1
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Chen YL, Jones AN, Crawford A, Sattler M, Ettinger A, Torres-Padilla ME. Determinants of minor satellite RNA function in chromosome segregation in mouse embryonic stem cells. J Cell Biol 2024; 223:e202309027. [PMID: 38625077 PMCID: PMC11022885 DOI: 10.1083/jcb.202309027] [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: 09/05/2023] [Revised: 03/06/2024] [Accepted: 03/29/2024] [Indexed: 04/17/2024] Open
Abstract
The centromere is a fundamental higher-order structure in chromosomes ensuring their faithful segregation upon cell division. Centromeric transcripts have been described in several species and suggested to participate in centromere function. However, low sequence conservation of centromeric repeats appears inconsistent with a role in recruiting highly conserved centromeric proteins. Here, we hypothesized that centromeric transcripts may function through a secondary structure rather than sequence conservation. Using mouse embryonic stem cells (ESCs), we show that an imbalance in the levels of forward or reverse minor satellite (MinSat) transcripts leads to severe chromosome segregation defects. We further show that MinSat RNA adopts a stem-loop secondary structure, which is conserved in human α-satellite transcripts. We identify an RNA binding region in CENPC and demonstrate that MinSat transcripts function through the structured region of the RNA. Importantly, mutants that disrupt MinSat secondary structure do not cause segregation defects. We propose that the conserved role of centromeric transcripts relies on their secondary RNA structure.
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Affiliation(s)
- Yung-Li Chen
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Munich, München, Germany
| | - Alisha N. Jones
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
| | - Amy Crawford
- Department of Chemistry, New York University, New York, NY, USA
| | - Michael Sattler
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, Bavarian NMR Center, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Andreas Ettinger
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Munich, München, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Munich, München, Germany
- Faculty of Biology, Ludwig-Maximilians Universität, München, Germany
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2
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Arora UP, Dumont BL. Molecular evolution of the mammalian kinetochore complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.600994. [PMID: 38979348 PMCID: PMC11230421 DOI: 10.1101/2024.06.27.600994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Mammalian centromeres are satellite-rich chromatin domains that serve as sites for kinetochore complex assembly. Centromeres are highly variable in sequence and satellite organization across species, but the processes that govern the co-evolutionary dynamics between rapidly evolving centromeres and their associated kinetochore proteins remain poorly understood. Here, we pursue a course of phylogenetic analyses to investigate the molecular evolution of the complete kinetochore complex across primate and rodent species with divergent centromere repeat sequences and features. We show that many protein components of the core centromere associated network (CCAN) harbor signals of adaptive evolution, consistent with their intimate association with centromere satellite DNA and roles in the stability and recruitment of additional kinetochore proteins. Surprisingly, CCAN and outer kinetochore proteins exhibit comparable rates of adaptive divergence, suggesting that changes in centromere DNA can ripple across the kinetochore to drive adaptive protein evolution within distant domains of the complex. Our work further identifies kinetochore proteins subject to lineage-specific adaptive evolution, including rapidly evolving proteins in species with centromere satellites characterized by higher-order repeat structure and lacking CENP-B boxes. Thus, features of centromeric chromatin beyond the linear DNA sequence may drive selection on kinetochore proteins. Overall, our work spotlights adaptively evolving proteins with diverse centromere-associated functions, including centromere chromatin structure, kinetochore protein assembly, kinetochore-microtubule association, cohesion maintenance, and DNA damage response pathways. These adaptively evolving kinetochore protein candidates present compelling opportunities for future functional investigations exploring how their concerted changes with centromere DNA ensure the maintenance of genome stability.
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Affiliation(s)
- Uma P Arora
- The Jackson Laboratory, 600 Main Street, Bar Harbor ME 04609
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston MA 02111
| | - Beth L Dumont
- The Jackson Laboratory, 600 Main Street, Bar Harbor ME 04609
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston MA 02111
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, 04469
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3
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Voleníková A, Lukšíková K, Mora P, Pavlica T, Altmanová M, Štundlová J, Pelikánová Š, Simanovsky SA, Jankásek M, Reichard M, Nguyen P, Sember A. Fast satellite DNA evolution in Nothobranchius annual killifishes. Chromosome Res 2023; 31:33. [PMID: 37985497 PMCID: PMC10661780 DOI: 10.1007/s10577-023-09742-8] [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: 05/20/2023] [Revised: 10/04/2023] [Accepted: 10/28/2023] [Indexed: 11/22/2023]
Abstract
Satellite DNA (satDNA) is a rapidly evolving class of tandem repeats, with some monomers being involved in centromere organization and function. To identify repeats associated with (peri)centromeric regions, we investigated satDNA across Southern and Coastal clades of African annual killifishes of the genus Nothobranchius. Molecular cytogenetic and bioinformatic analyses revealed that two previously identified satellites, designated here as NkadSat01-77 and NfurSat01-348, are associated with (peri)centromeres only in one lineage of the Southern clade. NfurSat01-348 was, however, additionally detected outside centromeres in three members of the Coastal clade. We also identified a novel satDNA, NrubSat01-48, associated with (peri)centromeres in N. foerschi, N. guentheri, and N. rubripinnis. Our findings revealed fast turnover of satDNA associated with (peri)centromeres and different trends in their evolution in two clades of the genus Nothobranchius.
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Affiliation(s)
- Anna Voleníková
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Karolína Lukšíková
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Pablo Mora
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Department of Experimental Biology, Genetics Area, University of Jaén, Jaén, Spain
| | - Tomáš Pavlica
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Marie Altmanová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jana Štundlová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Šárka Pelikánová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Sergey A Simanovsky
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Marek Jankásek
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Reichard
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Department of Ecology and Vertebrate Zoology, University of Łódź, Łódź, Poland
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petr Nguyen
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic.
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
| | - Alexandr Sember
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic.
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4
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Klimas A, Gallagher BR, Wijesekara P, Fekir S, DiBernardo EF, Cheng Z, Stolz DB, Cambi F, Watkins SC, Brody SL, Horani A, Barth AL, Moore CI, Ren X, Zhao Y. Magnify is a universal molecular anchoring strategy for expansion microscopy. Nat Biotechnol 2023; 41:858-869. [PMID: 36593399 PMCID: PMC10264239 DOI: 10.1038/s41587-022-01546-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/05/2022] [Indexed: 01/03/2023]
Abstract
Expansion microscopy enables nanoimaging with conventional microscopes by physically and isotropically magnifying preserved biological specimens embedded in a crosslinked water-swellable hydrogel. Current expansion microscopy protocols require prior treatment with reactive anchoring chemicals to link specific labels and biomolecule classes to the gel. We describe a strategy called Magnify, which uses a mechanically sturdy gel that retains nucleic acids, proteins and lipids without the need for a separate anchoring step. Magnify expands biological specimens up to 11 times and facilitates imaging of cells and tissues with effectively around 25-nm resolution using a diffraction-limited objective lens of about 280 nm on conventional optical microscopes or with around 15 nm effective resolution if combined with super-resolution optical fluctuation imaging. We demonstrate Magnify on a broad range of biological specimens, providing insight into nanoscopic subcellular structures, including synaptic proteins from mouse brain, podocyte foot processes in formalin-fixed paraffin-embedded human kidney and defects in cilia and basal bodies in drug-treated human lung organoids.
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Affiliation(s)
- Aleksandra Klimas
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Brendan R Gallagher
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Piyumi Wijesekara
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Sinda Fekir
- Department of Neuroscience, Brown University, Providence, RI, USA
- Carney Institute for Brain Science, Brown University, Providence, RI, USA
| | - Emma F DiBernardo
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Zhangyu Cheng
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Donna B Stolz
- Department of Cell Biology, Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA, USA
| | - Franca Cambi
- Veterans Administration Pittsburgh, Pittsburgh, PA, USA
- Department of Neurology/PIND, University of Pittsburgh, Pittsburgh, PA, USA
| | - Simon C Watkins
- Department of Cell Biology, Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA, USA
| | - Steven L Brody
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Amjad Horani
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Alison L Barth
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Christopher I Moore
- Department of Neuroscience, Brown University, Providence, RI, USA
- Carney Institute for Brain Science, Brown University, Providence, RI, USA
| | - Xi Ren
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yongxin Zhao
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.
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5
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The Sequence Dependent Nanoscale Structure of CENP-A Nucleosomes. Int J Mol Sci 2022; 23:ijms231911385. [PMID: 36232691 PMCID: PMC9569828 DOI: 10.3390/ijms231911385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
CENP-A is a histone variant found in high abundance at the centromere in humans. At the centromere, this histone variant replaces the histone H3 found throughout the bulk chromatin. Additionally, the centromere comprises tandem repeats of α-satellite DNA, which CENP-A nucleosomes assemble upon. However, the effect of the DNA sequence on the nucleosome assembly and centromere formation remains poorly understood. Here, we investigated the structure of nucleosomes assembled with the CENP-A variant using Atomic Force Microscopy. We assembled both CENP-A nucleosomes and H3 nucleosomes on a DNA substrate containing an α-satellite motif and characterized their positioning and wrapping efficiency. We also studied CENP-A nucleosomes on the 601-positioning motif and non-specific DNA to compare their relative positioning and stability. CENP-A nucleosomes assembled on α-satellite DNA did not show any positional preference along the substrate, which is similar to both H3 nucleosomes and CENP-A nucleosomes on non-specific DNA. The range of nucleosome wrapping efficiency was narrower on α-satellite DNA compared with non-specific DNA, suggesting a more stable complex. These findings indicate that DNA sequence and histone composition may be two of many factors required for accurate centromere assembly.
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Population Scale Analysis of Centromeric Satellite DNA Reveals Highly Dynamic Evolutionary Patterns and Genomic Organization in Long-Tailed and Rhesus Macaques. Cells 2022; 11:cells11121953. [PMID: 35741082 PMCID: PMC9221937 DOI: 10.3390/cells11121953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 02/04/2023] Open
Abstract
Centromeric satellite DNA (cen-satDNA) consists of highly divergent repeat monomers, each approximately 171 base pairs in length. Here, we investigated the genetic diversity in the centromeric region of two primate species: long-tailed (Macaca fascicularis) and rhesus (Macaca mulatta) macaques. Fluorescence in situ hybridization and bioinformatic analysis showed the chromosome-specific organization and dynamic nature of cen-satDNAsequences, and their substantial diversity, with distinct subfamilies across macaque populations, suggesting increased turnovers. Comparative genomics identified high level polymorphisms spanning a 120 bp deletion region and a remarkable interspecific variability in cen-satDNA size and structure. Population structure analysis detected admixture patterns within populations, indicating their high divergence and rapid evolution. However, differences in cen-satDNA profiles appear to not be involved in hybrid incompatibility between the two species. Our study provides a genomic landscape of centromeric repeats in wild macaques and opens new avenues for exploring their impact on the adaptive evolution and speciation of primates.
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7
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Wang Z, Rouard M, Biswas MK, Droc G, Cui D, Roux N, Baurens FC, Ge XJ, Schwarzacher T, Heslop-Harrison P(JS, Liu Q. A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae. Gigascience 2022; 11:6576245. [PMID: 35488861 PMCID: PMC9055855 DOI: 10.1093/gigascience/giac027] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/26/2022] [Accepted: 02/22/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Ensete glaucum (2n = 2x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana (Musa). A high-quality reference genome sequence assembly of E. glaucum is a resource for functional and evolutionary studies of Ensete, Musaceae, and the Zingiberales. FINDINGS Using Oxford Nanopore Technologies, chromosome conformation capture (Hi-C), Illumina and RNA survey sequence, supported by molecular cytogenetics, we report a high-quality 481.5 Mb genome assembly with 9 pseudo-chromosomes and 36,836 genes. A total of 55% of the genome is composed of repetitive sequences with predominantly LTR-retroelements (37%) and DNA transposons (7%). The single 5S ribosomal DNA locus had an exceptionally long monomer length of 1,056 bp, more than twice that of the monomers at multiple loci in Musa. A tandemly repeated satellite (1.1% of the genome, with no similar sequence in Musa) was present around all centromeres, together with a few copies of a long interspersed nuclear element (LINE) retroelement. The assembly enabled us to characterize in detail the chromosomal rearrangements occurring between E. glaucum and the x = 11 species of Musa. One E. glaucum chromosome has the same gene content as Musa acuminata, while others show multiple, complex, but clearly defined evolutionary rearrangements in the change between x= 9 and 11. CONCLUSIONS The advance towards a Musaceae pangenome including E. glaucum, tolerant of extreme environments, makes a complete set of gene alleles, copy number variation, and a reference for structural variation available for crop breeding and understanding environmental responses. The chromosome-scale genome assembly shows the nature of chromosomal fusion and translocation events during speciation, and features of rapid repetitive DNA change in terms of copy number, sequence, and genomic location, critical to understanding its role in diversity and evolution.
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Affiliation(s)
- Ziwei Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France,French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Alliance Bioversity and CIAT, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Manosh Kumar Biswas
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Gaetan Droc
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Alliance Bioversity and CIAT, CIRAD, INRAE, IRD, F-34398 Montpellier, France,CIRAD, UMR AGAP Institut, F-34398 Montpellier, France,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Dongli Cui
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Pat (J S) Heslop-Harrison
- Correspondence address. Qing Liu. Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China. Pat Heslop-Harrison. Department of Genetics and Genome Biology, University of Leicester, Leicester, LE 7RH, UK Qing Liu. Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China E-mail:
| | - Qing Liu
- Correspondence address. Pat Heslop-Harrison. Department of Genetics and Genome Biology, University of Leicester, Leicester, LE 7RH, UK. E-mail:
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Vozdova M, Kubickova S, Martínková N, Galindo DJ, Bernegossi AM, Cernohorska H, Kadlcikova D, Musilová P, Duarte JM, Rubes J. Satellite DNA in Neotropical Deer Species. Genes (Basel) 2021; 12:genes12010123. [PMID: 33478071 PMCID: PMC7835801 DOI: 10.3390/genes12010123] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 01/04/2023] Open
Abstract
The taxonomy and phylogenetics of Neotropical deer have been mostly based on morphological criteria and needs a critical revision on the basis of new molecular and cytogenetic markers. In this study, we used the variation in the sequence, copy number, and chromosome localization of satellite I-IV DNA to evaluate evolutionary relationships among eight Neotropical deer species. Using FISH with satI-IV probes derived from Mazama gouazoubira, we proved the presence of satellite DNA blocks in peri/centromeric regions of all analyzed deer. Satellite DNA was also detected in the interstitial chromosome regions of species of the genus Mazama with highly reduced chromosome numbers. In contrast to Blastocerus dichotomus, Ozotoceros bezoarticus, and Odocoileus virginianus, Mazama species showed high abundance of satIV DNA by FISH. The phylogenetic analysis of the satellite DNA showed close relationships between O. bezoarticus and B. dichotomus. Furthermore, the Neotropical and Nearctic populations of O. virginianus formed a single clade. However, the satellite DNA phylogeny did not allow resolving the relationships within the genus Mazama. The high abundance of the satellite DNA in centromeres probably contributes to the formation of chromosomal rearrangements, thus leading to a fast and ongoing speciation in this genus, which has not yet been reflected in the satellite DNA sequence diversification.
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Affiliation(s)
- Miluse Vozdova
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (D.K.); (P.M.); (J.R.)
- Correspondence: ; Tel.: +4205-3333-1422
| | - Svatava Kubickova
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (D.K.); (P.M.); (J.R.)
| | - Natália Martínková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Kvetna 8, 603 65 Brno, Czech Republic;
| | - David Javier Galindo
- Deer Research and Conservation Center (NUPECCE), School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), 14884-900 Jaboticabal, Brazil; (D.J.G.); (A.M.B.); (J.M.D.)
| | - Agda Maria Bernegossi
- Deer Research and Conservation Center (NUPECCE), School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), 14884-900 Jaboticabal, Brazil; (D.J.G.); (A.M.B.); (J.M.D.)
| | - Halina Cernohorska
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (D.K.); (P.M.); (J.R.)
| | - Dita Kadlcikova
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (D.K.); (P.M.); (J.R.)
| | - Petra Musilová
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (D.K.); (P.M.); (J.R.)
| | - Jose Mauricio Duarte
- Deer Research and Conservation Center (NUPECCE), School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), 14884-900 Jaboticabal, Brazil; (D.J.G.); (A.M.B.); (J.M.D.)
| | - Jiri Rubes
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (D.K.); (P.M.); (J.R.)
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9
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Suntronpong A, Singchat W, Kruasuwan W, Prakhongcheep O, Sillapaprayoon S, Muangmai N, Somyong S, Indananda C, Kraichak E, Peyachoknagul S, Srikulnath K. Characterization of centromeric satellite DNAs (MALREP) in the Asian swamp eel (Monopterus albus) suggests the possible origin of repeats from transposable elements. Genomics 2020; 112:3097-3107. [PMID: 32470643 DOI: 10.1016/j.ygeno.2020.05.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/21/2020] [Accepted: 05/24/2020] [Indexed: 01/04/2023]
Abstract
Centromeric satellite DNA (cen-satDNA) sequences of the Asian swamp eel (Monopterus albus) were characterized. Three GC-rich cen-satDNA sequences were detected as a 233 bp MALREP-A and a 293 bp MALREP-B localized to all chromosomes, and a 293 bp MALREP-C distributed on eight chromosome pairs. Sequence lengths of MALREP-B and MALREP-C were 60 bp larger than that of MALREP-A, showing partial homology with core sequences (233 bp). Size differences between MALREP-A and MALREP-B/C suggest the possible occurrence of two satDNA families. The presence of an additional 60 bp in MALREP-B/C resulted from an ancient dimer of 233 bp monomers and subsequent mutation and homogenization between the two monomers. All MALREPs showed partial homology with transposable elements (TEs), suggesting that the MALREPs originated from the TEs. The MALREPs might have been acquired in the Asian swamp eel, thereby promoting fixation in the species.
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Affiliation(s)
- Aorarat Suntronpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand.
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand.
| | - Worarat Kruasuwan
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Ornjira Prakhongcheep
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Siwapech Sillapaprayoon
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand.
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand.
| | - Suthasinee Somyong
- National Omics Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani 12120, Thailand.
| | - Chantra Indananda
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Ekaphan Kraichak
- Department of Botany, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand; Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok 10900, Thailand; Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand; Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand; Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan.
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10
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Gamba R, Fachinetti D. From evolution to function: Two sides of the same CENP-B coin? Exp Cell Res 2020; 390:111959. [DOI: 10.1016/j.yexcr.2020.111959] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/07/2020] [Accepted: 03/12/2020] [Indexed: 10/24/2022]
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11
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Ohzeki JI, Otake K, Masumoto H. Human artificial chromosome: Chromatin assembly mechanisms and CENP-B. Exp Cell Res 2020; 389:111900. [PMID: 32044309 DOI: 10.1016/j.yexcr.2020.111900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 12/12/2022]
Abstract
The centromere is a specialized chromosomal locus required for accurate chromosome segregation. Heterochromatin also assembles around centromere chromatin and forms a base that supports sister chromatid cohesion until anaphase begins. Both centromere chromatin and heterochromatin assemble on a centromeric DNA sequence, a highly repetitive sequence called alphoid DNA (α-satellite DNA) in humans. Alphoid DNA can form a de novo centromere and subsequent human artificial chromosome (HAC) when introduced into the human culture cells HT1080. HAC is maintained stably as a single chromosome independent of other human chromosomes. For de novo centromere assembly and HAC formation, the centromere protein CENP-B and its binding sites, CENP-B boxes, are required in the repeating units of alphoid DNA. CENP-B has multiple roles in de novo centromere chromatin assembly and stabilization and in heterochromatin formation upon alphoid DNA introduction into the cells. Here we review recent progress in human artificial chromosome construction and centromere/heterochromatin assembly and maintenance, focusing on the involvement of human centromere DNA and CENP-B protein.
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Affiliation(s)
- Jun-Ichirou Ohzeki
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818, Japan
| | - Koichiro Otake
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818, Japan
| | - Hiroshi Masumoto
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818, Japan.
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12
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Diversity of PBI-DdeI satellite DNA in snakes correlates with rapid independent evolution and different functional roles. Sci Rep 2019; 9:15459. [PMID: 31664097 PMCID: PMC6820872 DOI: 10.1038/s41598-019-51863-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 10/09/2019] [Indexed: 11/24/2022] Open
Abstract
To better understand PBI-DdeI satellite DNA located in the centromeric region of python, molecular evolution analysis was conducted on 40 snake species. A ladder-like pattern of DNA bands with repetition of the 194–210 bp monomer was observed in 15 species using PCR. Molecular cloning was performed to obtain 97 AT-rich monomer sequences. Phylogenetic and network analyses showed three PBI-DdeI subfamilies with sequences grouped in species-specific clusters, suggesting rapid evolution. Slow evolution was found in eight species with shared PBI-DdeI sequences, suggesting recent species diversification, allowing PBI-DdeI no time to diverge, with limited homogenization and fixation processes. Quantitative real-time PCR showed large differences in copy number between Python bivittatus and other snakes, consistent with repeat scanning of whole genome sequences. Copy numbers were significantly higher in female Naja kaouthia than in males, concurring with chromosomal distribution of PBI-DdeI specifically localized to female W chromosomes. PBI-DdeI might act as an evolutionary driver with several repeats to promote W chromosome differentiation and heterochromatinization in N. kaouthia. Analysis revealed PBI-DdeI with a reduced copy number, compared to P. bivittatus, in most snakes studied, and it is possible that it subsequently dispersed and amplified on W chromosomes with different functional roles in N. kaouthia.
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13
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Ohzeki J, Larionov V, Earnshaw WC, Masumoto H. De novo formation and epigenetic maintenance of centromere chromatin. Curr Opin Cell Biol 2019; 58:15-25. [PMID: 30654232 DOI: 10.1016/j.ceb.2018.12.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/30/2018] [Accepted: 12/07/2018] [Indexed: 12/12/2022]
Abstract
Accurate chromosome segregation is essential for cell proliferation. The centromere is a specialized chromosomal locus, on which the kinetochore structure is formed. The centromere/kinetochore is required for the equal separation of sister chromatids to daughter cells. Here, we review recent findings on centromere-specific chromatin, including its constitutive protein components, its de novo formation and maintenance mechanisms, and our progress in analyses with synthetic human artificial chromosomes (HACs).
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Affiliation(s)
- Junichirou Ohzeki
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan
| | - Vladimir Larionov
- Genome Structure and Function Group, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Hiroshi Masumoto
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan.
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14
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Koga A, Tanabe H, Hirai Y, Imai H, Imamura M, Oishi T, Stanyon R, Hirai H. Co-Opted Megasatellite DNA Drives Evolution of Secondary Night Vision in Azara's Owl Monkey. Genome Biol Evol 2017; 9:1963-1970. [PMID: 28810713 PMCID: PMC5553404 DOI: 10.1093/gbe/evx142] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2017] [Indexed: 11/12/2022] Open
Abstract
Owl monkeys (genus Aotus) are the only taxon in simian primates that consists of nocturnal or otherwise cathemeral species. Their night vision is superior to that of other monkeys, apes, and humans but not as good as that of typical nocturnal mammals. This incomplete night vision has been used to conclude that these monkeys only secondarily adapted to a nocturnal lifestyle, or to their cathemeral lifestyle that involves high night-time activity. It is known that the rod cells of many nocturnal mammals possess a unique nuclear architecture in which heterochromatin is centrally located. This "inverted nuclear architecture", in contrast with "conventional nuclear architecture", provides elevated night vision by passing light efficiently to the outer segments of photoreceptors. Owl monkey rod cells exhibit an intermediate chromatin distribution, which may provide them with less efficient night vision than other nocturnal mammals. Recently, we identified three megasatellite DNAs in the genome of Azara's owl monkey (Aotus azarae). In the present study, we show that one of the three megasatellite DNAs, OwlRep, serves as the primary component of the heterochromatin block located in the central space of the rod nucleus in A. azarae. This satellite DNA is likely to have emerged in the Aotus lineage after its divergence from those of other platyrrhini taxa and underwent a rapid expansion in the genome. Our results indicate that the heterochromatin core in the A. azarae rod nucleus was newly formed in A. azarae or its recent ancestor, and supports the hypothesis that A. azarae, and with all probability other Aotus species, secondarily acquired night vision.
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Affiliation(s)
- Akihiko Koga
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Hideyuki Tanabe
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Yuriko Hirai
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Hiroo Imai
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | | | - Takao Oishi
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | | | - Hirohisa Hirai
- Primate Research Institute, Kyoto University, Inuyama, Japan
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15
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Prakhongcheep O, Thapana W, Suntronpong A, Singchat W, Pattanatanang K, Phatcharakullawarawat R, Muangmai N, Peyachoknagul S, Matsubara K, Ezaz T, Srikulnath K. Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata). BMC Evol Biol 2017; 17:193. [PMID: 28814266 PMCID: PMC5559828 DOI: 10.1186/s12862-017-1044-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 08/08/2017] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Satellite DNAs (stDNAs) are highly repeated sequences that constitute large portions of any genome. The evolutionary dynamics of stDNA (e.g. copy number, nucleotide sequence, location) can, therefore, provide an insight into genome organization and evolution. We investigated the evolutionary origin of VSAREP stDNA in 17 monitor lizards (seven Asian, five Australian, and five African) at molecular and cytogenetic level. RESULTS Results revealed that VSAREP is conserved in the genome of Asian and Australian varanids, but not in African varanids, suggesting that these sequences are either differentiated or lost in the African varanids. Phylogenetic and arrangement network analyses revealed the existence of at least four VSAREP subfamilies. The similarity of each sequence unit within the same VSAREP subfamily from different species was higher than those of other VSAREP subfamilies belonging to the same species. Additionally, all VSAREP subfamilies isolated from the three Australian species (Varanus rosenbergi, V. gouldii, and V. acanthurus) were co-localized near the centromeric or pericentromeric regions of the macrochromosomes, except for chromosomes 3 and 4 in each Australian varanid. However, their chromosomal arrangements were different among species. CONCLUSIONS The VSAREP stDNA family lack homogenized species-specific nucleotide positions in varanid lineage. Most VSAREP sequences were shared among varanids within the four VSAREP subfamilies. This suggests that nucleotide substitutions in each varanid species accumulated more slowly than homogenization rates in each VSAREP subfamily, resulting in non-species-specific evolution of stDNA profiles. Moreover, changes in location of VSAREP stDNA in each Australian varanid suggests a correlation with chromosomal rearrangements, leading to karyotypic differences among these species.
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Affiliation(s)
- Ornjira Prakhongcheep
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Animal Breeding and Genetics Consortium - Kasetsart University (ABG - KU), 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU), Kasetsart University, Bangkok, 10900, Thailand
| | - Watcharaporn Thapana
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Animal Breeding and Genetics Consortium - Kasetsart University (ABG - KU), 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU), Kasetsart University, Bangkok, 10900, Thailand
| | - Aorarat Suntronpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Animal Breeding and Genetics Consortium - Kasetsart University (ABG - KU), 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Animal Breeding and Genetics Consortium - Kasetsart University (ABG - KU), 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Khampee Pattanatanang
- Department of Parasitology, Faculty of Veterinary Medicine, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Real Zoo, The Sky Shopping Center, Ayutthaya, 13210, Thailand
| | | | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU), Kasetsart University, Bangkok, 10900, Thailand
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Kazumi Matsubara
- Wildlife Genetics Laboratory, Institute for Applied Ecology, University of Canberra, Canberra, ACT 2600, Australia
| | - Tariq Ezaz
- Wildlife Genetics Laboratory, Institute for Applied Ecology, University of Canberra, Canberra, ACT 2600, Australia
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Animal Breeding and Genetics Consortium - Kasetsart University (ABG - KU), 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU), Kasetsart University, Bangkok, 10900, Thailand.
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16
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Dumont M, Fachinetti D. DNA Sequences in Centromere Formation and Function. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2017; 56:305-336. [PMID: 28840243 DOI: 10.1007/978-3-319-58592-5_13] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Faithful chromosome segregation during cell division depends on the centromere, a complex DNA/protein structure that links chromosomes to spindle microtubules. This chromosomal domain has to be marked throughout cell division and its chromosomal localization preserved across cell generations. From fission yeast to human, centromeres are established on a series of repetitive DNA sequences and on specialized centromeric chromatin. This chromatin is enriched with the histone H3 variant, named CENP-A, that was demonstrated to be the epigenetic mark that maintains centromere identity and function indefinitely. Although centromere identity is thought to be exclusively epigenetic, the presence of specific DNA sequences in the majority of eukaryotes and of the centromeric protein CENP-B that binds to these sequences, suggests the existence of a genetic component as well. In this review, we will highlight the importance of centromeric sequences for centromere formation and function, and discuss the centromere DNA sequence/CENP-B paradox.
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Affiliation(s)
- M Dumont
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005, Paris, France
| | - D Fachinetti
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005, Paris, France.
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17
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Kugou K, Hirai H, Masumoto H, Koga A. Formation of functional CENP-B boxes at diverse locations in repeat units of centromeric DNA in New World monkeys. Sci Rep 2016; 6:27833. [PMID: 27292628 PMCID: PMC4904201 DOI: 10.1038/srep27833] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 05/25/2016] [Indexed: 12/17/2022] Open
Abstract
Centromere protein B, which is involved in centromere formation, binds to centromeric repetitive DNA by recognizing a nucleotide motif called the CENP-B box. Humans have large numbers of CENP-B boxes in the centromeric repetitive DNA of their autosomes and X chromosome. The current understanding is that these CENP-B boxes are located at identical positions in the repeat units of centromeric DNA. Great apes also have CENP-B boxes in locations that are identical to humans. The purpose of the present study was to examine the location of CENP-B box in New World monkeys. We recently identified CENP-B box in one species of New World monkeys (marmosets). In this study, we found functional CENP-B boxes in CENP-A-assembled repeat units of centromeric DNA in 2 additional New World monkeys (squirrel monkeys and tamarins) by immunostaining and ChIP-qPCR analyses. The locations of the 3 CENP-B boxes in the repeat units differed from one another. The repeat unit size of centromeric DNA of New World monkeys (340–350 bp) is approximately twice that of humans and great apes (171 bp). This might be, associated with higher-order repeat structures of centromeric DNA, a factor for the observed variation in the CENP-B box location in New World monkeys.
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Affiliation(s)
- Kazuto Kugou
- Department of Frontier Research, Kazusa DNA Research Institute, Kisarazu 292-0818, Japan
| | - Hirohisa Hirai
- Primate Research Institute, Kyoto University, Inuyama 484-8506, Japan
| | - Hiroshi Masumoto
- Department of Frontier Research, Kazusa DNA Research Institute, Kisarazu 292-0818, Japan
| | - Akihiko Koga
- Primate Research Institute, Kyoto University, Inuyama 484-8506, Japan
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