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Lin J, Carman PJ, Gambogi CW, Kendsersky NM, Chuang E, Gates SN, Yokom AL, Rizo AN, Southworth DR, Shorter J. Design principles to tailor Hsp104 therapeutics. bioRxiv 2024:2024.04.26.591398. [PMID: 38712168 PMCID: PMC11071516 DOI: 10.1101/2024.04.26.591398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The hexameric AAA+ disaggregase, Hsp104, collaborates with Hsp70 and Hsp40 via its autoregulatory middle domain (MD) to solubilize aggregated protein conformers. However, how ATP- or ADP-specific MD configurations regulate Hsp104 hexamers remains poorly understood. Here, we define an ATP-specific network of interprotomer contacts between nucleotide-binding domain 1 (NBD1) and MD helix L1, which tunes Hsp70 collaboration. Manipulating this network can: (a) reduce Hsp70 collaboration without enhancing activity; (b) generate Hsp104 hypomorphs that collaborate selectively with class B Hsp40s; (c) produce Hsp70-independent potentiated variants; or (d) create species barriers between Hsp104 and Hsp70. Conversely, ADP-specific intraprotomer contacts between MD helix L2 and NBD1 restrict activity, and their perturbation frequently potentiates Hsp104. Importantly, adjusting the NBD1:MD helix L1 rheostat via rational design enables finely tuned collaboration with Hsp70 to safely potentiate Hsp104, minimize off-target toxicity, and counteract FUS proteinopathy in human cells. Thus, we establish important design principles to tailor Hsp104 therapeutics.
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Affiliation(s)
- JiaBei Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
| | - Peter J. Carman
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
| | - Craig W. Gambogi
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
| | - Nathan M. Kendsersky
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Pharmacology Graduate Group Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
| | - Edward Chuang
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Pharmacology Graduate Group Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
| | - Stephanie N. Gates
- Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109. U.S.A
- Current address: Department of Biochemistry, University of Missouri, Columbia, MO 65211. U.S.A
| | - Adam L. Yokom
- Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109. U.S.A
- Current address: Department of Biochemistry, University of Missouri, Columbia, MO 65211. U.S.A
| | - Alexandrea N. Rizo
- Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109. U.S.A
| | - Daniel R. Southworth
- Department of Biochemistry and Biophysics and the Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158. U.S.A
| | - James Shorter
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Pharmacology Graduate Group Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
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Gambogi CW, Birchak GJ, Mer E, Brown DM, Yankson G, Kixmoeller K, Gavade JN, Espinoza JL, Kashyap P, Dupont CL, Logsdon GA, Heun P, Glass JI, Black BE. Efficient formation of single-copy human artificial chromosomes. Science 2024; 383:1344-1349. [PMID: 38513017 PMCID: PMC11059994 DOI: 10.1126/science.adj3566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 01/23/2024] [Indexed: 03/23/2024]
Abstract
Large DNA assembly methodologies underlie milestone achievements in synthetic prokaryotic and budding yeast chromosomes. While budding yeast control chromosome inheritance through ~125-base pair DNA sequence-defined centromeres, mammals and many other eukaryotes use large, epigenetic centromeres. Harnessing centromere epigenetics permits human artificial chromosome (HAC) formation but is not sufficient to avoid rampant multimerization of the initial DNA molecule upon introduction to cells. We describe an approach that efficiently forms single-copy HACs. It employs a ~750-kilobase construct that is sufficiently large to house the distinct chromatin types present at the inner and outer centromere, obviating the need to multimerize. Delivery to mammalian cells is streamlined by employing yeast spheroplast fusion. These developments permit faithful chromosome engineering in the context of metazoan cells.
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Affiliation(s)
- Craig W. Gambogi
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | - Gabriel J. Birchak
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Graduate Program in Cell and Molecular Biology Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | - Elie Mer
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | | | - George Yankson
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Kathryn Kixmoeller
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | - Janardan N. Gavade
- Department of Biochemistry and Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | | | - Prakriti Kashyap
- Department of Biochemistry and Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | | | - Glennis A. Logsdon
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | - Patrick Heun
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | | | - Ben E. Black
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
- Graduate Program in Cell and Molecular Biology Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
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3
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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. Sci Adv 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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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Gambogi CW, Mer E, Brown DM, Yankson G, Gavade JN, Logsdon GA, Heun P, Glass JI, Black BE. Efficient Formation of Single-copy Human Artificial Chromosomes. bioRxiv 2023:2023.06.30.547284. [PMID: 37546784 PMCID: PMC10402137 DOI: 10.1101/2023.06.30.547284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Large DNA assembly methodologies underlie milestone achievements in synthetic prokaryotic and budding yeast chromosomes. While budding yeast control chromosome inheritance through ~125 bp DNA sequence-defined centromeres, mammals and many other eukaryotes use large, epigenetic centromeres. Harnessing centromere epigenetics permits human artificial chromosome (HAC) formation but is not sufficient to avoid rampant multimerization of the initial DNA molecule upon introduction to cells. Here, we describe an approach that efficiently forms single-copy HACs. It employs a ~750 kb construct that is sufficiently large to house the distinct chromatin types present at the inner and outer centromere, obviating the need to multimerize. Delivery to mammalian cells is streamlined by employing yeast spheroplast fusion. These developments permit faithful chromosome engineering in the context of metazoan cells.
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Affiliation(s)
- Craig W. Gambogi
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | - Elie Mer
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | | | - George Yankson
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Janardan N. Gavade
- 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 Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | - Patrick Heun
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | | | - Ben E. Black
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
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5
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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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7
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Gambogi CW, Dawicki-McKenna JM, Logsdon GA, Black BE. The unique kind of human artificial chromosome: Bypassing the requirement for repetitive centromere DNA. Exp Cell Res 2020; 391:111978. [PMID: 32246994 DOI: 10.1016/j.yexcr.2020.111978] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 12/20/2022]
Abstract
Centromeres are essential components of all eukaryotic chromosomes, including artificial/synthetic ones built in the laboratory. In humans, centromeres are typically located on repetitive α-satellite DNA, and these sequences are the "major ingredient" in first-generation human artificial chromosomes (HACs). Repetitive centromeric sequences present a major challenge for the design of synthetic mammalian chromosomes because they are difficult to synthesize, assemble, and characterize. Additionally, in most eukaryotes, centromeres are defined epigenetically. Here, we review the role of the genetic and epigenetic contributions to establishing centromere identity, highlighting recent work to hijack the epigenetic machinery to initiate centromere identity on a new generation of HACs built without α-satellite DNA. We also discuss the opportunities and challenges in developing useful unique sequence-based HACs.
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Affiliation(s)
- Craig W Gambogi
- Department of Biochemistry and Biophysics, Graduate Program in Biochemistry and Molecular Biophysics, Penn Center for Genome Integrity, and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jennine M Dawicki-McKenna
- Department of Biochemistry and Biophysics, Graduate Program in Biochemistry and Molecular Biophysics, Penn Center for Genome Integrity, and 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
| | - Ben E Black
- Department of Biochemistry and Biophysics, Graduate Program in Biochemistry and Molecular Biophysics, Penn Center for Genome Integrity, and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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8
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Logsdon GA, Gambogi CW, Liskovykh MA, Barrey EJ, Larionov V, Miga KH, Heun P, Black BE. Human Artificial Chromosomes that Bypass Centromeric DNA. Cell 2019; 178:624-639.e19. [PMID: 31348889 PMCID: PMC6657561 DOI: 10.1016/j.cell.2019.06.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 04/07/2019] [Accepted: 06/03/2019] [Indexed: 11/29/2022]
Abstract
Recent breakthroughs with synthetic budding yeast chromosomes expedite the creation of synthetic mammalian chromosomes and genomes. Mammals, unlike budding yeast, depend on the histone H3 variant, CENP-A, to epigenetically specify the location of the centromere-the locus essential for chromosome segregation. Prior human artificial chromosomes (HACs) required large arrays of centromeric α-satellite repeats harboring binding sites for the DNA sequence-specific binding protein, CENP-B. We report the development of a type of HAC that functions independently of these constraints. Formed by an initial CENP-A nucleosome seeding strategy, a construct lacking repetitive centromeric DNA formed several self-sufficient HACs that showed no uptake of genomic DNA. In contrast to traditional α-satellite HAC formation, the non-repetitive construct can form functional HACs without CENP-B or initial CENP-A nucleosome seeding, revealing distinct paths to centromere formation for different DNA sequence types. Our developments streamline the construction and characterization of HACs to facilitate mammalian synthetic genome efforts.
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Affiliation(s)
- Glennis A Logsdon
- Department of Biochemistry and Biophysics, Graduate Program in Biochemistry and Molecular Biophysics, and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Craig W Gambogi
- Department of Biochemistry and Biophysics, Graduate Program in Biochemistry and Molecular Biophysics, and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mikhail A Liskovykh
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Evelyne J Barrey
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Karen H Miga
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Patrick Heun
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Ben E Black
- Department of Biochemistry and Biophysics, Graduate Program in Biochemistry and Molecular Biophysics, and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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