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Bui M, Baek S, Bentahar RS, Melters DP, Dalal Y. Native and tagged CENP-A histones are functionally inequivalent. Epigenetics Chromatin 2024; 17:19. [PMID: 38825690 PMCID: PMC11145777 DOI: 10.1186/s13072-024-00543-9] [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: 02/07/2024] [Accepted: 05/22/2024] [Indexed: 06/04/2024] Open
Abstract
BACKGROUND Over the past several decades, the use of biochemical and fluorescent tags has elucidated mechanistic and cytological processes that would otherwise be impossible. The challenging nature of certain nuclear proteins includes low abundancy, poor antibody recognition, and transient dynamics. One approach to get around those issues is the addition of a peptide or larger protein tag to the target protein to improve enrichment, purification, and visualization. However, many of these studies were done under the assumption that tagged proteins can fully recapitulate native protein function. RESULTS We report that when C-terminally TAP-tagged CENP-A histone variant is introduced, it undergoes altered kinetochore protein binding, differs in post-translational modifications (PTMs), utilizes histone chaperones that differ from that of native CENP-A, and can partially displace native CENP-A in human cells. Additionally, these tagged CENP-A-containing nucleosomes have reduced centromeric incorporation at early G1 phase and poorly associates with linker histone H1.5 compared to native CENP-A nucleosomes. CONCLUSIONS These data suggest expressing tagged versions of histone variant CENP-A may result in unexpected utilization of non-native pathways, thereby altering the biological function of the histone variant.
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Affiliation(s)
- Minh Bui
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, 41 Medlars Drive, Bldg 41/Rm B1300, Bethesda, MD, 20892, USA.
| | - Songjoon Baek
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, 41 Medlars Drive, Bldg 41/Rm B1300, Bethesda, MD, 20892, USA
| | - Reda S Bentahar
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, 41 Medlars Drive, Bldg 41/Rm B1300, Bethesda, MD, 20892, USA
| | - Daniël P Melters
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, 41 Medlars Drive, Bldg 41/Rm B1300, Bethesda, MD, 20892, USA
| | - Yamini Dalal
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, 41 Medlars Drive, Bldg 41/Rm B1300, Bethesda, MD, 20892, USA.
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2
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Naish M, Henderson IR. The structure, function, and evolution of plant centromeres. Genome Res 2024; 34:161-178. [PMID: 38485193 PMCID: PMC10984392 DOI: 10.1101/gr.278409.123] [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] [Indexed: 03/22/2024]
Abstract
Centromeres are essential regions of eukaryotic chromosomes responsible for the formation of kinetochore complexes, which connect to spindle microtubules during cell division. Notably, although centromeres maintain a conserved function in chromosome segregation, the underlying DNA sequences are diverse both within and between species and are predominantly repetitive in nature. The repeat content of centromeres includes high-copy tandem repeats (satellites), and/or specific families of transposons. The functional region of the centromere is defined by loading of a specific histone 3 variant (CENH3), which nucleates the kinetochore and shows dynamic regulation. In many plants, the centromeres are composed of satellite repeat arrays that are densely DNA methylated and invaded by centrophilic retrotransposons. In some cases, the retrotransposons become the sites of CENH3 loading. We review the structure of plant centromeres, including monocentric, holocentric, and metapolycentric architectures, which vary in the number and distribution of kinetochore attachment sites along chromosomes. We discuss how variation in CENH3 loading can drive genome elimination during early cell divisions of plant embryogenesis. We review how epigenetic state may influence centromere identity and discuss evolutionary models that seek to explain the paradoxically rapid change of centromere sequences observed across species, including the potential roles of recombination. We outline putative modes of selection that could act within the centromeres, as well as the role of repeats in driving cycles of centromere evolution. Although our primary focus is on plant genomes, we draw comparisons with animal and fungal centromeres to derive a eukaryote-wide perspective of centromere structure and function.
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Affiliation(s)
- Matthew Naish
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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3
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Wang ML, Lin XJ, Mo BX, Kong WW. Plant Artificial Chromosomes: Construction and Transformation. ACS Synth Biol 2024; 13:15-24. [PMID: 38163256 DOI: 10.1021/acssynbio.3c00555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
With the decline of cultivated land and increase of the population in recent years, an agricultural revolution is urgently needed to produce more food to improve the living standards of humans. As one of the foundations of synthetic biology, artificial chromosomes hold great potential for advancing crop improvement. They offer opportunities to increase crop yield and quality, while enhancing crop resistance to disease. The progress made in plant artificial chromosome technology enables selective modification of existing chromosomes or the synthesis of new ones to improve crops and study gene function. However, current artificial chromosome technologies still face limitations, particularly in the synthesis of repeat sequences and the transformation of large DNA fragments. In this review, we will introduce the structure of plant centromeres, the construction of plant artificial chromosomes, and possible methods for transforming large fragments into plant cells.
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Affiliation(s)
- Ming L Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xiao J Lin
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Bei X Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Wen W Kong
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
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4
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Wang Y, Li Y, Zhou F, Zhang L, Gong J, Cheng C, Chen J, Lou Q. Genome-wide characterization, phylogenetic and expression analysis of Histone gene family in cucumber (Cucumis sativus L.). Int J Biol Macromol 2023; 230:123401. [PMID: 36702227 DOI: 10.1016/j.ijbiomac.2023.123401] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023]
Abstract
Histones are essential components of chromatin and play an important role in regulating gene transcription and participating in DNA replication. Here, we performed a comprehensive analysis of this gene family. In this study, we identified 37 CsHistones that were classified into five groups (H1, H2A, H2B, H3 and H4). The closely linked subfamilies exhibited more similarity in terms of motifs and intron/exon numbers. Segmental duplication (SD) is the main driving force of cucumber CsHistones expansion. Analysis of cis-regulatory elements in the promoter region of CsHistones showed that CsHistones can respond to a variety of stresses. RNA-Seq analysis indicated that the expression of most CsHistones was associated with different stresses, including downy mildew, powdery mildew, wilt, heat, cold, salt stress, and waterlogging. Expression analysis showed that several genes of H3 group were highly expressed in different reproductive organs. Notably, CsCENH3 (CsHistone30) has the characteristics of a variant histone, and we demonstrated that CsCENH3 was localized on the nucleus and its proteins were expressed in centromere region. These findings provide valuable information for the identification and potential functions of Histone genes and ideas for the cultivation of CENH3-mediated haploid induction lines in cucumber.
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Affiliation(s)
- Yi Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangang Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Fang Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Lu Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianlei Gong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunyan Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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Liu X, Kong W, Xiao N, Huang L, Zhang Y, Chen W, Mo B, Yu Y. A simple and efficient carbon nanotube-based nanocarriers simultaneously delivers multiple plasmids into diverse mature tissues of monocotyledonous crops. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2266-0. [PMID: 36738434 DOI: 10.1007/s11427-022-2266-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 12/19/2022] [Indexed: 02/05/2023]
Affiliation(s)
- Xuedong Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Wenwen Kong
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Nian Xiao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Lijuan Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Yu Zhang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.,Instrumental Analysis Center of Shenzhen University (Lihu Campus), Shenzhen University, Shenzhen, 518060, China
| | - Weizhao Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Yu Yu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
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Uncovering natural allelic and structural variants of OsCENH3 gene by targeted resequencing and in silico mining in genus Oryza. Sci Rep 2023; 13:830. [PMID: 36646847 PMCID: PMC9842635 DOI: 10.1038/s41598-023-28053-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Plant breeding efforts to boost rice productivity have focused on developing a haploid development pipeline. CENH3 gene has emerged as a leading player that can be manipulated to engineer haploid induction system. Currently, allele mining for the OsCENH3 gene was done by PCR-based resequencing of 33 wild species accessions of genus Oryza and in silico mining of alleles from pre-existing data. We have identified and characterized CENH3 variants in genus Oryza. Our results indicated that the majority CENH3 alleles present in the Oryza gene pool carry synonymous substitutions. A few non-synonymous substitutions occur in the N-terminal Tail domain (NTT). SNP A/G at position 69 was found in accessions of AA genome and non-AA genome species. Phylogenetic analysis revealed that non-synonymous substitutions carrying alleles follow pre-determined evolutionary patterns. O. longistaminata accessions carry SNPs in four codons along with indels in introns 3 and 6. Fifteen haplotypes were mined from our panel; representative mutant alleles exhibited structural variations upon modeling. Structural analysis indicated that more than one structural variant may be exhibited by different accessions of single species (Oryza barthii). NTT allelic mutants, though not directly implicated in HI, may show variable interactions. HI and interactive behavior could be ascertained in future investigations.
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7
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Shen K, Qu M, Zhao P. The Roads to Haploid Embryogenesis. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12020243. [PMID: 36678955 PMCID: PMC9865920 DOI: 10.3390/plants12020243] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/19/2022] [Accepted: 12/30/2022] [Indexed: 05/31/2023]
Abstract
Although zygotic embryogenesis is usually studied in the field of seed biology, great attention has been paid to the methods used to generate haploid embryos due to their applications in crop breeding. These mainly include two methods for haploid embryogenesis: in vitro microspore embryogenesis and in vivo haploid embryogenesis. Although microspore culture systems and maize haploid induction systems were discovered in the 1960s, little is known about the molecular mechanisms underlying haploid formation. In recent years, major breakthroughs have been made in in vivo haploid induction systems, and several key factors, such as the matrilineal (MTL), baby boom (BBM), domain of unknown function 679 membrane protein (DMP), and egg cell-specific (ECS) that trigger in vivo haploid embryo production in both the crops and Arabidopsis models have been identified. The discovery of these haploid inducers indicates that haploid embryogenesis is highly related to gamete development, fertilization, and genome stability in ealry embryos. Here, based on recent efforts to identify key players in haploid embryogenesis and to understand its molecular mechanisms, we summarize the different paths to haploid embryogenesis, and we discuss the mechanisms of haploid generation and its potential applications in crop breeding. Although these haploid-inducing factors could assist egg cells in bypassing fertilization to initiate embryogenesis or trigger genome elimination in zygotes after fertilization to form haploid embryos, the fertilization of central cells to form endosperms is a prerequisite step for haploid formation. Deciphering the molecular and cellular mechanisms for haploid embryogenesis, increasing the haploid induction efficiency, and establishing haploid induction systems in other crops are critical for promoting the application of haploid technology in crop breeding, and these should be addressed in further studies.
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Affiliation(s)
- Kun Shen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Mengxue Qu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Peng Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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8
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Zhou J, Liu Y, Guo X, Birchler JA, Han F, Su H. Centromeres: From chromosome biology to biotechnology applications and synthetic genomes in plants. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2051-2063. [PMID: 35722725 PMCID: PMC9616519 DOI: 10.1111/pbi.13875] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 05/11/2023]
Abstract
Centromeres are the genomic regions that organize and regulate chromosome behaviours during cell cycle, and their variations are associated with genome instability, karyotype evolution and speciation in eukaryotes. The highly repetitive and epigenetic nature of centromeres were documented during the past half century. With the aid of rapid expansion in genomic biotechnology tools, the complete sequence and structural organization of several plant and human centromeres were revealed recently. Here, we systematically summarize the current knowledge of centromere biology with regard to the DNA compositions and the histone H3 variant (CENH3)-dependent centromere establishment and identity. We discuss the roles of centromere to ensure cell division and to maintain the three-dimensional (3D) genomic architecture in different species. We further highlight the potential applications of manipulating centromeres to generate haploids or to induce polyploids offspring in plant for breeding programs, and of targeting centromeres with CRISPR/Cas for chromosome engineering and speciation. Finally, we also assess the challenges and strategies for de novo design and synthesis of centromeres in plant artificial chromosomes. The biotechnology applications of plant centromeres will be of great potential for the genetic improvement of crops and precise synthetic breeding in the future.
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Affiliation(s)
- Jingwei Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryShenzhen Institute of Nutrition and Health, Huazhong Agricultural UniversityWuhanChina
| | - Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Xianrui Guo
- Laboratory of Plant Chromosome Biology and Genomic Breeding, School of Life SciencesLinyi UniversityLinyiChina
| | - James A. Birchler
- Division of Biological SciencesUniversity of MissouriColumbiaMissouriUSA
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Handong Su
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryShenzhen Institute of Nutrition and Health, Huazhong Agricultural UniversityWuhanChina
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
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Meng D, Luo H, Dong Z, Huang W, Liu F, Li F, Chen S, Yu H, Jin W. Overexpression of Modified CENH3 in Maize Stock6-Derived Inducer Lines Can Effectively Improve Maternal Haploid Induction Rates. FRONTIERS IN PLANT SCIENCE 2022; 13:892055. [PMID: 35481149 PMCID: PMC9036175 DOI: 10.3389/fpls.2022.892055] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/22/2022] [Indexed: 05/29/2023]
Abstract
Maize (Zea mays) doubled haploid (DH) breeding is a technology that can efficiently generate inbred lines with homozygous genetic backgrounds. Haploids are usually produced through in vivo induction by haploid inducer lines in maize. Currently, two approaches are usually used to develop maize haploid inducer lines. One is through the conventional breeding improvement based on the Stock6 germplasm, and this strategy is extensively used to induce maternal haploids in commercial maize DH breeding. Another strategy, newly developed but less utilized so far, is by genetic manipulation of the Centromeric Histone3 (CENH3) in regular lines. However, whether both approaches can be combined to develop the haploid inducer line with higher maternal haploid induction rate (HIR) has not been reported. In this study, we manipulated the Stock6-derived inducer lines by overexpressing maize CENH3 fused with different fluorescent protein tags and found that the engineered Stock6-derived lines showed an obvious increase in the maternal HIR. Intriguingly, this above strategy could be further improved by substituting a tail-altered CENH3 for the full-length CENH3 in the tagged expression cassette, resulting in a maternal HIR up to 16.3% that was increased by ~6.1% than Stock6-derived lines control. These results suggested that integration of two in vivo haploid induction methods could rapidly and effectively improve the maternal HIRs of maize Stock6-derived inducer lines, and provided a potentially feasible solution for further optimizing the process of commercial maize DH breeding.
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Affiliation(s)
- Dexuan Meng
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Haishan Luo
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Zhaobin Dong
- State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Wei Huang
- State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Fang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Fenghai Li
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Shaojiang Chen
- State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Haiqiu Yu
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Weiwei Jin
- State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Department of Agronomy, College of Agriculture and Resources and Environmental Sciences, Tianjin Agricultural University, Tianjin, China
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Elisafenko EA, Evtushenko EV, Vershinin AV. The origin and evolution of a two-component system of paralogous genes encoding the centromeric histone CENH3 in cereals. BMC PLANT BIOLOGY 2021; 21:541. [PMID: 34794377 PMCID: PMC8603533 DOI: 10.1186/s12870-021-03264-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 10/12/2021] [Indexed: 06/07/2023]
Abstract
BACKGROUND The cereal family Poaceae is one of the largest and most diverse angiosperm families. The central component of centromere specification and function is the centromere-specific histone H3 (CENH3). Some cereal species (maize, rice) have one copy of the gene encoding this protein, while some (wheat, barley, rye) have two. We applied a homology-based approach to sequenced cereal genomes, in order to finally trace the mutual evolution of the structure of the CENH3 genes and the nearby regions in various tribes. RESULTS We have established that the syntenic group or the CENH3 locus with the CENH3 gene and the boundaries defined by the CDPK2 and bZIP genes first appeared around 50 Mya in a common ancestor of the subfamilies Bambusoideae, Oryzoideae and Pooideae. This locus came to Pooideae with one copy of CENH3 in the most ancient tribes Nardeae and Meliceae. The βCENH3 gene as a part of the locus appeared in the tribes Stipeae and Brachypodieae around 35-40 Mya. The duplication was accompanied by changes in the exon-intron structure. Purifying selection acts mostly on αCENH3s, while βCENH3s form more heterogeneous structures, in which clade-specific amino acid motifs are present. In barley species, the βCENH3 gene assumed an inverted orientation relative to αCENH3 and the CDPK2 gene was substituted with LHCB-l. As the evolution and domestication of plant species went on, the locus was growing in size due to an increasing distance between αCENH3 and βCENH3 because of a massive insertion of the main LTR-containing retrotransposon superfamilies, gypsy and copia, without any evolutionary preference on either of them. A comparison of the molecular structure of the locus in the A, B and D subgenomes of the hexaploid wheat T. aestivum showed that invasion by mobile elements and concomitant rearrangements took place in an independent way even in evolutionarily close species. CONCLUSIONS The CENH3 duplication in cereals was accompanied by changes in the exon-intron structure of the βCENH3 paralog. The observed general tendency towards the expansion of the CENH3 locus reveals an amazing diversity of ways in which different species implement the scenario described in this paper.
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Affiliation(s)
- Evgeny A Elisafenko
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, 630090, Russia
| | - Elena V Evtushenko
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, 630090, Russia
| | - Alexander V Vershinin
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia.
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11
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Li J, Wang Y, Zou W, Jian L, Fu Y, Zhao J. AtNUF2 modulates spindle microtubule organization and chromosome segregation during mitosis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:801-816. [PMID: 33993566 DOI: 10.1111/tpj.15347] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
The NDC80 complex is a conserved eukaryotic complex composed of four subunits (NUF2, SPC25, NDC80, and SPC24). In yeast and animal cells, the complex is located at the outer layer of the kinetochore, connecting the inner layer of the kinetochore and spindle microtubules (MTs) during cell division. In higher plants, the relationship of the NDC80 complex with MTs is still unclear. In this study, we characterized the biological function of AtNUF2, a subunit of the Arabidopsis NDC80 complex. We found that AtNUF2 is widely expressed in various organs, especially in different stages of embryonic development. It was verified that AtNUF2 co-localized with α-tubulin on MTs during mitosis by immunohistochemical assays. Mutation of AtNUF2 led to severe mitotic defects, not only in the embryo and endosperm, but also in seedlings, resulting in seed abortion and stagnating seedling growth. Furthermore, the biological function of AtNUF2 was studied using partially complemented nuf2-3/-DD45;ABI3pro::AtNUF2 (nuf2-3/-DA ) seedlings. The chromosome bridge and lagging chromatids occurred in nuf2-3/-DA root apical meristem cells, along with aberration of spindle MTs, resulting in blocked root growth. Meanwhile, the direct binding of AtNUF2 and AtSPC25 to MTs was determined by an MT co-sedimentation assay in vitro. This study revealed the function of AtNUF2 in mitosis and the underlying mechanisms, modulating spindle MT organization and ensuring chromosome segregation during embryo, endosperm, and root development, laying the foundation for subsequent research of the NDC80 complex.
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Affiliation(s)
- Jin Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yutao Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Wenxuan Zou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Liufang Jian
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ying Fu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jie Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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12
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Wang N, Liu J, Ricci WA, Gent JI, Dawe RK. Maize centromeric chromatin scales with changes in genome size. Genetics 2021; 217:iyab020. [PMID: 33857306 PMCID: PMC8049547 DOI: 10.1093/genetics/iyab020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/30/2021] [Indexed: 11/14/2022] Open
Abstract
Centromeres are defined by the location of Centromeric Histone H3 (CENP-A/CENH3) which interacts with DNA to define the locations and sizes of functional centromeres. An analysis of 26 maize genomes including 110 fully assembled centromeric regions revealed positive relationships between centromere size and genome size. These effects are independent of variation in the amounts of the major centromeric satellite sequence CentC. We also backcrossed known centromeres into two different lines with larger genomes and observed consistent increases in functional centromere sizes for multiple centromeres. Although changes in centromere size involve changes in bound CENH3, we could not mimic the effect by overexpressing CENH3 by threefold. Literature from other fields demonstrate that changes in genome size affect protein levels, organelle size and cell size. Our data demonstrate that centromere size is among these scalable features, and that multiple limiting factors together contribute to a stable centromere size equilibrium.
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Affiliation(s)
- Na Wang
- Department of Plant Biology, University of Georgia, Athens GA 30602, USA
| | - Jianing Liu
- Department of Genetics, University of Georgia, Athens GA 30602, USA
| | - William A Ricci
- Department of Plant Biology, University of Georgia, Athens GA 30602, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens GA 30602, USA
| | - R Kelly Dawe
- Department of Plant Biology, University of Georgia, Athens GA 30602, USA
- Department of Genetics, University of Georgia, Athens GA 30602, USA
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Hesami M, Yoosefzadeh Najafabadi M, Adamek K, Torkamaneh D, Jones AMP. Synergizing Off-Target Predictions for In Silico Insights of CENH3 Knockout in Cannabis through CRISPR/Cas. Molecules 2021; 26:molecules26072053. [PMID: 33916717 PMCID: PMC8038328 DOI: 10.3390/molecules26072053] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 12/13/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-mediated genome editing system has recently been used for haploid production in plants. Haploid induction using the CRISPR/Cas system represents an attractive approach in cannabis, an economically important industrial, recreational, and medicinal plant. However, the CRISPR system requires the design of precise (on-target) single-guide RNA (sgRNA). Therefore, it is essential to predict off-target activity of the designed sgRNAs to avoid unexpected outcomes. The current study is aimed to assess the predictive ability of three machine learning (ML) algorithms (radial basis function (RBF), support vector machine (SVM), and random forest (RF)) alongside the ensemble-bagging (E-B) strategy by synergizing MIT and cutting frequency determination (CFD) scores to predict sgRNA off-target activity through in silico targeting a histone H3-like centromeric protein, HTR12, in cannabis. The RF algorithm exhibited the highest precision, recall, and F-measure compared to all the tested individual algorithms with values of 0.61, 0.64, and 0.62, respectively. We then used the RF algorithm as a meta-classifier for the E-B method, which led to an increased precision with an F-measure of 0.62 and 0.66, respectively. The E-B algorithm had the highest area under the precision recall curves (AUC-PRC; 0.74) and area under the receiver operating characteristic (ROC) curves (AUC-ROC; 0.71), displaying the success of using E-B as one of the common ensemble strategies. This study constitutes a foundational resource of utilizing ML models to predict gRNA off-target activities in cannabis.
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Affiliation(s)
- Mohsen Hesami
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.H.); (M.Y.N.); (K.A.); (D.T.)
| | | | - Kristian Adamek
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.H.); (M.Y.N.); (K.A.); (D.T.)
| | - Davoud Torkamaneh
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.H.); (M.Y.N.); (K.A.); (D.T.)
- Département de Phytologie, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Andrew Maxwell Phineas Jones
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.H.); (M.Y.N.); (K.A.); (D.T.)
- Correspondence:
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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.
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15
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Wang N, Gent JI, Dawe RK. Haploid induction by a maize cenh3 null mutant. SCIENCE ADVANCES 2021; 7:7/4/eabe2299. [PMID: 33523932 PMCID: PMC7817090 DOI: 10.1126/sciadv.abe2299] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/05/2020] [Indexed: 05/03/2023]
Abstract
The production of haploids is an important first step in creating many new plant varieties. One approach used in Arabidopsis involves crossing plants expressing different forms of centromeric histone H3 (CENP-A/CENH3) and subsequent loss of genome with weaker centromeres. However, the method has been ineffective in crop plants. Here, we describe a greatly simplified method based on crossing maize lines that are heterozygous for a cenh3 null mutation. Crossing +/cenh3 to wild-type plants in both directions yielded haploid progeny. Genome elimination was determined by the cenh3 genotype of the gametophyte, suggesting that centromere failure is caused by CENH3 dilution during the postmeiotic cell divisions that precede gamete formation. The cenh3 haploid inducer works as a vigorous hybrid and can be transferred to other lines in a single cross, making it versatile for a variety of applications.
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Affiliation(s)
- Na Wang
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - R Kelly Dawe
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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Achrem M, Szućko I, Kalinka A. The epigenetic regulation of centromeres and telomeres in plants and animals. COMPARATIVE CYTOGENETICS 2020; 14:265-311. [PMID: 32733650 PMCID: PMC7360632 DOI: 10.3897/compcytogen.v14i2.51895] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/18/2020] [Indexed: 05/10/2023]
Abstract
The centromere is a chromosomal region where the kinetochore is formed, which is the attachment point of spindle fibers. Thus, it is responsible for the correct chromosome segregation during cell division. Telomeres protect chromosome ends against enzymatic degradation and fusions, and localize chromosomes in the cell nucleus. For this reason, centromeres and telomeres are parts of each linear chromosome that are necessary for their proper functioning. More and more research results show that the identity and functions of these chromosomal regions are epigenetically determined. Telomeres and centromeres are both usually described as highly condensed heterochromatin regions. However, the epigenetic nature of centromeres and telomeres is unique, as epigenetic modifications characteristic of both eu- and heterochromatin have been found in these areas. This specificity allows for the proper functioning of both regions, thereby affecting chromosome homeostasis. This review focuses on demonstrating the role of epigenetic mechanisms in the functioning of centromeres and telomeres in plants and animals.
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Affiliation(s)
- Magdalena Achrem
- Institute of Biology, University of Szczecin, Szczecin, PolandUniversity of SzczecinSzczecinPoland
- Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, PolandUniversity of SzczecinSzczecinPoland
| | - Izabela Szućko
- Institute of Biology, University of Szczecin, Szczecin, PolandUniversity of SzczecinSzczecinPoland
- Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, PolandUniversity of SzczecinSzczecinPoland
| | - Anna Kalinka
- Institute of Biology, University of Szczecin, Szczecin, PolandUniversity of SzczecinSzczecinPoland
- Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, PolandUniversity of SzczecinSzczecinPoland
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