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Teng Z, Yang L, Zhang Q, Chen Y, Wang X, Zheng Y, Tian A, Tian D, Lin Z, Deng WM, Liu H. Topoisomerase I is an evolutionarily conserved key regulator for satellite DNA transcription. Nat Commun 2024; 15:5151. [PMID: 38886382 PMCID: PMC11183047 DOI: 10.1038/s41467-024-49567-5] [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: 03/26/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024] Open
Abstract
RNA Polymerase (RNAP) II transcription on non-coding repetitive satellite DNAs plays an important role in chromosome segregation, but a little is known about the regulation of satellite transcription. We here show that Topoisomerase I (TopI), not TopII, promotes the transcription of α-satellite DNAs, the main type of satellite DNAs on human centromeres. Mechanistically, TopI localizes to centromeres, binds RNAP II and facilitates RNAP II elongation. Interestingly, in response to DNA double-stranded breaks (DSBs), α-satellite transcription is dramatically stimulated in a DNA damage checkpoint-independent but TopI-dependent manner, and these DSB-induced α-satellite RNAs form into strong speckles in the nucleus. Remarkably, TopI-dependent satellite transcription also exists in mouse 3T3 and Drosophila S2 cells and in Drosophila larval imaginal wing discs and tumor tissues. Altogether, our findings herein reveal an evolutionally conserved mechanism with TopI as a key player for the regulation of satellite transcription at both cellular and animal levels.
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Affiliation(s)
- Zhen Teng
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Lu Yang
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Qian Zhang
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Yujue Chen
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Xianfeng Wang
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Yiran Zheng
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Aiguo Tian
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
- Tulane Aging Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Di Tian
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Zhen Lin
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Wu-Min Deng
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Hong Liu
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA.
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
- Tulane Aging Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
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Teng Z, Yang L, Zhang Q, Chen Y, Wang X, Zheng Y, Tian A, Tian D, Lin Z, Deng WM, Liu H. Topoisomerase I is an Evolutionarily Conserved Key Regulator for Satellite DNA Transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592391. [PMID: 38746280 PMCID: PMC11092777 DOI: 10.1101/2024.05.03.592391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Repetitive satellite DNAs, divergent in nucleic-acid sequence and size across eukaryotes, provide a physical site for centromere assembly to orchestrate chromosome segregation during the cell cycle. These non-coding DNAs are transcribed by RNA polymerase (RNAP) II and the transcription has been shown to play a role in chromosome segregation, but a little is known about the regulation of centromeric transcription, especially in higher organisms with tandemly-repeated-DNA-sequence centromeres. Using RNA interference knockdown, chemical inhibition and AID/IAA degradation, we show that Topoisomerase I (TopI), not TopII, promotes the transcription of α-satellite DNAs, the main type of satellite on centromeres in human cells. Mechanistically, TopI localizes to centromeres, binds RNAP II and facilitates RNAP II elongation on centromeres. Interestingly, in response to DNA double-stranded breaks (DSBs) induced by chemotherapy drugs or CRSPR/Cas9, α-satellite transcription is dramatically stimulated in a DNA damage checkpoint-independent but TopI-dependent manner. These DSB-induced α-satellite RNAs were predominantly derived from the α-satellite high-order repeats of human centromeres and forms into strong speckles in the nucleus. Remarkably, TopI-dependent satellite transcription also exists in mouse 3T3 and Drosophila S2 cells and in Drosophila larval imaginal wing discs and tumor tissues. Altogether, our findings herein reveal an evolutionally conserved mechanism with TopI as a key player for the regulation of satellite transcription at both cellular and animal levels.
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Affiliation(s)
- Zhen Teng
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
- Contribute equally
| | - Lu Yang
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
- Contribute equally
| | - Qian Zhang
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
- Contribute equally
| | - Yujue Chen
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Xianfeng Wang
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Yiran Zheng
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Aiguo Tian
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
- Tulane Aging Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Di Tian
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Zhen Lin
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Wu-Min Deng
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Hong Liu
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
- Tulane Aging Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
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Koo DH, Ju Y, Putta K, Sathishraj R, Roma-Burgos N, Jugulam M, Friebe B, Gill BS. Extrachromosomal DNA-mediated glyphosate resistance in Italian ryegrass. PEST MANAGEMENT SCIENCE 2023; 79:4290-4294. [PMID: 37345512 DOI: 10.1002/ps.7626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/25/2023] [Accepted: 06/22/2023] [Indexed: 06/23/2023]
Abstract
BACKGROUND An Italian ryegrass population from Arkansas, USA developed glyphosate resistance due to 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene amplification. The plants in this population with approximately 70 EPSPS copies were used in the present study for the physical mapping of amplified copies of EPSPS gene to determine the possible mechanism of EPSPS gene amplification conferring glyphosate resistance in Italian ryegrass. RESULT Fluorescence in situ hybridization (FISH) analysis of glyphosate resistant (GR) Italian ryegrass plants with approximately 70 EPSPS copies displayed EPSPS hybridization signals randomly on most of the metaphase chromosomes. Glyphosate susceptible (GS) Italian ryegrass plants with one EPSPS copy displayed single prominent EPSPS hybridization signal, which was co-localized with 5S rDNA locus along with few additional signals on the outside of chromosomes. Pulsed-field gel electrophoresis (PFGE) followed by DNA blot using EPSPS gene as a probe identified a prominent EPSPS hybridization around the 400 kb region in GR DNA samples, but not in GS DNA samples. CONCLUSION We report the extrachromosomal DNA-mediated glyphosate resistance in Italian ryegrass. Physical mapping of amplified copies of EPSPS gene in Italian ryegrass by FISH gives us a clue that the amplified copies of EPSPS gene may be present in the extrachromosomal DNA elements. Further analysis by PFGE followed by DNA blotting revealed that the extrachromosomal DNA containing EPSPS is approximately 400 kb similar in size with that of eccDNA replicon in Amaranthus palmeri. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Dal-Hoe Koo
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Yoonha Ju
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Karthik Putta
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Rajendran Sathishraj
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Nilda Roma-Burgos
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Bernd Friebe
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Bikram S Gill
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
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Multiple heterochromatin diversification events in the genome of fungus-farming ants: insights from repetitive sequences. Chromosoma 2022; 131:59-75. [PMID: 35325297 DOI: 10.1007/s00412-022-00770-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/18/2022] [Accepted: 02/21/2022] [Indexed: 11/03/2022]
Abstract
A substantial portion of the eukaryotic genome includes repetitive DNA, which is important for its stability, regulation, and architecture. Fungus-farming ant genomes show remarkable structural rearrangement rates that were necessary for the establishment of their agriculture-based lifestyle, highlighting the relevance of this peculiar group in understanding the repetitive portion of ant genome. Chromosomal banding studies are in accordance with genomic data because they show that repetitive heterochromatic sequences of basal and derivative Attina species are GC-rich, an uncommon trait in Formicidae. To understand the evolutionary dynamics of heterochromatin in Attina, we compared GC-rich heterochromatin patterns between the Paleoattina and Neoattina clades of this subtribe. To this end, we hybridized the Mrel-C0t probe (highly and moderately repetitive DNA) obtained from Mycetomoellerius relictus, Neoattina with GC-rich heterochromatin, in karyotypes of Paleoattina and Neoattina species. Additionally, we mapped the repetitive sequences (GA)15 and (TTAGG)6 in species of the two clades to investigate their organization and evolutionary patterns in the genome of Attina. The Mrel-C0t probe marked the heterochromatin in M. relictus, in other Mycetomoellerius spp., and in species of Mycetarotes, Cyphomyrmex, and Sericomyrmex (Neoattina). In Mycetomoellerius urichii, only pericentromeric heterochromatin was marked with Mrel-C0t. No marking was observed in Paleoattina species or in Atta and Acromyrmex (Neoattina). These results indicated that different evolutionary events led to heterochromatin differentiation in Attina. The most likely hypothesis is that GC-rich heterochromatin arose in the common ancestor of the two clades and accumulated various changes throughout evolution. The sequences (GA)15 and (TTAGG)6 located in euchromatin and telomeres, respectively, showed more homogeneous results among the species.
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Šimoníková D, Čížková J, Zoulová V, Christelová P, Hřibová E. Advances in the Molecular Cytogenetics of Bananas, Family Musaceae. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040482. [PMID: 35214815 PMCID: PMC8879896 DOI: 10.3390/plants11040482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 05/03/2023]
Abstract
The banana is a staple food crop and represents an important trade commodity for millions of people living in tropical and subtropical countries. The most important edible banana clones originated from natural crosses between diploid Musa balbisiana and various subspecies of M. acuminata. It is worth mentioning that evolution and speciation in the Musaceae family were accompanied by large-scale chromosome structural changes, indicating possible reasons for lower fertility or complete sterility of these vegetatively propagated clones. Chromosomal changes, often accompanied by changes in genome size, are one of the driving forces underlying speciation in plants. They can clarify the genomic constitution of edible bananas and shed light on their origin and on diversification processes in members of the Musaceae family. This article reviews the development of molecular cytogenetic approaches, ranging from classical fluorescence in situ hybridization (FISH) using common cytogenetic markers to oligo painting FISH. We discuss differences in genome size and chromosome number across the Musaceae family in addition to the development of new chromosome-specific cytogenetic probes and their use in genome structure and comparative karyotype analysis. The impact of these methodological advances on our knowledge of Musa genome evolution at the chromosomal level is demonstrated. In addition to citing published results, we include our own new unpublished results and outline future applications of molecular cytogenetics in banana research.
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Affiliation(s)
- Denisa Šimoníková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic; (D.Š.); (J.Č.); (V.Z.); (P.C.)
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic; (D.Š.); (J.Č.); (V.Z.); (P.C.)
| | - Veronika Zoulová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic; (D.Š.); (J.Č.); (V.Z.); (P.C.)
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, 77900 Olomouc, Czech Republic
| | - Pavla Christelová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic; (D.Š.); (J.Č.); (V.Z.); (P.C.)
| | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic; (D.Š.); (J.Č.); (V.Z.); (P.C.)
- Correspondence: ; Tel.: +420-585-238-713
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Chen Y, Zhang Q, Liu H. An emerging role of transcription in chromosome segregation: Ongoing centromeric transcription maintains centromeric cohesion. Bioessays 2021; 44:e2100201. [PMID: 34761408 DOI: 10.1002/bies.202100201] [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: 08/19/2021] [Revised: 10/19/2021] [Accepted: 10/26/2021] [Indexed: 01/09/2023]
Abstract
Non-coding centromeres, which dictate kinetochore formation for proper chromosome segregation, are extremely divergent in DNA sequences across species but are under active transcription carried out by RNA polymerase (RNAP) II. The RNAP II-mediated centromeric transcription has been shown to facilitate the deposition of the centromere protein A (CENP-A) to centromeres, establishing a conserved and critical role of centromeric transcription in centromere maintenance. Our recent work revealed another role of centromeric transcription in chromosome segregation: maintaining centromeric cohesion during mitosis. Interestingly, this role appears to be fulfilled through ongoing centromeric transcription rather than centromeric transcripts. In addition, we found that centromeric transcription may not require some of the traditional transcription initiation factors, suggestive of "uniqueness" in its regulation. In this review, we discuss the novel role and regulation of centromeric transcription as well as the potential underlying mechanisms.
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Affiliation(s)
- Yujue Chen
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, 70112, USA
| | - Qian Zhang
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, 70112, USA
| | - Hong Liu
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, 70112, USA.,Tulane Cancer Center, Tulane University School of Medicine, New Orleans, 70112, USA.,Tulane Aging Center, Tulane University School of Medicine, New Orleans, 70112, USA
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Lin G, He C, Zheng J, Koo DH, Le H, Zheng H, Tamang TM, Lin J, Liu Y, Zhao M, Hao Y, McFraland F, Wang B, Qin Y, Tang H, McCarty DR, Wei H, Cho MJ, Park S, Kaeppler H, Kaeppler SM, Liu Y, Springer N, Schnable PS, Wang G, White FF, Liu S. Chromosome-level genome assembly of a regenerable maize inbred line A188. Genome Biol 2021; 22:175. [PMID: 34108023 PMCID: PMC8188678 DOI: 10.1186/s13059-021-02396-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 05/28/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies. RESULTS Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus. CONCLUSIONS The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues.
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Affiliation(s)
- Guifang Lin
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Center, Manhattan, KS, 66506-5502, USA
| | - Cheng He
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Center, Manhattan, KS, 66506-5502, USA
| | - Jun Zheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dal-Hoe Koo
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Center, Manhattan, KS, 66506-5502, USA
| | - Ha Le
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Center, Manhattan, KS, 66506-5502, USA
| | - Huakun Zheng
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Center, Manhattan, KS, 66506-5502, USA
| | - Tej Man Tamang
- Department of Horticulture and Natural Resources, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Jinguang Lin
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Center, Manhattan, KS, 66506-5502, USA
- Present Address, Corvallis, OR, 97330, USA
| | - Yan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mingxia Zhao
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Center, Manhattan, KS, 66506-5502, USA
| | - Yangfan Hao
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Center, Manhattan, KS, 66506-5502, USA
| | - Frank McFraland
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Yang Qin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haibao Tang
- Center for Genomics and Biotechnology and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Donald R McCarty
- Department of Horticulture, University of Florida, Gainesville, FL, 32611-0680, USA
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Myeong-Je Cho
- Innovative Genomics Institute, University of California-Berkeley, Sunnyvale, CA, 94704, USA
| | - Sunghun Park
- Department of Horticulture and Natural Resources, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Heidi Kaeppler
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yunjun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Nathan Springer
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Patrick S Schnable
- Department of Agronomy, Iowa State University, Ames, IA, 50011-3605, USA
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611-0680, USA
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Center, Manhattan, KS, 66506-5502, USA.
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Abstract
Hibiscus exhibits high variation in chromosome number both within and among species. The Hibiscus mutabilis L. karyotype was analyzed in detail using fluorescence in situ hybridization (FISH) with oligonucleotide probes for (AG3T3)3 and 5S rDNA, which were tested here for the first time. In total, 90 chromosomes were counted in prometaphase and metaphase, and all exhibited similarly intense (AG3T3)3 signals at both ends. (AG3T3)3 showed little variation and thus did not allow discrimination among H. mutabilis chromosomes, but its location at both ends confirmed the integrity of each chromosome, thus contributing to accurate counting of the numerous, small chromosomes. Oligo-5S rDNA marked the proximal/distal regions of six chromosomes: weak signals on chromosomes 7 and 8, slightly stronger signals on chromosomes 15 and 16, and very strong signals on chromosomes 17 and 18. Therefore, 5S rDNA could assist in chromosome identification in H. mutabilis. Metaphase chromosome lengths ranged from 3.00 to 1.18 μm, indicating small chromosomes. The ratios of longest to shortest chromosome length in prometaphase and metaphase were 2.58 and 2.54, respectively, indicating karyotype asymmetry in H. mutabilis. These results provide an exact chromosome number and a physical map, which will be useful for genome assembly and contribute to molecular cytogenetics in the genus Hibiscus.
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Affiliation(s)
- Xiaomei Luo
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, China.,College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, China
| | - Zhoujian He
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, China.,College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, China
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Agrawal N, Gupta M, Banga SS, Heslop-Harrison JS(P. Identification of Chromosomes and Chromosome Rearrangements in Crop Brassicas and Raphanus sativus: A Cytogenetic Toolkit Using Synthesized Massive Oligonucleotide Libraries. FRONTIERS IN PLANT SCIENCE 2020; 11:598039. [PMID: 33414797 PMCID: PMC7783396 DOI: 10.3389/fpls.2020.598039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 11/30/2020] [Indexed: 05/10/2023]
Abstract
Crop brassicas include three diploid [Brassica rapa (AA; 2n = 2x = 16), B. nigra (BB; 2n = 2x = 18), and B. oleracea (CC; 2n = 2x = 20)] and three derived allotetraploid species. It is difficult to distinguish Brassica chromosomes as they are small and morphologically similar. We aimed to develop a genome-sequence based cytogenetic toolkit for reproducible identification of Brassica chromosomes and their structural variations. A bioinformatic pipeline was used to extract repeat-free sequences from the whole genome assembly of B. rapa. Identified sequences were subsequently used to develop four c. 47-mer oligonucleotide libraries comprising 27,100, 11,084, 9,291, and 16,312 oligonucleotides. We selected these oligonucleotides after removing repeats from 18 identified sites (500-1,000 kb) with 1,997-5,420 oligonucleotides localized at each site in B. rapa. For one set of probes, a new method for amplification or immortalization of the library is described. oligonucleotide probes produced specific and reproducible in situ hybridization patterns for all chromosomes belonging to A, B, C, and R (Raphanus sativus) genomes. The probes were able to identify structural changes between the genomes, including translocations, fusions, and deletions. Furthermore, the probes were able to identify a structural translocation between a pak choi and turnip cultivar of B. rapa. Overall, the comparative chromosomal mapping helps understand the role of chromosome structural changes during genome evolution and speciation in the family Brassicaceae. The probes can also be used to identify chromosomes in aneuploids such as addition lines used for gene mapping, and to track transfer of chromosomes in hybridization and breeding programs.
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Affiliation(s)
- Neha Agrawal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Mehak Gupta
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Surinder S. Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - JS (Pat) Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Bury L, Moodie B, Ly J, McKay LS, Miga KH, Cheeseman IM. Alpha-satellite RNA transcripts are repressed by centromere-nucleolus associations. eLife 2020; 9:59770. [PMID: 33174837 PMCID: PMC7679138 DOI: 10.7554/elife.59770] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/09/2020] [Indexed: 01/03/2023] Open
Abstract
Although originally thought to be silent chromosomal regions, centromeres are instead actively transcribed. However, the behavior and contributions of centromere-derived RNAs have remained unclear. Here, we used single-molecule fluorescence in-situ hybridization (smFISH) to detect alpha-satellite RNA transcripts in intact human cells. We find that alpha-satellite RNA-smFISH foci levels vary across cell lines and over the cell cycle, but do not remain associated with centromeres, displaying localization consistent with other long non-coding RNAs. Alpha-satellite expression occurs through RNA polymerase II-dependent transcription, but does not require established centromere or cell division components. Instead, our work implicates centromere–nucleolar interactions as repressing alpha-satellite expression. The fraction of nucleolar-localized centromeres inversely correlates with alpha-satellite transcripts levels across cell lines and transcript levels increase substantially when the nucleolus is disrupted. The control of alpha-satellite transcripts by centromere-nucleolar contacts provides a mechanism to modulate centromere transcription and chromatin dynamics across diverse cell states and conditions.
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Affiliation(s)
- Leah Bury
- Whitehead Institute for Biomedical Research, Cambridge, United States
| | - Brittania Moodie
- Whitehead Institute for Biomedical Research, Cambridge, United States
| | - Jimmy Ly
- Whitehead Institute for Biomedical Research, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Liliana S McKay
- Whitehead Institute for Biomedical Research, Cambridge, United States
| | - Karen Hh Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, United States
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
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11
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Arunkumar G, Melters DP. Centromeric Transcription: A Conserved Swiss-Army Knife. Genes (Basel) 2020; 11:E911. [PMID: 32784923 PMCID: PMC7463856 DOI: 10.3390/genes11080911] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 12/11/2022] Open
Abstract
In most species, the centromere is comprised of repetitive DNA sequences, which rapidly evolve. Paradoxically, centromeres fulfill an essential function during mitosis, as they are the chromosomal sites wherein, through the kinetochore, the mitotic spindles bind. It is now generally accepted that centromeres are transcribed, and that such transcription is associated with a broad range of functions. More than a decade of work on this topic has shown that centromeric transcripts are found across the eukaryotic tree and associate with heterochromatin formation, chromatin structure, kinetochore structure, centromeric protein loading, and inner centromere signaling. In this review, we discuss the conservation of small and long non-coding centromeric RNAs, their associations with various centromeric functions, and their potential roles in disease.
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Affiliation(s)
| | - Daniël P. Melters
- Chromatin Structure and Epigenetic Mechanisms, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA;
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12
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Application and prospects of CRISPR/Cas9-based methods to trace defined genomic sequences in living and fixed plant cells. Chromosome Res 2019; 28:7-17. [PMID: 31792795 DOI: 10.1007/s10577-019-09622-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 11/15/2019] [Accepted: 11/19/2019] [Indexed: 02/08/2023]
Abstract
The 3D organization of chromatin plays an important role in genome stability and many other pivotal biological programs. Therefore, the establishment of imaging methods, which enable us to study the dynamics of chromatin in living cells, is necessary. Although primary live cell imaging methods were a breakthrough, there is a need to develop more specific labeling techniques. With the discovery of programmable DNA binding proteins, such zinc finger proteins (ZFP), transcription activator-like effectors (TALE), and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), a major leap forward was made. Here, we review the applications and potential of fluorescent repressor-operator systems, programmable DNA binding proteins with an emphasis on CRISPR-based chromatin imaging in living and fixed cells, and their potential application in plant science.
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13
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Šimoníková D, Němečková A, Karafiátová M, Uwimana B, Swennen R, Doležel J, Hřibová E. Chromosome Painting Facilitates Anchoring Reference Genome Sequence to Chromosomes In Situ and Integrated Karyotyping in Banana ( Musa Spp.). FRONTIERS IN PLANT SCIENCE 2019; 10:1503. [PMID: 31824534 DOI: 10.3389/fpls.2019.01503/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/29/2019] [Indexed: 05/24/2023]
Abstract
Oligo painting FISH was established to identify all chromosomes in banana (Musa spp.) and to anchor pseudomolecules of reference genome sequence of Musa acuminata spp. malaccensis "DH Pahang" to individual chromosomes in situ. A total of 19 chromosome/chromosome-arm specific oligo painting probes were developed and were shown to be suitable for molecular cytogenetic studies in genus Musa. For the first time, molecular karyotypes of diploid M. acuminata spp. malaccensis (A genome), M. balbisiana (B genome), and M. schizocarpa (S genome) from the Eumusa section of Musa, which contributed to the evolution of edible banana cultivars, were established. This was achieved after a combined use of oligo painting probes and a set of previously developed banana cytogenetic markers. The density of oligo painting probes was sufficient to study chromosomal rearrangements on mitotic as well as on meiotic pachytene chromosomes. This advance will enable comparative FISH mapping and identification of chromosomal translocations which accompanied genome evolution and speciation in the family Musaceae.
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Affiliation(s)
- Denisa Šimoníková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Alžbeěta Němečková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Brigitte Uwimana
- Banana Breeding, International Institute of Tropical Agriculture, Kampala, Uganda
| | - Rony Swennen
- Bioversity International, Banana Genetic Resources, Heverlee, Belgium
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, Katholieke Universiteit Leuven, Leuven, Belgium
- Banana Breeding, International Institute of Tropical Agriculture, Arusha, Tanzania
| | - Jaroslav Doležel
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Eva Hřibová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
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14
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Duda Z, Trusiak S, O'Neill R. Centromere Transcription: Means and Motive. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019; 56:257-281. [PMID: 28840241 DOI: 10.1007/978-3-319-58592-5_11] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The chromosome biology field at large has benefited from studies of the cell cycle components, protein cascades and genomic landscape that are required for centromere identity, assembly and stable transgenerational inheritance. Research over the past 20 years has challenged the classical descriptions of a centromere as a stable, unmutable, and transcriptionally silent chromosome component. Instead, based on studies from a broad range of eukaryotic species, including yeast, fungi, plants, and animals, the centromere has been redefined as one of the more dynamic areas of the eukaryotic genome, requiring coordination of protein complex assembly, chromatin assembly, and transcriptional activity in a cell cycle specific manner. What has emerged from more recent studies is the realization that the transcription of specific types of nucleic acids is a key process in defining centromere integrity and function. To illustrate the transcriptional landscape of centromeres across eukaryotes, we focus this review on how transcripts interact with centromere proteins, when in the cell cycle centromeric transcription occurs, and what types of sequences are being transcribed. Utilizing data from broadly different organisms, a picture emerges that places centromeric transcription as an integral component of centromere function.
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Affiliation(s)
- Zachary Duda
- Department of Molecular and Cell Biology, The Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
| | - Sarah Trusiak
- Department of Molecular and Cell Biology, The Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
| | - Rachel O'Neill
- Department of Molecular and Cell Biology, The Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA.
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15
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Luo X, Liu J. Fluorescence In Situ Hybridization (FISH) Analysis of the Locations of the Oligonucleotides 5S rDNA, (AGGGTTT) 3, and (TTG) 6 in Three Genera of Oleaceae and Their Phylogenetic Framework. Genes (Basel) 2019; 10:genes10050375. [PMID: 31108932 PMCID: PMC6562466 DOI: 10.3390/genes10050375] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 11/29/2022] Open
Abstract
We report the cytogenetic map for a collection of species in the Oleaceae, and test similarities among the karyotypes relative to their known species phylogeny. The oligonucleotides 5S ribosomal DNA (rDNA), (AGGGTTT)3, and (TTG)6 were used as fluorescence in situ hybridization (FISH) probes to locate the corresponding chromosomes in three Oleaceae genera: Fraxinus pennsylvanica, Syringa oblata, Ligustrum lucidum, and Ligustrum × vicaryi. Forty-six small chromosomes were identified in four species. (AGGGTTT)3 signals were observed on almost all chromosome ends of four species, but (AGGGTTT)3 played no role in distinguishing the chromosomes but displayed intact chromosomes and could thus be used as a guide for finding chromosome counts. (TTG)6 and 5S rDNA signals discerned several chromosomes located at subterminal or central regions. Based on the similarity of the signal pattern (mainly in number and location and less in intensity) of the four species, the variations in the 5S rDNA and (TTG)6 distribution can be ordered as L. lucidum < L. × vicaryi < F. pennsylvanica < S. oblata. Variations have observed in the three genera. The molecular cytogenetic data presented here might serve as a starting point for further larger-scale elucidation of the structure of the Oleaceae genome, and comparison with the known phylogeny of Oleaceae family.
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Affiliation(s)
- Xiaomei Luo
- College of Forestry, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
| | - Juncheng Liu
- College of Forestry, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
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16
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Deng H, Xiang S, Guo Q, Jin W, Cai Z, Liang G. Molecular cytogenetic analysis of genome-specific repetitive elements in Citrus clementina Hort. Ex Tan. and its taxonomic implications. BMC PLANT BIOLOGY 2019; 19:77. [PMID: 30770721 PMCID: PMC6377768 DOI: 10.1186/s12870-019-1676-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 02/07/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Clementine mandarin (Citrus clementina Hort. ex Tan.) is one of the most famous and widely grown citrus cultivars worldwide. Variations in relation to the composition and distribution of repetitive DNA sequences that dominate greatly in eukaryote genomes are considered to be species-, genome-, or even chromosome-specific. Repetitive DNA-based fluorescence in situ hybridization (FISH) is a powerful tool for molecular cytogenetic study. However, to date few studies have involved in the repetitive elements and cytogenetic karyotype of Clementine. RESULTS A graph-based similarity sequence read clustering methodology was performed to analyze the repetitive DNA families in the Clementine genome. The bioinformatics analysis showed that repetitive DNAs constitute 41.95% of the Clementine genome, and the majority of repetitive elements are retrotransposons and satellite DNAs. Sequential multicolor FISH using a probe mix that contained CL17, four satellite DNAs, two rDNAs and an oligonucleotide of (TTTAGGG)3 was performed with Clementine somatic metaphase chromosomes. An integrated karyotype of Clementine was established based on unequivocal and reproducible chromosome discriminations. The distribution patterns of these probes in several Citrus, Poncirus and Fortunella species were summarized through extensive FISH analyses. Polymorphism and heterozygosity were commonly observed in the three genera. Some asymmetrical FISH loci in Clementine were in agreement with its hybrid origin. CONCLUSIONS The composition and abundance of repetitive elements in the Clementine genome were reanalyzed. Multicolor FISH-based karyotyping provided direct visual proof of the heterozygous nature of Clementine chromosomes with conspicuous asymmetrical FISH hybridization signals. We detected some similar and variable distribution patterns of repetitive DNAs in Citrus, Poncirus, and Fortunella, which revealed notable conservation among these genera, as well as obvious polymorphism and heterozygosity, indicating the potential utility of these repetitive element markers for the study of taxonomic, phylogenetic and evolutionary relationships in the future.
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Affiliation(s)
- Honghong Deng
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715 China
| | - Suqiong Xiang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715 China
| | - Qigao Guo
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715 China
| | - Weiwei Jin
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Zexi Cai
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Guolu Liang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715 China
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17
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Abstract
Fluorescence in situ hybridization (FISH) is used to examine chromosomal abnormalities and DNA damage. Developed in the early 1980s, this technique remains an important tool for understanding chromosome biology and diagnosing genetic disease and cancer. Use of FISH on metaphase chromosomes allows the visualization of chromosomal abnormalities at specific loci. Here, we describe methods for creating metaphase chromosome spreads and the use of telomere FISH probes to detect chromosome ends.
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Affiliation(s)
- P Logan Schuck
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Jason A Stewart
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.
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18
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Šimoníková D, Němečková A, Karafiátová M, Uwimana B, Swennen R, Doležel J, Hřibová E. Chromosome Painting Facilitates Anchoring Reference Genome Sequence to Chromosomes In Situ and Integrated Karyotyping in Banana ( Musa Spp.). FRONTIERS IN PLANT SCIENCE 2019; 10:1503. [PMID: 31824534 PMCID: PMC6879668 DOI: 10.3389/fpls.2019.01503] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/29/2019] [Indexed: 05/04/2023]
Abstract
Oligo painting FISH was established to identify all chromosomes in banana (Musa spp.) and to anchor pseudomolecules of reference genome sequence of Musa acuminata spp. malaccensis "DH Pahang" to individual chromosomes in situ. A total of 19 chromosome/chromosome-arm specific oligo painting probes were developed and were shown to be suitable for molecular cytogenetic studies in genus Musa. For the first time, molecular karyotypes of diploid M. acuminata spp. malaccensis (A genome), M. balbisiana (B genome), and M. schizocarpa (S genome) from the Eumusa section of Musa, which contributed to the evolution of edible banana cultivars, were established. This was achieved after a combined use of oligo painting probes and a set of previously developed banana cytogenetic markers. The density of oligo painting probes was sufficient to study chromosomal rearrangements on mitotic as well as on meiotic pachytene chromosomes. This advance will enable comparative FISH mapping and identification of chromosomal translocations which accompanied genome evolution and speciation in the family Musaceae.
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Affiliation(s)
- Denisa Šimoníková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Alžbeěta Němečková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Brigitte Uwimana
- Banana Breeding, International Institute of Tropical Agriculture, Kampala, Uganda
| | - Rony Swennen
- Bioversity International, Banana Genetic Resources, Heverlee, Belgium
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, Katholieke Universiteit Leuven, Leuven, Belgium
- Banana Breeding, International Institute of Tropical Agriculture, Arusha, Tanzania
| | - Jaroslav Doležel
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Eva Hřibová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
- *Correspondence: Eva Hřibová,
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19
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Talbert PB, Henikoff S. Transcribing Centromeres: Noncoding RNAs and Kinetochore Assembly. Trends Genet 2018; 34:587-599. [DOI: 10.1016/j.tig.2018.05.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 12/20/2022]
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20
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Koo DH, Molin WT, Saski CA, Jiang J, Putta K, Jugulam M, Friebe B, Gill BS. Extrachromosomal circular DNA-based amplification and transmission of herbicide resistance in crop weed Amaranthus palmeri. Proc Natl Acad Sci U S A 2018; 115:3332-3337. [PMID: 29531028 PMCID: PMC5879691 DOI: 10.1073/pnas.1719354115] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Gene amplification has been observed in many bacteria and eukaryotes as a response to various selective pressures, such as antibiotics, cytotoxic drugs, pesticides, herbicides, and other stressful environmental conditions. An increase in gene copy number is often found as extrachromosomal elements that usually contain autonomously replicating extrachromosomal circular DNA molecules (eccDNAs). Amaranthus palmeri, a crop weed, can develop herbicide resistance to glyphosate [N-(phosphonomethyl) glycine] by amplification of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene, the molecular target of glyphosate. However, biological questions regarding the source of the amplified EPSPS, the nature of the amplified DNA structures, and mechanisms responsible for maintaining this gene amplification in cells and their inheritance remain unknown. Here, we report that amplified EPSPS copies in glyphosate-resistant (GR) A. palmeri are present in the form of eccDNAs with various conformations. The eccDNAs are transmitted during cell division in mitosis and meiosis to the soma and germ cells and the progeny by an as yet unknown mechanism of tethering to mitotic and meiotic chromosomes. We propose that eccDNAs are one of the components of McClintock's postulated innate systems [McClintock B (1978) Stadler Genetics Symposium] that can rapidly produce soma variation, amplify EPSPS genes in the sporophyte that are transmitted to germ cells, and modulate rapid glyphosate resistance through genome plasticity and adaptive evolution.
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Affiliation(s)
- Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506
| | - William T Molin
- Crop Production Systems Research Unit, US Department of Agriculture-Agricultural Research Services, Stoneville, MS 38776
| | | | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824
- Department of Horticulture, Michigan State University, East Lansing, MI 48824
| | - Karthik Putta
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - Bernd Friebe
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506
| | - Bikram S Gill
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506;
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21
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Dreissig S, Schiml S, Schindele P, Weiss O, Rutten T, Schubert V, Gladilin E, Mette MF, Puchta H, Houben A. Live-cell CRISPR imaging in plants reveals dynamic telomere movements. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:565-573. [PMID: 28509419 PMCID: PMC5599988 DOI: 10.1111/tpj.13601] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/11/2017] [Accepted: 05/09/2017] [Indexed: 05/11/2023]
Abstract
Elucidating the spatiotemporal organization of the genome inside the nucleus is imperative to our understanding of the regulation of genes and non-coding sequences during development and environmental changes. Emerging techniques of chromatin imaging promise to bridge the long-standing gap between sequencing studies, which reveal genomic information, and imaging studies that provide spatial and temporal information of defined genomic regions. Here, we demonstrate such an imaging technique based on two orthologues of the bacterial clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein 9 (Cas9). By fusing eGFP/mRuby2 to catalytically inactive versions of Streptococcus pyogenes and Staphylococcus aureus Cas9, we show robust visualization of telomere repeats in live leaf cells of Nicotiana benthamiana. By tracking the dynamics of telomeres visualized by CRISPR-dCas9, we reveal dynamic telomere movements of up to 2 μm over 30 min during interphase. Furthermore, we show that CRISPR-dCas9 can be combined with fluorescence-labelled proteins to visualize DNA-protein interactions in vivo. By simultaneously using two dCas9 orthologues, we pave the way for the imaging of multiple genomic loci in live plants cells. CRISPR imaging bears the potential to significantly improve our understanding of the dynamics of chromosomes in live plant cells.
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Affiliation(s)
- Steven Dreissig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466SeelandGermany
| | - Simon Schiml
- Botanical InstituteKarlsruhe Institute of TechnologyPOB 698076049KarlsruheGermany
| | - Patrick Schindele
- Botanical InstituteKarlsruhe Institute of TechnologyPOB 698076049KarlsruheGermany
| | - Oda Weiss
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466SeelandGermany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466SeelandGermany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466SeelandGermany
| | - Evgeny Gladilin
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466SeelandGermany
| | - Michael F. Mette
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466SeelandGermany
- Present address:
King Abdullah University of Science & TechnologyThuwal23955‐6900Saudi Arabia
| | - Holger Puchta
- Botanical InstituteKarlsruhe Institute of TechnologyPOB 698076049KarlsruheGermany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466SeelandGermany
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22
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Bilinski P, Han Y, Hufford MB, Lorant A, Zhang P, Estep MC, Jiang J, Ross-Ibarra J. Genomic abundance is not predictive of tandem repeat localization in grass genomes. PLoS One 2017; 12:e0177896. [PMID: 28570674 PMCID: PMC5453492 DOI: 10.1371/journal.pone.0177896] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 05/04/2017] [Indexed: 11/25/2022] Open
Abstract
Highly repetitive regions have historically posed a challenge when investigating sequence variation and content. High-throughput sequencing has enabled researchers to use whole-genome shotgun sequencing to estimate the abundance of repetitive sequence, and these methodologies have been recently applied to centromeres. Previous research has investigated variation in centromere repeats across eukaryotes, positing that the highest abundance tandem repeat in a genome is often the centromeric repeat. To test this assumption, we used shotgun sequencing and a bioinformatic pipeline to identify common tandem repeats across a number of grass species. We find that de novo assembly and subsequent abundance ranking of repeats can successfully identify tandem repeats with homology to known tandem repeats. Fluorescent in-situ hybridization shows that de novo assembly and ranking of repeats from non-model taxa identifies chromosome domains rich in tandem repeats both near pericentromeres and elsewhere in the genome.
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Affiliation(s)
- Paul Bilinski
- Dept. of Plant Sciences, University of California, Davis, Davis, CA, United States of America
- * E-mail: (PB); (JRI)
| | - Yonghua Han
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Dept. of Horticulture, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Matthew B. Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States of America
| | - Anne Lorant
- Dept. of Plant Sciences, University of California, Davis, Davis, CA, United States of America
| | - Pingdong Zhang
- Dept. of Horticulture, University of Wisconsin-Madison, Madison, WI, United States of America
- College of Bioscience and Biotechnology, Beijing Forestry University, Beijing, China
| | - Matt C. Estep
- Dept. of Biology, Appalachian State University, Boone, NC, United States of America
| | - Jiming Jiang
- Dept. of Horticulture, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Jeffrey Ross-Ibarra
- Dept. of Plant Sciences, University of California, Davis, Davis, CA, United States of America
- Genome Center and Center for Population Biology, University of California, Davis, Davis, CA, United States of America
- * E-mail: (PB); (JRI)
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23
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Friedman S, Freitag M. Centrochromatin of Fungi. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2017; 56:85-109. [PMID: 28840234 DOI: 10.1007/978-3-319-58592-5_4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The centromere is an essential chromosomal locus that dictates the nucleation point for assembly of the kinetochore and subsequent attachment of spindle microtubules during chromosome segregation. Research over the last decades demonstrated that centromeres are defined by a combination of genetic and epigenetic factors. Recent work showed that centromeres are quite diverse and flexible and that many types of centromere sequences and centromeric chromatin ("centrochromatin") have evolved. The kingdom of the fungi serves as an outstanding example of centromere plasticity, including organisms with centromeres as diverse as 0.15-300 kb in length, and with different types of chromatin states for most species examined thus far. Some of the species in the less familiar taxa provide excellent opportunities to help us better understand centromere biology in all eukaryotes, which may improve treatment options against fungal infection, and biotechnologies based on fungi. This review summarizes the current knowledge of fungal centromeres and centrochromatin, including an outlook for future research.
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Affiliation(s)
- Steven Friedman
- Department of Biochemistry and Biophysics, Oregon State University, 2011 ALS Bldg, Corvallis, OR, 97331, USA
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, 2011 ALS Bldg, Corvallis, OR, 97331, USA.
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