1
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Pei D, Yu X, Fu W, Ma X, Fang J. The evolution and formation of centromeric repeats analysis in Vitis vinifera. PLANTA 2024; 259:99. [PMID: 38522063 DOI: 10.1007/s00425-024-04374-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/03/2024] [Indexed: 03/25/2024]
Abstract
MAIN CONCLUSION Six grape centromere-specific markers for cytogenetics were mined by combining genetic and immunological assays, and the possible evolution mechanism of centromeric repeats was analyzed. Centromeric histone proteins are functionally conserved; however, centromeric repetitive DNA sequences may represent considerable diversity in related species. Therefore, studying the characteristics and structure of grape centromere repeat sequences contributes to a deeper understanding of the evolutionary process of grape plants, including their origin and mechanisms of polyploidization. Plant centromeric regions are mainly composed of repetitive sequences, including SatDNA and transposable elements (TE). In this research, the characterization of centromere sequences in the whole genome of grapevine (Vitis vinifera L.) has been conducted. Five centromeric tandem repeat sequences (Vv1, Vv2, Vv5, Vv6, and Vv8) and one long terminal repeat (LTR) sequence Vv24 were isolated. These sequences had different centromeric distributions, which indicates that grape centromeric sequences may undergo rapid evolution. The existence of extrachromosomal circular DNA (eccDNA) and gene expression in CenH3 subdomain region may provide various potential mechanisms for the generation of new centromeric regions.
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Affiliation(s)
- Dan Pei
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xue Yu
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Weihong Fu
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xuhui Ma
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277000, China
| | - Jinggui Fang
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095, China.
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2
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Soares SC, Eler ES, E Silva CEF, da Silva MNF, Araújo NP, Svartman M, Feldberg E. LINE-1 and SINE-B1 mapping and genome diversification in Proechimys species (Rodentia: Echimyidae). Life Sci Alliance 2022; 5:5/6/e202101104. [PMID: 35304430 PMCID: PMC8932440 DOI: 10.26508/lsa.202101104] [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: 04/22/2021] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 11/24/2022] Open
Abstract
This study aimed to understand the impact of LINE-1 and SINE-B1 retroelements on the architecture and karyotypic diversification of five rodent species of the genus Proechimys from different regions of the Amazon. Karyotype comparisons were performed using fluorescent interspecific in situ hybridization. The L1 and B1 retroelements showed a non-random arrangement and a conserved pattern when the genomes of the five species of Proechimys were compared, including the two cytotypes of Proechimys guyannensis The signal homeology among the chromosomes and the degree of similarity among the formed clusters indicate rearrangements such as fusion/fission, and demonstrates that these retroelements can behave as derived characters shared in Proechimys The differentiated distribution and organization of these retroelements in the karyotypes and in the chromosomal fiber, respectively, may represent a strong indication of their role as generating sources of karyotypic diversity in the genus Proechimys and provide insights into the evolutionary relationships between taxa.
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Affiliation(s)
- Simone Cardoso Soares
- Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil .,Laboratório de Genética Animal (LGA), Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil.,Universidade do Estado do Amazonas, Manaus, Brazil
| | - Eduardo Schmidt Eler
- Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Carlos Eduardo Faresin E Silva
- Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil.,Laboratório de Genética Animal (LGA), Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | | | - Naiara Pereira Araújo
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Instituto Federal de Educação, Ciência e Tecnologia de Rondônia campus Jaru, Jaru, Brazil
| | - Marta Svartman
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Eliana Feldberg
- Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil.,Laboratório de Genética Animal (LGA), Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
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3
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Molecular and FISH analysis of 45S rDNA on BAC molecule of Saccharina japonica. AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2021.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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4
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Franek M, Kilar A, Fojtík P, Olšinová M, Benda A, Rotrekl V, Dvořáčková M, Fajkus J. Super-resolution microscopy of chromatin fibers and quantitative DNA methylation analysis of DNA fiber preparations. J Cell Sci 2021; 134:jcs258374. [PMID: 34350964 DOI: 10.1242/jcs.258374] [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: 01/06/2021] [Accepted: 07/05/2021] [Indexed: 11/20/2022] Open
Abstract
Analysis of histone variants and epigenetic marks is dominated by genome-wide approaches in the form of chromatin immunoprecipitation-sequencing (ChIP-seq) and related methods. Although uncontested in their value for single-copy genes, mapping the chromatin of DNA repeats is problematic for biochemical techniques that involve averaging of cell populations or analysis of clusters of tandem repeats in a single-cell analysis. Extending chromatin and DNA fibers allows us to study the epigenetics of individual repeats in their specific chromosomal context, and thus constitutes an important tool for gaining a complete understanding of the epigenetic organization of genomes. We report that using an optimized fiber extension protocol is essential in order to obtain more reproducible data and to minimize the clustering of fibers. We also demonstrate that the use of super-resolution microscopy is important for reliable evaluation of the distribution of histone modifications on individual fibers. Furthermore, we introduce a custom script for the analysis of methylation levels on DNA fibers and apply it to map the methylation of telomeres, ribosomal genes and centromeres.
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Affiliation(s)
- Michal Franek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Agata Kilar
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-61137 Brno, Czech Republic
| | - Petr Fojtík
- International Clinical Research Center (ICRC) at St. Anne's University Hospital, Pekařská 53, CZ-65691 Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Marie Olšinová
- Charles University, Faculty of Science, Biology Section, Imaging methods core facility at BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Aleš Benda
- Charles University, Faculty of Science, Biology Section, Imaging methods core facility at BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Vladimír Rotrekl
- International Clinical Research Center (ICRC) at St. Anne's University Hospital, Pekařská 53, CZ-65691 Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Jíří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-61137 Brno, Czech Republic
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5
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Huang Y, Ding W, Zhang M, Han J, Jing Y, Yao W, Hasterok R, Wang Z, Wang K. The formation and evolution of centromeric satellite repeats in Saccharum species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:616-629. [PMID: 33547688 DOI: 10.1111/tpj.15186] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 01/25/2021] [Accepted: 01/29/2021] [Indexed: 05/04/2023]
Abstract
Centromeres in eukaryotes are composed of tandem DNAs and retrotransposons. However, centromeric repeats exhibit considerable diversity, even among closely related species, and their origin and evolution are largely unknown. We conducted a genome-wide characterization of the centromeric sequences in sugarcane (Saccharum officinarum). Four centromeric tandem repeat sequences, So1, So103, So137 and So119, were isolated. So1 has a monomeric length of 137 bp, typical of a centromeric satellite, and has evolved four variants. However, these So1 variants had distinct centromere distributions and some were unique to an individual centromere. The distributions of the So1 variants were unexpectedly consistent among the Saccharum species that had different basic chromosome numbers or ploidy levels, thus suggesting evolutionary stability for approximately 7 million years in sugarcane. So103, So137 and So119 had unusually longer monomeric lengths that ranged from 327 to 1371 bp and lacked translational phasing on the CENH3 nucleosomes. Moreover, So103, So137 and So119 seemed to be highly similar to retrotransposons, which suggests that they originated from these mobile elements. Notably, all three repeats were flanked by direct repeats, and formed extrachromosomal circular DNAs (eccDNAs). The presence of circular molecules for these retrotransposon-derived centromeric satellites suggests an eccDNA-mediated centromeric satellite formation pathway in sugarcane.
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Affiliation(s)
- Yongji Huang
- Guangxi Key Laboratory of Sugarcane Biology & Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops (MOE), College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Wenjie Ding
- Guangxi Key Laboratory of Sugarcane Biology & Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops (MOE), College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Muqing Zhang
- Guangxi Key Laboratory of Sugarcane Biology & Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops (MOE), College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro- Bioresources, Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Jinlei Han
- Guangxi Key Laboratory of Sugarcane Biology & Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops (MOE), College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yanfen Jing
- Ruili Breeding Station, Sugarcane Institute, Yunnan Academy of Agricultural Sciences, Ruili, 678600, China
| | - Wei Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro- Bioresources, Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, 40-032, Poland
| | - Zonghua Wang
- Guangxi Key Laboratory of Sugarcane Biology & Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops (MOE), College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Kai Wang
- Guangxi Key Laboratory of Sugarcane Biology & Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops (MOE), College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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6
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Xia QM, Miao LK, Xie KD, Yin ZP, Wu XM, Chen CL, Grosser JW, Guo WW. Localization and characterization of Citrus centromeres by combining half-tetrad analysis and CenH3-associated sequence profiling. PLANT CELL REPORTS 2020; 39:1609-1622. [PMID: 32897396 DOI: 10.1007/s00299-020-02587-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
The physical locations of citrus centromere are revealed by combining genetic and immunological assays for the first time and nine citrus centromere-specific markers for cytogenetics are mined. Centromere localization is challenging, because highly redundant repetitive sequences in centromeric regions make sequence assembly difficult. Although several citrus genomes have been released, the centromeric regions and their characteristics remain to be elucidated. Here, we mapped citrus centromeres through half-tetrad analysis (HTA) that included the genotyping of 54 tetraploid hybrids derived from 2n megagametophytes of Nadorcott tangor with 212 single nucleotide polymorphism (SNP) markers. The sizes of centromeric regions, which estimated based on the heterozygosity restitution rate pattern along the chromosomes, ranged from 1.12 to 18.19 Mb. We also profiled the binding sequences with the centromere-specific histone variant CenH3 by chromatin immunoprecipitation sequencing (ChIP-seq). Based on the positions of the top ten CenH3-enriched contigs, the sizes of centromeric regions were estimated to range from 0.01 to 7.60 Mb and were either adjacent to or included in the centromeric regions identified by HTA. We used DNA probes from two repeats selected from the centromeric regions and seven CenH3-binding centromeric repeats to verify centromeric locations by fluorescence in situ hybridization (FISH). Centromere localization in citrus will contribute to the mining of centromeric/pericentromeric markers, thus to facilitate the rapid identification of mechanisms underlying 2n gamete formation and serve the polyploidy breeding.
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Affiliation(s)
- Qiang-Ming Xia
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lu-Ke Miao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kai-Dong Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Zhao-Ping Yin
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiao-Meng Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chun-Li Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jude W Grosser
- Citrus Research and Education Center, University of Florida, 700 Experiment Station Road, Lake Alfred, FL, 33850, USA
| | - Wen-Wu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
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7
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Kalinka A, Achrem M. The distribution pattern of 5-methylcytosine in rye (Secale L.) chromosomes. PLoS One 2020; 15:e0240869. [PMID: 33057421 PMCID: PMC7561101 DOI: 10.1371/journal.pone.0240869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/04/2020] [Indexed: 12/02/2022] Open
Abstract
The rye (Secale L.) genome is large, and it contains many classes of repetitive sequences. Secale species differ in terms of genome size, heterochromatin content, and global methylation level; however, the organization of individual types of sequences in chromosomes is relatively similar. The content of the abundant subtelomeric heterochromatin fraction in rye do not correlate with the global level of cytosine methylation, hence immunofluorescence detection of 5-methylcytosine (5-mC) distribution in metaphase chromosomes was performed. The distribution patterns of 5-methylcytosine in the chromosomes of Secale species/subspecies were generally similar. 5-methylcytosine signals were dispersed along the entire length of the chromosome arms of all chromosomes, indicating high levels of methylation, especially at retrotransposon sequences. 5-mC signals were absent in the centromeric and telomeric regions, as well as in subtelomeric blocks of constitutive heterochromatin, in each of the taxa studied. Pericentromeric domains were methylated, however, there was a certain level of polymorphism in these areas, as was the case with the nucleolus organizer region. Sequence methylation within the region of the heterochromatin intercalary bands were also demonstrated to be heterogenous. Unexpectedly, there was a lack of methylation in rye subtelomeres, indicating that heterochromatin is a very diverse fraction of chromatin, and its epigenetic regulation or potential influence on adjacent regions can be more complex than has conventionally been thought. Like telomeres and centromeres, subtelomeric heterochromatin can has a specific role, and the absence of 5-mC is required to maintain the heterochromatin state.
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Affiliation(s)
- Anna Kalinka
- Institute of Biology, University of Szczecin, Szczecin, Poland
- Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, Poland
- * E-mail:
| | - Magdalena Achrem
- Institute of Biology, University of Szczecin, Szczecin, Poland
- Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, Poland
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8
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Kahl VFS, Allen JAM, Nelson CB, Sobinoff AP, Lee M, Kilo T, Vasireddy RS, Pickett HA. Telomere Length Measurement by Molecular Combing. Front Cell Dev Biol 2020; 8:493. [PMID: 32612998 PMCID: PMC7308456 DOI: 10.3389/fcell.2020.00493] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/25/2020] [Indexed: 12/14/2022] Open
Abstract
Telomeres are repetitive regions of DNA bound by specialized proteins at the termini of linear chromosomes that prevent the natural chromosome ends from being recognized as DNA double strand breaks. Telomeric DNA is gradually eroded with each round of cell division, resulting in the accumulation of critically short or dysfunctional telomeres that eventually trigger cellular senescence. Consequently, telomere length is indicative of the proliferative capacity of a cell. Multiple methods exist to measure telomere length and telomere content, but a simple and reliable technique to accurately measure individual telomere lengths is currently lacking. We have developed the Telomere length Combing Assay (TCA) to measure telomere length on stretched DNA fibers. We used TCA to measure telomere erosion in primary human fibroblasts, and to detect telomere lengthening in response to activation of telomere maintenance pathways. TCA was also used to accurately measure telomere length in healthy individuals, and to identify critically short telomeres in patients with telomere biology disorders. TCA is performed on isolated DNA, negating the need for cycling cells. TCA is amenable to semi-automated image analysis, and can be fully automated using the Genomic Vision molecular combing platform. This not only precludes sampling bias, but also provides the potential for high-throughput applications and clinical development. TCA is a simple and versatile technique to measure the distribution of individual telomere lengths in a cell population, offering improved accuracy, and more detailed biological insight for telomere length measurement applications.
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Affiliation(s)
- Vivian F S Kahl
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Joshua A M Allen
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Christopher B Nelson
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Alexander P Sobinoff
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Michael Lee
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Tatjana Kilo
- Department of Hematology, Children's Hospital at Westmead, Sydney Children's Hospitals Network, Sydney, NSW, Australia
| | - Raja S Vasireddy
- Department of Hematology, Children's Hospital at Westmead, Sydney Children's Hospitals Network, Sydney, NSW, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
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9
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Lazniewski M, Dawson WK, Rusek AM, Plewczynski D. One protein to rule them all: The role of CCCTC-binding factor in shaping human genome in health and disease. Semin Cell Dev Biol 2019; 90:114-127. [PMID: 30096365 PMCID: PMC6642822 DOI: 10.1016/j.semcdb.2018.08.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 08/06/2018] [Indexed: 12/12/2022]
Abstract
The eukaryotic genome, constituting several billion base pairs, must be contracted to fit within the volume of a nucleus where the diameter is on the scale of μm. The 3D structure and packing of such a long sequence cannot be left to pure chance, as DNA must be efficiently used for its primary roles as a matrix for transcription and replication. In recent years, methods like chromatin conformation capture (including 3C, 4C, Hi-C, ChIA-PET and Multi-ChIA) and optical microscopy have advanced substantially and have shed new light on how eukaryotic genomes are hierarchically organized; first into 10-nm fiber, next into DNA loops, topologically associated domains and finally into interphase or mitotic chromosomes. This knowledge has allowed us to revise our understanding regarding the mechanisms governing the process of DNA organization. Mounting experimental evidence suggests that the key element in the formation of loops is the binding of the CCCTC-binding factor (CTCF) to DNA; a protein that can be referred to as the chief organizer of the genome. However, CTCF does not work alone but in cooperation with other proteins, such as cohesin or Yin Yang 1 (YY1). In this short review, we briefly describe our current understanding of the structure of eukaryotic genomes, how they are established and how the formation of DNA loops can influence gene expression. We discuss the recent discoveries describing the 3D structure of the CTCF-DNA complex and the role of CTCF in establishing genome structure. Finally, we briefly explain how various genetic disorders might arise as a consequence of mutations in the CTCF target sequence or alteration of genomic imprinting.
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Affiliation(s)
- Michal Lazniewski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland
| | - Wayne K Dawson
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 103-8657, Japan
| | - Anna Maria Rusek
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; Clinical Molecular Biology Department, Medical University of Bialystok, Bialystok, Poland
| | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; Centre for Innovative Research, Medical University of Bialystok, Bialystok, Poland; Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland.
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10
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Bačovský V, Hobza R, Vyskot B. Technical Review: Cytogenetic Tools for Studying Mitotic Chromosomes. Methods Mol Biol 2018; 1675:509-535. [PMID: 29052211 DOI: 10.1007/978-1-4939-7318-7_30] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Significant advances in chromosome preparation and other techniques have greatly increased the potential of plant cytogenetics in recent years. Increase in longitudinal resolution using DNA extended fibers as well as new developments in imaging and signal amplification technologies have enhanced the ability of FISH to detect small gene targets. The combination of fluorescence in situ hybridization with immunocytochemistry allows the investigation of cell events, chromosomal rearrangements and chromatin features typical for plant nuclei. Chromosome manipulation techniques using microdissection and flow sorting have accelerated the analysis of complex plant genomes. Together, the different cytogenetic approaches are invaluable for the unravelling of detailed structures of plant chromosomes, which are of utmost importance for the study of genome properties, DNA replication and gene regulation. In this technical review, different cytogenetic approaches are discussed for the analysis of plant chromosomes, with a focus on mitotic chromosomes.
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Affiliation(s)
- Václaclav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Boris Vyskot
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic.
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11
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Findley SD, Birchler JA, Stacey G. Metaphase Chromosome Preparation from Soybean (Glycine max) Root Tips. ACTA ACUST UNITED AC 2017; 2:78-88. [PMID: 31725978 DOI: 10.1002/cppb.20046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This unit presents a highly reliable protocol to produce and screen metaphase chromosome spreads from root tip cell suspensions of soybean (Glycine max), or other legumes. The procedures represent soybean-optimized versions of protocols developed for maize. The use of pressurized nitrous oxide to reliably generate metaphase-arrested chromosomes is crucial to overcoming one of the challenges of working with tiny and numerous soybean chromosomes. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Seth D Findley
- University of Missouri, Division of Plant Sciences, Columbia, Missouri
| | - James A Birchler
- University of Missouri, Division of Biological Sciences, Columbia, Missouri
| | - Gary Stacey
- University of Missouri, Division of Plant Sciences, Columbia, Missouri
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12
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Isolation and characterization of centromeric repetitive DNA sequences in Saccharum spontaneum. Sci Rep 2017; 7:41659. [PMID: 28134354 PMCID: PMC5278356 DOI: 10.1038/srep41659] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 12/21/2016] [Indexed: 01/05/2023] Open
Abstract
Sugarcane (Saccharum hybrids spp.) is the most important sugar crop that accounts for ~75% of the world’s sugar production. Recently, a whole-genome sequencing project was launched on the wild species S. spontaneum. To obtain information on the DNA composition of the repeat-enriched region of the centromere, we conducted a genome-wide analysis of the DNA sequences associated with CenH3 (a mutant of histone H3 located in eukaryote centromeres) using chromatin immunoprecipitation followed by sequencing (ChIP-seq) method. We demonstrate that the centromeres contain mainly SCEN-like single satellite repeat (Ss1) and several Ty3/gypsy retrotransposon-related repeats (Ss166, Ss51, and Ss68). Ss1 dominates in the centromeric regions and spans up to 500 kb. In contrast, the Ty3/gypsy retrotransposon-related repeats are either clustered spanning over a short range, or dispersed in the centromere regions. Interestingly, Ss1 exhibits a chromosome-specific enrichment in the wild species S. spontaneum and S. robustum, but not in the domesticated species S. officinarum and modern sugarcane cultivars. This finding suggests an autopolyploid genome identity of S. spontaneum with a high level of homology among its eight sub-genomes. We also conducted a genome-wide survey of the repetitive DNAs in S. spontaneum following a similarity-based sequence clustering strategy. These results provide insight into the composition of sugarcane genome as well as the genome assembly of S. spontaneum.
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Abstract
High resolution fiber-Fluorescence in situ hybridization (FISH) is an advanced FISH technology that can effectively bridge the resolution gap between probe hybridizing on DNA molecules and chromosomal regions. Since various types of DNA and chromatin fibers can be generated reflecting different degrees of DNA/chromatin packaging status, fiber-FISH technology has been successfully used in diverse molecular cytogenetic/cytogenomic studies. Following a brief review of this technology, including its major development and increasing applications, typical protocols to generate DNA/chromatin fiber will be described, coupled with rationales, as well as technical tips. These released DNA/chromatin fibers are suitable for an array of cytogenetic/cytogenomic analyses.
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Affiliation(s)
- Christine J Ye
- The Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Henry H Heng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 3226 Scott Hall, 540 E, Detroit, MI, 48201, USA.
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
- Karmanos Cancer Institute, Detroit, MI, 48201, USA.
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15
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Abstract
Fluorescence in situ hybridization (FISH) is widely used in cytogenetics to determine the localization of DNA sequences on target chromosomes, to provide visible information regarding the physical position of DNA sequences, to determine the abundance and distribution of repetitive sequences that comprise a large proportion of genomes, and to determine the relative chromosome positions of multiple sequences in physical mapping. By mapping on extended chromatin fibers, fiber-FISH can be used to determine the structure and organization of genes or DNA sequences with a high resolution (to a few kilobases). The protocols described here will provide procedures of FISH on metaphase chromosomes and extended chromatin fibers of rice (Oryza sativa). © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Kai Wang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fujian, China
| | - Weichang Yu
- Shenzhen Research Institute of the Chinese University of Hong Kong, Shenzhen, China
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Deen J, Sempels W, De Dier R, Vermant J, Dedecker P, Hofkens J, Neely RK. Combing of genomic DNA from droplets containing picograms of material. ACS NANO 2015; 9:809-816. [PMID: 25561163 PMCID: PMC4344373 DOI: 10.1021/nn5063497] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/05/2015] [Indexed: 05/30/2023]
Abstract
Deposition of linear DNA molecules is a critical step in many single-molecule genomic approaches including DNA mapping, fiber-FISH, and several emerging sequencing technologies. In the ideal situation, the DNA that is deposited for these experiments is absolutely linear and uniformly stretched, thereby enabling accurate distance measurements. However, this is rarely the case, and furthermore, current approaches for the capture and linearization of DNA on a surface tend to require complex surface preparation and large amounts of starting material to achieve genomic-scale mapping. This makes them technically demanding and prevents their application in emerging fields of genomics, such as single-cell based analyses. Here we describe a simple and extremely efficient approach to the deposition and linearization of genomic DNA molecules. We employ droplets containing as little as tens of picograms of material and simply drag them, using a pipet tip, over a polymer-coated coverslip. In this report we highlight one particular polymer, Zeonex, which is remarkably efficient at capturing DNA. We characterize the method of DNA capture on the Zeonex surface and find that the use of droplets greatly facilitates the efficient deposition of DNA. This is the result of a circulating flow in the droplet that maintains a high DNA concentration at the interface of the surface/solution. Overall, our approach provides an accessible route to the study of genomic structural variation from samples containing no more than a handful of cells.
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Affiliation(s)
- Jochem Deen
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
| | - Wouter Sempels
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
| | - Raf De Dier
- Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46, Heverlee 3001, Belgium
| | - Jan Vermant
- Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46, Heverlee 3001, Belgium
- Department of Materials, ETH Zürich, Vladimir Prelog Weg 5, CH 8093 Zürich, Switzerland
| | - Peter Dedecker
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
| | - Johan Hofkens
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Robert K. Neely
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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Zhang W, Cao Y, Wang K, Zhao T, Chen J, Pan M, Wang Q, Feng S, Guo W, Zhou B, Zhang T. Identification of centromeric regions on the linkage map of cotton using centromere-related repeats. Genomics 2014; 104:587-93. [PMID: 25238895 DOI: 10.1016/j.ygeno.2014.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 08/16/2014] [Accepted: 09/07/2014] [Indexed: 12/16/2022]
Abstract
Centromere usually contains high-copy-number retrotransposons and satellite repeats, which are difficult to map, clone and sequence. Currently, very little is known about the centromere in cotton. Here, we sequenced a bacterial artificial chromosome (BAC) mapping to the centromeric region and predicted four long-terminal-repeat (LTR) retrotransposons. They were located in the heterochromatic centromeric regions of all 52 pachytene chromosomes in Gossypium hirsutum. Fiber-FISH mapping revealed that these retrotransposons span an area of at least 1.8Mb in the centromeric region. Comparative analysis showed that these retrotransposons generated similar, strong fluorescent signals in the D progenitor Gossypium raimondii but not in the A progenitor Gossypium herbaceum, suggesting that the centromere sequence of tetraploid cotton might be derived from the D progenitor. Centromeric regions were anchored on 13 chromosomes of D-genome sequence. Characterization of these centromere-related repeats and regions will enhance cotton centromere mapping, sequencing and evolutionary studies.
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Affiliation(s)
- Wenpan Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, China
| | - Yujie Cao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, China
| | - Kai Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, China
| | - Ting Zhao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiedan Chen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengqiao Pan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiong Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, China
| | - Shouli Feng
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, China
| | - Wangzhen Guo
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, China
| | - Baoliang Zhou
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, China.
| | - Tianzhen Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, China.
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