1
|
Kuo YT, Schubert V, Marques A, Schubert I, Houben A. Centromere diversity: How different repeat-based holocentromeres may have evolved. Bioessays 2024; 46:e2400013. [PMID: 38593286 DOI: 10.1002/bies.202400013] [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: 01/16/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/11/2024]
Abstract
In addition to monocentric eukaryotes, which have a single localized centromere on each chromosome, there are holocentric species, with extended repeat-based or repeat-less centromeres distributed over the entire chromosome length. At least two types of repeat-based holocentromeres exist, one composed of many small repeat-based centromere units (small unit-type), and another one characterized by a few large centromere units (large unit-type). We hypothesize that the transposable element-mediated dispersal of hundreds of short satellite arrays formed the small centromere unit-type holocentromere in Rhynchospora pubera. The large centromere unit-type of the plant Chionographis japonica is likely a product of simultaneous DNA double-strand breaks (DSBs), which initiated the de novo formation of repeat-based holocentromeres via insertion of satellite DNA, derived from extra-chromosomal circular DNAs (eccDNAs). The number of initial DSBs along the chromosomes must be higher than the number of centromere units since only a portion of the breaks will have incorporated eccDNA at an appropriate position to serve as future centromere unit sites. Subsequently, preferential incorporation of the centromeric histone H3 variant at these positions is assumed. The identification of repeat-based holocentromeres across lineages will unveil the centromere plasticity and elucidate the mechanisms underlying the diverse formation of holocentromeres.
Collapse
Affiliation(s)
- Yi-Tzu Kuo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| |
Collapse
|
2
|
Hockens C, Lorenzi H, Wang TT, Lei EP, Rosin LF. Chromosome segregation during spermatogenesis occurs through a unique center-kinetic mechanism in holocentric moth species. PLoS Genet 2024; 20:e1011329. [PMID: 38913752 PMCID: PMC11226059 DOI: 10.1371/journal.pgen.1011329] [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: 10/13/2023] [Revised: 07/05/2024] [Accepted: 06/03/2024] [Indexed: 06/26/2024] Open
Abstract
Precise regulation of chromosome dynamics in the germline is essential for reproductive success across species. Yet, the mechanisms underlying meiotic chromosomal events such as homolog pairing and chromosome segregation are not fully understood in many species. Here, we employ Oligopaint DNA FISH to investigate mechanisms of meiotic homolog pairing and chromosome segregation in the holocentric pantry moth, Plodia interpunctella, and compare our findings to new and previous studies in the silkworm moth, Bombyx mori, which diverged from P. interpunctella over 100 million years ago. We find that pairing in both Bombyx and Plodia spermatogenesis is initiated at gene-rich chromosome ends. Additionally, both species form rod shaped cruciform-like bivalents at metaphase I. However, unlike the telomere-oriented chromosome segregation mechanism observed in Bombyx, Plodia can orient bivalents in multiple different ways at metaphase I. Surprisingly, in both species we find that kinetochores consistently assemble at non-telomeric loci toward the center of chromosomes regardless of where chromosome centers are located in the bivalent. Additionally, sister kinetochores do not seem to be paired in these species. Instead, four distinct kinetochores are easily observed at metaphase I. Despite this, we find clear end-on microtubule attachments and not lateral microtubule attachments co-orienting these separated kinetochores. These findings challenge the classical view of segregation where paired, poleward-facing kinetochores are required for accurate homolog separation in meiosis I. Our studies here highlight the importance of exploring fundamental processes in non-model systems, as employing novel organisms can lead to the discovery of novel biology.
Collapse
Affiliation(s)
- Clio Hockens
- Unit on Chromosome Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hernan Lorenzi
- TriLab Bioinformatics Group, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tricia T. Wang
- Unit on Chromosome Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Elissa P. Lei
- Nuclear Organization and Gene Expression Section; Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Leah F. Rosin
- Unit on Chromosome Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| |
Collapse
|
3
|
Boman J, Wiklund C, Vila R, Backström N. Meiotic drive against chromosome fusions in butterfly hybrids. Chromosome Res 2024; 32:7. [PMID: 38702576 PMCID: PMC11068667 DOI: 10.1007/s10577-024-09752-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/21/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Species frequently differ in the number and structure of chromosomes they harbor, but individuals that are heterozygous for chromosomal rearrangements may suffer from reduced fitness. Chromosomal rearrangements like fissions and fusions can hence serve as a mechanism for speciation between incipient lineages, but their evolution poses a paradox. How can rearrangements get fixed between populations if heterozygotes have reduced fitness? One solution is that this process predominantly occurs in small and isolated populations, where genetic drift can override natural selection. However, fixation is also more likely if a novel rearrangement is favored by a transmission bias, such as meiotic drive. Here, we investigate chromosomal transmission distortion in hybrids between two wood white (Leptidea sinapis) butterfly populations with extensive karyotype differences. Using data from two different crossing experiments, we uncover that there is a transmission bias favoring the ancestral chromosomal state for derived fusions, a result that shows that chromosome fusions actually can fix in populations despite being counteracted by meiotic drive. This means that meiotic drive not only can promote runaway chromosome number evolution and speciation, but also that it can be a conservative force acting against karyotypic change and the evolution of reproductive isolation. Based on our results, we suggest a mechanistic model for why chromosome fusion mutations may be opposed by meiotic drive and discuss factors contributing to karyotype evolution in Lepidoptera.
Collapse
Affiliation(s)
- Jesper Boman
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden.
| | - Christer Wiklund
- Department of Zoology: Division of Ecology, Stockholm University, Stockholm, Sweden
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra), Passeig Marítim de La Barceloneta 37-49, 08003, Barcelona, Spain
| | - Niclas Backström
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| |
Collapse
|
4
|
Xiang Y, Tsuchiya D, Yu Z, Zhao X, McKinney S, Unruh J, Slaughter B, Lake CM, Hawley RS. Multiple reorganizations of the lateral elements of the synaptonemal complex facilitate homolog segregation in Bombyx mori oocytes. Curr Biol 2024; 34:352-360.e4. [PMID: 38176417 DOI: 10.1016/j.cub.2023.12.018] [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: 10/03/2023] [Revised: 11/29/2023] [Accepted: 12/07/2023] [Indexed: 01/06/2024]
Abstract
Although Lepidopteran females build a synaptonemal complex (SC) in pachytene, homologs do not crossover, necessitating an alternative method of homolog conjunction. In Bombyx mori oocytes, the SC breaks down at the end of pachytene, and homolog associations are maintained by a large oocyte-specific structure, which we call the bivalent bridge (BB), connecting paired homologs. The BB is derived from at least some components of the SC lateral elements (LEs). It contains the HORMAD protein HOP1 and the LE protein SYCP2 and is formed by the fusion of the two LE derivatives. As diplotene progresses, the BB increases in width and acquires a layered structure with a thick band of HOP1 separating two layers of SYCP2. The HOP1 interacting protein, PCH2, joins the BB in mid-diplotene, and by late-diplotene, it lies in the middle of the HOP1 filament. This structure is maintained through metaphase I. SYCP2 and PCH2 are lost at anaphase I, and the BB no longer connects the separating homologs. However, a key component of the BB, HOP1, remains at the metaphase I plate. These changes in organization of the BB occur simultaneously with the movement of the kinetochore protein, DSN1, from within the BB at mid-diplotene to the edge of the homologs facing the poles by metaphase I. We view these data in context of models in which SC components and regulators can be repurposed to achieve different functions, a fascinating example of evolution achieving homolog conjunction in an alternative way with recycling of SC proteins.
Collapse
Affiliation(s)
- Youbin Xiang
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Dai Tsuchiya
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Zulin Yu
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Xia Zhao
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Sean McKinney
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Jay Unruh
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Brian Slaughter
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Cathleen M Lake
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - R Scott Hawley
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, MO 66160, USA.
| |
Collapse
|
5
|
Zhou KD, Zhang CX, Niu FR, Bai HC, Wu DD, Deng JC, Qian HY, Jiang YL, Ma W. Exploring Plant Meiosis: Insights from the Kinetochore Perspective. Curr Issues Mol Biol 2023; 45:7974-7995. [PMID: 37886947 PMCID: PMC10605258 DOI: 10.3390/cimb45100504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/12/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023] Open
Abstract
The central player for chromosome segregation in both mitosis and meiosis is the macromolecular kinetochore structure, which is assembled by >100 structural and regulatory proteins on centromere DNA. Kinetochores play a crucial role in cell division by connecting chromosomal DNA and microtubule polymers. This connection helps in the proper segregation and alignment of chromosomes. Additionally, kinetochores can act as a signaling hub, regulating the start of anaphase through the spindle assembly checkpoint, and controlling the movement of chromosomes during anaphase. However, the role of various kinetochore proteins in plant meiosis has only been recently elucidated, and these proteins differ in their functionality from those found in animals. In this review, our current knowledge of the functioning of plant kinetochore proteins in meiosis will be summarized. In addition, the functional similarities and differences of core kinetochore proteins in meiosis between plants and other species are discussed, and the potential applications of manipulating certain kinetochore genes in meiosis for breeding purposes are explored.
Collapse
Affiliation(s)
- Kang-Di Zhou
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China; (K.-D.Z.); (C.-X.Z.)
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China; (H.-C.B.); (J.-C.D.); (H.-Y.Q.); (Y.-L.J.)
| | - Cai-Xia Zhang
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China; (K.-D.Z.); (C.-X.Z.)
| | - Fu-Rong Niu
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China;
| | - Hao-Chen Bai
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China; (H.-C.B.); (J.-C.D.); (H.-Y.Q.); (Y.-L.J.)
| | - Dan-Dan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China;
| | - Jia-Cheng Deng
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China; (H.-C.B.); (J.-C.D.); (H.-Y.Q.); (Y.-L.J.)
| | - Hong-Yuan Qian
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China; (H.-C.B.); (J.-C.D.); (H.-Y.Q.); (Y.-L.J.)
| | - Yun-Lei Jiang
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China; (H.-C.B.); (J.-C.D.); (H.-Y.Q.); (Y.-L.J.)
| | - Wei Ma
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China; (K.-D.Z.); (C.-X.Z.)
| |
Collapse
|
6
|
Fukagawa T, Kakutani T. Transgenerational epigenetic control of constitutive heterochromatin, transposons, and centromeres. Curr Opin Genet Dev 2023; 78:102021. [PMID: 36716679 DOI: 10.1016/j.gde.2023.102021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/20/2022] [Accepted: 01/04/2023] [Indexed: 01/30/2023]
Abstract
Epigenetic mechanisms are important not only for development but also for genome stability and chromosome dynamics. The latter types of epigenetic controls can often be transgenerational. Here, we review recent progress in two examples of transgenerational epigenetic control: i) the control of constitutive heterochromatin and transposable elements and ii) epigenetic mechanisms that regulate centromere specification and functions. We also discuss the biological significance of enigmatic associations among centromeres, transposons, and constitutive heterochromatin.
Collapse
Affiliation(s)
- Tatsuo Fukagawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan. https://twitter.com/tatsuofukagawa1
| | - Tetsuji Kakutani
- Department of Biological Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.
| |
Collapse
|
7
|
Macas J, Ávila Robledillo L, Kreplak J, Novák P, Koblížková A, Vrbová I, Burstin J, Neumann P. Assembly of the 81.6 Mb centromere of pea chromosome 6 elucidates the structure and evolution of metapolycentric chromosomes. PLoS Genet 2023; 19:e1010633. [PMID: 36735726 PMCID: PMC10027222 DOI: 10.1371/journal.pgen.1010633] [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: 11/23/2022] [Revised: 03/20/2023] [Accepted: 01/23/2023] [Indexed: 02/04/2023] Open
Abstract
Centromeres in the legume genera Pisum and Lathyrus exhibit unique morphological characteristics, including extended primary constrictions and multiple separate domains of centromeric chromatin. These so-called metapolycentromeres resemble an intermediate form between monocentric and holocentric types, and therefore provide a great opportunity for studying the transitions between different types of centromere organizations. However, because of the exceedingly large and highly repetitive nature of metapolycentromeres, highly contiguous assemblies needed for these studies are lacking. Here, we report on the assembly and analysis of a 177.6 Mb region of pea (Pisum sativum) chromosome 6, including the 81.6 Mb centromere region (CEN6) and adjacent chromosome arms. Genes, DNA methylation profiles, and most of the repeats were uniformly distributed within the centromere, and their densities in CEN6 and chromosome arms were similar. The exception was an accumulation of satellite DNA in CEN6, where it formed multiple arrays up to 2 Mb in length. Centromeric chromatin, characterized by the presence of the CENH3 protein, was predominantly associated with arrays of three different satellite repeats; however, five other satellites present in CEN6 lacked CENH3. The presence of CENH3 chromatin was found to determine the spatial distribution of the respective satellites during the cell cycle. Finally, oligo-FISH painting experiments, performed using probes specifically designed to label the genomic regions corresponding to CEN6 in Pisum, Lathyrus, and Vicia species, revealed that metapolycentromeres evolved via the expansion of centromeric chromatin into neighboring chromosomal regions and the accumulation of novel satellite repeats. However, in some of these species, centromere evolution also involved chromosomal translocations and centromere repositioning.
Collapse
Affiliation(s)
- Jiří Macas
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, Czech Republic
| | - Laura Ávila Robledillo
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, Czech Republic
| | - Jonathan Kreplak
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Petr Novák
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, Czech Republic
| | - Andrea Koblížková
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, Czech Republic
| | - Iva Vrbová
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, Czech Republic
| | - Judith Burstin
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Pavel Neumann
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, Czech Republic
| |
Collapse
|
8
|
Mon H, Sato M, Lee JM, Kusakabe T. Construction of gene co-expression networks in cultured silkworm cells and identification of previously uncharacterized lepidopteran-specific genes required for chromosome dynamics. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 151:103875. [PMID: 36410580 DOI: 10.1016/j.ibmb.2022.103875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/01/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
Advances in sequencing technology and bioinformatics have accelerated gene discovery and homology-based functional annotation in many species, and numerous targeted gene studies have greatly expanded the understanding of gene functions. Nevertheless, there are still many genes that lack homology with genes in other evolutionary lineages and are left as genes with unknown functions. We constructed a gene co-expression network from the Bombyx mori ovary-derived cell line, BmN4, and attempted to infer the biological roles of uncharacterized genes based on the correlation between the function-known and unknown genes. Within this network, we focused on the co-expression modules involved in chromosome architecture, dynamics, and integrity, and selected the uncharacterized genes for subsequent RNAi-based phenotypic screening. This approach enabled the identification of 5 genes whose knockdown led to abnormalities in chromosome dynamics and spindle morphology in mitosis. One of them was a recently characterized gene, BmCenp-T, which plays a central role in building the kinetochore protein complex on the silkworm holocentric chromosomes. In this study, we suggest a method for constructing the gene co-expression network and selecting candidate genes for small-scale RNAi screening. This approach is complementary to homology-based annotation and may be useful for the analysis of lineage-specific uncharacterized genes such as orphan genes.
Collapse
Affiliation(s)
- Hiroaki Mon
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Masanao Sato
- Laboratory of Applied Molecular Entomology, Division of Applied Bioscience, Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Jae Man Lee
- Laboratory of Creative Science for Insect Industries, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Takahiro Kusakabe
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan.
| |
Collapse
|
9
|
Dong Q, Li F. Cell cycle control of kinetochore assembly. Nucleus 2022; 13:208-220. [PMID: 36037227 PMCID: PMC9427032 DOI: 10.1080/19491034.2022.2115246] [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] [Indexed: 10/28/2022] Open
Abstract
The kinetochore is a large proteinaceous structure assembled on the centromeres of chromosomes. The complex machinery links chromosomes to the mitotic spindle and is essential for accurate chromosome segregation during cell division. The kinetochore is composed of two submodules: the inner and outer kinetochore. The inner kinetochore is assembled on centromeric chromatin and persists with centromeres throughout the cell cycle. The outer kinetochore attaches microtubules to the inner kinetochore, and assembles only during mitosis. The review focuses on recent advances in our understanding of the mechanisms governing the proper assembly of the outer kinetochore during mitosis and highlights open questions for future investigation.
Collapse
Affiliation(s)
- Qianhua Dong
- Department of Biology, New York University, New York, NY, USA
| | - Fei Li
- Department of Biology, New York University, New York, NY, USA
| |
Collapse
|
10
|
Caro L, Raman P, Steiner FA, Ailion M, Malik HS. Recurrent but Short-Lived Duplications of Centromeric Proteins in Holocentric Caenorhabditis Species. Mol Biol Evol 2022; 39:6731087. [PMID: 36173809 PMCID: PMC9577544 DOI: 10.1093/molbev/msac206] [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] [Indexed: 12/15/2022] Open
Abstract
Centromeric histones (CenH3s) are essential for chromosome inheritance during cell division in most eukaryotes. CenH3 genes have rapidly evolved and undergone repeated gene duplications and diversification in many plant and animal species. In Caenorhabditis species, two independent duplications of CenH3 (named hcp-3 for HoloCentric chromosome-binding Protein 3) were previously identified in C. elegans and C. remanei. Using phylogenomic analyses in 32 Caenorhabditis species, we find strict retention of the ancestral hcp-3 gene and 10 independent duplications. Most hcp-3L (hcp-3-like) paralogs are only found in 1-2 species, are expressed in both males and females/hermaphrodites, and encode histone fold domains with 69-100% identity to ancestral hcp-3. We identified novel N-terminal protein motifs, including putative kinetochore protein-interacting motifs and a potential separase cleavage site, which are well conserved across Caenorhabditis HCP-3 proteins. Other N-terminal motifs vary in their retention across paralogs or species, revealing potential subfunctionalization or functional loss following duplication. An N-terminal extension in the hcp-3L gene of C. afra revealed an unprecedented protein fusion, where hcp-3L fused to duplicated segments from hcp-4 (nematode CENP-C). By extending our analyses beyond CenH3, we found gene duplications of six inner and outer kinetochore genes in Caenorhabditis, which appear to have been retained independent of hcp-3 duplications. Our findings suggest that centromeric protein duplications occur frequently in Caenorhabditis nematodes, are selectively retained for short evolutionary periods, then degenerate or are lost entirely. We hypothesize that unique challenges associated with holocentricity in Caenorhabditis may lead to this rapid "revolving door" of kinetochore protein paralogs.
Collapse
Affiliation(s)
- Lews Caro
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA.,Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Pravrutha Raman
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Florian A Steiner
- Department of Molecular Biology and Cellular Biology, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Michael Ailion
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA.,Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.,Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| |
Collapse
|
11
|
Brusini L, Dos Santos Pacheco N, Tromer EC, Soldati-Favre D, Brochet M. Composition and organization of kinetochores show plasticity in apicomplexan chromosome segregation. J Cell Biol 2022; 221:213421. [PMID: 36006241 PMCID: PMC9418836 DOI: 10.1083/jcb.202111084] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 05/31/2022] [Accepted: 07/15/2022] [Indexed: 01/01/2023] Open
Abstract
Kinetochores are multiprotein assemblies directing mitotic spindle attachment and chromosome segregation. In apicomplexan parasites, most known kinetochore components and associated regulators are apparently missing, suggesting a minimal structure with limited control over chromosome segregation. In this study, we use interactomics combined with deep homology searches to identify 13 previously unknown components of kinetochores in Apicomplexa. Apicomplexan kinetochores are highly divergent in sequence and composition from animal and fungal models. The nanoscale organization includes at least four discrete compartments, each displaying different biochemical interactions, subkinetochore localizations and evolutionary rates across the phylum. We reveal alignment of kinetochores at the metaphase plate in both Plasmodium berghei and Toxoplasma gondii, suggestive of a conserved "hold signal" that prevents precocious entry into anaphase. Finally, we show unexpected plasticity in kinetochore composition and segregation between apicomplexan lifecycle stages, suggestive of diverse requirements to maintain fidelity of chromosome segregation across parasite modes of division.
Collapse
Affiliation(s)
- Lorenzo Brusini
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland,Correspondence to Lorenzo Brusini:
| | - Nicolas Dos Santos Pacheco
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Eelco C. Tromer
- Cell Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, Groningen, Netherlands
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Mathieu Brochet
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland,Mathieu Brochet:
| |
Collapse
|
12
|
Hofstatter PG, Thangavel G, Lux T, Neumann P, Vondrak T, Novak P, Zhang M, Costa L, Castellani M, Scott A, Toegelová H, Fuchs J, Mata-Sucre Y, Dias Y, Vanzela AL, Huettel B, Almeida CC, Šimková H, Souza G, Pedrosa-Harand A, Macas J, Mayer KF, Houben A, Marques A. Repeat-based holocentromeres influence genome architecture and karyotype evolution. Cell 2022; 185:3153-3168.e18. [DOI: 10.1016/j.cell.2022.06.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/24/2022] [Accepted: 06/24/2022] [Indexed: 01/30/2023]
|
13
|
Wang Y, Wu L, Yuen KWY. The roles of transcription, chromatin organisation and chromosomal processes in holocentromere establishment and maintenance. Semin Cell Dev Biol 2022; 127:79-89. [PMID: 35042676 DOI: 10.1016/j.semcdb.2022.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/09/2022] [Accepted: 01/09/2022] [Indexed: 12/15/2022]
Abstract
The centromere is a unique functional region on each eukaryotic chromosome where the kinetochore assembles and orchestrates microtubule attachment and chromosome segregation. Unlike monocentromeres that occupy a specific region on the chromosome, holocentromeres are diffused along the length of the chromosome. Despite being less common, holocentromeres have been verified in almost 800 nematode, insect, and plant species. Understanding of the molecular and epigenetic regulation of holocentromeres is lagging that of monocentromeres. Here we review how permissive locations for holocentromeres are determined across the genome, potentially by chromatin organisation, transcription, and non-coding RNAs, specifically in the nematode C. elegans. In addition, we discuss how holocentric CENP-A or CENP-T-containing nucleosomes are recruited and deposited, through the help of histone chaperones, licensing factors, and condensin complexes, both during de novo holocentromere establishment, and in each mitotic cell cycle. The process of resolving sister centromeres after DNA replication in holocentric organisms is also mentioned. Conservation and diversity between holocentric and monocentric organisms are highlighted, and outstanding questions are proposed.
Collapse
Affiliation(s)
- Yue Wang
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong
| | - Lillian Wu
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong; Epigenetics and Genome Stability Team, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom
| | - Karen Wing Yee Yuen
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong.
| |
Collapse
|
14
|
Senaratne AP, Cortes-Silva N, Drinnenberg IA. Evolution of holocentric chromosomes: Drivers, diversity, and deterrents. Semin Cell Dev Biol 2022; 127:90-99. [PMID: 35031207 DOI: 10.1016/j.semcdb.2022.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/14/2021] [Accepted: 01/05/2022] [Indexed: 02/06/2023]
Abstract
Centromeres are specialized chromosomal regions that recruit kinetochore proteins and mediate spindle microtubule attachment to ensure faithful chromosome segregation during mitosis and meiosis. Centromeres can be restricted to one region of the chromosome. Named "monocentromere", this type represents the most commonly found centromere organization across eukaryotes. Alternatively, centromeres can also be assembled at sites chromosome-wide. This second type is called "holocentromere". Despite their early description over 100 years ago, research on holocentromeres has lagged behind that of monocentromeres. Nevertheless, the application of next generation sequencing approaches and advanced microscopic technologies enabled recent advances understanding the molecular organization and regulation of holocentromeres in different organisms. Here we review the current state of research on holocentromeres focusing on evolutionary considerations. First, we provide a brief historical perspective on the discovery of holocentric chromosomes. We then discuss models/drivers that have been proposed over the years to explain the evolutionary transition from mono- to holocentric chromosomes. We continue to review the description of holocentric chromosomes in diverse eukaryotic groups and then focus our discussion on a specific and recently characterized type of holocentromere organization in insects that functions independently of the otherwise essential centromeric marker protein CenH3, thus providing novel insights into holocentromere evolution in insects. Finally, we propose reasons to explain why the holocentric trait is not more frequent across eukaryotes despite putative selective advantages.
Collapse
Affiliation(s)
| | - Nuria Cortes-Silva
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Ines A Drinnenberg
- Institut Curie, PSL Research University, CNRS, UMR3664, F-75005 Paris, France; Sorbonne Université, Institut Curie, CNRS, UMR3664, F-75005 Paris, France.
| |
Collapse
|
15
|
Sridhar S, Fukagawa T. Kinetochore Architecture Employs Diverse Linker Strategies Across Evolution. Front Cell Dev Biol 2022; 10:862637. [PMID: 35800888 PMCID: PMC9252888 DOI: 10.3389/fcell.2022.862637] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/23/2022] [Indexed: 01/09/2023] Open
Abstract
The assembly of a functional kinetochore on centromeric chromatin is necessary to connect chromosomes to the mitotic spindle, ensuring accurate chromosome segregation. This connecting function of the kinetochore presents multiple internal and external structural challenges. A microtubule interacting outer kinetochore and centromeric chromatin interacting inner kinetochore effectively confront forces from the external spindle and centromere, respectively. While internally, special inner kinetochore proteins, defined as “linkers,” simultaneously interact with centromeric chromatin and the outer kinetochore to enable association with the mitotic spindle. With the ability to simultaneously interact with outer kinetochore components and centromeric chromatin, linker proteins such as centromere protein (CENP)-C or CENP-T in vertebrates and, additionally CENP-QOkp1-UAme1 in yeasts, also perform the function of force propagation within the kinetochore. Recent efforts have revealed an array of linker pathways strategies to effectively recruit the largely conserved outer kinetochore. In this review, we examine these linkages used to propagate force and recruit the outer kinetochore across evolution. Further, we look at their known regulatory pathways and implications on kinetochore structural diversity and plasticity.
Collapse
|
16
|
Yatskevich S, Muir KW, Bellini D, Zhang Z, Yang J, Tischer T, Predin M, Dendooven T, McLaughlin SH, Barford D. Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome. Science 2022; 376:844-852. [PMID: 35420891 PMCID: PMC7612757 DOI: 10.1126/science.abn3810] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Kinetochores assemble onto specialized centromeric CENP-A (centromere protein A) nucleosomes (CENP-ANuc) to mediate attachments between chromosomes and the mitotic spindle. We describe cryo-electron microscopy structures of the human inner kinetochore constitutive centromere associated network (CCAN) complex bound to CENP-ANuc reconstituted onto α-satellite DNA. CCAN forms edge-on contacts with CENP-ANuc, and a linker DNA segment of the α-satellite repeat emerges from the fully wrapped end of the nucleosome to thread through the central CENP-LN channel that tightly grips the DNA. The CENP-TWSX histone-fold module further augments DNA binding and partially wraps the linker DNA in a manner reminiscent of canonical nucleosomes. Our study suggests that the topological entrapment of the linker DNA by CCAN provides a robust mechanism by which kinetochores withstand both pushing and pulling forces exerted by the mitotic spindle.
Collapse
Affiliation(s)
- Stanislau Yatskevich
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Kyle W. Muir
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Dom Bellini
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Ziguo Zhang
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jing Yang
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Thomas Tischer
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Masa Predin
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Tom Dendooven
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | | | - David Barford
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| |
Collapse
|
17
|
Hattersley N, Schlientz AJ, Prevo B, Oegema K, Desai A. MEL-28/ELYS and CENP-C coordinately control outer kinetochore assembly and meiotic chromosome-microtubule interactions. Curr Biol 2022; 32:2563-2571.e4. [PMID: 35609608 DOI: 10.1016/j.cub.2022.04.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/23/2022] [Accepted: 04/14/2022] [Indexed: 10/18/2022]
Abstract
During mitosis and meiosis in the majority of eukaryotes, centromeric chromatin comprised of CENP-A nucleosomes and their reader CENP-C recruits components of the outer kinetochore to build an interface with spindle microtubules.1,2 One exception is C. elegans oocyte meiosis, where outer kinetochore proteins form cup-like structures on chromosomes independently of centromeric chromatin.3 Here, we show that the nucleoporin MEL-28 (ortholog of human ELYS) and CENP-CHCP-4 act in parallel to recruit outer kinetochore components to oocyte meiotic chromosomes. Unexpectedly, co-inhibition of MEL-28 and CENP-CHCP-4 resulted in chromosomes being expelled from the meiotic spindle prior to anaphase onset, a more severe phenotype than what was observed following ablation of the outer kinetochore.4,5 This observation suggested that MEL-28 and the outer kinetochore independently link chromosomes to spindle microtubules. Consistent with this, the chromosome expulsion defect was observed following co-inhibition of MEL-28 and the microtubule-coupling KNL-1/MIS-12/NDC-80 (KMN) network of the outer kinetochore. Use of engineered mutants showed that MEL-28 acts in conjunction with the microtubule-binding NDC-80 complex to keep chromosomes within the oocyte meiotic spindle and that this function likely involves the Y-complex of nucleoporins that associate with MEL-28; by contrast, the ability to dock protein phosphatase 1, shared by MEL-28 and KNL-1, is not involved. These results highlight nuclear pore-independent functions for a conserved nucleoporin and explain two unusual features of oocyte meiotic chromosome segregation in C. elegans: centromeric chromatin-independent outer kinetochore assembly, and dispensability of the outer kinetochore for constraining chromosomes in the acentrosomal meiotic spindle.
Collapse
Affiliation(s)
- Neil Hattersley
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA 92093, USA
| | - Aleesa J Schlientz
- Division of Biological Sciences & Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Bram Prevo
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA 92093, USA
| | - Karen Oegema
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA 92093, USA; Division of Biological Sciences & Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Arshad Desai
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA 92093, USA; Division of Biological Sciences & Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
18
|
Abstract
Centromeres, the chromosomal loci where spindle fibers attach during cell division to segregate chromosomes, are typically found within satellite arrays in plants and animals. Satellite arrays have been difficult to analyze because they comprise megabases of tandem head-to-tail highly repeated DNA sequences. Much evidence suggests that centromeres are epigenetically defined by the location of nucleosomes containing the centromere-specific histone H3 variant cenH3, independently of the DNA sequences where they are located; however, the reason that cenH3 nucleosomes are generally found on rapidly evolving satellite arrays has remained unclear. Recently, long-read sequencing technology has clarified the structures of satellite arrays and sparked rethinking of how they evolve, and new experiments and analyses have helped bring both understanding and further speculation about the role these highly repeated sequences play in centromere identification.
Collapse
Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| |
Collapse
|
19
|
Takenoshita Y, Hara M, Fukagawa T. Recruitment of two Ndc80 complexes via the CENP-T pathway is sufficient for kinetochore functions. Nat Commun 2022; 13:851. [PMID: 35165266 PMCID: PMC8844409 DOI: 10.1038/s41467-022-28403-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/18/2022] [Indexed: 12/27/2022] Open
Abstract
To form functional kinetochores, CENP-C and CENP-T independently recruit the KMN (Knl1C, Mis12C, and Ndc80C) network onto the kinetochores. To clarify the functions of the KMN network on CENP-T, we evaluated its roles in chicken DT40 cell lines lacking the CENP-C-KMN network interaction. By analyzing mutants lacking both CENP-T-Mis12C and CENP-C-Mis12C interactions, we demonstrated that Knl1C and Mis12C (KM) play critical roles in the cohesion of sister chromatids or the recruitment of spindle checkpoint proteins onto kinetochores. Two copies of Ndc80C (N-N) exist on CENP-T via Mis12C or direct binding. Analyses of cells specifically lacking the Mis12C-Ndc80C interaction revealed that N-N is needed for proper kinetochore-microtubule interactions. However, using artificial engineering to directly bind the two copies of Ndc80C to CENP-T, we demonstrated that N-N functions without direct Mis12C binding to Ndc80C in native kinetochores. This study demonstrated the mechanisms by which complicated networks play roles in native kinetochores. The kinetochores contain multiple protein interaction networks. Takenoshita et al. analyzed the complicated networks using the genetic method and revealed that two copies of Ndc80 complexes on CENP-T are sufficient for kinetochore functions.
Collapse
|
20
|
Ishii M, Akiyoshi B. Plasticity in centromere organization and kinetochore composition: Lessons from diversity. Curr Opin Cell Biol 2022; 74:47-54. [PMID: 35108654 PMCID: PMC9089191 DOI: 10.1016/j.ceb.2021.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022]
Abstract
Kinetochores are the macromolecular protein complexes that govern chromosome movement by binding spindle microtubules during mitosis and meiosis. Centromeres are the specific chromosomal regions that serve as the platform on which kinetochores assemble. Despite their essentiality for proper chromosome segregation, the size and organization of centromeres vary dramatically between species, while different compositions of kinetochores are found among eukaryotes. Here we discuss recent progress in understanding centromeres and kinetochores in non-traditional model eukaryotes. We specifically focus on select lineages (holocentric insects, early diverging fungi, and kinetoplastids) that lack CENP-A, a centromere-specific histone H3 variant that is critical for kinetochore specification and assembly in many eukaryotes. We also highlight some organisms that might have hitherto unknown types of kinetochore proteins.
Collapse
Affiliation(s)
- Midori Ishii
- Department of Biochemistry, University of Oxford, UK
| | | |
Collapse
|
21
|
Nhim S, Gimenez S, Nait-Saidi R, Severac D, Nam K, d'Alençon E, Nègre N. H3K9me2 genome-wide distribution in the holocentric insect Spodoptera frugiperda (Lepidoptera: Noctuidae). Genomics 2021; 114:384-397. [PMID: 34971718 DOI: 10.1016/j.ygeno.2021.12.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/02/2021] [Accepted: 12/15/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND Eukaryotic genomes are packaged by Histone proteins in a structure called chromatin. There are different chromatin types. Euchromatin is typically associated with decondensed, transcriptionally active regions and heterochromatin to more condensed regions of the chromosomes. Methylation of Lysine 9 of Histone H3 (H3K9me) is a conserved biochemical marker of heterochromatin. In many organisms, heterochromatin is usually localized at telomeric as well as pericentromeric regions but can also be found at interstitial chromosomal loci. This distribution may vary in different species depending on their general chromosomal organization. Holocentric species such as Spodoptera frugiperda (Lepidoptera: Noctuidae) possess dispersed centromeres instead of a monocentric one and thus no observable pericentromeric compartment. To identify the localization of heterochromatin in such species we performed ChIP-Seq experiments and analyzed the distribution of the heterochromatin marker H3K9me2 in the Sf9 cell line and whole 4th instar larvae (L4) in relation to RNA-Seq data. RESULTS In both samples we measured an enrichment of H3K9me2 at the (sub) telomeres, rDNA loci, and satellite DNA sequences, which could represent dispersed centromeric regions. We also observed that density of H3K9me2 is positively correlated with transposable elements and protein-coding genes. But contrary to most model organisms, H3K9me2 density is not correlated with transcriptional repression. CONCLUSION This is the first genome-wide ChIP-Seq analysis conducted in S. frugiperda for H3K9me2. Compared to model organisms, this mark is found in expected chromosomal compartments such as rDNA and telomeres. However, it is also localized at numerous dispersed regions, instead of the well described large pericentromeric domains, indicating that H3K9me2 might not represent a classical heterochromatin marker in Lepidoptera. (242 words).
Collapse
Affiliation(s)
- Sandra Nhim
- DGIMI, Univ Montpellier, INRAE, Montpellier, France
| | | | | | - Dany Severac
- MGX, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Kiwoong Nam
- DGIMI, Univ Montpellier, INRAE, Montpellier, France
| | | | - Nicolas Nègre
- DGIMI, Univ Montpellier, INRAE, Montpellier, France.
| |
Collapse
|
22
|
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.
Collapse
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.
| |
Collapse
|
23
|
Harrison PM. fLPS 2.0: rapid annotation of compositionally-biased regions in biological sequences. PeerJ 2021; 9:e12363. [PMID: 34760378 PMCID: PMC8557692 DOI: 10.7717/peerj.12363] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/30/2021] [Indexed: 12/12/2022] Open
Abstract
Compositionally-biased (CB) regions in biological sequences are enriched for a subset of sequence residue types. These can be shorter regions with a concentrated bias (i.e., those termed ‘low-complexity’), or longer regions that have a compositional skew. These regions comprise a prominent class of the uncharacterized ‘dark matter’ of the protein universe. Here, I report the latest version of the fLPS package for the annotation of CB regions, which includes added consideration of DNA sequences, to label the eight possible biased regions of DNA. In this version, the user is now able to restrict analysis to a specified subset of residue types, and also to filter for previously annotated domains to enable detection of discontinuous CB regions. A ‘thorough’ option has been added which enables the labelling of subtler biases, typically made from a skew for several residue types. In the output, protein CB regions are now labelled with bias classes reflecting the physico-chemical character of the biasing residues. The fLPS 2.0 package is available from: https://github.com/pmharrison/flps2 or in a Supplemental File of this paper.
Collapse
Affiliation(s)
- Paul M Harrison
- Department of Biology, McGill University, Montreal, QC, Canada
| |
Collapse
|
24
|
Kumon T, Ma J, Akins RB, Stefanik D, Nordgren CE, Kim J, Levine MT, Lampson MA. Parallel pathways for recruiting effector proteins determine centromere drive and suppression. Cell 2021; 184:4904-4918.e11. [PMID: 34433012 PMCID: PMC8448984 DOI: 10.1016/j.cell.2021.07.037] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 06/07/2021] [Accepted: 07/29/2021] [Indexed: 12/19/2022]
Abstract
Selfish centromere DNA sequences bias their transmission to the egg in female meiosis. Evolutionary theory suggests that centromere proteins evolve to suppress costs of this "centromere drive." In hybrid mouse models with genetically different maternal and paternal centromeres, selfish centromere DNA exploits a kinetochore pathway to recruit microtubule-destabilizing proteins that act as drive effectors. We show that such functional differences are suppressed by a parallel pathway for effector recruitment by heterochromatin, which is similar between centromeres in this system. Disrupting the kinetochore pathway with a divergent allele of CENP-C reduces functional differences between centromeres, whereas disrupting heterochromatin by CENP-B deletion amplifies the differences. Molecular evolution analyses using Murinae genomes identify adaptive evolution in proteins in both pathways. We propose that centromere proteins have recurrently evolved to minimize the kinetochore pathway, which is exploited by selfish DNA, relative to the heterochromatin pathway that equalizes centromeres, while maintaining essential functions.
Collapse
Affiliation(s)
- Tomohiro Kumon
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jun Ma
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - R Brian Akins
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Derek Stefanik
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - C Erik Nordgren
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Junhyong Kim
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mia T Levine
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael A Lampson
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
25
|
Vanpoperinghe L, Carlier-Grynkorn F, Cornilleau G, Kusakabe T, Drinnenberg IA, Tran PT. Live-cell imaging reveals square shape spindles and long mitosis duration in the silkworm holocentric cells. MICROPUBLICATION BIOLOGY 2021; 2021. [PMID: 34514356 PMCID: PMC8411215 DOI: 10.17912/micropub.biology.000441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Accepted: 08/21/2021] [Indexed: 01/17/2023]
Abstract
Proper chromosome segregation during mitosis requires both the assembly of a microtubule (MT)-based spindle and the assembly of DNA-centromere-based kinetochore structure. Kinetochore-to-MT attachment enables chromosome separation. Monocentric cells, such as found in human, have one unique kinetochore per chromosome. Holocentric cells, such as found in the silkworm, in contrast, have multiple kinetochore structures per chromosome. Interestingly, some human cancer chromosomes contain more than one kinetochore, a condition called di- and tricentric. Thus, comparing how wild-type mono- and holocentric cells perform mitosis may provide novel insights into cancer di- and tricentric cell mitosis. We present here live-cell imaging of human RPE1 and silkworm BmN4 cells, revealing striking differences in spindle architecture and dynamics, and highlighting differential kinesin function between mono- and holocentric cells.
Collapse
Affiliation(s)
- Lucien Vanpoperinghe
- Institut Curie, PSL Université, Sorbonne Université, CNRS, Paris, France.,Médicine Sorbonne Université, École Normale Supérieure, Paris, France
| | | | - Gaetan Cornilleau
- Institut Curie, PSL Université, Sorbonne Université, CNRS, Paris, France
| | - Takahiro Kusakabe
- Kyushu University, Department of Bioresource Sciences, Laboratory of Insect Genome Science, Fukuoka, Japan
| | - Ines A Drinnenberg
- Institut Curie, PSL Université, Sorbonne Université, CNRS, Paris, France
| | - Phong T Tran
- Institut Curie, PSL Université, Sorbonne Université, CNRS, Paris, France.,University of Pennsylvania, Department of Cell and Developmental Biology, Philadephia, PA, United States
| |
Collapse
|
26
|
Rosin LF, Gil J, Drinnenberg IA, Lei EP. Oligopaint DNA FISH reveals telomere-based meiotic pairing dynamics in the silkworm, Bombyx mori. PLoS Genet 2021; 17:e1009700. [PMID: 34319984 PMCID: PMC8351950 DOI: 10.1371/journal.pgen.1009700] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/09/2021] [Accepted: 07/07/2021] [Indexed: 12/04/2022] Open
Abstract
Accurate chromosome segregation during meiosis is essential for reproductive success. Yet, many fundamental aspects of meiosis remain unclear, including the mechanisms regulating homolog pairing across species. This gap is partially due to our inability to visualize individual chromosomes during meiosis. Here, we employ Oligopaint FISH to investigate homolog pairing and compaction of meiotic chromosomes and resurrect a classical model system, the silkworm Bombyx mori. Our Oligopaint design combines multiplexed barcoding with secondary oligo labeling for high flexibility and low cost. These studies illustrate that Oligopaints are highly specific in whole-mount gonads and on meiotic squashes. We show that meiotic pairing is robust in both males and females and that pairing can occur through numerous partially paired intermediate structures. We also show that pairing in male meiosis occurs asynchronously and seemingly in a transcription-biased manner. Further, we reveal that meiotic bivalent formation in B. mori males is highly similar to bivalent formation in C. elegans, with both of these pathways ultimately resulting in the pairing of chromosome ends with non-paired ends facing the spindle pole. Additionally, microtubule recruitment in both C. elegans and B. mori is likely dependent on kinetochore proteins but independent of the centromere-specifying histone CENP-A. Finally, using super-resolution microscopy in the female germline, we show that homologous chromosomes remain associated at telomere domains in the absence of chiasma and after breakdown and modification to the synaptonemal complex in pachytene. These studies reveal novel insights into mechanisms of meiotic homolog pairing both with or without recombination.
Collapse
Affiliation(s)
- Leah F. Rosin
- Nuclear Organization and Gene Expression Section; Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jose Gil
- Institut Curie, PSL Research University, CNRS, Paris, France; Sorbonne Université, Institut Curie, CNRS, Paris, France
| | - Ines A. Drinnenberg
- Institut Curie, PSL Research University, CNRS, Paris, France; Sorbonne Université, Institut Curie, CNRS, Paris, France
| | - Elissa P. Lei
- Nuclear Organization and Gene Expression Section; Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| |
Collapse
|
27
|
Navarro AP, Cheeseman IM. Kinetochore assembly throughout the cell cycle. Semin Cell Dev Biol 2021; 117:62-74. [PMID: 33753005 DOI: 10.1016/j.semcdb.2021.03.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 11/29/2022]
Abstract
The kinetochore plays an essential role in facilitating chromosome segregation during cell division. This massive protein complex assembles onto the centromere of chromosomes and enables their attachment to spindle microtubules during mitosis. The kinetochore also functions as a signaling hub to regulate cell cycle progression, and is crucial to ensuring the fidelity of chromosome segregation. Despite the fact that kinetochores are large and robust molecular assemblies, they are also highly dynamic structures that undergo structural and organizational changes throughout the cell cycle. This review will highlight our current understanding of kinetochore structure and function, focusing on the dynamic processes that underlie kinetochore assembly.
Collapse
Affiliation(s)
- Alexandra P Navarro
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| |
Collapse
|
28
|
Krátká M, Šmerda J, Lojdová K, Bureš P, Zedek F. Holocentric Chromosomes Probably Do Not Prevent Centromere Drive in Cyperaceae. FRONTIERS IN PLANT SCIENCE 2021; 12:642661. [PMID: 33679859 PMCID: PMC7933567 DOI: 10.3389/fpls.2021.642661] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/29/2021] [Indexed: 05/05/2023]
Abstract
Centromere drive model describes an evolutionary process initiated by centromeric repeats expansion, which leads to the recruitment of excess kinetochore proteins and consequent preferential segregation of an expanded centromere to the egg during female asymmetric meiosis. In response to these selfish centromeres, the histone protein CenH3, which recruits kinetochore components, adaptively evolves to restore chromosomal parity and counter the detrimental effects of centromere drive. Holocentric chromosomes, whose kinetochores are assembled along entire chromosomes, have been hypothesized to prevent expanded centromeres from acquiring a selective advantage and initiating centromere drive. In such a case, CenH3 would be subjected to less frequent or no adaptive evolution. Using codon substitution models, we analyzed 36 CenH3 sequences from 35 species of the holocentric family Cyperaceae. We found 10 positively selected codons in the CenH3 gene [six codons in the N-terminus and four in the histone fold domain (HFD)] and six branches of its phylogeny along which the positive selection occurred. One of the positively selected codons was found in the centromere targeting domain (CATD) that directly interacts with DNA and its mutations may be important in centromere drive suppression. The frequency of these positive selection events was comparable to the frequency of positive selection in monocentric clades with asymmetric female meiosis. Taken together, these results suggest that preventing centromere drive is not the primary adaptive role of holocentric chromosomes, and their ability to suppress it likely depends on their kinetochore structure in meiosis.
Collapse
Affiliation(s)
| | | | | | | | - František Zedek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| |
Collapse
|
29
|
Gassmann R. Cell Division: Chromatin Dynamics Shape Insect Holocentromeres. Curr Biol 2021; 31:R34-R37. [PMID: 33434487 DOI: 10.1016/j.cub.2020.10.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Centromeres, the chromosomal loci that ensure chromosome segregation by directing kinetochore assembly, are typically marked by the histone CENP-A. A study in CENP-A-deficient insects finds that virtually any chromosomal region with low nucleosome turnover can assemble kinetochores, highlighting the extraordinary plasticity of holocentromeres.
Collapse
Affiliation(s)
- Reto Gassmann
- Instituto de Investigação e Inovação em Saúde - i3S, Universidade do Porto, 4200-135 Porto, Portugal.
| |
Collapse
|
30
|
Karimi-Ashtiyani R. Centromere Engineering as an Emerging Tool for Haploid Plant Production: Advances and Challenges. Methods Mol Biol 2021; 2289:3-22. [PMID: 34270060 DOI: 10.1007/978-1-0716-1331-3_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Haploid production is of great importance in plant breeding programs. Doubled haploid technology accelerates the generation of inbred lines with homozygosity in all loci in a single year. Haploids can be induced in vitro via cultivating the haploid gametes or in vivo through inter- and intraspecific hybridization. Haploid induction through centromere engineering is a novel system that is theoretically applicable to many plant species. The present review chapter discusses the proposed molecular mechanisms of selective chromosome elimination in early embryogenesis and the effects of kinetochore component modifications on proper chromosome segregation. Finally, the advantages and limitations of the CENH3-mediated haploidization approach and its applications are highlighted.
Collapse
|
31
|
Abstract
The kinetochore is a complex structure whose function is absolutely essential. Unlike the centromere, the kinetochore at first appeared remarkably well conserved from yeast to humans, especially the microtubule-binding outer kinetochore. However, recent efforts towards biochemical reconstitution of diverse kinetochores challenge the notion of a similarly conserved architecture for the constitutively centromere-associated network of the inner kinetochore. This review briefly summarizes the evidence from comparative genomics for interspecific variability in inner kinetochore composition and focuses on novel biochemical evidence indicating that even homologous inner kinetochore protein complexes are put to different uses in different organisms.
Collapse
Affiliation(s)
- G E Hamilton
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - T N Davis
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| |
Collapse
|
32
|
Gržan T, Despot-Slade E, Meštrović N, Plohl M, Mravinac B. CenH3 distribution reveals extended centromeres in the model beetle Tribolium castaneum. PLoS Genet 2020; 16:e1009115. [PMID: 33125365 PMCID: PMC7598501 DOI: 10.1371/journal.pgen.1009115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/14/2020] [Indexed: 11/18/2022] Open
Abstract
Centromeres are chromosomal domains essential for kinetochore assembly and correct chromosome segregation. Inconsistent in their underlying DNA sequences, centromeres are defined epigenetically by the presence of the centromere-specific histone H3 variant CenH3. Most of the analyzed eukaryotes have monocentric chromosomes in which CenH3 proteins deposit into a single, primary constriction visible at metaphase chromosomes. Contrary to monocentrics, evolutionary sporadic holocentric chromosomes lack a primary constriction and have kinetochore activity distributed along the entire chromosome length. In this work, we identified cCENH3 protein, the centromeric H3 histone of the coleopteran model beetle Tribolium castaneum. By ChIP-seq analysis we disclosed that cCENH3 chromatin assembles upon a repertoire of repetitive DNAs. cCENH3 in situ mapping revealed unusually elongated T. castaneum centromeres that comprise approximately 40% of the chromosome length. Being the longest insect regional centromeres evidenced so far, T. castaneum centromeres are characterized by metapolycentric structure composed of several individual cCENH3-containing domains. We suggest that the model beetle T. castaneum with its metapolycentromeres could represent an excellent model for further studies of non-canonical centromeres in insects.
Collapse
Affiliation(s)
- Tena Gržan
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | | | - Nevenka Meštrović
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Miroslav Plohl
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- * E-mail: (MP); (BM)
| | - Brankica Mravinac
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- * E-mail: (MP); (BM)
| |
Collapse
|
33
|
Senaratne AP, Muller H, Fryer KA, Kawamoto M, Katsuma S, Drinnenberg IA. Formation of the CenH3-Deficient Holocentromere in Lepidoptera Avoids Active Chromatin. Curr Biol 2020; 31:173-181.e7. [PMID: 33125865 DOI: 10.1016/j.cub.2020.09.078] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 12/23/2022]
Abstract
Despite the essentiality for faithful chromosome segregation, centromere architectures are diverse among eukaryotes1,2 and embody two main configurations: mono- and holocentromeres, referring, respectively, to localized or unrestricted distribution of centromeric activity. Of the two, some holocentromeres offer the curious condition of having arisen independently in multiple insects, most of which have lost the otherwise essential centromere-specifying factor CenH33 (first described as CENP-A in humans).4-7 The loss of CenH3 raises intuitive questions about how holocentromeres are organized and regulated in CenH3-lacking insects. Here, we report the first chromatin-level description of CenH3-deficient holocentromeres by leveraging recently identified centromere components6,7 and genomics approaches to map and characterize the holocentromeres of the silk moth Bombyx mori, a representative lepidopteran insect lacking CenH3. This uncovered a robust correlation between the distribution of centromere sites and regions of low chromatin activity along B. mori chromosomes. Transcriptional perturbation experiments recapitulated the exclusion of B. mori centromeres from active chromatin. Based on reciprocal centromere occupancy patterns observed along differentially expressed orthologous genes of Lepidoptera, we further found that holocentromere formation in a manner that is recessive to chromatin dynamics is evolutionarily conserved. Our results help us discuss the plasticity of centromeres in the context of a role for the chromosome-wide chromatin landscape in conferring centromere identity rather than the presence of CenH3. Given the co-occurrence of CenH3 loss and holocentricity in insects,7 we further propose that the evolutionary establishment of holocentromeres in insects was facilitated through the loss of a CenH3-specified centromere.
Collapse
Affiliation(s)
- Aruni P Senaratne
- Institut Curie, PSL Research University, CNRS, UMR3664, 75005 Paris, France; Sorbonne Université, Institut Curie, CNRS, UMR3664, 75005 Paris, France
| | - Héloïse Muller
- Institut Curie, PSL Research University, CNRS, UMR3664, 75005 Paris, France; Sorbonne Université, Institut Curie, CNRS, UMR3664, 75005 Paris, France
| | - Kelsey A Fryer
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA 94305-5307, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA
| | - Munetaka Kawamoto
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Susumu Katsuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ines A Drinnenberg
- Institut Curie, PSL Research University, CNRS, UMR3664, 75005 Paris, France; Sorbonne Université, Institut Curie, CNRS, UMR3664, 75005 Paris, France.
| |
Collapse
|
34
|
Hinshaw SM, Harrison SC. The Structural Basis for Kinetochore Stabilization by Cnn1/CENP-T. Curr Biol 2020; 30:3425-3431.e3. [DOI: 10.1016/j.cub.2020.06.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 12/22/2022]
|
35
|
Duan J, Li Y, Du J, Duan E, Lei Y, Liang S, Zhang X, Zhao X, Kan Y, Yao L, Yang X, Zhang X, Wu X. A chromosome‐scale genome assembly of
Antheraea pernyi
(Saturniidae, Lepidoptera). Mol Ecol Resour 2020; 20:1372-1383. [DOI: 10.1111/1755-0998.13199] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Jianping Duan
- Henan Key Laboratory of Funiu Mountain Insect Biology, Henan Engineering Lab of Insects Bio‐reactor College of Agricultural Engineering, Nanyang Normal University Nanyang China
| | - Ying Li
- Henan Key Laboratory of Funiu Mountain Insect Biology, Henan Engineering Lab of Insects Bio‐reactor College of Agricultural Engineering, Nanyang Normal University Nanyang China
| | - Jie Du
- Henan Key Laboratory of Funiu Mountain Insect Biology, Henan Engineering Lab of Insects Bio‐reactor College of Agricultural Engineering, Nanyang Normal University Nanyang China
| | - Erzhen Duan
- College of Biological Engineering Henan University of Technology Zhengzhou China
| | - Yuyu Lei
- Henan Key Laboratory of Funiu Mountain Insect Biology, Henan Engineering Lab of Insects Bio‐reactor College of Agricultural Engineering, Nanyang Normal University Nanyang China
| | - Shimei Liang
- Henan Key Laboratory of Funiu Mountain Insect Biology, Henan Engineering Lab of Insects Bio‐reactor College of Agricultural Engineering, Nanyang Normal University Nanyang China
| | - Xian Zhang
- Henan Key Laboratory of Funiu Mountain Insect Biology, Henan Engineering Lab of Insects Bio‐reactor College of Agricultural Engineering, Nanyang Normal University Nanyang China
| | - Xin Zhao
- Henan Key Laboratory of Funiu Mountain Insect Biology, Henan Engineering Lab of Insects Bio‐reactor College of Agricultural Engineering, Nanyang Normal University Nanyang China
| | - Yunchao Kan
- Henan Key Laboratory of Funiu Mountain Insect Biology, Henan Engineering Lab of Insects Bio‐reactor College of Agricultural Engineering, Nanyang Normal University Nanyang China
| | - Lunguang Yao
- Henan Key Laboratory of Funiu Mountain Insect Biology, Henan Engineering Lab of Insects Bio‐reactor College of Agricultural Engineering, Nanyang Normal University Nanyang China
| | - Xinfeng Yang
- Henan Institute of Sericulture Science Zhengzhou China
| | - Xingtan Zhang
- Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry University Fuzhou China
| | | |
Collapse
|
36
|
Balzano E, Giunta S. Centromeres under Pressure: Evolutionary Innovation in Conflict with Conserved Function. Genes (Basel) 2020; 11:E912. [PMID: 32784998 PMCID: PMC7463522 DOI: 10.3390/genes11080912] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 12/22/2022] Open
Abstract
Centromeres are essential genetic elements that enable spindle microtubule attachment for chromosome segregation during mitosis and meiosis. While this function is preserved across species, centromeres display an array of dynamic features, including: (1) rapidly evolving DNA; (2) wide evolutionary diversity in size, shape and organization; (3) evidence of mutational processes to generate homogenized repetitive arrays that characterize centromeres in several species; (4) tolerance to changes in position, as in the case of neocentromeres; and (5) intrinsic fragility derived by sequence composition and secondary DNA structures. Centromere drive underlies rapid centromere DNA evolution due to the "selfish" pursuit to bias meiotic transmission and promote the propagation of stronger centromeres. Yet, the origins of other dynamic features of centromeres remain unclear. Here, we review our current understanding of centromere evolution and plasticity. We also detail the mutagenic processes proposed to shape the divergent genetic nature of centromeres. Changes to centromeres are not simply evolutionary relics, but ongoing shifts that on one side promote centromere flexibility, but on the other can undermine centromere integrity and function with potential pathological implications such as genome instability.
Collapse
Affiliation(s)
- Elisa Balzano
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, 00185 Roma, Italy;
| | - Simona Giunta
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| |
Collapse
|
37
|
Hamilton GE, Helgeson LA, Noland CL, Asbury CL, Dimitrova YN, Davis TN. Reconstitution reveals two paths of force transmission through the kinetochore. eLife 2020; 9:56582. [PMID: 32406818 PMCID: PMC7367685 DOI: 10.7554/elife.56582] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/13/2020] [Indexed: 01/23/2023] Open
Abstract
Partitioning duplicated chromosomes equally between daughter cells is a microtubule-mediated process essential to eukaryotic life. A multi-protein machine, the kinetochore, drives chromosome segregation by coupling the chromosomes to dynamic microtubule tips, even as the tips grow and shrink through the gain and loss of subunits. The kinetochore must harness, transmit, and sense mitotic forces, as a lack of tension signals incorrect chromosome-microtubule attachment and precipitates error correction mechanisms. But though the field has arrived at a ‘parts list’ of dozens of kinetochore proteins organized into subcomplexes, the path of force transmission through these components has remained unclear. Here we report reconstitution of functional Saccharomyces cerevisiae kinetochore assemblies from recombinantly expressed proteins. The reconstituted kinetochores are capable of self-assembling in vitro, coupling centromeric nucleosomes to dynamic microtubules, and withstanding mitotically relevant forces. They reveal two distinct pathways of force transmission and Ndc80c recruitment.
Collapse
Affiliation(s)
- Grace E Hamilton
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Luke A Helgeson
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Cameron L Noland
- Department of Structural Biology, Genentech Inc, South San Francisco, United States
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Yoana N Dimitrova
- Department of Structural Biology, Genentech Inc, South San Francisco, United States
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, United States
| |
Collapse
|
38
|
Navarro AP, Cheeseman IM. Chromosome Segregation: Evolving a Plastic Chromosome-Microtubule Interface. Curr Biol 2020; 30:R174-R177. [PMID: 32097646 DOI: 10.1016/j.cub.2019.12.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Despite a conserved requirement in mediating chromosome segregation, kinetochores display remarkable plasticity in their structure and composition. New work in holocentric insect species highlights the molecular rewiring that occurs when key structural components of the kinetochore are lost and centromere structure is changed.
Collapse
Affiliation(s)
- Alexandra P Navarro
- Whitehead Institute for Biomedical Research, and Department of Biology, Massachusetts Institute of Technology, 455 Main Street, Cambridge, MA 02142, USA
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, and Department of Biology, Massachusetts Institute of Technology, 455 Main Street, Cambridge, MA 02142, USA.
| |
Collapse
|