, Oxendine K, Henderson L, Horner VL, Weaver BA, Burkard ME. A survey of chromosomal instability measures across mechanistic models. Proc Natl Acad Sci U S A 2024; 121:e2309621121. [PMID: 38588415 PMCID: PMC11032477 DOI: 10.1073/pnas.2309621121] [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: 06/22/2023] [Accepted: 01/25/2024] [Indexed: 04/10/2024] Open
Abstract
Chromosomal instability (CIN) is the persistent reshuffling of cancer karyotypes via chromosome mis-segregation during cell division. In cancer, CIN exists at varying levels that have differential effects on tumor progression. However, mis-segregation rates remain challenging to assess in human cancer despite an array of available measures. We evaluated measures of CIN by comparing quantitative methods using specific, inducible phenotypic CIN models of chromosome bridges, pseudobipolar spindles, multipolar spindles, and polar chromosomes. For each, we measured CIN fixed and timelapse fluorescence microscopy, chromosome spreads, six-centromere FISH, bulk transcriptomics, and single-cell DNA sequencing (scDNAseq). As expected, microscopy of tumor cells in live and fixed samples significantly correlated (R = 0.72; P < 0.001) and sensitively detect CIN. Cytogenetics approaches include chromosome spreads and 6-centromere FISH, which also significantly correlate (R = 0.76; P < 0.001) but had limited sensitivity for lower rates of CIN. Bulk genomic DNA signatures and bulk transcriptomic scores, CIN70 and HET70, did not detect CIN. By contrast, scDNAseq detects CIN with high sensitivity, and significantly correlates with imaging methods (R = 0.82; P < 0.001). In summary, single-cell methods such as imaging, cytogenetics, and scDNAseq can measure CIN, with the latter being the most comprehensive method accessible to clinical samples. To facilitate the comparison of CIN rates between phenotypes and methods, we propose a standardized unit of CIN: Mis-segregations per Diploid Division. This systematic analysis of common CIN measures highlights the superiority of single-cell methods and provides guidance for measuring CIN in the clinical setting.
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Affiliation(s)
- Andrew R. Lynch
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, WI53705
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI53705
| | - Shermineh Bradford
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, WI53705
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI53705
| | - Amber S. Zhou
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, WI53705
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI53705
| | - Kim Oxendine
- Cytogenetic and Molecular Genetic Services Laboratory, Wisconsin State Laboratory of Hygiene, University of Wisconsin–Madison, Madison, WI53706
| | - Les Henderson
- Cytogenetic and Molecular Genetic Services Laboratory, Wisconsin State Laboratory of Hygiene, University of Wisconsin–Madison, Madison, WI53706
| | - Vanessa L. Horner
- Cytogenetic and Molecular Genetic Services Laboratory, Wisconsin State Laboratory of Hygiene, University of Wisconsin–Madison, Madison, WI53706
| | - Beth A. Weaver
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, WI53705
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI53705
- Department of Cell and Regenerative Biology, University of Wisconsin–Madison, Madison, WI53705
| | - Mark E. Burkard
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, WI53705
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI53705
- Division of Hematology Oncology and Palliative Care, Department of Medicine University of Wisconsin–Madison, Madison, WI53705
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5
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Yin K, Büttner M, Deligiannis IK, Strzelecki M, Zhang L, Talavera-López C, Theis F, Odom DT, Martinez-Jimenez CP. Polyploidisation pleiotropically buffers ageing in hepatocytes. J Hepatol 2024:S0168-8278(24)00227-7. [PMID: 38583492 DOI: 10.1016/j.jhep.2024.03.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND & AIMS Polyploidy in hepatocytes has been proposed as a genetic mechanism to buffer against transcriptional dysregulation. Here, we aim to demonstrate the role of polyploidy in modulating gene regulatory networks in hepatocytes during ageing. METHODS We performed single-nucleus RNA-sequencing in hepatocyte nuclei of different ploidy levels isolated from young and old wild-type mice. Changes in the gene expression and regulatory network were compared to three independent haploinsufficient strains for HNF4A, CEBPA or CTCF, representing non-deleterious perturbations. Phenotypic characteristics of the liver section were additionally evaluated histologically, whereas the genomic allele composition of hepatocytes was analysed by BaseScope. RESULTS We observed that ageing in wild-type mice results in nuclei polyploidy and marked increase in steatosis. Haploinsufficiency of liver-specific master regulators (HFN4A or CEBPA) results in the enrichment of hepatocytes with tetraploid nuclei at a young age, affecting the genomic regulatory network, and dramatically suppressing ageing-related steatosis tissue-wide. Notably, these phenotypes are not the result of subtle disruption to liver-specific transcriptional networks, since haploinsufficiency in CTCF insulator protein resulted in the same phenotype. Further quantification of genotypes of tetraploid hepatocytes in young and old HFN4A haploinsufficient mice revealed that during ageing, tetraploid hepatocytes lead to the selection of wild-type alleles, restoring non-deleterious genetic perturbation. ConclusionsOur results suggest a model whereby polyploidisation leads to fundamentally different cell states. Polyploid conversion enables pleiotropic buffering against age-related decline via non-random allelic segregation to restore a wild-type genome.
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Affiliation(s)
- Kelvin Yin
- Helmholtz Pioneer Campus (HPC), Helmholtz Munich, Neuherberg, Germany
| | - Maren Büttner
- Institute of Computational Biology, Computational Health Department, Helmholtz Munich, Neuherberg, Germany
| | | | - Mateusz Strzelecki
- Helmholtz Pioneer Campus (HPC), Helmholtz Munich, Neuherberg, Germany; German Cancer Research Centre, Heidelberg, Germany
| | - Liwei Zhang
- Helmholtz Pioneer Campus (HPC), Helmholtz Munich, Neuherberg, Germany
| | - Carlos Talavera-López
- Institute of Computational Biology, Computational Health Department, Helmholtz Munich, Neuherberg, Germany; TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Fabian Theis
- Institute of Computational Biology, Computational Health Department, Helmholtz Munich, Neuherberg, Germany; Würzburg Institute for Systems Immunology, Faculty of Medicine, Julius-Maximilian-Universität, Würzburg, Germany
| | - Duncan T Odom
- Technical University of Munich, Department of Mathematics, 85748 Garching. Munich, Germany
| | - Celia P Martinez-Jimenez
- Helmholtz Pioneer Campus (HPC), Helmholtz Munich, Neuherberg, Germany; German Cancer Research Centre, Heidelberg, Germany; Institute of Biotechnology and Biomedicine (BIOTECMED), Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, Spain.
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6
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Baker TM, Waise S, Tarabichi M, Van Loo P. Aneuploidy and complex genomic rearrangements in cancer evolution. NATURE CANCER 2024; 5:228-239. [PMID: 38286829 PMCID: PMC7616040 DOI: 10.1038/s43018-023-00711-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/14/2023] [Indexed: 01/31/2024]
Abstract
Mutational processes that alter large genomic regions occur frequently in developing tumors. They range from simple copy number gains and losses to the shattering and reassembly of entire chromosomes. These catastrophic events, such as chromothripsis, chromoplexy and the formation of extrachromosomal DNA, affect the expression of many genes and therefore have a substantial effect on the fitness of the cells in which they arise. In this review, we cover large genomic alterations, the mechanisms that cause them and their effect on tumor development and evolution.
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Affiliation(s)
- Toby M Baker
- The Francis Crick Institute, London, UK
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sara Waise
- The Francis Crick Institute, London, UK
- Cancer Sciences Unit, University of Southampton, Southampton, UK
| | - Maxime Tarabichi
- The Francis Crick Institute, London, UK
- Institute for Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium
| | - Peter Van Loo
- The Francis Crick Institute, London, UK.
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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7
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Popovic M, Borot L, Lorenzon AR, Lopes ALRDC, Sakkas D, Lledó B, Morales R, Ortiz JA, Polyzos NP, Parriego M, Azpiroz F, Galain M, Pujol A, Menten B, Dhaenens L, Vanden Meerschaut F, Stoop D, Rodriguez M, de la Blanca EP, Rodríguez A, Vassena R. Implicit bias in diagnosing mosaicism amongst preimplantation genetic testing providers: results from a multicenter study of 36 395 blastocysts. Hum Reprod 2024; 39:258-274. [PMID: 37873575 DOI: 10.1093/humrep/dead213] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/15/2023] [Indexed: 10/25/2023] Open
Abstract
STUDY QUESTION Does the diagnosis of mosaicism affect ploidy rates across different providers offering preimplantation genetic testing for aneuploidies (PGT-A)? SUMMARY ANSWER Our analysis of 36 395 blastocyst biopsies across eight genetic testing laboratories revealed that euploidy rates were significantly higher in providers reporting low rates of mosaicism. WHAT IS KNOWN ALREADY Diagnoses consistent with chromosomal mosaicism have emerged as a third category of possible embryo ploidy outcomes following PGT-A. However, in the era of mosaicism, embryo selection has become increasingly complex. Biological, technical, analytical, and clinical complexities in interpreting such results have led to substantial variability in mosaicism rates across PGT-A providers and clinics. Critically, it remains unknown whether these differences impact the number of euploid embryos available for transfer. Ultimately, this may significantly affect clinical outcomes, with important implications for PGT-A patients. STUDY DESIGN, SIZE, DURATION In this international, multicenter cohort study, we reviewed 36 395 consecutive PGT-A results, obtained from 10 035 patients across 11 867 treatment cycles, conducted between October 2015 and October 2021. A total of 17 IVF centers, across eight PGT-A providers, five countries and three continents participated in the study. All blastocysts were tested using trophectoderm biopsy and next-generation sequencing. Both autologous and donation cycles were assessed. Cycles using preimplantation genetic testing for structural rearrangements were excluded from the analysis. PARTICIPANTS/MATERIALS, SETTING, METHODS The PGT-A providers were randomly categorized (A to H). Providers B, C, D, E, F, G, and H all reported mosaicism, whereas Provider A reported embryos as either euploid or aneuploid. Ploidy rates were analyzed using multilevel mixed linear regression. Analyses were adjusted for maternal age, paternal age, oocyte source, number of embryos biopsied, day of biopsy, and PGT-A provider, as appropriate. We compared associations between genetic testing providers and PGT-A outcomes, including the number of chromosomally normal (euploid) embryos determined to be suitable for transfer. MAIN RESULTS AND THE ROLE OF CHANCE The mean maternal age (±SD) across all providers was 36.2 (±5.2). Our findings reveal a strong association between PGT-A provider and the diagnosis of euploidy and mosaicism. Amongst the seven providers that reported mosaicism, the rates varied from 3.1% to 25.0%. After adjusting for confounders, we observed a significant difference in the likelihood of diagnosing mosaicism across providers (P < 0.001), ranging from 6.5% (95% CI: 5.2-7.4%) for Provider B to 35.6% (95% CI: 32.6-38.7%) for Provider E. Notably, adjusted euploidy rates were highest for providers that reported the lowest rates of mosaicism (Provider B: euploidy, 55.7% (95% CI: 54.1-57.4%), mosaicism, 6.5% (95% CI: 5.2-7.4%); Provider H: euploidy, 44.5% (95% CI: 43.6-45.4%), mosaicism, 9.9% (95% CI: 9.2-10.6%)); and Provider D: euploidy, 43.8% (95% CI: 39.2-48.4%), mosaicism, 11.0% (95% CI: 7.5-14.5%)). Moreover, the overall chance of having at least one euploid blastocyst available for transfer was significantly higher when mosaicism was not reported, when we compared Provider A to all other providers (OR = 1.30, 95% CI: 1.13-1.50). Differences in diagnosing and interpreting mosaic results across PGT-A laboratories raise further concerns regarding the accuracy and relevance of mosaicism predictions. While we confirmed equivalent clinical outcomes following the transfer of mosaic and euploid blastocysts, we found that a significant proportion of mosaic embryos are not used for IVF treatment. LIMITATIONS, REASONS FOR CAUTION Due to the retrospective nature of the study, associations can be ascertained, however, causality cannot be established. Certain parameters such as blastocyst grade were not available in the dataset. Furthermore, certain platform-related and clinic-specific factors may not be readily quantifiable or explicitly captured in our dataset. As such, a full elucidation of all potential confounders accounting for variability may not be possible. WIDER IMPLICATIONS OF THE FINDINGS Our findings highlight the strong need for standardization and quality assurance in the industry. The decision not to transfer mosaic embryos may ultimately reduce the chance of success of a PGT-A cycle by limiting the pool of available embryos. Until we can be certain that mosaic diagnoses accurately reflect biological variability, reporting mosaicism warrants utmost caution. A prudent approach is imperative, as it may determine the difference between success or failure for some patients. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the Torres Quevedo Grant, awarded to M.P. (PTQ2019-010494) by the Spanish State Research Agency, Ministry of Science and Innovation, Spain. M.P., L.B., A.R.L., A.L.R.d.C.L., N.P.P., M.P., D.S., F.A., A.P., B.M., L.D., F.V.M., D.S., M.R., E.P.d.l.B., A.R., and R.V. have no competing interests to declare. B.L., R.M., and J.A.O. are full time employees of IB Biotech, the genetics company of the Instituto Bernabeu group, which performs preimplantation genetic testing. M.G. is a full time employee of Novagen, the genetics company of Cegyr, which performs preimplantation genetic testing. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Mina Popovic
- Research and Development, Eugin Group, Barcelona, Spain
| | - Lorena Borot
- Research and Development, Eugin Group, Barcelona, Spain
| | | | | | | | | | | | | | - Nikolaos P Polyzos
- Clínica Dexeus Mujer, Dexeus University Hospital, Barcelona, Spain
- Department of Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - Mónica Parriego
- Clínica Dexeus Mujer, Dexeus University Hospital, Barcelona, Spain
| | - Felicitas Azpiroz
- Research and Development, Eugin Group, Barcelona, Spain
- Cegyr-Medicina y Genética Reproductiva-Eugin Group, Buenos Aires, Argentina
| | - Micaela Galain
- Cegyr-Medicina y Genética Reproductiva-Eugin Group, Buenos Aires, Argentina
| | - Aïda Pujol
- Center for Infertility and Human Reproduction, CIRH-Eugin Group, Barcelona, Spain
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Lien Dhaenens
- Department of Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | | | - Dominic Stoop
- Department of Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | | | | | | | - Rita Vassena
- Research and Development, Eugin Group, Barcelona, Spain
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Gambogi CW, Pandey N, Dawicki-McKenna JM, Arora UP, Liskovykh MA, Ma J, Lamelza P, Larionov V, Lampson MA, Logsdon GA, Dumont BL, Black BE. Centromere innovations within a mouse species. SCIENCE ADVANCES 2023; 9:eadi5764. [PMID: 37967185 PMCID: PMC10651114 DOI: 10.1126/sciadv.adi5764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/13/2023] [Indexed: 11/17/2023]
Abstract
Mammalian centromeres direct faithful genetic inheritance and are typically characterized by regions of highly repetitive and rapidly evolving DNA. We focused on a mouse species, Mus pahari, that we found has evolved to house centromere-specifying centromere protein-A (CENP-A) nucleosomes at the nexus of a satellite repeat that we identified and termed π-satellite (π-sat), a small number of recruitment sites for CENP-B, and short stretches of perfect telomere repeats. One M. pahari chromosome, however, houses a radically divergent centromere harboring ~6 mega-base pairs of a homogenized π-sat-related repeat, π-satB, that contains >20,000 functional CENP-B boxes. There, CENP-B abundance promotes accumulation of microtubule-binding components of the kinetochore and a microtubule-destabilizing kinesin of the inner centromere. We propose that the balance of pro- and anti-microtubule binding by the new centromere is what permits it to segregate during cell division with high fidelity alongside the older ones whose sequence creates a markedly different molecular composition.
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Affiliation(s)
- Craig W. Gambogi
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nootan Pandey
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennine M. Dawicki-McKenna
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Uma P. Arora
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Mikhail A. Liskovykh
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jun Ma
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Piero Lamelza
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael A. Lampson
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Glennis A. Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Beth L. Dumont
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469, USA
| | - Ben E. Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
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9
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Miga KH, Eichler EE. Envisioning a new era: Complete genetic information from routine, telomere-to-telomere genomes. Am J Hum Genet 2023; 110:1832-1840. [PMID: 37922882 PMCID: PMC10645551 DOI: 10.1016/j.ajhg.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 11/07/2023] Open
Abstract
Advances in long-read sequencing and assembly now mean that individual labs can generate phased genomes that are more accurate and more contiguous than the original human reference genome. With declining costs and increasing democratization of technology, we suggest that complete genome assemblies, where both parental haplotypes are phased telomere to telomere, will become standard in human genetics. Soon, even in clinical settings where rigorous sample-handling standards must be met, affected individuals could have reference-grade genomes fully sequenced and assembled in just a few hours given advances in technology, computational processing, and annotation. Complete genetic variant discovery will transform how we map, catalog, and associate variation with human disease and fundamentally change our understanding of the genetic diversity of all humans.
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Affiliation(s)
- Karen H Miga
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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10
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Chong MK, Rosas-Salvans M, Tran V, Dumont S. Chromosome size-dependent polar ejection force impairs mammalian mitotic error correction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562637. [PMID: 37905080 PMCID: PMC10614862 DOI: 10.1101/2023.10.16.562637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Accurate chromosome segregation requires sister kinetochores to biorient, attaching to opposite spindle poles. To this end, the mammalian kinetochore destabilizes incorrect attachments and stabilizes correct ones, but how it discriminates between these is not yet clear. Here, we test the model that kinetochore tension is the stabilizing cue and ask how chromosome size impacts that model. We live image PtK2 cells, with just 14 chromosomes, widely ranging in size, and find that long chromosomes align at the metaphase plate later than short chromosomes. Enriching for errors and imaging error correction live, we show that long chromosomes exhibit a specific delay in correcting attachments. Using chromokinesin overexpression and laser ablation to perturb polar ejection forces, we find that chromosome size and force on arms determine alignment order. Thus, we propose a model where increased force on long chromosomes can falsely stabilize incorrect attachments, delaying their biorientation. As such, long chromosomes may require compensatory mechanisms for correcting errors to avoid chromosomal instability.
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Affiliation(s)
- Megan K. Chong
- Tetrad Graduate Program, UCSF, San Francisco, CA 94158, USA
- Department of Bioengineering & Therapeutic Sciences, UCSF, San Francisco, CA 94158, USA
| | - Miquel Rosas-Salvans
- Department of Bioengineering & Therapeutic Sciences, UCSF, San Francisco, CA 94158, USA
| | - Vanna Tran
- Tetrad Graduate Program, UCSF, San Francisco, CA 94158, USA
- Department of Bioengineering & Therapeutic Sciences, UCSF, San Francisco, CA 94158, USA
| | - Sophie Dumont
- Tetrad Graduate Program, UCSF, San Francisco, CA 94158, USA
- Department of Bioengineering & Therapeutic Sciences, UCSF, San Francisco, CA 94158, USA
- Department of Biochemistry & Biophysics, UCSF San Francisco 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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11
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Zhou AS, Tucker JB, Scribano CM, Lynch AR, Carlsen CL, Pop-Vicas ST, Pattaswamy SM, Burkard ME, Weaver BA. Diverse microtubule-targeted anticancer agents kill cells by inducing chromosome missegregation on multipolar spindles. PLoS Biol 2023; 21:e3002339. [PMID: 37883329 PMCID: PMC10602348 DOI: 10.1371/journal.pbio.3002339] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 09/18/2023] [Indexed: 10/28/2023] Open
Abstract
Microtubule-targeted agents are commonly used for cancer treatment, though many patients do not benefit. Microtubule-targeted drugs were assumed to elicit anticancer activity via mitotic arrest because they cause cell death following mitotic arrest in cell culture. However, we recently demonstrated that intratumoral paclitaxel concentrations are insufficient to induce mitotic arrest and rather induce chromosomal instability (CIN) via multipolar mitotic spindles. Here, we show in metastatic breast cancer and relevant human cellular models that this mechanism is conserved among clinically useful microtubule poisons. While multipolar divisions typically produce inviable progeny, multipolar spindles can be focused into near-normal bipolar spindles at any stage of mitosis. Using a novel method to quantify the rate of CIN, we demonstrate that cell death positively correlates with net loss of DNA. Spindle focusing decreases CIN and causes resistance to diverse microtubule poisons, which can be counteracted by addition of a drug that increases CIN without affecting spindle polarity. These results demonstrate conserved mechanisms of action and resistance for diverse microtubule-targeted agents. Trial registration: clinicaltrials.gov, NCT03393741.
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Affiliation(s)
- Amber S. Zhou
- Molecular and Cellular Pharmacology Graduate Training Program, University of Wisconsin, Madison, Wisconsin, United States of America
| | - John B. Tucker
- Cancer Biology Graduate Training Program, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Christina M. Scribano
- Molecular and Cellular Pharmacology Graduate Training Program, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Andrew R. Lynch
- Cellular and Molecular Pathology Graduate Training Program, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Caleb L. Carlsen
- Cellular and Molecular Biology Graduate Training Program, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Sophia T. Pop-Vicas
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Srishrika M. Pattaswamy
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Mark E. Burkard
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
- Department of Oncology/McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, United States of America
- Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Beth A. Weaver
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, Wisconsin, United States of America
- Department of Oncology/McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, United States of America
- Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin, United States of America
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12
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Truong MA, Cané-Gasull P, Lens SMA. Modeling specific aneuploidies: from karyotype manipulations to biological insights. Chromosome Res 2023; 31:25. [PMID: 37640903 PMCID: PMC10462580 DOI: 10.1007/s10577-023-09735-7] [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: 04/28/2023] [Revised: 07/11/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023]
Abstract
An abnormal chromosome number, or aneuploidy, underlies developmental disorders and is a common feature of cancer, with different cancer types exhibiting distinct patterns of chromosomal gains and losses. To understand how specific aneuploidies emerge in certain tissues and how they contribute to disease development, various methods have been developed to alter the karyotype of mammalian cells and mice. In this review, we provide an overview of both classic and novel strategies for inducing or selecting specific chromosomal gains and losses in human and murine cell systems. We highlight how these customized aneuploidy models helped expanding our knowledge of the consequences of specific aneuploidies to (cancer) cell physiology.
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Affiliation(s)
- My Anh Truong
- Oncode Institute and Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584, CG, Utrecht, The Netherlands
| | - Paula Cané-Gasull
- Oncode Institute and Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584, CG, Utrecht, The Netherlands
| | - Susanne M A Lens
- Oncode Institute and Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584, CG, Utrecht, The Netherlands.
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13
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Shih J, Sarmashghi S, Zhakula-Kostadinova N, Zhang S, Georgis Y, Hoyt SH, Cuoco MS, Gao GF, Spurr LF, Berger AC, Ha G, Rendo V, Shen H, Meyerson M, Cherniack AD, Taylor AM, Beroukhim R. Cancer aneuploidies are shaped primarily by effects on tumour fitness. Nature 2023; 619:793-800. [PMID: 37380777 PMCID: PMC10529820 DOI: 10.1038/s41586-023-06266-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
Aneuploidies-whole-chromosome or whole-arm imbalances-are the most prevalent alteration in cancer genomes1,2. However, it is still debated whether their prevalence is due to selection or ease of generation as passenger events1,2. Here we developed a method, BISCUT, that identifies loci subject to fitness advantages or disadvantages by interrogating length distributions of telomere- or centromere-bounded copy-number events. These loci were significantly enriched for known cancer driver genes, including genes not detected through analysis of focal copy-number events, and were often lineage specific. BISCUT identified the helicase-encoding gene WRN as a haploinsufficient tumour-suppressor gene on chromosome 8p, which is supported by several lines of evidence. We also formally quantified the role of selection and mechanical biases in driving aneuploidy, finding that rates of arm-level copy-number alterations are most highly correlated with their effects on cellular fitness1,2. These results provide insight into the driving forces behind aneuploidy and its contribution to tumorigenesis.
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Affiliation(s)
- Juliann Shih
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Tufts University School of Medicine, Boston, MA, USA
- Department of Internal Medicine, Kirk Kerkorian School of Medicine at the University of Nevada, Las Vegas, NV, USA
| | - Shahab Sarmashghi
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nadja Zhakula-Kostadinova
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Shu Zhang
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yohanna Georgis
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Stephanie H Hoyt
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael S Cuoco
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Galen F Gao
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Liam F Spurr
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ashton C Berger
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gavin Ha
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Veronica Rendo
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Hui Shen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Matthew Meyerson
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Andrew D Cherniack
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alison M Taylor
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Rameen Beroukhim
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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14
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Angrisani A, Fachinetti D. The KaryoCreate technology generates specific aneuploid karyotypes on demand. CELL REPORTS METHODS 2023; 3:100514. [PMID: 37426746 PMCID: PMC10326432 DOI: 10.1016/j.crmeth.2023.100514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
In a recent issue of Cell, Bosco et al. present an innovative methodology named KaryoCreate that allows the generation of chromosome-specific aneuploidy in human cells in order to investigate the ontogenesis and the multifaceted aspects of aneuploidy in physio-pathological contexts.
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15
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Lynch AR, Bradford S, Zhou AS, Oxendine K, Henderson L, Horner VL, Weaver BA, Burkard ME. A survey of CIN measures across mechanistic models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.15.544840. [PMID: 37398147 PMCID: PMC10312700 DOI: 10.1101/2023.06.15.544840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Chromosomal instability (CIN) is the persistent reshuffling of cancer karyotypes via chromosome mis-segregation during cell division. In cancer, CIN exists at varying levels that have differential effects on tumor progression. However, mis-segregation rates remain challenging to assess in human cancer despite an array of available measures. We evaluated measures of CIN by comparing quantitative methods using specific, inducible phenotypic CIN models of chromosome bridges, pseudobipolar spindles, multipolar spindles, and polar chromosomes. For each, we measured CIN fixed and timelapse fluorescence microscopy, chromosome spreads, 6-centromere FISH, bulk transcriptomics, and single cell DNA sequencing (scDNAseq). As expected, microscopy of tumor cells in live and fixed samples correlated well (R=0.77; p<0.01) and sensitively detect CIN. Cytogenetics approaches include chromosome spreads and 6-centromere FISH, which also correlate well (R=0.77; p<0.01) but had limited sensitivity for lower rates of CIN. Bulk genomic DNA signatures and bulk transcriptomic scores, CIN70 and HET70, did not detect CIN. By contrast, single-cell DNA sequencing (scDNAseq) detects CIN with high sensitivity, and correlates very well with imaging methods (R=0.83; p<0.01). In summary, single-cell methods such as imaging, cytogenetics, and scDNAseq can measure CIN, with the latter being the most comprehensive method accessible to clinical samples. To facilitate comparison of CIN rates between phenotypes and methods, we propose a standardized unit of CIN: Mis-segregations per Diploid Division (MDD). This systematic analysis of common CIN measures highlights the superiority of single-cell methods and provides guidance for measuring CIN in the clinical setting.
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Affiliation(s)
- Andrew R. Lynch
- Carbone Cancer Center, University of Wisconsin – Madison, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin – Madison, Madison, WI, USA
| | - Shermineh Bradford
- Carbone Cancer Center, University of Wisconsin – Madison, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin – Madison, Madison, WI, USA
| | - Amber S. Zhou
- Carbone Cancer Center, University of Wisconsin – Madison, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin – Madison, Madison, WI, USA
| | - Kim Oxendine
- Wisconsin State Laboratory of Hygiene, University of Wisconsin – Madison, Madison, WI, USA
| | - Les Henderson
- Wisconsin State Laboratory of Hygiene, University of Wisconsin – Madison, Madison, WI, USA
| | - Vanessa L. Horner
- Wisconsin State Laboratory of Hygiene, University of Wisconsin – Madison, Madison, WI, USA
| | - Beth A. Weaver
- Carbone Cancer Center, University of Wisconsin – Madison, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin – Madison, Madison, WI, USA
- Department of Cell and Regenerative Biology, University of Wisconsin – Madison, Madison, WI, USA
| | - Mark E. Burkard
- Carbone Cancer Center, University of Wisconsin – Madison, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin – Madison, Madison, WI, USA
- Division of Hematology Oncology and Palliative Care, Department of Medicine, University of Wisconsin – Madison, Madison, WI, USA
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16
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Tovini L, Johnson SC, Guscott MA, Andersen AM, Spierings DCJ, Wardenaar R, Foijer F, McClelland SE. Targeted assembly of ectopic kinetochores to induce chromosome-specific segmental aneuploidies. EMBO J 2023; 42:e111587. [PMID: 37063065 PMCID: PMC10183824 DOI: 10.15252/embj.2022111587] [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: 05/03/2022] [Revised: 03/31/2023] [Accepted: 04/05/2023] [Indexed: 04/18/2023] Open
Abstract
Cancer cells display persistent underlying chromosomal instability, with individual tumour types intriguingly exhibiting characteristic subsets of whole, and subchromosomal aneuploidies. Few methods to induce specific aneuploidies will exist, hampering investigation of functional consequences of recurrent aneuploidies, as well as the acute consequences of specific chromosome mis-segregation. We therefore investigated the possibility of sabotaging the mitotic segregation of specific chromosomes using nuclease-dead CRISPR-Cas9 (dCas9) as a cargo carrier to specific genomic loci. We recruited the kinetochore-nucleating domain of centromere protein CENP-T to assemble ectopic kinetochores either near the centromere of chromosome 9, or the telomere of chromosome 1. Ectopic kinetochore assembly led to increased chromosome instability and partial aneuploidy of the target chromosomes, providing the potential to induce specific chromosome mis-segregation events in a range of cell types. We also provide an analysis of putative endogenous repeats that could support ectopic kinetochore formation. Overall, our findings provide new insights into ectopic kinetochore biology and represent an important step towards investigating the role of specific aneuploidy and chromosome mis-segregation events in diseases associated with aneuploidy.
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Affiliation(s)
| | - Sarah C Johnson
- Centre for Cancer Genomics and Computational BiologyBarts Cancer Institute, Queen Mary University of LondonLondonUK
| | - Molly A Guscott
- Centre for Cancer Genomics and Computational BiologyBarts Cancer Institute, Queen Mary University of LondonLondonUK
| | - Alexander M Andersen
- Centre for Cancer Genomics and Computational BiologyBarts Cancer Institute, Queen Mary University of LondonLondonUK
| | - Diana Carolina Johanna Spierings
- European Research Institute for the Biology of AgeingUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - René Wardenaar
- European Research Institute for the Biology of AgeingUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of AgeingUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Sarah E McClelland
- Centre for Cancer Genomics and Computational BiologyBarts Cancer Institute, Queen Mary University of LondonLondonUK
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17
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Gambogi CW, Pandey N, Dawicki-McKenna JM, Arora UP, Liskovykh MA, Ma J, Lamelza P, Larionov V, Lampson MA, Logsdon GA, Dumont BL, Black BE. Centromere Innovations Within a Mouse Species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540353. [PMID: 37333154 PMCID: PMC10274901 DOI: 10.1101/2023.05.11.540353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Mammalian centromeres direct faithful genetic inheritance and are typically characterized by regions of highly repetitive and rapidly evolving DNA. We focused on a mouse species, Mus pahari, that we found has evolved to house centromere-specifying CENP-A nucleosomes at the nexus of a satellite repeat that we identified and term π-satellite (π-sat), a small number of recruitment sites for CENP-B, and short stretches of perfect telomere repeats. One M. pahari chromosome, however, houses a radically divergent centromere harboring ~6 Mbp of a homogenized π-sat-related repeat, π-satB, that contains >20,000 functional CENP-B boxes. There, CENP-B abundance drives accumulation of microtubule-binding components of the kinetochore, as well as a microtubule-destabilizing kinesin of the inner centromere. The balance of pro- and anti-microtubule-binding by the new centromere permits it to segregate during cell division with high fidelity alongside the older ones whose sequence creates a markedly different molecular composition.
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Affiliation(s)
- Craig W. Gambogi
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA 19104
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104
| | - Nootan Pandey
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA 19104
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
| | - Jennine M. Dawicki-McKenna
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA 19104
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
| | - Uma P. Arora
- The Jackson Laboratory, Bar Harbor, ME 04609
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111
| | - Mikhail A. Liskovykh
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892
| | - Jun Ma
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Piero Lamelza
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892
| | - Michael A. Lampson
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Glennis A. Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
| | - Beth L. Dumont
- The Jackson Laboratory, Bar Harbor, ME 04609
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111
| | - Ben E. Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA 19104
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104
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18
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Bosco N, Goldberg A, Zhao X, Mays JC, Cheng P, Johnson AF, Bianchi JJ, Toscani C, Di Tommaso E, Katsnelson L, Annuar D, Mei S, Faitelson RE, Pesselev IY, Mohamed KS, Mermerian A, Camacho-Hernandez EM, Gionco CA, Manikas J, Tseng YS, Sun Z, Fani S, Keegan S, Lippman SM, Fenyö D, Giunta S, Santaguida S, Davoli T. KaryoCreate: A CRISPR-based technology to study chromosome-specific aneuploidy by targeting human centromeres. Cell 2023; 186:1985-2001.e19. [PMID: 37075754 PMCID: PMC10676289 DOI: 10.1016/j.cell.2023.03.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 11/17/2022] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
Abstract
Aneuploidy, the presence of chromosome gains or losses, is a hallmark of cancer. Here, we describe KaryoCreate (karyotype CRISPR-engineered aneuploidy technology), a system that enables the generation of chromosome-specific aneuploidies by co-expression of an sgRNA targeting chromosome-specific CENPA-binding ɑ-satellite repeats together with dCas9 fused to mutant KNL1. We design unique and highly specific sgRNAs for 19 of the 24 chromosomes. Expression of these constructs leads to missegregation and induction of gains or losses of the targeted chromosome in cellular progeny, with an average efficiency of 8% for gains and 12% for losses (up to 20%) validated across 10 chromosomes. Using KaryoCreate in colon epithelial cells, we show that chromosome 18q loss, frequent in gastrointestinal cancers, promotes resistance to TGF-β, likely due to synergistic hemizygous deletion of multiple genes. Altogether, we describe an innovative technology to create and study chromosome missegregation and aneuploidy in the context of cancer and beyond.
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Affiliation(s)
- Nazario Bosco
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Aleah Goldberg
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Xin Zhao
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Joseph C Mays
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Pan Cheng
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Adam F Johnson
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Joy J Bianchi
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Cecilia Toscani
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Elena Di Tommaso
- Department of Biology and Biotechnology Charles Darwin, University of Rome "La Sapienza", 00185 Rome, Italy
| | - Lizabeth Katsnelson
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Dania Annuar
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Sally Mei
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Roni E Faitelson
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Ilan Y Pesselev
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Kareem S Mohamed
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Angela Mermerian
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Elaine M Camacho-Hernandez
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Courtney A Gionco
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Julie Manikas
- Department of Cell Biology, NYU Langone Health, New York, NY, USA
| | - Yi-Shuan Tseng
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Zhengxi Sun
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Somayeh Fani
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Sarah Keegan
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Scott M Lippman
- Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Simona Giunta
- Department of Biology and Biotechnology Charles Darwin, University of Rome "La Sapienza", 00185 Rome, Italy
| | - Stefano Santaguida
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy
| | - Teresa Davoli
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.
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19
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Heiser HC, Cagnin NF, de Souza MU, Ali TM, Estrada PRQ, de Souza CCWD, Coprerski B, Rubio C, Riboldi M. The embryo mosaicism profile of next-generation sequencing PGT-A in different clinical conditions and their associations. FRONTIERS IN REPRODUCTIVE HEALTH 2023; 5:1132662. [PMID: 37050939 PMCID: PMC10083245 DOI: 10.3389/frph.2023.1132662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
IntroductionUniform chromosome abnormalities are commonly seen in early pregnancy loss, with analyses of the product of conception suggesting the presence of mosaic autosomal trisomy in ∼10% of cases. Although chromosomal mosaicism occurs in a minority of embryos, their relative commonality and uncertainty regarding associated transfer outcomes have created discussion at both the clinical and research levels, highlighting the need to understand the clinical conditions associated with the incidence of embryo mosaicism.MethodsWe took advantage of a preimplantation genetic testing for aneuploidy (PGT-A) database created from 2019 to 2022 in more than 160 in vitro fertilization (IVF) clinics in Brazil, the second-largest world market for IVF. We carried out descriptive statistical and associative analyses to assess the proportions of mosaicism associated with clinical conditions and reported incidence by chromosome, clinic origin, and biopsy operator.ResultsChromosomal analysis revealed that most mosaic aneuploidies occurred in the last three chromosomes, with 78.06% of cases having only one chromosome affected. Low mosaicism in trisomy represented the most ordinary form, followed by low mosaicism in monosomy. We identified associations between low (negatively-associated) and high mosaicism (positively-associated) and maternal age, indication (male factor and uterus/ovarian factor negatively associated with low and high mosaic, respectively), day of blastocyst development (day five has an overall better outcome), morphology grade (lower quality increased the chances of low and high mosaicism), origin (vitrified oocyte and embryo increased the rates of low and high mosaicism, respectively), and embryo sex (male embryos negatively associated with low mosaic).DiscussionWith these results, we hope to foster an improved understanding of the chromosomal mosaicism linked with distinct clinical conditions and their associations in Brazil.
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Affiliation(s)
| | | | | | | | | | | | - Bruno Coprerski
- Laboratory of Genetic Medicine, Igenomix Brasil, São Paulo, Brazil
| | | | - Marcia Riboldi
- Laboratory of Genetic Medicine, Igenomix Brasil, São Paulo, Brazil
- Correspondence: Marcia Riboldi
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20
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Aberrant HMGA2 Expression Sustains Genome Instability That Promotes Metastasis and Therapeutic Resistance in Colorectal Cancer. Cancers (Basel) 2023; 15:cancers15061735. [PMID: 36980621 PMCID: PMC10046046 DOI: 10.3390/cancers15061735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/06/2023] [Accepted: 03/11/2023] [Indexed: 03/16/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most lethal cancers worldwide, accounting for nearly ~10% of all cancer diagnoses and deaths. Current therapeutic approaches have considerably increased survival for patients diagnosed at early stages; however, ~20% of CRC patients are diagnosed with late-stage, metastatic CRC, where 5-year survival rates drop to 6–13% and treatment options are limited. Genome instability is an enabling hallmark of cancer that confers increased acquisition of genetic alterations, mutations, copy number variations and chromosomal rearrangements. In that regard, research has shown a clear association between genome instability and CRC, as the accumulation of aberrations in cancer-related genes provides subpopulations of cells with several advantages, such as increased proliferation rates, metastatic potential and therapeutic resistance. Although numerous genes have been associated with CRC, few have been validated as predictive biomarkers of metastasis or therapeutic resistance. A growing body of evidence suggests a member of the High-Mobility Group A (HMGA) gene family, HMGA2, is a potential biomarker of metastatic spread and therapeutic resistance. HMGA2 is expressed in embryonic tissues and is frequently upregulated in aggressively growing cancers, including CRC. As an architectural, non-histone chromatin binding factor, it initiates chromatin decompaction to facilitate transcriptional regulation. HMGA2 maintains the capacity for stem cell renewal in embryonic and cancer tissues and is a known promoter of epithelial-to-mesenchymal transition in tumor cells. This review will focus on the known molecular mechanisms by which HMGA2 exerts genome protective functions that contribute to cancer cell survival and chemoresistance in CRC.
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21
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Mahlke MA, Lumerman L, Ly P, Nechemia-Arbely Y. Epigenetic centromere identity is precisely maintained through DNA replication but is uniquely specified among human cells. Life Sci Alliance 2023; 6:e202201807. [PMID: 36596606 PMCID: PMC9811134 DOI: 10.26508/lsa.202201807] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 01/05/2023] Open
Abstract
Centromere identity is defined and maintained epigenetically by the presence of the histone variant CENP-A. How centromeric CENP-A position is specified and precisely maintained through DNA replication is not fully understood. The recently released Telomere-to-Telomere (T2T) genome assembly containing the first complete human centromere sequences provides a new resource for examining CENP-A position. Mapping CENP-A position in clones of the same cell line to the T2T assembly identified highly similar CENP-A position after multiple cell divisions. In contrast, centromeric CENP-A epialleles were evident at several centromeres of different human cell lines, demonstrating the location of CENP-A enrichment and the site of kinetochore recruitment vary among human cells. Across the cell cycle, CENP-A molecules deposited in G1 phase are maintained in their precise position through DNA replication. Thus, despite CENP-A dilution during DNA replication, CENP-A is precisely reloaded onto the same sequences within the daughter centromeres, maintaining unique centromere identity among human cells.
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Affiliation(s)
- Megan A Mahlke
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lior Lumerman
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yael Nechemia-Arbely
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
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22
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Kawashima Y, Oda AH, Hikida Y, Ohta K. Chromosome-dependent aneuploid formation in Spo11-less meiosis. Genes Cells 2023; 28:129-148. [PMID: 36530025 PMCID: PMC10107155 DOI: 10.1111/gtc.12998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/21/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
Deficiency in meiotic recombination leads to aberrant chromosome disjunction during meiosis, often resulting in the lethality of gametes or genetic disorders due to aneuploidy formation. Budding yeasts lacking Spo11, which is essential for initiation of meiotic recombination, produce many inviable spores in meiosis, while very rarely all sets of 16 chromosomes are coincidentally assorted into gametes to form viable spores. We induced meiosis in a spo11∆ diploid, in which homolog pairs can be distinguished by single nucleotide polymorphisms and determined whole-genome sequences of their exceptionally viable spores. We detected no homologous recombination in the viable spores of spo11∆ diploid. Point mutations were fewer in spo11∆ than in wild-type. We observed spo11∆ viable spores carrying a complete diploid set of homolog pairs or haploid spores with a complete haploid set of homologs but with aneuploidy in some chromosomes. In the latter, we found the chromosome-dependence in the aneuploid incidence, which was positively and negatively influenced by the chromosome length and the impact of dosage-sensitive genes, respectively. Selection of aneuploidy during meiosis II or mitosis after spore germination was also chromosome dependent. These results suggest a pathway by which specific chromosomes are more prone to cause aneuploidy, as observed in Down syndrome.
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Affiliation(s)
- Yuri Kawashima
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Arisa H Oda
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Yasushi Hikida
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
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23
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Dunkley S, Mogessie B. Actin limits egg aneuploidies associated with female reproductive aging. SCIENCE ADVANCES 2023; 9:eadc9161. [PMID: 36662854 PMCID: PMC9858517 DOI: 10.1126/sciadv.adc9161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Aging-related centromeric cohesion loss underlies premature separation of sister chromatids and egg aneuploidy in reproductively older females. Here, we show that F-actin maintains chromatid association after cohesion deterioration in aged eggs. F-actin disruption in aged mouse eggs exacerbated untimely dissociation of sister chromatids, while its removal in young eggs induced extensive chromatid separation events generally only seen in advanced reproductive ages. In young eggs containing experimentally reduced cohesion, F-actin removal accelerated premature splitting and scattering of sister chromatids in a microtubule dynamics-dependent manner, suggesting that actin counteracts chromatid-pulling spindle forces. Consistently, F-actin stabilization restricted scattering of unpaired chromatids generated by complete degradation of centromeric cohesion proteins. We conclude that actin mitigates egg aneuploidies arising from age-related cohesion depletion by limiting microtubule-driven separation and dispersion of sister chromatids. This is supported by our finding that spindle-associated F-actin structures are disrupted in eggs of reproductively older females.
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Affiliation(s)
- Sam Dunkley
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Binyam Mogessie
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
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24
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High-throughput telomere length measurement at nucleotide resolution using the PacBio high fidelity sequencing platform. Nat Commun 2023; 14:281. [PMID: 36650155 PMCID: PMC9845338 DOI: 10.1038/s41467-023-35823-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 12/20/2022] [Indexed: 01/19/2023] Open
Abstract
Telomeres are specialized nucleoprotein structures at the ends of linear chromosomes. The progressive shortening of steady-state telomere length in normal human somatic cells is a promising biomarker for age-associated diseases. However, there remain substantial challenges in quantifying telomere length due to the lack of high-throughput method with nucleotide resolution for individual telomere. Here, we describe a workflow to capture telomeres using newly designed telobaits in human culture cell lines as well as clinical patient samples and measure their length accurately at nucleotide resolution using single-molecule real-time (SMRT) sequencing. Our results also reveal the extreme heterogeneity of telomeric variant sequences (TVSs) that are dispersed throughout the telomere repeat region. The presence of TVSs disrupts the continuity of the canonical (5'-TTAGGG-3')n telomere repeats, which affects the binding of shelterin complexes at the chromosomal ends and telomere protection. These findings may have profound implications in human aging and diseases.
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25
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Chromosome Inequality: Causes and Consequences of Non-Random Segregation Errors in Mitosis and Meiosis. Cells 2022; 11:cells11223564. [PMID: 36428993 PMCID: PMC9688425 DOI: 10.3390/cells11223564] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Aneuploidy is a hallmark of cancer and a major cause of miscarriages in humans. It is caused by chromosome segregation errors during cell divisions. Evidence is mounting that the probability of specific chromosomes undergoing a segregation error is non-random. In other words, some chromosomes have a higher chance of contributing to aneuploid karyotypes than others. This could have important implications for the origins of recurrent aneuploidy patterns in cancer and developing embryos. Here, we review recent progress in understanding the prevalence and causes of non-random chromosome segregation errors in mammalian mitosis and meiosis. We evaluate its potential impact on cancer and human reproduction and discuss possible research avenues.
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26
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Shaikh N, Mazzagatti A, De Angelis S, Johnson SC, Bakker B, Spierings DCJ, Wardenaar R, Maniati E, Wang J, Boemo MA, Foijer F, McClelland SE. Replication stress generates distinctive landscapes of DNA copy number alterations and chromosome scale losses. Genome Biol 2022; 23:223. [PMID: 36266663 PMCID: PMC9583511 DOI: 10.1186/s13059-022-02781-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 10/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A major driver of cancer chromosomal instability is replication stress, the slowing or stalling of DNA replication. How replication stress and genomic instability are connected is not known. Aphidicolin-induced replication stress induces breakages at common fragile sites, but the exact causes of fragility are debated, and acute genomic consequences of replication stress are not fully explored. RESULTS We characterize DNA copy number alterations (CNAs) in single, diploid non-transformed cells, caused by one cell cycle in the presence of either aphidicolin or hydroxyurea. Multiple types of CNAs are generated, associated with different genomic regions and features, and observed copy number landscapes are distinct between aphidicolin and hydroxyurea-induced replication stress. Coupling cell type-specific analysis of CNAs to gene expression and single-cell replication timing analyses pinpointed the causative large genes of the most recurrent chromosome-scale CNAs in aphidicolin. These are clustered on chromosome 7 in RPE1 epithelial cells but chromosome 1 in BJ fibroblasts. Chromosome arm level CNAs also generate acentric lagging chromatin and micronuclei containing these chromosomes. CONCLUSIONS Chromosomal instability driven by replication stress occurs via focal CNAs and chromosome arm scale changes, with the latter confined to a very small subset of chromosome regions, potentially heavily skewing cancer genome evolution. Different inducers of replication stress lead to distinctive CNA landscapes providing the opportunity to derive copy number signatures of specific replication stress mechanisms. Single-cell CNA analysis thus reveals the impact of replication stress on the genome, providing insights into the molecular mechanisms which fuel chromosomal instability in cancer.
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Affiliation(s)
- Nadeem Shaikh
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Alice Mazzagatti
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Simone De Angelis
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Sarah C Johnson
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Bjorn Bakker
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, AV, the Netherlands
- Current address: The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, AV, the Netherlands
| | - René Wardenaar
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, AV, the Netherlands
| | - Eleni Maniati
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Jun Wang
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Michael A Boemo
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, AV, the Netherlands
| | - Sarah E McClelland
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK.
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27
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Matson MEH, Liang Q, Lonardi S, Judelson HS. Karyotype variation, spontaneous genome rearrangements affecting chemical insensitivity, and expression level polymorphisms in the plant pathogen Phytophthora infestans revealed using its first chromosome-scale assembly. PLoS Pathog 2022; 18:e1010869. [PMID: 36215336 PMCID: PMC9584435 DOI: 10.1371/journal.ppat.1010869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/20/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022] Open
Abstract
Natural isolates of the potato and tomato pathogen Phytophthora infestans exhibit substantial variation in virulence, chemical sensitivity, ploidy, and other traits. A chromosome-scale assembly was developed to expand genomic resources for this oomyceteous microbe, and used to explore the basis of variation. Using PacBio and Illumina data, a long-range linking library, and an optical map, an assembly was created and coalesced into 15 pseudochromosomes spanning 219 Mb using SNP-based genetic linkage data. De novo gene prediction combined with transcript evidence identified 19,981 protein-coding genes, plus about eight thousand tRNA genes. The chromosomes were comprised of a mosaic of gene-rich and gene-sparse regions plus very long centromeres. Genes exhibited a biased distribution across chromosomes, especially members of families encoding RXLR and CRN effectors which clustered on certain chromosomes. Strikingly, half of F1 progeny of diploid parents were polyploid or aneuploid. Substantial expression level polymorphisms between strains were identified, much of which could be attributed to differences in chromosome dosage, transposable element insertions, and adjacency to repetitive DNA. QTL analysis identified a locus on the right arm of chromosome 3 governing sensitivity to the crop protection chemical metalaxyl. Strains heterozygous for resistance often experienced megabase-sized deletions of that part of the chromosome when cultured on metalaxyl, increasing resistance due to loss of the sensitive allele. This study sheds light on diverse phenomena affecting variation in P. infestans and relatives, helps explain the prevalence of polyploidy in natural populations, and provides a new foundation for biologic and genetic investigations.
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Affiliation(s)
- Michael E. H. Matson
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Qihua Liang
- Department of Computer Science and Engineering, University of California, Riverside, California, United States of America
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, California, United States of America
| | - Howard S. Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
- * E-mail:
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28
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HJURP inhibits proliferation of ovarian cancer cells by regulating CENP-A/CENP-N. Bull Cancer 2022; 109:1007-1016. [DOI: 10.1016/j.bulcan.2021.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/08/2021] [Accepted: 12/13/2021] [Indexed: 11/19/2022]
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Cechova M, Miga KH. Satellite DNAs and human sex chromosome variation. Semin Cell Dev Biol 2022; 128:15-25. [PMID: 35644878 DOI: 10.1016/j.semcdb.2022.04.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022]
Abstract
Satellite DNAs are present on every chromosome in the cell and are typically enriched in repetitive, heterochromatic parts of the human genome. Sex chromosomes represent a unique genomic and epigenetic context. In this review, we first report what is known about satellite DNA biology on human X and Y chromosomes, including repeat content and organization, as well as satellite variation in typical euploid individuals. Then, we review sex chromosome aneuploidies that are among the most common types of aneuploidies in the general population, and are better tolerated than autosomal aneuploidies. This is demonstrated also by the fact that aging is associated with the loss of the X, and especially the Y chromosome. In addition, supernumerary sex chromosomes enable us to study general processes in a cell, such as analyzing heterochromatin dosage (i.e. additional Barr bodies and long heterochromatin arrays on Yq) and their downstream consequences. Finally, genomic and epigenetic organization and regulation of satellite DNA could influence chromosome stability and lead to aneuploidy. In this review, we argue that the complete annotation of satellite DNA on sex chromosomes in human, and especially in centromeric regions, will aid in explaining the prevalence and the consequences of sex chromosome aneuploidies.
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Affiliation(s)
- Monika Cechova
- Faculty of Informatics, Masaryk University, Czech Republic
| | - Karen H Miga
- Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA; UC Santa Cruz Genomics Institute, University of California Santa Cruz, CA 95064, USA
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30
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Billmyre KK. Chromosome-specific behaviors during early meiosis. Curr Top Dev Biol 2022; 151:127-154. [PMID: 36681468 DOI: 10.1016/bs.ctdb.2022.05.002] [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] [Indexed: 01/25/2023]
Abstract
Inheriting the wrong number of chromosomes is one of the leading causes of infertility and birth defects in humans. However, in many organisms, individual chromosomes vary dramatically in both organization, sequence, and size. Chromosome segregation systems must be capable of accounting for these differences to reliably segregate chromosomes. During gametogenesis, meiosis ensures that all chromosomes segregate properly into gametes (i.e., egg or sperm). Interestingly, not all chromosomes exhibit the same dynamics during meiosis, which can lead to chromosome-specific behaviors and defects. This review will summarize some of the chromosome-specific meiotic events that are currently known and discuss their impact on meiotic outcomes.
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31
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Klaasen SJ, Truong MA, van Jaarsveld RH, Koprivec I, Štimac V, de Vries SG, Risteski P, Kodba S, Vukušić K, de Luca KL, Marques JF, Gerrits EM, Bakker B, Foijer F, Kind J, Tolić IM, Lens SMA, Kops GJPL. Nuclear chromosome locations dictate segregation error frequencies. Nature 2022; 607:604-609. [PMID: 35831506 PMCID: PMC9300461 DOI: 10.1038/s41586-022-04938-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 06/07/2022] [Indexed: 12/25/2022]
Abstract
Chromosome segregation errors during cell divisions generate aneuploidies and micronuclei, which can undergo extensive chromosomal rearrangements such as chromothripsis1-5. Selective pressures then shape distinct aneuploidy and rearrangement patterns-for example, in cancer6,7-but it is unknown whether initial biases in segregation errors and micronucleation exist for particular chromosomes. Using single-cell DNA sequencing8 after an error-prone mitosis in untransformed, diploid cell lines and organoids, we show that chromosomes have different segregation error frequencies that result in non-random aneuploidy landscapes. Isolation and sequencing of single micronuclei from these cells showed that mis-segregating chromosomes frequently also preferentially become entrapped in micronuclei. A similar bias was found in naturally occurring micronuclei of two cancer cell lines. We find that segregation error frequencies of individual chromosomes correlate with their location in the interphase nucleus, and show that this is highest for peripheral chromosomes behind spindle poles. Randomization of chromosome positions, Cas9-mediated live tracking and forced repositioning of individual chromosomes showed that a greater distance from the nuclear centre directly increases the propensity to mis-segregate. Accordingly, chromothripsis in cancer genomes9 and aneuploidies in early development10 occur more frequently for larger chromosomes, which are preferentially located near the nuclear periphery. Our findings reveal a direct link between nuclear chromosome positions, segregation error frequencies and micronucleus content, with implications for our understanding of tumour genome evolution and the origins of specific aneuploidies during development.
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Affiliation(s)
- Sjoerd J Klaasen
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands
| | - My Anh Truong
- Oncode Institute, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Richard H van Jaarsveld
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands
| | | | | | - Sippe G de Vries
- Oncode Institute, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | | | | | - Kim L de Luca
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Joana F Marques
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Elianne M Gerrits
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Bjorn Bakker
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Floris Foijer
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Jop Kind
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands.,Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | | | - Susanne M A Lens
- Oncode Institute, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Geert J P L Kops
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands.
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32
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Vukušić K, Tolić IM. Polar Chromosomes—Challenges of a Risky Path. Cells 2022; 11:cells11091531. [PMID: 35563837 PMCID: PMC9101661 DOI: 10.3390/cells11091531] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/28/2022] [Accepted: 04/30/2022] [Indexed: 12/29/2022] Open
Abstract
The process of chromosome congression and alignment is at the core of mitotic fidelity. In this review, we discuss distinct spatial routes that the chromosomes take to align during prometaphase, which are characterized by distinct biomolecular requirements. Peripheral polar chromosomes are an intriguing case as their alignment depends on the activity of kinetochore motors, polar ejection forces, and a transition from lateral to end-on attachments to microtubules, all of which can result in the delayed alignment of these chromosomes. Due to their undesirable position close to and often behind the spindle pole, these chromosomes may be particularly prone to the formation of erroneous kinetochore-microtubule interactions, such as merotelic attachments. To prevent such errors, the cell employs intricate mechanisms to preposition the spindle poles with respect to chromosomes, ensure the formation of end-on attachments in restricted spindle regions, repair faulty attachments by error correction mechanisms, and delay segregation by the spindle assembly checkpoint. Despite this protective machinery, there are several ways in which polar chromosomes can fail in alignment, mis-segregate, and lead to aneuploidy. In agreement with this, polar chromosomes are present in certain tumors and may even be involved in the process of tumorigenesis.
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33
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Lynch AR, Arp NL, Zhou AS, Weaver BA, Burkard ME. Quantifying chromosomal instability from intratumoral karyotype diversity using agent-based modeling and Bayesian inference. eLife 2022; 11:e69799. [PMID: 35380536 PMCID: PMC9054132 DOI: 10.7554/elife.69799] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 04/01/2022] [Indexed: 12/03/2022] Open
Abstract
Chromosomal instability (CIN)-persistent chromosome gain or loss through abnormal mitotic segregation-is a hallmark of cancer that drives aneuploidy. Intrinsic chromosome mis-segregation rate, a measure of CIN, can inform prognosis and is a promising biomarker for response to anti-microtubule agents. However, existing methodologies to measure this rate are labor intensive, indirect, and confounded by selection against aneuploid cells, which reduces observable diversity. We developed a framework to measure CIN, accounting for karyotype selection, using simulations with various levels of CIN and models of selection. To identify the model parameters that best fit karyotype data from single-cell sequencing, we used approximate Bayesian computation to infer mis-segregation rates and karyotype selection. Experimental validation confirmed the extensive chromosome mis-segregation rates caused by the chemotherapy paclitaxel (18.5 ± 0.5/division). Extending this approach to clinical samples revealed that inferred rates fell within direct observations of cancer cell lines. This work provides the necessary framework to quantify CIN in human tumors and develop it as a predictive biomarker.
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Affiliation(s)
- Andrew R Lynch
- Carbone Cancer Center, University of Wisconsin-MadisonMadisonUnited States
- McArdle Laboratory for Cancer Research, University of Wisconsin-MadisonMadisonUnited States
| | - Nicholas L Arp
- Carbone Cancer Center, University of Wisconsin-MadisonMadisonUnited States
| | - Amber S Zhou
- Carbone Cancer Center, University of Wisconsin-MadisonMadisonUnited States
- McArdle Laboratory for Cancer Research, University of Wisconsin-MadisonMadisonUnited States
| | - Beth A Weaver
- Carbone Cancer Center, University of Wisconsin-MadisonMadisonUnited States
- McArdle Laboratory for Cancer Research, University of Wisconsin-MadisonMadisonUnited States
- Department of Cell and Regenerative Biology, University of WisconsinMadisonUnited States
| | - Mark E Burkard
- Carbone Cancer Center, University of Wisconsin-MadisonMadisonUnited States
- McArdle Laboratory for Cancer Research, University of Wisconsin-MadisonMadisonUnited States
- Division of Hematology Medical Oncology and Palliative Care, Department of Medicine University of WisconsinMadisonUnited States
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34
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Altemose N, Glennis A, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ, Sauria MEG, Borchers M, Gershman A, Mikheenko A, Shepelev VA, Dvorkina T, Kunyavskaya O, Vollger MR, Rhie A, McCartney AM, Asri M, Lorig-Roach R, Shafin K, Aganezov S, Olson D, de Lima LG, Potapova T, Hartley GA, Haukness M, Kerpedjiev P, Gusev F, Tigyi K, Brooks S, Young A, Nurk S, Koren S, Salama SR, Paten B, Rogaev EI, Streets A, Karpen GH, Dernburg AF, Sullivan BA, Straight AF, Wheeler TJ, Gerton JL, Eichler EE, Phillippy AM, Timp W, Dennis MY, O'Neill RJ, Zook JM, Schatz MC, Pevzner PA, Diekhans M, Langley CH, Alexandrov IA, Miga KH. Complete genomic and epigenetic maps of human centromeres. Science 2022; 376:eabl4178. [PMID: 35357911 PMCID: PMC9233505 DOI: 10.1126/science.abl4178] [Citation(s) in RCA: 171] [Impact Index Per Article: 85.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, and functions, which include facilitating proper chromosome segregation. Now, a complete, telomere-to-telomere human genome assembly (T2T-CHM13) has enabled us to comprehensively characterize pericentromeric and centromeric repeats, which constitute 6.2% of the genome (189.9 megabases). Detailed maps of these regions revealed multimegabase structural rearrangements, including in active centromeric repeat arrays. Analysis of centromere-associated sequences uncovered a strong relationship between the position of the centromere and the evolution of the surrounding DNA through layered repeat expansions. Furthermore, comparisons of chromosome X centromeres across a diverse panel of individuals illuminated high degrees of structural, epigenetic, and sequence variation in these complex and rapidly evolving regions.
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Affiliation(s)
- Nicolas Altemose
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - A. Glennis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Andrey V. Bzikadze
- Graduate Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA
| | - Pragya Sidhwani
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Sasha A. Langley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gina V. Caldas
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Savannah J. Hoyt
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Lev Uralsky
- Sirius University of Science and Technology, Sochi, Russia
- Vavilov Institute of General Genetics, Moscow, Russia
| | | | - Colin J. Shew
- Genome Center, MIND Institute, and Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
| | | | | | - Ariel Gershman
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | | | - Tatiana Dvorkina
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Olga Kunyavskaya
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Mitchell R. Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ann M. McCartney
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mobin Asri
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Ryan Lorig-Roach
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kishwar Shafin
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Sergey Aganezov
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Daniel Olson
- Department of Computer Science, University of Montana, Missoula, MT. USA
| | | | - Tamara Potapova
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Gabrielle A. Hartley
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | | | - Fedor Gusev
- Vavilov Institute of General Genetics, Moscow, Russia
| | - Kristof Tigyi
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Shelise Brooks
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alice Young
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sofie R. Salama
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA
| | - Evgeny I. Rogaev
- Sirius University of Science and Technology, Sochi, Russia
- Vavilov Institute of General Genetics, Moscow, Russia
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, USA
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aaron Streets
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Gary H. Karpen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- BioEngineering and BioMedical Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Abby F. Dernburg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - Beth A. Sullivan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | | | - Travis J. Wheeler
- Department of Computer Science, University of Montana, Missoula, MT. USA
| | - Jennifer L. Gerton
- Stowers Institute for Medical Research, Kansas City, MO, USA
- University of Kansas Medical School, Department of Biochemistry and Molecular Biology and Cancer Center, University of Kansas, Kansas City, KS, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Megan Y. Dennis
- Genome Center, MIND Institute, and Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
| | - Rachel J. O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Justin M. Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Pavel A. Pevzner
- Department of Computer Science and Engineering, University of California at San Diego, San Diego, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Charles H. Langley
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Ivan A. Alexandrov
- Vavilov Institute of General Genetics, Moscow, Russia
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA
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35
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Dunkley S, Scheffler K, Mogessie B. Cytoskeletal form and function in mammalian oocytes and zygotes. Curr Opin Cell Biol 2022; 75:102073. [PMID: 35364486 DOI: 10.1016/j.ceb.2022.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/09/2022] [Accepted: 02/17/2022] [Indexed: 11/28/2022]
Abstract
The actin and microtubule cytoskeletons of mammalian oocytes and zygotes exist in distinct forms at various subcellular locations. This enables each cytoskeletal system to perform vastly different functions in time and space within the same cell. In recent years, key discovery enabling tools including light-sensitive microscopy assays have helped to illuminate cytoskeletal form and function in female reproductive cell biology. New findings include unexpected participation of F-actin in oocyte chromosome segregation, oocyte specific modes of spindle self-organization as well as existence of nuclear actin polymers whose functions are only starting to emerge. Functional actin-microtubule interactions have also been identified as an important feature that supports mammalian embryo development. Other advances have revealed reproductive age-related changes in chromosome structure and dynamics that predispose mammalian eggs to aneuploidy.
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Affiliation(s)
- Sam Dunkley
- School of Biochemistry, University of Bristol, BS8 1TD, Bristol, UK
| | | | - Binyam Mogessie
- School of Biochemistry, University of Bristol, BS8 1TD, Bristol, UK; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06511, USA.
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36
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Chardon F, Japaridze A, Witt H, Velikovsky L, Chakraborty C, Wilhelm T, Dumont M, Yang W, Kikuti C, Gangnard S, Mace AS, Wuite G, Dekker C, Fachinetti D. CENP-B-mediated DNA loops regulate activity and stability of human centromeres. Mol Cell 2022; 82:1751-1767.e8. [PMID: 35320753 DOI: 10.1016/j.molcel.2022.02.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 12/25/2022]
Abstract
Chromosome inheritance depends on centromeres, epigenetically specified regions of chromosomes. While conventional human centromeres are known to be built of long tandem DNA repeats, much of their architecture remains unknown. Using single-molecule techniques such as AFM, nanopores, and optical tweezers, we find that human centromeric DNA exhibits complex DNA folds such as local hairpins. Upon binding to a specific sequence within centromeric regions, the DNA-binding protein CENP-B compacts centromeres by forming pronounced DNA loops between the repeats, which favor inter-chromosomal centromere compaction and clustering. This DNA-loop-mediated organization of centromeric chromatin participates in maintaining centromere position and integrity upon microtubule pulling during mitosis. Our findings emphasize the importance of DNA topology in centromeric regulation and stability.
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Affiliation(s)
- Florian Chardon
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Aleksandre Japaridze
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Hannes Witt
- Department of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, the Netherlands
| | - Leonid Velikovsky
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Camellia Chakraborty
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Therese Wilhelm
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Marie Dumont
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Wayne Yang
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Carlos Kikuti
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Stephane Gangnard
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Anne-Sophie Mace
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Gijs Wuite
- Department of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, the Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France.
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37
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Abstract
Aneuploidy, a genomic alternation characterized by deviations in the copy number of chromosomes, affects organisms from early development through to aging. Although it is a main cause of human pregnancy loss and a hallmark of cancer, how aneuploidy affects cellular function has been elusive. The last two decades have seen rapid advances in the understanding of the causes and consequences of aneuploidy at the molecular and cellular levels. These studies have uncovered effects of aneuploidy that can be beneficial or detrimental to cells and organisms in an environmental context-dependent and karyotype-dependent manner. Aneuploidy also imposes general stress on cells that stems from an imbalanced genome and, consequently, also an imbalanced proteome. These insights provide the fundamental framework for understanding the impact of aneuploidy in genome evolution, human pathogenesis and drug resistance.
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38
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Jeffery D, Lochhead M, Almouzni G. CENP-A: A Histone H3 Variant with Key Roles in Centromere Architecture in Healthy and Diseased States. Results Probl Cell Differ 2022; 70:221-261. [PMID: 36348109 DOI: 10.1007/978-3-031-06573-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Centromeres are key architectural components of chromosomes. Here, we examine their construction, maintenance, and functionality. Focusing on the mammalian centromere- specific histone H3 variant, CENP-A, we highlight its coevolution with both centromeric DNA and its chaperone, HJURP. We then consider CENP-A de novo deposition and the importance of centromeric DNA recently uncovered with the added value from new ultra-long-read sequencing. We next review how to ensure the maintenance of CENP-A at the centromere throughout the cell cycle. Finally, we discuss the impact of disrupting CENP-A regulation on cancer and cell fate.
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Affiliation(s)
- Daniel Jeffery
- Equipe Labellisée Ligue contre le Cancer, Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, UMR3664, Paris, France
| | - Marina Lochhead
- Equipe Labellisée Ligue contre le Cancer, Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, UMR3664, Paris, France
| | - Geneviève Almouzni
- Equipe Labellisée Ligue contre le Cancer, Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, UMR3664, Paris, France.
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39
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Kirsch-Volders M, Fenech M. Aneuploidy, inflammation and diseases. Mutat Res 2022; 824:111777. [PMID: 35358789 DOI: 10.1016/j.mrfmmm.2022.111777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/22/2022] [Accepted: 03/15/2022] [Indexed: 05/23/2023]
Abstract
This review discusses how numerical aneuploidy may trigger inflammation in somatic cells and its consequences. Therefore we: i) summarized current knowledge on the cellular and molecular pathological effects of aneuploidy; ii) considered which of these aspects are able to trigger inflammation; iii) determined the genetic and environmental factors which may modulate the link between aneuploidy and inflammation; iv) explored the rôle of diet in prevention of aneuploidy and inflammation; v) examined whether aneuploidy and inflammation are causes and/or consequences of diseases; vi) identified the knowledge gaps and research needed to translate these observations into improved health care and disease prevention. The relationships between aneuploidy, inflammation and diseases are complex, because they depend on which chromosomes are involved, the proportion of cells affected and which organs are aneuploid in the case of mosaic aneuploidy. Therefore, a systemic approach is recommended to understand the emergence of aneuploidy-driven diseases and to take preventive measures to protect individuals from exposure to aneugenic conditions.
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Affiliation(s)
- Micheline Kirsch-Volders
- Laboratory for Cell Genetics, Department Biology, Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Michael Fenech
- Genome Health Foundation, North Brighton, SA 5048, Australia; Clinical and Health Sciences, University of South Australia, SA 5000, Australia.
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40
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Barbosa AC, Xu Z, Karari K, Williams W, Hauf S, Brown WRA. Mutation and selection explain why many eukaryotic centromeric DNA sequences are often A + T rich. Nucleic Acids Res 2021; 50:579-596. [PMID: 34928384 PMCID: PMC8754631 DOI: 10.1093/nar/gkab1219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/16/2021] [Accepted: 11/30/2021] [Indexed: 01/10/2023] Open
Abstract
We have used chromosome engineering to replace native centromeric DNA with different test sequences at native centromeres in two different strains of the fission yeast Schizosaccharomyces pombe and have discovered that A + T rich DNA, whether synthetic or of bacterial origin, will function as a centromere in this species. Using genome size as a surrogate for the inverse of effective population size (Ne) we also show that the relative A + T content of centromeric DNA scales with Ne across 43 animal, fungal and yeast (Opisthokonta) species. This suggests that in most of these species the A + T content of the centromeric DNA is determined by a balance between selection and mutation. Combining the experimental results and the evolutionary analyses allows us to conclude that A + T rich DNA of almost any sequence will function as a centromere in most Opisthokonta species. The fact that many G/C to A/T substitutions are unlikely to be selected against may contribute to the rapid evolution of centromeric DNA. We also show that a neo-centromere sequence is not simply a weak version of native centromeric DNA and suggest that neo-centromeres require factors either for their propagation or establishment in addition to those required by native centromeres.
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Affiliation(s)
- Anne C Barbosa
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, NG7 2UH, UK
| | - Zhengyao Xu
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, NG7 2UH, UK
| | - Kazhal Karari
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, NG7 2UH, UK
| | - Wendi Williams
- Virginia Tech, Department of Biological Sciences, Fralin Life Sciences Institute, 1015 Life Science Circle, Blacksburg, VA 24061, USA
| | - Silke Hauf
- Virginia Tech, Department of Biological Sciences, Fralin Life Sciences Institute, 1015 Life Science Circle, Blacksburg, VA 24061, USA
| | - William R A Brown
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, NG7 2UH, UK
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41
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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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42
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Abstract
We are entering a new era in genomics where entire centromeric regions are accurately represented in human reference assemblies. Access to these high-resolution maps will enable new surveys of sequence and epigenetic variation in the population and offer new insight into satellite array genomics and centromere function. Here, we focus on the sequence organization and evolution of alpha satellites, which are credited as the genetic and genomic definition of human centromeres due to their interaction with inner kinetochore proteins and their importance in the development of human artificial chromosome assays. We provide an overview of alpha satellite repeat structure and array organization in the context of these high-quality reference data sets; discuss the emergence of variation-based surveys; and provide perspective on the role of this new source of genetic and epigenetic variation in the context of chromosome biology, genome instability, and human disease.
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Affiliation(s)
- Karen H Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California 95064, USA; .,Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Ivan A Alexandrov
- Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia; .,Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg 199004, Russia.,Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
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43
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Abstract
The centromere performs a universally conserved function, to accurately partition genetic information upon cell division. Yet, centromeres are among the most rapidly evolving regions of the genome and are bound by a varying assortment of centromere-binding factors that are themselves highly divergent at the protein-sequence level. A common thread in most species is the dependence on the centromere-specific histone variant CENP-A for the specification of the centromere site. However, CENP-A is not universally required in all species or cell types, making the identification of a general mechanism for centromere specification challenging. In this review, we examine our current understanding of the mechanisms of centromere specification in CENP-A-dependent and independent systems, focusing primarily on recent work.
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Affiliation(s)
- Barbara G Mellone
- Department of Molecular and Cell Biology, and Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, F-75005 Paris, France.
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Salinas-Luypaert C, Allu PK, Logsdon GA, Dawicki-McKenna JM, Gambogi CW, Fachinetti D, Black BE. Gene replacement strategies validate the use of functional tags on centromeric chromatin and invalidate an essential role for CENP-A K124ub. Cell Rep 2021; 37:109924. [PMID: 34731637 PMCID: PMC8643106 DOI: 10.1016/j.celrep.2021.109924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 08/31/2021] [Accepted: 10/12/2021] [Indexed: 12/17/2022] Open
Abstract
Functional tags are ubiquitous in cell biology, and for studies of one chromosomal locus, the centromere, tags have been remarkably useful. The centromere directs chromosome inheritance at cell division. The location of the centromere is defined by a histone H3 variant, CENP-A. The regulation of the chromatin assembly pathway essential for centromere inheritance and function includes posttranslational modification (PTM) of key components, including CENP-A itself. Others have recently called into question the use of functional tags, with the claim that at least two widely used tags obscured the essentiality of one particular PTM, CENP-AK124 ubiquitination (ub). Here, we employ three independent gene replacement strategies that eliminate large, lysine-containing tags to interrogate these claims. Using these approaches, we find no evidence to support an essential function of CENP-AK124ub. Our general methodology will be useful to validate discoveries permitted by powerful functional tagging schemes at the centromere and other cellular locations. Using three gene replacement strategies, Salinas-Luypaert et al. demonstrate that CENP-AK124ub is not essential for CENP-A function at centromeres. Thus, functional tags do not mask the role of K124 when it is mutated. These strategies can be employed to interrogate posttranslational modifications at the centromere and other cellular locations.
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Affiliation(s)
| | - Praveen Kumar Allu
- Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jennine M Dawicki-McKenna
- Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Craig W Gambogi
- Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Program in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniele Fachinetti
- Institut Curie, PSL University, CNRS, UMR 144, 26 rue d'Ulm, 75005, Paris, France.
| | - Ben E Black
- Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Program in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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45
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Miga KH, Sullivan BA. Expanding studies of chromosome structure and function in the era of T2T genomics. Hum Mol Genet 2021; 30:R198-R205. [PMID: 34302168 PMCID: PMC8631062 DOI: 10.1093/hmg/ddab214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
The recent accomplishment of a truly complete human genome has afforded a new view of chromosome structure and function that was limited 30 years ago. Here, we discuss the expansion of knowledge from the early cytological studies of the genome to the current high-resolution genomic, epigenetic and functional maps that have been achieved by recent technology and computational advances. These studies have revealed unexpected complexities of genome organization and function and uncovered new views of fundamental chromosomal elements. Comprehensive genomic maps will enable accurate diagnosis of human diseases caused by altered chromosome structure and function, facilitate development of chromosome-based therapies and shape the future of preventative medicine and healthcare.
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Affiliation(s)
- Karen H Miga
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Beth A Sullivan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
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46
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Joshi A, Musicante MJ, Wheeler BS. Defining the consequences of endogenous genetic variation within a novel family of Schizosaccharomyces pombe heterochromatin nucleating sequences. G3 GENES|GENOMES|GENETICS 2021; 11:6291246. [PMID: 34849813 PMCID: PMC8496282 DOI: 10.1093/g3journal/jkab185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 05/20/2021] [Indexed: 11/13/2022]
Abstract
Centromeres are essential for genetic inheritance—they prevent aneuploidy by providing a physical link between DNA and chromosome segregation machinery. In many organisms, centromeres form at sites of repetitive DNAs that help establish the chromatin architecture required for centromere function. These repeats are often rapidly evolving and subject to homogenization, which causes the expansion of novel repeats and sequence turnover. Thus, centromere sequence varies between individuals and across species. This variation can affect centromere function. We utilized Schizosaccharomyces pombe to assess the relationship between centromere sequence and chromatin structure and determine how sensitive this relationship is to genetic variation. In S. pombe, nucleating sequences within centromere repeats recruit heterochromatin via multiple mechanisms, which include RNA-interference (RNAi) . Heterochromatin, in turn, contributes to centromere function through its participation in three essential processes; establishment of a kinetochore, cohesion of sister chromatids, and suppression of recombination. Here, we show that a centromere element containing RevCen, a target of the RNAi pathway, establishes heterochromatin and gene silencing when relocated to a chromosome arm. Within this RevCen-containing element (RCE), a highly conserved domain is necessary for full heterochromatin nucleation but cannot establish heterochromatin independently. We characterize the 10 unique RCEs in the S. pombe centromere assembly, which range from 60% to 99.6% identical, and show that all are sufficient to establish heterochromatin. These data affirm the importance of centromere repeats in establishing heterochromatin and suggest there is flexibility within the sequences that mediate this process. Such flexibility may preserve centromere function despite the rapid evolution of centromere repeats.
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Affiliation(s)
- Arati Joshi
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
| | | | - Bayly S Wheeler
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
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47
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MacDonald C, McClelland SE. Chromosome Instability through the Ages: Parallels between Speciation and Somatic (Cancer) Evolution. Trends Genet 2021; 37:691-694. [PMID: 34083067 DOI: 10.1016/j.tig.2021.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 11/25/2022]
Abstract
Cancer research has recently benefitted from the integration of evolutionary theory to study somatic genome evolution during tumor development. Here, we explore how investigating mechanistic principles of chromosomal instability during both species and somatic evolution can reciprocally inform each field.
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Affiliation(s)
- Catriona MacDonald
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, 4 Royal College St, London, NW1 0TU, UK
| | - Sarah E McClelland
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, UK.
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48
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Hartley GA, Okhovat M, O'Neill RJ, Carbone L. Comparative analyses of gibbon centromeres reveal dynamic genus specific shifts in repeat composition. Mol Biol Evol 2021; 38:3972-3992. [PMID: 33983366 PMCID: PMC8382927 DOI: 10.1093/molbev/msab148] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Centromeres are functionally conserved chromosomal loci essential for proper chromosome segregation during cell division, yet they show high sequence diversity across species. Despite their variation, a near universal feature of centromeres is the presence of repetitive sequences, such as DNA satellites and transposable elements (TEs). Because of their rapidly evolving karyotypes, gibbons represent a compelling model to investigate divergence of functional centromere sequences across short evolutionary timescales. In this study, we use ChIP-seq, RNA-seq, and fluorescence in situ hybridization to comprehensively investigate the centromeric repeat content of the four extant gibbon genera (Hoolock, Hylobates, Nomascus, and Siamang). In all gibbon genera, we find that CENP-A nucleosomes and the DNA-proteins that interface with the inner kinetochore preferentially bind retroelements of broad classes rather than satellite DNA. A previously identified gibbon-specific composite retrotransposon, LAVA, known to be expanded within the centromere regions of one gibbon genus (Hoolock), displays centromere- and species-specific sequence differences, potentially as a result of its co-option to a centromeric function. When dissecting centromere satellite composition, we discovered the presence of the retroelement-derived macrosatellite SST1 in multiple centromeres of Hoolock, whereas alpha-satellites represent the predominate satellite in the other genera, further suggesting an independent evolutionary trajectory for Hoolock centromeres. Finally, using de novo assembly of centromere sequences, we determined that transcripts originating from gibbon centromeres recapitulate the species-specific TE composition. Combined, our data reveal dynamic shifts in the repeat content that define gibbon centromeres and coincide with the extensive karyotypic diversity within this lineage.
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Affiliation(s)
- Gabrielle A Hartley
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269
| | - Mariam Okhovat
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, 97239
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269.,Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269.,Department of Genomics and Genome Sciences, UConn Health, Farmington, CT, 06030
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, 97239.,Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, 97006.,Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, 97239.,Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, 97239
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49
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Wang N, Liu J, Ricci WA, Gent JI, Dawe RK. Maize centromeric chromatin scales with changes in genome size. Genetics 2021; 217:iyab020. [PMID: 33857306 PMCID: PMC8049547 DOI: 10.1093/genetics/iyab020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/30/2021] [Indexed: 11/14/2022] Open
Abstract
Centromeres are defined by the location of Centromeric Histone H3 (CENP-A/CENH3) which interacts with DNA to define the locations and sizes of functional centromeres. An analysis of 26 maize genomes including 110 fully assembled centromeric regions revealed positive relationships between centromere size and genome size. These effects are independent of variation in the amounts of the major centromeric satellite sequence CentC. We also backcrossed known centromeres into two different lines with larger genomes and observed consistent increases in functional centromere sizes for multiple centromeres. Although changes in centromere size involve changes in bound CENH3, we could not mimic the effect by overexpressing CENH3 by threefold. Literature from other fields demonstrate that changes in genome size affect protein levels, organelle size and cell size. Our data demonstrate that centromere size is among these scalable features, and that multiple limiting factors together contribute to a stable centromere size equilibrium.
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Affiliation(s)
- Na Wang
- Department of Plant Biology, University of Georgia, Athens GA 30602, USA
| | - Jianing Liu
- Department of Genetics, University of Georgia, Athens GA 30602, USA
| | - William A Ricci
- Department of Plant Biology, University of Georgia, Athens GA 30602, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens GA 30602, USA
| | - R Kelly Dawe
- Department of Plant Biology, University of Georgia, Athens GA 30602, USA
- Department of Genetics, University of Georgia, Athens GA 30602, USA
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50
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Wallander K, Thutkawkorapin J, Sahlin E, Lindblom A, Lagerstedt-Robinson K. Massive parallel sequencing in a family with rectal cancer. Hered Cancer Clin Pract 2021; 19:23. [PMID: 33827643 PMCID: PMC8028209 DOI: 10.1186/s13053-021-00181-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/30/2021] [Indexed: 12/29/2022] Open
Abstract
Background We have previously reported a family with a suspected autosomal dominant rectal and gastric cancer syndrome without any obvious causative genetic variant. Here, we focused the study on a potentially isolated rectal cancer syndrome in this family. Methods We included seven family members (six obligate carriers). Whole-exome sequencing and whole-genome sequencing data were analyzed and filtered for shared coding and splicing sequence and structural variants among the affected individuals. Results When considering family members with rectal cancer or advanced adenomas as affected, we found six new potentially cancer-associated variants in the genes CENPB, ZBTB20, CLINK, LRRC26, TRPM1, and NPEPL1. All variants were missense variants and none of the genes have previously been linked to inherited rectal cancer. No structural variant was found. Conclusion By massive parallel sequencing in a family suspected of carrying a highly penetrant rectal cancer predisposing genetic variant, we found six genetic missense variants with a potential connection to the rectal cancer in this family. One of them could be a high-risk genetic variant, or one or more of them could be low risk variants. The p.(Glu438Lys) variant in the CENPB gene was found to be of particular interest. The CENPB protein binds DNA and helps form centromeres during mitosis. It is involved in the WNT signaling pathway, which is critical for colorectal cancer development and its role in inherited rectal cancer needs to be further examined. Supplementary Information The online version contains supplementary material available at 10.1186/s13053-021-00181-2.
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Affiliation(s)
- Karin Wallander
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Solna, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Jessada Thutkawkorapin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Ellika Sahlin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Solna, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Solna, Stockholm, Sweden. .,Department of Clinical Genetics, Karolinska University Hospital, Solna, Stockholm, Sweden.
| | - Kristina Lagerstedt-Robinson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Solna, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Solna, Stockholm, Sweden
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