1
|
Vashisht I, Dhaka N, Jain R, Sood A, Sharma N, Sharma MK, Sharma R. Non-coding RNAs-mediated environmental surveillance determines male fertility in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108030. [PMID: 37708711 DOI: 10.1016/j.plaphy.2023.108030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/16/2023]
Abstract
Plants are continuously exposed to environmental stresses leading to significant yield losses. With the changing climatic conditions, the intensity and duration of these stresses are expected to increase, posing a severe threat to crop productivity worldwide. Male gametogenesis is one of the most sensitive developmental stages. Exposure to environmental stresses during this stage leads to male sterility and yield loss. Elucidating the underlying molecular mechanism of environment-affected male sterility is essential to address this challenge. High-throughput RNA sequencing studies, loss-of-function phenotypes of sRNA biogenesis genes and functional genomics studies with non-coding RNAs have started to unveil the roles of small RNAs, long non-coding RNAs and the complex regulatory interactions between them in regulating male fertility under different growth regimes. Here, we discuss the current understanding of the non-coding RNA-mediated environmental stress surveillance and regulation of male fertility in plants. The candidate ncRNAs emerging from these studies can be leveraged to generate environment-sensitive male sterile lines for hybrid breeding or mitigate the impact of climate change on male fertility, as the situation demands.
Collapse
Affiliation(s)
- Ira Vashisht
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Namrata Dhaka
- Department of Biotechnology, Central University of Haryana, Mahendergarh, Haryana, 123031, India
| | - Rubi Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India; Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Rajasthan, 333031, India
| | - Akanksha Sood
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Rajasthan, 333031, India
| | - Niharika Sharma
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW, 2800, Australia
| | - Manoj K Sharma
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rita Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Rajasthan, 333031, India.
| |
Collapse
|
2
|
Yang W, Bai Q, Li Y, Chen J, Liu C. Epigenetic modifications: Allusive clues of lncRNA functions in plants. Comput Struct Biotechnol J 2023; 21:1989-1994. [PMID: 36950220 PMCID: PMC10025020 DOI: 10.1016/j.csbj.2023.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 02/25/2023] [Accepted: 03/08/2023] [Indexed: 03/13/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been verified as flexible and important factors in various biological processes of multicellular eukaryotes, including plants. The respective intricate crosstalk among multiple epigenetic modifications has been examined to some extent. However, only a small proportion of lncRNAs has been functionally well characterized. Moreover, the relationship between lncRNAs and other epigenetic modifications has not been systematically studied. In this mini-review, we briefly summarize the representative biological functions of lncRNAs in developmental programs and environmental responses in plants. In addition, we particularly discuss the intimate relationship between lncRNAs and other epigenetic modifications, and we outline the underlying avenues and challenges for future research on plant lncRNAs.
Collapse
Affiliation(s)
- Wenjing Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Quanzi Bai
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yan Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianghua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, China
- Corresponding author at: CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China.
| |
Collapse
|
3
|
Genome-wide analysis of long noncoding RNAs, 24-nt siRNAs, DNA methylation and H3K27me3 marks in Brassica rapa. PLoS One 2021; 16:e0242530. [PMID: 33788851 PMCID: PMC8011741 DOI: 10.1371/journal.pone.0242530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/18/2021] [Indexed: 11/30/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are RNA fragments that generally do not code for a protein but are involved in epigenetic gene regulation. In this study, lncRNAs of Brassica rapa were classified into long intergenic noncoding RNAs, natural antisense RNAs, and intronic noncoding RNAs and their expression analyzed in relation to genome-wide 24-nt small interfering RNAs (siRNAs), DNA methylation, and histone H3 lysine 27 trimethylation marks (H3K27me3). More than 65% of the lncRNAs analyzed consisted of one exon, and more than 55% overlapped with inverted repeat regions (IRRs). Overlap of lncRNAs with IRRs or genomic regions encoding for 24-nt siRNAs resulted in increased DNA methylation levels when both were present. LncRNA did not overlap greatly with H3K27me3 marks, but the expression level of intronic noncoding RNAs that did coincide with H3K27me3 marks was higher than without H3K27me3 marks. The Brassica genus comprises important vegetables and oil seed crops grown across the world. B. rapa is a diploid (AA genome) thought to be one of the ancestral species of both B. juncea (AABB genome) and B. napus (AACC) through genome merging (allotetrapolyploidization). Complex genome restructuring and epigenetic alterations are thought to be involved in these allotetrapolyploidization events. Comparison of lncRNAs between B. rapa and B. nigra, B. oleracea, B. juncea, and B. napus showed the highest conservation with B. oleracea. This study presents a comprehensive analysis of the epigenome structure of B. rapa at multi-epigenetic levels (siRNAs, DNA methylation, H3K27me3, and lncRNAs) and identified a suite of candidate lncRNAs that may be epigenetically regulated in the Brassica genus.
Collapse
|
4
|
Abbas A, Yu P, Sun L, Yang Z, Chen D, Cheng S, Cao L. Exploiting Genic Male Sterility in Rice: From Molecular Dissection to Breeding Applications. FRONTIERS IN PLANT SCIENCE 2021; 12:629314. [PMID: 33763090 PMCID: PMC7982899 DOI: 10.3389/fpls.2021.629314] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/28/2021] [Indexed: 06/12/2023]
Abstract
Rice (Oryza sativa L.) occupies a very salient and indispensable status among cereal crops, as its vast production is used to feed nearly half of the world's population. Male sterile plants are the fundamental breeding materials needed for specific propagation in order to meet the elevated current food demands. The development of the rice varieties with desired traits has become the ultimate need of the time. Genic male sterility is a predominant system that is vastly deployed and exploited for crop improvement. Hence, the identification of new genetic elements and the cognizance of the underlying regulatory networks affecting male sterility in rice are crucial to harness heterosis and ensure global food security. Over the years, a variety of genomics studies have uncovered numerous mechanisms regulating male sterility in rice, which provided a deeper and wider understanding on the complex molecular basis of anther and pollen development. The recent advances in genomics and the emergence of multiple biotechnological methods have revolutionized the field of rice breeding. In this review, we have briefly documented the recent evolution, exploration, and exploitation of genic male sterility to the improvement of rice crop production. Furthermore, this review describes future perspectives with focus on state-of-the-art developments in the engineering of male sterility to overcome issues associated with male sterility-mediated rice breeding to address the current challenges. Finally, we provide our perspectives on diversified studies regarding the identification and characterization of genic male sterility genes, the development of new biotechnology-based male sterility systems, and their integrated applications for hybrid rice breeding.
Collapse
Affiliation(s)
- Adil Abbas
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Ping Yu
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Lianping Sun
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhengfu Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Daibo Chen
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Shihua Cheng
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Liyong Cao
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- Northern Center of China National Rice Research Institute, Shuangyashan, China
| |
Collapse
|
5
|
Zhou C, Zhou H, Ma X, Yang H, Wang P, Wang G, Zheng L, Zhang Y, Liu X. Genome-Wide Identification and Characterization of Main Histone Modifications in Sorghum Decipher Regulatory Mechanisms Involved by mRNA and Long Noncoding RNA Genes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2337-2347. [PMID: 33555853 DOI: 10.1021/acs.jafc.0c07035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Post-translational modifications of histones play an important chromatic role of a transcript activity in eukaryotes. Even though mRNA and long noncoding RNA (lncRNA) genes share similar biogenetic processes, these transcript classes may differ in many ways. However, knowledge about the crosstalk between histone methylations and the two types of sorghum genes is still ambiguous. In the present study, we reveal the genome-wide distribution of six histone modifications, namely, di- and trimethylation of H3K4 (H3K4me2 and H3K4me3), H3K27 (H3K27me2 and H3K27me3), and H3K36 (H3K36me2 and H3K36me3) in sorghum and analyze their functional relationships. Unlike other histone methylation, the codecoration of H3K4me3 and H3K36me3 is negatively associated with the production of lincRNAs in the context of active expression of mRNA genes. Our data demonstrated that H3K4me3 may act as a complementary component to H3K36me3 in the transcriptional regulatory process. Moreover, we observe that both H3K4me3 and H3K36me3 are involved in the negative-going regulation of plant lincRNA and mRNA genes. Our data provide a genome-wide landscape of histone methylation in sorghum, decrypt its reciprocity, and shed light on its transcriptional regulation roles in mRNA and lncRNA genes.
Collapse
Affiliation(s)
- Chao Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang 443002, China
| | - Hanlin Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang 443002, China
| | - Xueping Ma
- Laboratory of Medicinal Plant, Institute of Basic Medical Sciences, School of Basic Medicine, Biomedical Research Institute, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| | - Huilan Yang
- Institute for Interdisciplinary Research, Jianghan University, Wuhan 430056, China
| | - Ping Wang
- Institute for Interdisciplinary Research, Jianghan University, Wuhan 430056, China
| | - Guodong Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Lanlan Zheng
- Laboratory of Medicinal Plant, Institute of Basic Medical Sciences, School of Basic Medicine, Biomedical Research Institute, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| | - Yonghong Zhang
- Laboratory of Medicinal Plant, Institute of Basic Medical Sciences, School of Basic Medicine, Biomedical Research Institute, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| | - Xiaoyun Liu
- Institute for Interdisciplinary Research, Jianghan University, Wuhan 430056, China
| |
Collapse
|
6
|
Jin J, Lu P, Xu Y, Li Z, Yu S, Liu J, Wang H, Chua NH, Cao P. PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs. Nucleic Acids Res 2021; 49:D1489-D1495. [PMID: 33079992 PMCID: PMC7778960 DOI: 10.1093/nar/gkaa910] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/30/2020] [Accepted: 10/03/2020] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides with little or no protein coding potential. The expanding list of lncRNAs and accumulating evidence of their functions in plants have necessitated the creation of a comprehensive database for lncRNA research. However, currently available plant lncRNA databases have some deficiencies, including the lack of lncRNA data from some model plants, uneven annotation standards, a lack of visualization for expression patterns, and the absence of epigenetic information. To overcome these problems, we upgraded our Plant Long noncoding RNA Database (PLncDB, http://plncdb.tobaccodb.org/), which was based on a uniform annotation pipeline. PLncDB V2.0 currently contains 1 246 372 lncRNAs for 80 plant species based on 13 834 RNA-Seq datasets, integrating lncRNA information from four other resources including EVLncRNAs, RNAcentral and etc. Expression patterns and epigenetic signals can be visualized using multiple tools (JBrowse, eFP Browser and EPexplorer). Targets and regulatory networks for lncRNAs are also provided for function exploration. In addition, PLncDB V2.0 is hierarchical and user-friendly and has five built-in search engines. We believe PLncDB V2.0 is useful for the plant lncRNA community and data mining studies and provides a comprehensive resource for data-driven lncRNA research in plants.
Collapse
Affiliation(s)
- Jingjing Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Peng Lu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Yalong Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Zefeng Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Shizhou Yu
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco, Guiyang 550081, China
| | - Jun Liu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Nam-Hai Chua
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore.,Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, USA
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| |
Collapse
|
7
|
Pecinka A, Chevalier C, Colas I, Kalantidis K, Varotto S, Krugman T, Michailidis C, Vallés MP, Muñoz A, Pradillo M. Chromatin dynamics during interphase and cell division: similarities and differences between model and crop plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5205-5222. [PMID: 31626285 DOI: 10.1093/jxb/erz457] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Genetic information in the cell nucleus controls organismal development and responses to the environment, and finally ensures its own transmission to the next generations. To achieve so many different tasks, the genetic information is associated with structural and regulatory proteins, which orchestrate nuclear functions in time and space. Furthermore, plant life strategies require chromatin plasticity to allow a rapid adaptation to abiotic and biotic stresses. Here, we summarize current knowledge on the organization of plant chromatin and dynamics of chromosomes during interphase and mitotic and meiotic cell divisions for model and crop plants differing as to genome size, ploidy, and amount of genomic resources available. The existing data indicate that chromatin changes accompany most (if not all) cellular processes and that there are both shared and unique themes in the chromatin structure and global chromosome dynamics among species. Ongoing efforts to understand the molecular mechanisms involved in chromatin organization and remodeling have, together with the latest genome editing tools, potential to unlock crop genomes for innovative breeding strategies and improvements of various traits.
Collapse
Affiliation(s)
- Ales Pecinka
- Institute of Experimental Botany, Czech Acad Sci, Centre of the Region Haná for Agricultural and Biotechnological Research, Olomouc, Czech Republic
| | | | - Isabelle Colas
- James Hutton Institute, Cell and Molecular Science, Pr Waugh's Lab, Invergowrie, Dundee, UK
| | - Kriton Kalantidis
- Department of Biology, University of Crete, and Institute of Molecular Biology Biotechnology, FoRTH, Heraklion, Greece
| | - Serena Varotto
- Department of Agronomy Animal Food Natural Resources and Environment (DAFNAE) University of Padova, Agripolis viale dell'Università, Legnaro (PD), Italy
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Christos Michailidis
- Institute of Experimental Botany, Czech Acad Sci, Praha 6 - Lysolaje, Czech Republic
| | - María-Pilar Vallés
- Department of Genetics and Plant Breeding, Estación Experimental Aula Dei (EEAD), Spanish National Research Council (CSIC), Zaragoza, Spain
| | - Aitor Muñoz
- Department of Plant Molecular Genetics, National Center of Biotechnology/Superior Council of Scientific Research, Autónoma University of Madrid, Madrid, Spain
| | - Mónica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
| |
Collapse
|
8
|
Pourkheirandish M, Golicz AA, Bhalla PL, Singh MB. Global Role of Crop Genomics in the Face of Climate Change. FRONTIERS IN PLANT SCIENCE 2020; 11:922. [PMID: 32765541 PMCID: PMC7378793 DOI: 10.3389/fpls.2020.00922] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 06/05/2020] [Indexed: 05/05/2023]
Abstract
The development of climate change resilient crops is necessary if we are to meet the challenge of feeding the growing world's population. We must be able to increase food production despite the projected decrease in arable land and unpredictable environmental conditions. This review summarizes the technological and conceptual advances that have the potential to transform plant breeding, help overcome the challenges of climate change, and initiate the next plant breeding revolution. Recent developments in genomics in combination with high-throughput and precision phenotyping facilitate the identification of genes controlling critical agronomic traits. The discovery of these genes can now be paired with genome editing techniques to rapidly develop climate change resilient crops, including plants with better biotic and abiotic stress tolerance and enhanced nutritional value. Utilizing the genetic potential of crop wild relatives (CWRs) enables the domestication of new species and the generation of synthetic polyploids. The high-quality crop plant genome assemblies and annotations provide new, exciting research targets, including long non-coding RNAs (lncRNAs) and cis-regulatory regions. Metagenomic studies give insights into plant-microbiome interactions and guide selection of optimal soils for plant cultivation. Together, all these advances will allow breeders to produce improved, resilient crops in relatively short timeframes meeting the demands of the growing population and changing climate.
Collapse
Affiliation(s)
| | | | | | - Mohan B. Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| |
Collapse
|
9
|
Lu Y, Zhou DX, Zhao Y. Understanding epigenomics based on the rice model. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1345-1363. [PMID: 31897514 DOI: 10.1007/s00122-019-03518-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/18/2019] [Indexed: 05/26/2023]
Abstract
The purpose of this paper provides a comprehensive overview of the recent researches on rice epigenomics, including DNA methylation, histone modifications, noncoding RNAs, and three-dimensional genomics. The challenges and perspectives for future research in rice are discussed. Rice as a model plant for epigenomic studies has much progressed current understanding of epigenetics in plants. Recent results on rice epigenome profiling and three-dimensional chromatin structure studies reveal specific features and implication in gene regulation during rice plant development and adaptation to environmental changes. Results on rice chromatin regulator functions shed light on mechanisms of establishment, recognition, and resetting of epigenomic information in plants. Cloning of several rice epialleles associated with important agronomic traits highlights importance of epigenomic variation in rice plant growth, fitness, and yield. In this review, we summarize and analyze recent advances in rice epigenomics and discuss challenges and directions for future research in the field.
Collapse
Affiliation(s)
- Yue Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Institute of Plant Science of Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University Paris-Saclay, 91405, Orsay, France
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
10
|
Li C, Xu H, Fu FF, Russell SD, Sundaresan V, Gent JI. Genome-wide redistribution of 24-nt siRNAs in rice gametes. Genome Res 2020; 30:173-184. [PMID: 31896557 PMCID: PMC7050532 DOI: 10.1101/gr.253674.119] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/23/2019] [Indexed: 12/13/2022]
Abstract
Gametes constitute a critical stage of the plant life cycle during which the genome undergoes reprogramming in preparation for embryogenesis. Here, we examined genome-wide distributions of small RNAs in the sperm and egg cells of rice. We found that 24-nt siRNAs, which are a hallmark of RNA-directed DNA methylation (RdDM) in plants, were depleted from heterochromatin boundaries in both gametes relative to vegetative tissues, reminiscent of siRNA patterns in DDM1-type nucleosome remodeler mutants. In sperm cells, 24-nt siRNAs were spread across heterochromatic regions, while in egg cells, 24-nt siRNAs were concentrated at a smaller number of heterochromatic loci throughout the genome, especially at loci which also produced siRNAs in other tissues. In both gametes, patterns of CHH methylation, typically a strong indicator of RdDM, were similar to vegetative tissues, although lower in magnitude. These findings indicate that the small RNA transcriptome undergoes large-scale redistribution in both male and female gametes, which is not correlated with recruitment of DNA methyltransferases in gametes and suggestive of unexplored regulatory activities of gamete small RNAs.
Collapse
Affiliation(s)
- Chenxin Li
- Department of Plant Biology, University of California, Davis, California 95616, USA
| | - Hengping Xu
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Fang-Fang Fu
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Scott D Russell
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Venkatesan Sundaresan
- Department of Plant Biology, University of California, Davis, California 95616, USA.,Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| |
Collapse
|
11
|
Wang Y, Zhang H, Li Q, Jin J, Chen H, Zou Y, Huang X, Ding Y. Genome-Wide Identification of lncRNAs Involved in Fertility Transition in the Photo-Thermosensitive Genic Male Sterile Rice Line Wuxiang S. FRONTIERS IN PLANT SCIENCE 2020; 11:580050. [PMID: 33519839 PMCID: PMC7840536 DOI: 10.3389/fpls.2020.580050] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 12/22/2020] [Indexed: 05/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) act as universal regulators of various biological processes, but no genome-wide screening of lncRNAs involved in the fertility transition of the photo-thermosensitive genic male sterile (PTGMS) rice line has been reported. Here, we performed strand-specific RNA sequencing at three developmental stages of a novel PTGMS line Wuxiang S (WXS). A total of 3,948 lncRNAs were identified; 622 of these were detected as differentially expressed lncRNAs (DE-lncRNAs) between male-sterile WXS (WXS-S) and male-fertile WXS (WXS-F). A large proportion of lncRNAs differentially expressed at the stage of pollen mother cells meiosis, suggested that it may be the most critical stage for fertility transition of WXS. Furthermore, functional annotation of the cis- and trans- targets of DE-lncRNAs showed that 150 targets corresponding to 141 DE-lncRNAs were identified as involved in anther and pollen development. Moreover, computational analysis predicted 97 lncRNAs as precursors for 72 miRNAs, and 94 DE-lncRNAs as potential endogenous target mimics (eTMs) for 150 miRNAs. Finally, using the dual luciferase reporter assays, we demonstrated that two lncRNAs act as eTMs to regulate the expression of the SPL and GRF genes by competing for the shared osa-miR156 and osa-miR396, respectively. These genomic characteristics, differential expression, and interaction of lncRNAs with miRNAs and mRNAs contribute to our understanding of the roles of lncRNAs during the fertility transition in PTGMS rice lines.
Collapse
Affiliation(s)
- Ying Wang
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hongyuan Zhang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Qian Li
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jing Jin
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hao Chen
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yu Zou
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xingguo Huang
- Wuhan Wuda Tianyuau Bio-Tech Co., Ltd., Wuhan, China
| | - Yi Ding
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, China
- *Correspondence: Yi Ding,
| |
Collapse
|