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Topoisomerase VI participates in an insulator-like function that prevents H3K9me2 spreading. Proc Natl Acad Sci U S A 2022; 119:e2001290119. [PMID: 35759655 PMCID: PMC9271158 DOI: 10.1073/pnas.2001290119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The organization of the genome into transcriptionally active and inactive chromatin domains requires well-delineated chromatin boundaries and insulator functions in order to maintain the identity of adjacent genomic loci with antagonistic chromatin marks and functionality. In plants that lack known chromatin insulators, the mechanisms that prevent heterochromatin spreading into euchromatin remain to be identified. Here, we show that DNA Topoisomerase VI participates in a chromatin boundary function that safeguards the expression of genes in euchromatin islands within silenced heterochromatin regions. While some transposable elements are reactivated in mutants of the Topoisomerase VI complex, genes insulated in euchromatin islands within heterochromatic regions of the Arabidopsis thaliana genome are specifically down-regulated. H3K9me2 levels consistently increase at euchromatin island loci and decrease at some transposable element loci. We further show that Topoisomerase VI physically interacts with S-adenosylmethionine synthase methionine adenosyl transferase 3 (MAT3), which is required for H3K9me2. A Topoisomerase VI defect affects MAT3 occupancy on heterochromatic elements and its exclusion from euchromatic islands, thereby providing a possible mechanistic explanation to the essential role of Topoisomerase VI in the delimitation of chromatin domains.
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Wang X, Shen C, Meng P, Tan G, Lv L. Analysis and review of trichomes in plants. BMC PLANT BIOLOGY 2021; 21:70. [PMID: 33526015 PMCID: PMC7852143 DOI: 10.1186/s12870-021-02840-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/11/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND Trichomes play a key role in the development of plants and exist in a wide variety of species. RESULTS In this paper, it was reviewed that the structure and morphology characteristics of trichomes, alongside the biological functions and classical regulatory mechanisms of trichome development in plants. The environment factors, hormones, transcription factor, non-coding RNA, etc., play important roles in regulating the initialization, branching, growth, and development of trichomes. In addition, it was further investigated the atypical regulation mechanism in a non-model plant, found that regulating the growth and development of tea (Camellia sinensis) trichome is mainly affected by hormones and the novel regulation factors. CONCLUSIONS This review further displayed the complex and differential regulatory networks in trichome initiation and development, provided a reference for basic and applied research on trichomes in plants.
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Affiliation(s)
- Xiaojing Wang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, People's Republic of China
| | - Chao Shen
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, People's Republic of China
| | - Pinghong Meng
- Institute of Horticulture, Guizhou Province Academy of Agricultural Sciences, Guiyang, Guizhou, People's Republic of China
| | - Guofei Tan
- Institute of Horticulture, Guizhou Province Academy of Agricultural Sciences, Guiyang, Guizhou, People's Republic of China.
| | - Litang Lv
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, People's Republic of China.
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Sutormin DA, Galivondzhyan AK, Polkhovskiy AV, Kamalyan SO, Severinov KV, Dubiley SA. Diversity and Functions of Type II Topoisomerases. Acta Naturae 2021; 13:59-75. [PMID: 33959387 PMCID: PMC8084294 DOI: 10.32607/actanaturae.11058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/09/2020] [Indexed: 11/29/2022] Open
Abstract
The DNA double helix provides a simple and elegant way to store and copy genetic information. However, the processes requiring the DNA helix strands separation, such as transcription and replication, induce a topological side-effect - supercoiling of the molecule. Topoisomerases comprise a specific group of enzymes that disentangle the topological challenges associated with DNA supercoiling. They relax DNA supercoils and resolve catenanes and knots. Here, we review the catalytic cycles, evolution, diversity, and functional roles of type II topoisomerases in organisms from all domains of life, as well as viruses and other mobile genetic elements.
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Affiliation(s)
- D. A. Sutormin
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - A. K. Galivondzhyan
- Lomonosov Moscow State University, Moscow, 119991 Russia
- Institute of Molecular Genetics RAS, Moscow, 123182 Russia
| | - A. V. Polkhovskiy
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - S. O. Kamalyan
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - K. V. Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
- Centre for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, Moscow, 119334 Russia
- Waksman Institute for Microbiology, Piscataway, New Jersey, 08854 USA
| | - S. A. Dubiley
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
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Garg R, Singh VK, Rajkumar MS, Kumar V, Jain M. Global transcriptome and coexpression network analyses reveal cultivar-specific molecular signatures associated with seed development and seed size/weight determination in chickpea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:1088-1107. [PMID: 28640939 DOI: 10.1111/tpj.13621] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 06/02/2017] [Accepted: 06/09/2017] [Indexed: 05/22/2023]
Abstract
Seed development is an intricate process regulated via a complex transcriptional regulatory network. To understand the molecular mechanisms governing seed development and seed size/weight in chickpea, we performed a comprehensive analysis of transcriptome dynamics during seed development in two cultivars with contrasting seed size/weight (small-seeded, Himchana 1 and large-seeded, JGK 3). Our analysis identified stage-specific expression for a significant proportion (>13%) of the genes in each cultivar. About one half of the total genes exhibited significant differential expression in JGK 3 as compared with Himchana 1. We found that different seed development stages can be delineated by modules of coexpressed genes. A comparative analysis revealed differential developmental stage specificity of some modules between the two cultivars. Furthermore, we constructed transcriptional regulatory networks and identified key components determining seed size/weight. The results suggested that extended period of cell division during embryogenesis and higher level of endoreduplication along with more accumulation of storage compounds during maturation determine large seed size/weight. Further, we identified quantitative trait loci-associated candidate genes harboring single nucleotide polymorphisms in the promoter sequences that differentiate small- and large-seeded chickpea cultivars. The results provide a valuable resource to dissect the role of candidate genes governing seed development and seed size/weight in chickpea.
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Affiliation(s)
- Rohini Garg
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
| | - Vikash K Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mohan Singh Rajkumar
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vinay Kumar
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mukesh Jain
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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Fitzgerald TL, Powell JJ, Stiller J, Weese TL, Abe T, Zhao G, Jia J, McIntyre CL, Li Z, Manners JM, Kazan K. An assessment of heavy ion irradiation mutagenesis for reverse genetics in wheat (Triticum aestivum L.). PLoS One 2015; 10:e0117369. [PMID: 25719507 PMCID: PMC4342231 DOI: 10.1371/journal.pone.0117369] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 12/22/2014] [Indexed: 11/19/2022] Open
Abstract
Reverse genetic techniques harnessing mutational approaches are powerful tools that can provide substantial insight into gene function in plants. However, as compared to diploid species, reverse genetic analyses in polyploid plants such as bread wheat can present substantial challenges associated with high levels of sequence and functional similarity amongst homoeologous loci. We previously developed a high-throughput method to identify deletions of genes within a physically mutagenized wheat population. Here we describe our efforts to combine multiple homoeologous deletions of three candidate disease susceptibility genes (TaWRKY11, TaPFT1 and TaPLDß1). We were able to produce lines featuring homozygous deletions at two of the three homoeoloci for all genes, but this was dependent on the individual mutants used in crossing. Intriguingly, despite extensive efforts, viable lines possessing homozygous deletions at all three homoeoloci could not be produced for any of the candidate genes. To investigate deletion size as a possible reason for this phenomenon, we developed an amplicon sequencing approach based on synteny to Brachypodium distachyon to assess the size of the deletions removing one candidate gene (TaPFT1) in our mutants. These analyses revealed that genomic deletions removing the locus are relatively large, resulting in the loss of multiple additional genes. The implications of this work for the use of heavy ion mutagenesis for reverse genetic analyses in wheat are discussed.
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Affiliation(s)
- Timothy L. Fitzgerald
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane, QLD, 4067, Australia
- * E-mail: (TLF); (KK)
| | - Jonathan J. Powell
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane, QLD, 4067, Australia
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Jiri Stiller
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane, QLD, 4067, Australia
| | - Terri L. Weese
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane, QLD, 4067, Australia
| | - Tomoko Abe
- RIKEN Nishina Center for Accelerator-Based Science, 2-1 Hirosawa, Wako, Saitama, 351–0198, Japan
| | - Guangyao Zhao
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jizeng Jia
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - C. Lynne McIntyre
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane, QLD, 4067, Australia
| | - Zhongyi Li
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Black Mountain Laboratories, Clunies Ross St, Acton, ACT, 2601, Australia
| | - John M. Manners
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Black Mountain Laboratories, Clunies Ross St, Acton, ACT, 2601, Australia
| | - Kemal Kazan
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane, QLD, 4067, Australia
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, 4072, Australia
- * E-mail: (TLF); (KK)
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