101
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Zhang X, Dong J, Deng F, Wang W, Cheng Y, Song L, Hu M, Shen J, Xu Q, Shen F. The long non-coding RNA lncRNA973 is involved in cotton response to salt stress. BMC PLANT BIOLOGY 2019; 19:459. [PMID: 31666019 PMCID: PMC6822370 DOI: 10.1186/s12870-019-2088-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/20/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Long non-coding (lnc) RNAs are a class of functional RNA molecules greater than 200 nucleotides in length, and lncRNAs play important roles in various biological regulatory processes and response to the biotic and abiotic stresses. LncRNAs associated with salt stress in cotton have been identified through RNA sequencing, but the function of lncRNAs has not been reported. We previously identified salt stress-related lncRNAs in cotton (Gossypium spp.), and discovered the salt-related lncRNA-lncRNA973. RESULTS In this study, we identified the expression level, localization, function, and preliminary mechanism of action of lncRNA973. LncRNA973, which was localized in the nucleus, was expressed at a low level under nonstress conditions but can be significantly increased by salt treatments. Here lncRNA973 was transformed into Arabidopsis and overexpressed. Along with the increased expression compared with wild type under salt stress conditions in transgenic plants, the seed germination rate, fresh weights and root lengths of the transgenic plants increased. We also knocked down the expression of lncRNA973 using virus-induced gene silencing technology. The lncRNA973 knockdown plants wilted, and the leaves became yellowed and dropped under salt-stress conditions, indicating that the tolerance to salt stress had decreased compared with wild type. LncRNA973 may be involved in the regulation of reactive oxygen species-scavenging genes, transcription factors and genes involved in salt stress-related processes in response to cotton salt stress. CONCLUSIONS LncRNA973 was localized in the nucleus and its expression was increased by salt treatment. The lncRNA973-overexpression lines had increased salt tolerance compared with the wild type, while the lncRNA973 knockdown plants had reduced salt tolerance. LncRNA973 regulated cotton responses to salt stress by modulating the expression of a series of salt stress-related genes. The data provides a basis for further studies on the mechanisms of lncRNA973-associated responses to salt stress in cotton.
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Affiliation(s)
- Xiaopei Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai'an, Shandong, 271018, People's Republic of China
| | - Jie Dong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai'an, Shandong, 271018, People's Republic of China
| | - Fenni Deng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai'an, Shandong, 271018, People's Republic of China
| | - Wei Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai'an, Shandong, 271018, People's Republic of China
| | - Yingying Cheng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai'an, Shandong, 271018, People's Republic of China
| | - Lirong Song
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai'an, Shandong, 271018, People's Republic of China
| | - Mengjiao Hu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai'an, Shandong, 271018, People's Republic of China
| | - Jian Shen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai'an, Shandong, 271018, People's Republic of China
| | - Qingjiang Xu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai'an, Shandong, 271018, People's Republic of China
| | - Fafu Shen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai'an, Shandong, 271018, People's Republic of China.
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102
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Chen R, Li M, Zhang H, Duan L, Sun X, Jiang Q, Zhang H, Hu Z. Continuous salt stress-induced long non-coding RNAs and DNA methylation patterns in soybean roots. BMC Genomics 2019; 20:730. [PMID: 31606033 PMCID: PMC6790039 DOI: 10.1186/s12864-019-6101-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 09/12/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Environmental stimuli can activate a series of physiological and biochemical responses in plants accompanied by extensive transcriptional reprogramming. Long non-coding RNAs (lncRNAs), as versatile regulators, control gene expression in multiple ways and participate in the adaptation to biotic and abiotic stresses. RESULTS In this study, soybean seedlings were continuously cultured for 15 days with high salinity solutions started from seed germination. Strand-specific whole transcriptome sequencing and stringent bioinformatic analysis led to the identification of 3030 long intergenic non-coding RNAs (lincRNAs) and 275 natural antisense transcripts (lncNATs) in soybean roots. In contrast to mRNAs, newly identified lncRNAs exhibited less exons, similar AU content to UTRs, even distribution across the genome and low evolutionary conservation. Remarkably, more than 75% of discovered lncRNAs that were activated or up-regulated by continuous salt stress mainly targeted proteins with binding and catalytic activities. Furthermore, two DNA methylation maps with single-base resolution were generated by using reduced representation bisulfite sequencing, offering a genome-wide perspective and important clues for epigenetic regulation of stress-associated lncRNAs and protein-coding genes. CONCLUSIONS Taken together, our findings systematically demonstrated the characteristics of continuous salt stress-induced lncRNAs and extended the knowledge of corresponding methylation profiling, providing valuable evidence for a better understanding of how plants cope with long-term salt stress circumstances.
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Affiliation(s)
- Rui Chen
- Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.
| | - Ming Li
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Huiyuan Zhang
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lijin Duan
- Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China
| | - Xianjun Sun
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qiyan Jiang
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hui Zhang
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zheng Hu
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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103
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Ma J, Bai X, Luo W, Feng Y, Shao X, Bai Q, Sun S, Long Q, Wan D. Genome-Wide Identification of Long Noncoding RNAs and Their Responses to Salt Stress in Two Closely Related Poplars. Front Genet 2019; 10:777. [PMID: 31543901 PMCID: PMC6739720 DOI: 10.3389/fgene.2019.00777] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 07/23/2019] [Indexed: 12/23/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are involved in various biological regulatory processes, but their roles in plants resistance to salt stress remain largely unknown. To systematically explore the characteristics of lncRNAs and their roles in plant salt responses, we conducted strand-specific RNA-sequencing of four tissue types with salt treatments in two closely related poplars (Populus euphratica and Populus alba var. pyramidalis), and a total of 10,646 and 10,531 lncRNAs were identified, respectively. These lncRNAs showed significantly lower values in terms of length, expression, and expression correction than with mRNA. We further found that about 40% and 60% of these identified lncRNAs responded to salt stress with tissue-specific expression patterns across the two poplars. Furthermore, lncRNAs showed weak evolutionary conservation in sequences and exhibited diverse regulatory styles; in particular, tissue- and species-specific responses to salt stress varied greatly in two poplars, for example, 322 lncRNAs were found highly expressed in P. euphratica but not in P. alba var. pyramidalis and 3,425 lncRNAs were identified to be species-specific in P. euphratica in response to salt stress. Moreover, tissue-specific expression of lncRNAs in two poplars were identified with predicted target genes included Aux/IAA, NAC, MYB, involved in regulating plant growth and the plant stress response. Taken together, the systematic analysis of lncRNAs between sister species enhances our understanding of the characteristics of lncRNAs and their roles in plant growth and salt response.
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Affiliation(s)
- Jianchao Ma
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Xiaotao Bai
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Wenchun Luo
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yannan Feng
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xuemin Shao
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Qiuxian Bai
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Shujiao Sun
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Qiming Long
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
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104
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Potential of epigenetic events in human thyroid cancer. Cancer Genet 2019; 239:13-21. [PMID: 31472323 DOI: 10.1016/j.cancergen.2019.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/27/2019] [Accepted: 08/22/2019] [Indexed: 12/26/2022]
Abstract
Thyroid cancer remains the highest prevailing endocrine malignancy, and its incidence rate has progressively increased in the previous years. Above 95% of thyroid tumor are follicular cells types of carcinoma in which are considered invasive type of tumor. The pathogenesis and molecular mechanism of thyroid tumors are yet remains elucidated, in spite of activating RET, RAS and BRAF carcinogenesis have been well introduced. Nemours molecular alterations have been defined and have revealed promise for their diagnostic, prognostic and therapeutic capacity but still need further confirmation. Among different types of mechanisms, the current article reviews the importance of epigenetic modifications in thyroid cancer. Increasing data from previous reports demonstrate that acquired epigenetic abnormalities together with genetic changes plays an important role in alteration of gene expression patterns. Aberrant DNA methylation has been well known in the CpG regions and profile of microRNAs (mi-RNAs) expression also involved in cancer development. In addition, the gene expression through epigenetic control contribution to thyroid cancer is analyzed and it is semi considered in the clinic. However the epigenetic of the thyroid cancer is yet remains in its early stages, and it carries encouraging potential thyroid cancer detections in its early stages, assessment of prognosis and targeted cancer treatment.
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105
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Kim JH. Chromatin Remodeling and Epigenetic Regulation in Plant DNA Damage Repair. Int J Mol Sci 2019; 20:ijms20174093. [PMID: 31443358 PMCID: PMC6747262 DOI: 10.3390/ijms20174093] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/19/2022] Open
Abstract
DNA damage response (DDR) in eukaryotic cells is initiated in the chromatin context. DNA damage and repair depend on or have influence on the chromatin dynamics associated with genome stability. Epigenetic modifiers, such as chromatin remodelers, histone modifiers, DNA (de-)methylation enzymes, and noncoding RNAs regulate DDR signaling and DNA repair by affecting chromatin dynamics. In recent years, significant progress has been made in the understanding of plant DDR and DNA repair. SUPPRESSOR OF GAMMA RESPONSE1, RETINOBLASTOMA RELATED1 (RBR1)/E2FA, and NAC103 have been proven to be key players in the mediation of DDR signaling in plants, while plant-specific chromatin remodelers, such as DECREASED DNA METHYLATION1, contribute to chromatin dynamics for DNA repair. There is accumulating evidence that plant epigenetic modifiers are involved in DDR and DNA repair. In this review, I examine how DDR and DNA repair machineries are concertedly regulated in Arabidopsis thaliana by a variety of epigenetic modifiers directing chromatin remodeling and epigenetic modification. This review will aid in updating our knowledge on DDR and DNA repair in plants.
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Affiliation(s)
- Jin-Hong Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212, Korea.
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106
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Yu Y, Zhang Y, Chen X, Chen Y. Plant Noncoding RNAs: Hidden Players in Development and Stress Responses. Annu Rev Cell Dev Biol 2019; 35:407-431. [PMID: 31403819 DOI: 10.1146/annurev-cellbio-100818-125218] [Citation(s) in RCA: 196] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A large and significant portion of eukaryotic transcriptomes consists of noncoding RNAs (ncRNAs) that have minimal or no protein-coding capacity but are functional. Diverse ncRNAs, including both small RNAs and long ncRNAs (lncRNAs), play essential regulatory roles in almost all biological processes by modulating gene expression at the transcriptional and posttranscriptional levels. In this review, we summarize the current knowledge of plant small RNAs and lncRNAs, with a focus on their biogenesis, modes of action, local and systemic movement, and functions at the nexus of plant development and environmental responses. The complex connections among small RNAs, lncRNAs, and small peptides in plants are also discussed, along with the challenges of identifying and investigating new classes of ncRNAs.
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Affiliation(s)
- Yu Yu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Yuchan Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
| | - Xuemei Chen
- Department of Botany and Plant Sciences and Institute of Integrative Genome Biology, University of California, Riverside, California 92521, USA;
| | - Yueqin Chen
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
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107
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Sablok G, Sun K, Sun H. NAMS: Noncoding Assessment of long RNAs in Magnoliophyta Species. Methods Mol Biol 2019; 1933:257-264. [PMID: 30945190 DOI: 10.1007/978-1-4939-9045-0_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Regulation of plant transcriptional machinery has been recently demonstrated to be widely regulated by a class of long noncoding RNAs (lncRNAs) with size larger than 200 nt. The lncRNAs have been demonstrated to play key roles in abiotic stress. Taking into account the rapid pace in the development of the sequencing technologies, accelerated identification of lncRNAs with potential involvement in regulating the gene expression has been witnessed. Although progress has been made to identify the lncRNAs, however, accurate classification of the lncRNAs particularly in the case of plants is still challenging. In this protocol chapter, we present NAMS, which provides large-scale noncoding assessment of the lncRNAs specifically designed for Magnoliophyta species. We describe the approach and the usage of NAMS with potential applications for the lncRNA discovery.
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Affiliation(s)
- Gaurav Sablok
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Trento, Italy.
| | - Kun Sun
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Hao Sun
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong, China. .,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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108
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Hoang NV, Furtado A, Perlo V, Botha FC, Henry RJ. The Impact of cDNA Normalization on Long-Read Sequencing of a Complex Transcriptome. Front Genet 2019; 10:654. [PMID: 31396260 PMCID: PMC6664245 DOI: 10.3389/fgene.2019.00654] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 06/20/2019] [Indexed: 11/13/2022] Open
Abstract
Normalization of cDNA is widely used to improve the coverage of rare transcripts in analysis of transcriptomes employing next-generation sequencing. Recently, long-read technology has been emerging as a powerful tool for sequencing and construction of transcriptomes, especially for complex genomes containing highly similar transcripts and transcript-spliced isoforms. Here, we analyzed the transcriptome of sugarcane, a highly polyploidy plant genome, by PacBio isoform sequencing (Iso-Seq) of two different cDNA library preparations, with and without a normalization step. The results demonstrated that, while the two libraries included many of the same transcripts, many longer transcripts were removed, and many new generally shorter transcripts were detected by normalization. For the same input cDNA and data yield, the normalized library recovered more total transcript isoforms and number of predicted gene families and orthologous groups, resulting in a higher representation for the sugarcane transcriptome, compared to the non-normalized library. The non-normalized library, on the other hand, included a wider transcript length range with more longer transcripts above ∼1.25 kb and more transcript isoforms per gene family and gene ontology terms per transcript. A large proportion of the unique transcripts comprising ∼52% of the normalized library were expressed at a lower level than the unique transcripts from the non-normalized library, across three tissue types tested including leaf, stalk, and root. About 83% of the total 5,348 predicted long noncoding transcripts was derived from the normalized library, of which ∼80% was derived from the lowly expressed fraction. Functional annotation of the unique transcripts suggested that each library enriched different functional transcript fractions. This demonstrated the complementation of the two approaches in obtaining a complete transcriptome of a complex genome at the sequencing depth used in this study.
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Affiliation(s)
- Nam V. Hoang
- College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Virginie Perlo
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Frederik C. Botha
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- Sugar Research Australia, Indooroopilly, QLD, Australia
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
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109
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Narnoliya LK, Kaushal G, Singh SP. Long noncoding RNAs and miRNAs regulating terpene and tartaric acid biosynthesis in rose-scented geranium. FEBS Lett 2019; 593:2235-2249. [PMID: 31210363 DOI: 10.1002/1873-3468.13493] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This study aimed to explore the noncoding RNAs, which have emerged as key regulatory molecules in biological processes, in rose-scented geranium. We analyzed RNA-seq data revealing 26 784 long noncoding RNAs (lncRNAs) and 871 miRNAs in rose-scented geranium. A total of 466 lncRNAs were annotated using different plant lncRNA public databases. Furthermore, 372 lncRNAs and 99 miRNAs were detected that target terpene and tartarate biosynthetic pathways. An interactome, comprising of lncRNAs, miRNAs, and mRNAs, was constructed that represents a noncoding RNA regulatory network of the target mRNAs. Real-time quantitative PCR expression validation was done for selected lncRNAs involved in the regulation of terpene and tartaric acid pathways. This study provides the first insights into the regulatory functioning of noncoding RNAs in rose-scented geranium.
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Affiliation(s)
| | - Girija Kaushal
- Center of Innovative and Applied Bioprocessing, S.A.S. Nagar, Mohali, India
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing, S.A.S. Nagar, Mohali, India
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110
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Long noncoding RNAs in Brassica rapa L. following vernalization. Sci Rep 2019; 9:9302. [PMID: 31243302 PMCID: PMC6594933 DOI: 10.1038/s41598-019-45650-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 06/07/2019] [Indexed: 01/04/2023] Open
Abstract
Brassica rapa L. is an important agricultural crop that requires a period of prolonged cold for flowering. This process is known as vernalization. Studies have shown that long noncoding RNAs (lncRNAs) play important roles in abiotic stress responses and several cold-responsive noncoding RNAs have been suggested to be involved in vernalization. We examined the transcriptome of the Chinese cabbage inbred line (B. rapa L. var. pekinensis) RJKB-T24, and identified 1,444 long intergenic noncoding RNAs (lincRNAs), 551 natural antisense transcripts (NATs), and 93 intronic noncoding RNAs (incRNAs); 549 of the 2,088 lncRNAs significantly altered their expression in response to four weeks of cold treatment. Most differentially expressed lncRNAs did not lead to a change of expression levels in mRNAs covering or near lncRNAs, suggesting that the transcriptional responses to four weeks of cold treatment in lncRNA and mRNA are independent. However, some differentially expressed mRNAs had NATs with expression altered in the same direction. These genes were categorized as having an abiotic stress response, suggesting that the paired-expression may play a role in the transcriptional response to vernalization or cold treatment. We also identified short-term cold treatment induced NATs in BrFLC and BrMAF genes, which are involved in vernalization. The lncRNAs we identified differed from those reported in Arabidopsis thaliana, suggesting the role of lncRNAs in vernalization differ between these two species.
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111
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Discovery, Identification, and Functional Characterization of Plant Long Intergenic Noncoding RNAs After Virus Infection. Methods Mol Biol 2019. [PMID: 30945185 DOI: 10.1007/978-1-4939-9045-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Long intergenic noncoding RNAs (lincRNAs), which possess diverse features such as remodeling chromatin and genome architecture, RNA stabilization, and genome architecture, are important regulatory factors in plant genomes. They serve to fine-tune the expression of neighboring genes. Here, we describe a procedure of discovery, identification, and functional characterization of plant lincRNAs after virus infection. From high-throughput RNA-Seq transcriptome analysis, the noncoding RNA transcripts with significant fold changes (upregulation or downregulation) will be discovered and identified. The lincRNA of interest will be further confirmed and validated using rapid amplification of cDNA ends (RACE). In addition, functional characterization of the lincRNA will be followed up through overexpression and knockdown strategies.
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112
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Van Bel M, Bucchini F, Vandepoele K. Gene space completeness in complex plant genomes. CURRENT OPINION IN PLANT BIOLOGY 2019; 48:9-17. [PMID: 30797187 DOI: 10.1016/j.pbi.2019.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/10/2018] [Accepted: 01/21/2019] [Indexed: 05/22/2023]
Abstract
Genome annotations offer ample opportunities to study gene functions, biochemical and regulatory pathways, or quantitative trait loci in plants. Determining the quality and completeness of a genome annotation, and maintaining the balance between them, are major challenges, even for genomes of well-studied model organisms. In this review, we present a historical overview of the complexity in different plant genomes and discuss the hurdles and possible solutions in obtaining a complete and high-quality genome annotation. We illustrate there is no clear-cut answer to solve these challenges for different gene types, but provide tips on guiding the iterative process of generating a superior genome annotation, which is a moving target as our knowledge about plant genomics increases and additional data sources become available.
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Affiliation(s)
- Michiel Van Bel
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - François Bucchini
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium.
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113
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Zhang Z, Zheng Y, Ham BK, Zhang S, Fei Z, Lucas WJ. Plant lncRNAs are enriched in and move systemically through the phloem in response to phosphate deficiency. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:492-508. [PMID: 30171742 DOI: 10.1111/jipb.12715] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/29/2018] [Indexed: 05/08/2023]
Abstract
In response to phosphate (Pi) deficiency, it has been shown that micro-RNAs (miRNAs) and mRNAs are transported through the phloem for delivery to sink tissues. Growing evidence also indicates that long non-coding RNAs (lncRNAs) are critical regulators of Pi homeostasis in plants. However, whether lncRNAs are present in and move through the phloem, in response to Pi deficiency, remains to be established. Here, using cucumber as a model plant, we show that lncRNAs are enriched in the phloem translocation stream and respond, systemically, to an imposed Pi-stress. A well-known lncRNA, IPS1, the target mimic (TM) of miRNA399, accumulates to a high level in the phloem, but is not responsive to early Pi deficiency. An additional 24 miRNA TMs were also detected in the phloem translocation stream; among them miRNA171 TMs and miR166 TMs were induced in response to an imposed Pi stress. Grafting studies identified 22 lncRNAs which move systemically into developing leaves and root tips. A CU-rich PTB motif was further identified in these mobile lncRNAs. Our findings revealed that lncRNAs respond to Pi deficiency, non-cell-autonomously, and may act as systemic signaling agents to coordinate early Pi deficiency signaling, at the whole-plant level.
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Affiliation(s)
- Zhaoliang Zhang
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Yi Zheng
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Byung-Kook Ham
- Global Institute for Food Security, Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Shupei Zhang
- State Key Laboratory of Tea Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - William J Lucas
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, USA
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114
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Zhao L, Zhang H, Kohnen MV, Prasad KVSK, Gu L, Reddy ASN. Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing. Front Genet 2019; 10:253. [PMID: 30949200 PMCID: PMC6438080 DOI: 10.3389/fgene.2019.00253] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/06/2019] [Indexed: 12/18/2022] Open
Abstract
Nanopore sequencing from Oxford Nanopore Technologies (ONT) and Pacific BioSciences (PacBio) single-molecule real-time (SMRT) long-read isoform sequencing (Iso-Seq) are revolutionizing the way transcriptomes are analyzed. These methods offer many advantages over most widely used high-throughput short-read RNA sequencing (RNA-Seq) approaches and allow a comprehensive analysis of transcriptomes in identifying full-length splice isoforms and several other post-transcriptional events. In addition, direct RNA-Seq provides valuable information about RNA modifications, which are lost during the PCR amplification step in other methods. Here, we present a comprehensive summary of important applications of these technologies in plants, including identification of complex alternative splicing (AS), full-length splice variants, fusion transcripts, and alternative polyadenylation (APA) events. Furthermore, we discuss the impact of the newly developed nanopore direct RNA-Seq in advancing epitranscriptome research in plants. Additionally, we summarize computational tools for identifying and quantifying full-length isoforms and other co/post-transcriptional events and discussed some of the limitations with these methods. Sequencing of transcriptomes using these new single-molecule long-read methods will unravel many aspects of transcriptome complexity in unprecedented ways as compared to previous short-read sequencing approaches. Analysis of plant transcriptomes with these new powerful methods that require minimum sample processing is likely to become the norm and is expected to uncover novel co/post-transcriptional gene regulatory mechanisms that control biological outcomes during plant development and in response to various stresses.
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Affiliation(s)
- Liangzhen Zhao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Markus V. Kohnen
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kasavajhala V. S. K. Prasad
- Program in Cell and Molecular Biology, Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Anireddy S. N. Reddy
- Program in Cell and Molecular Biology, Department of Biology, Colorado State University, Fort Collins, CO, United States
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Genome-wide analysis of long non-coding RNAs unveils the regulatory roles in the heat tolerance of Chinese cabbage (Brassica rapa ssp.chinensis). Sci Rep 2019; 9:5002. [PMID: 30899041 PMCID: PMC6428831 DOI: 10.1038/s41598-019-41428-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 03/05/2019] [Indexed: 01/12/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) mediate important epigenetic regulation in various biological processes related to the stress response in plants. However, the systematic analysis of the lncRNAs expressed in Brassica rapa under heat stress has been elusive. In this study, we performed a genome-wide analysis of the lncRNA expression profiles in non-heading Chinese cabbage leaves using strand-specific RNA-sequencing. A total of 4594 putative lncRNAs were identified with a comprehensive landscape of dynamic lncRNA expression networks under heat stress. Co-expression networks of the interactions among the differentially expressed lncRNAs, mRNAs and microRNAs revealed that several phytohormones were associated with heat tolerance, including salicylic acid (SA) and brassinosteroid (BR) pathways. Of particular importance is the discovery of 25 lncRNAs that were highly co-expressed with 10 heat responsive genes. Thirty-nine lncRNAs were predicted as endogenous target mimics (eTMs) for 35 miRNAs, and five of them were validated to be involved in the heat tolerance of Chinese cabbage. Heat responsive lncRNA (TCONS_00048391) is an eTM for bra-miR164a, that could be a sponge for miRNA binding and may be a competing endogenous RNA (ceRNA) for the target gene NAC1 (Bra030820), affecting the expression of bra-miR164a in Chinese cabbage. Thus, these findings provide new insights into the functions of lncRNAs in heat tolerance and highlight a set of candidate lncRNAs for further studies in non-heading Chinese cabbage.
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Seo JS, Diloknawarit P, Park BS, Chua NH. ELF18-INDUCED LONG NONCODING RNA 1 evicts fibrillarin from mediator subunit to enhance PATHOGENESIS-RELATED GENE 1 (PR1) expression. THE NEW PHYTOLOGIST 2019; 221:2067-2079. [PMID: 30307032 DOI: 10.1111/nph.15530] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 10/02/2018] [Indexed: 05/20/2023]
Abstract
Plant immune response is initiated upon the recognition of pathogen-associated molecular patterns such as elf18. Previously, we identified an Arabidopsis ELF18-INDUCED LONG NONCODING RNA 1 (ELENA1), as a positive transcriptional regulator of immune responsive genes. ELENA1 associated with Mediator subunit 19a (MED19a) to enhance enrichment of the complex on PATHOGENESIS-RELATED GENE 1 (PR1) promoter. In vitro and in vivo RNA-protein interaction experiments showed that ELENA1 can also interact with FIBRILLARIN 2 (FIB2). Co-immunoprecipitation and bimolecular fluorescence complementation assay showed that FIB2 directly interacts with MED19a in nucleoplasm and nucleolus. Analysis of fib2 mutant showed that FIB2 functions as a negative transcriptional regulator for immune responsive genes, including PR1. Genetic and biochemical analyses demonstrated that ELENA1 can dissociate the FIB2/MED19a complex and release FIB2 from PR1 promoter to enhance PR1 expression. ELENA1 increases PR1 expression by evicting the repressor (FIB2) from the activator (MED19a). Our findings uncover an additional layer of complexity in the transcriptional regulation of plant immune responsive genes by long noncoding RNA.
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Affiliation(s)
- Jun Sung Seo
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore City, 117604, Singapore
| | - Piyarut Diloknawarit
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore City, 117604, Singapore
| | - Bong Soo Park
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore City, 117604, Singapore
| | - Nam-Hai Chua
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore City, 117604, Singapore
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117
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The susceptibility of sea-island cotton recombinant inbred lines to Fusarium oxysporum f. sp. vasinfectum infection is characterized by altered expression of long noncoding RNAs. Sci Rep 2019; 9:2894. [PMID: 30814537 PMCID: PMC6393425 DOI: 10.1038/s41598-019-39051-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 01/04/2019] [Indexed: 01/29/2023] Open
Abstract
Disease resistance is one of the most complicated yet important plant traits. The potential functions of long noncoding RNAs (lncRNAs) in response to pathogenic fungi remain unclear. In this study, we sequenced the transcriptomes of four different sea-island cotton (Gossypium barbadense) recombinant inbred lines (RILs) with susceptible, highly susceptible, highly resistant, or super highly resistant phenotypes and compared their responses to Fusarium oxysporum f. sp. vasinfectum (Fov) infection with those of their susceptible and resistant parents. Infection-induced protein coding genes were highly enriched in similar disease resistance-related pathways regardless of fungal susceptibility. In contrast, we found that the expression of a large number of Fov infection-induced lncRNAs was positively correlated with plant susceptibility. Bioinformatics analysis of potential target mRNAs of lncRNAs with both trans-acting and cis-acting mechanisms showed that mRNAs co-expressed or co-located with Fov-regulated lncRNAs were highly enriched in disease resistance-related pathways, including glutathione metabolism, glycolysis, plant hormone signal transduction, anthocyanin biosynthesis, and butanoate metabolism. Together these results suggest that lncRNAs could play a significant role in the response to pathogenic fungal infection and the establishment of disease resistance. The transcriptional regulation of these infection-susceptible lncRNAs could be coordinated with infection-susceptible mRNAs and integrated into a regulatory network to modulate plant-pathogen interactions and disease resistance. Fov-susceptible lncRNAs represent a novel class of molecular markers for breeding of Fov-resistant cotton cultivars.
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Vaattovaara A, Leppälä J, Salojärvi J, Wrzaczek M. High-throughput sequencing data and the impact of plant gene annotation quality. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1069-1076. [PMID: 30590678 PMCID: PMC6382340 DOI: 10.1093/jxb/ery434] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/28/2018] [Indexed: 06/02/2023]
Abstract
The use of draft genomes of different species and re-sequencing of accessions and populations are now common tools for plant biology research. The de novo assembled draft genomes make it possible to identify pivotal divergence points in the plant lineage and provide an opportunity to investigate the genomic basis and timing of biological innovations by inferring orthologs between species. Furthermore, re-sequencing facilitates the mapping and subsequent molecular characterization of causative loci for traits, such as those for plant stress tolerance and development. In both cases high-quality gene annotation-the identification of protein-coding regions, gene promoters, and 5'- and 3'-untranslated regions-is critical for investigation of gene function. Annotations are constantly improving but automated gene annotations still require manual curation and experimental validation. This is particularly important for genes with large introns, genes located in regions rich with transposable elements or repeats, large gene families, and segmentally duplicated genes. In this opinion paper, we highlight the impact of annotation quality on evolutionary analyses, genome-wide association studies, and the identification of orthologous genes in plants. Furthermore, we predict that incorporating accurate information from manual curation into databases will dramatically improve the performance of automated gene predictors.
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Affiliation(s)
- Aleksia Vaattovaara
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), Helsinki, Finland
| | - Johanna Leppälä
- Department of Ecology and Environmental Science, Umeå University, Linnaeus väg 6, Umeå, Sweden
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), Helsinki, Finland
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Michael Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), Helsinki, Finland
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Karlik E, Ari S, Gozukirmizi N. LncRNAs: genetic and epigenetic effects in plants. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1581085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Elif Karlik
- Department of Biotechnology Institute of Graduate Studies in Science and Engineering, Istanbul University, Istanbul, Turkey
- Department of Molecular Biology and Genetics Faculty of Science, Istinye University, Istanbul, Turkey
| | - Sule Ari
- Department of Molecular Biology and Genetics Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Nermin Gozukirmizi
- Department of Molecular Biology and Genetics Faculty of Science, Istanbul University, Istanbul, Turkey
- Department of Molecular Biology and Genetics Faculty of Science, Istinye University, Istanbul, Turkey
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Yu T, Tzeng DTW, Li R, Chen J, Zhong S, Fu D, Zhu B, Luo Y, Zhu H. Genome-wide identification of long non-coding RNA targets of the tomato MADS box transcription factor RIN and function analysis. ANNALS OF BOTANY 2019; 123:469-482. [PMID: 30376036 PMCID: PMC6377105 DOI: 10.1093/aob/mcy178] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 10/08/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS In recent years, increasing numbers of long non-coding RNAs (lncRNAs) have been identified in humans, animals and plants, and several of them have been shown to play important roles in diverse biological processes. However, little work has been performed on the regulation mechanism of lncRNA biogenesis and expression, especially in plants. Compared with studies of tomato MADS-box transcription factor RIPENING INHIBITOR (RIN) target coding genes, there are few reports on its relationship to non-coding RNAs. The aim of the present study was to identify and explore the specific role of RIN target lncRNAs in tomato fruit development and ripening. METHODS lncRNA targets of RIN were identified by chromatin immunoprecipitation sequencing (ChIP-seq) combined with RNA deep sequencing analysis. Six selected lncRNA targets were validated by quantitative real-time PCR, ChIP and electrophoretic mobility shift assays, and we further confirmed differential expression between wild-type and ripening-deficient mutant fruit, and RIN direct binding in the promoter regions. By means of virus-induced gene silencing (VIGS) assays and a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) genome editing strategy, the ripening-related function of a specific target lncRNA (lncRNA2155) was studied. KEY RESULTS We identified 187 lncRNAs as direct RIN targets, which exhibited RIN binding sites in their promoters and showed different expression between the wild-type and rin mutant. Six target lncRNAs were shown to bind with RIN directly in their promoters in vivo and in vitro. Moreover, using CRISPR/Cas9 technology to knock out the locus of the target lncRNA2155 indicated that it delayed fruit ripening in tomato. CONCLUSIONS Collectively, these findings provide new insight into RIN in the transcriptional regulation of lncRNAs and suggest that lncRNAs will contribute to a better understanding of the RIN regulatory network that controls fruit ripening.
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Affiliation(s)
- Tongtong Yu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - David T W Tzeng
- EG12 Science Centre School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Ran Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Jianye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bio resources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou, China
| | - Silin Zhong
- EG12 Science Centre School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Daqi Fu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Benzhong Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yunbo Luo
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- For correspondence: and
| | - Hongliang Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- For correspondence: and
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Wu X, Shi T, Iqbal S, Zhang Y, Liu L, Gao Z. Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume. BMC PLANT BIOLOGY 2019; 19:64. [PMID: 30744565 PMCID: PMC6371585 DOI: 10.1186/s12870-019-1672-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 02/01/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are transcripts more than 200 bp in length do not encode proteins. Up to the present, it has been reported that lncRNAs play an essential role in developmental processes through their regulatory functions. However, their characteristics, expression inheritance patterns, and functions in Prunus mume are quite unidentified. RESULTS In this present study, we exposed the specific characters of pistil development process between single pistil cv 'Qingjia No.2' (QJN2) and multiple pistils cv 'Da Yu' (DY). We found that early October is the key stage for pistil differentiation. The similarity epidermis was observed between two types of pistil. We also further investigated a complete pistil development lncRNA profiles through RNA-seq in Prunus mume. 2572 unique lncRNAs and 24,648 genes mapped to Prunus mume genome, furthermore, 591 novel lncRNAs were predicted. Both unique lncRNAs and novel lncRNAs are shorter in length than the mRNAs, and the overall expression level of lncRNAs was lower than mRNAs in Prunus mume. 186 known lncRNAs, 1638 genes and 89 novel lncRNAs were identified as significant differential expressed in QJN2 compared with DY. We predicted 421 target genes of differentially expressed known lncRNAs (DEKLs) and 254 target genes of differentially expressed novel lncRNAs (DENLs). 153 miRNAs were predicted interacted with 100 DEKLs while 112 miRNAs were predicted interacted with 55 DENLs. Further analysis of the DEKLs showed that the lncRNA of XR_514690.2 down-regulated its target ppe-miR172d, and up-regulated AP2, respectively. Meanwhile, the other lncRNA of TCONS_00032517 induced cytokinin negative regulator gene A-ARR expression via repressing its target miRNA ppe-miR160a/b in DY. At the same time we found that the AP2 expression was significantly up-regulated by zeatin (ZT) treatment in flower buds. Our experiments suggest that the two lncRNAs of XR_514690.2 and TCONS_00032517 might contribute the formation of multiple pistils in Prunus mume. CONCLUSION This study shows the first characterization of lncRNAs involved in pistil development and provides new indications to elucidate how lncRNAs and their targets play role in pistil differentiation and flower development in Prunus mume.
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Affiliation(s)
- Xinxin Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210095 China
| | - Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shahid Iqbal
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yong Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 China
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
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122
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Zhou Y, Cho WK, Byun HS, Chavan V, Kil EJ, Lee S, Hong SW. Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virus. PeerJ 2019; 7:e6286. [PMID: 30713817 PMCID: PMC6354667 DOI: 10.7717/peerj.6286] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/14/2018] [Indexed: 01/23/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play an important role in regulating many biological processes. In this study, tomato seeds were first irradiated by neutrons. Eight tomato mutants were then selected and infected by Tomato yellow leaf curl virus (TYLCV). RNA sequencing followed by bioinformatics analyses identified 1,563 tomato lncRNAs. About half of the lncRNAs were derived from intergenic regions, whereas antisense lncRNAs accounted for 35%. There were fewer lncRNAs identified in our study than in other studies identifying tomato lncRNAs. Functional classification of 794 lncRNAs associated with tomato genes showed that many lncRNAs were associated with binding functions required for interactions with other molecules and localized in the cytosol and membrane. In addition, we identified 19 up-regulated and 11 down-regulated tomato lncRNAs by comparing TYLCV infected plants to non-infected plants using previously published data. Based on these results, the lncRNAs identified in this study provide important resources for characterization of tomato lncRNAs in response to TYLCV infection.
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Affiliation(s)
- Yujie Zhou
- Department of Energy Science, Sungkyunkwan University, Suwon, South Korea
| | - Won Kyong Cho
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Hee-Seong Byun
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Vivek Chavan
- Department of Energy Science, Sungkyunkwan University, Suwon, South Korea
| | - Eui-Joon Kil
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Seung-Woo Hong
- Department of Physics, Sungkyunkwan University, Suwon, South Korea
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123
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Song Y, Li L, Yang Z, Zhao G, Zhang X, Wang L, Zheng L, Zhuo F, Yin H, Ge X, Zhang C, Yang Z, Ren M, Li F. Target of Rapamycin (TOR) Regulates the Expression of lncRNAs in Response to Abiotic Stresses in Cotton. Front Genet 2019; 9:690. [PMID: 30671083 PMCID: PMC6332313 DOI: 10.3389/fgene.2018.00690] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/11/2018] [Indexed: 12/11/2022] Open
Abstract
TOR (Target of Rapamycin) kinase is an evolutionarily conserved protein kinase, which integrates stress-related cues with growth and metabolic outputs. Long non-coding RNAs (lncRNAs) play a vital role in the regulation of eukaryotic genes. However, little is known about TOR's function in regulating the expression of lncRNAs in plants. In this study, four putative homologous genes encoding the TOR protein were identified by utilizing the recently completed cotton genome. Pharmacological experiments with TOR inhibitor AZD8055 and on silencing GhTOR genes resulted in obvious cotton growth retardation, indicating the conserved role of TOR in plant growth. The expression pattern analyses in different tissues reveal that TOR may play a role in root development, and the transcript levels of TOR genes were changed under different stress conditions. Importantly, we found TOR may be a key player in regulating the expression of long non-coding RNAs (lncRNAs). A total of 10,315 lncRNAs were discovered in cotton seedlings, 90.7% of which were long intergenic ncRNAs. Moreover, we identified the differentially expressed lncRNAs, of which 296 were significantly upregulated and 105 were downregulated in TOR inactivated plants. GO and KEGG analyses of differentially expressed lncRNA neighboring genes reveal that these differentially expressed lncRNA-targeted genes are involved in many life processes, including stress response, glutathione, and ribosomes in cotton. A series of differentially expressed lncRNAs potentially involved in plant stress response was identified under TOR inhibition. Collectively, these results suggest that cotton TOR proteins may directly modulate the expression of putative stress-related lncRNAs and eventually play a potential role in the cotton stress response.
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Affiliation(s)
- Yun Song
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Linxuan Li
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Zhaoen Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Ge Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xueyan Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lingling Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lei Zheng
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Fengping Zhuo
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Huan Yin
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xiaoyang Ge
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Chaojun Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zuoren Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Maozhi Ren
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
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Calixto CPG, Tzioutziou NA, James AB, Hornyik C, Guo W, Zhang R, Nimmo HG, Brown JWS. Cold-Dependent Expression and Alternative Splicing of Arabidopsis Long Non-coding RNAs. FRONTIERS IN PLANT SCIENCE 2019; 10:235. [PMID: 30891054 PMCID: PMC6413719 DOI: 10.3389/fpls.2019.00235] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/12/2019] [Indexed: 05/07/2023]
Abstract
Plants re-program their gene expression when responding to changing environmental conditions. Besides differential gene expression, extensive alternative splicing (AS) of pre-mRNAs and changes in expression of long non-coding RNAs (lncRNAs) are associated with stress responses. RNA-sequencing of a diel time-series of the initial response of Arabidopsis thaliana rosettes to low temperature showed massive and rapid waves of both transcriptional and AS activity in protein-coding genes. We exploited the high diversity of transcript isoforms in AtRTD2 to examine regulation and post-transcriptional regulation of lncRNA gene expression in response to cold stress. We identified 135 lncRNA genes with cold-dependent differential expression (DE) and/or differential alternative splicing (DAS) of lncRNAs including natural antisense RNAs, sORF lncRNAs, and precursors of microRNAs (miRNAs) and trans-acting small-interfering RNAs (tasiRNAs). The high resolution (HR) of the time-series allowed the dynamics of changes in transcription and AS to be determined and identified early and adaptive transcriptional and AS changes in the cold response. Some lncRNA genes were regulated only at the level of AS and using plants grown at different temperatures and a HR time-course of the first 3 h of temperature reduction, we demonstrated that the AS of some lncRNAs is highly sensitive to small temperature changes suggesting tight regulation of expression. In particular, a splicing event in TAS1a which removed an intron that contained the miR173 processing and phased siRNAs generation sites was differentially alternatively spliced in response to cold. The cold-induced reduction of the spliced form of TAS1a and of the tasiRNAs suggests that splicing may enhance production of the siRNAs. Our results identify candidate lncRNAs that may contribute to the regulation of expression that determines the physiological processes essential for acclimation and freezing tolerance.
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Affiliation(s)
- Cristiane P. G. Calixto
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Nikoleta A. Tzioutziou
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Allan B. James
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Csaba Hornyik
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Wenbin Guo
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Hugh G. Nimmo
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - John W. S. Brown
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- *Correspondence: John W. S. Brown,
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Li Y, Wu C, Liu C, Yu J, Duan X, Fan W, Wang J, Zhang X, Yan G, Li T, Zhang K. Functional identification of lncRNAs in sweet cherry ( Prunus avium) pollen tubes via transcriptome analysis using single-molecule long-read sequencing. HORTICULTURE RESEARCH 2019; 6:135. [PMID: 31814988 PMCID: PMC6885045 DOI: 10.1038/s41438-019-0218-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/27/2019] [Accepted: 10/27/2019] [Indexed: 05/05/2023]
Abstract
Sweet cherry (Prunus avium) is a popular fruit with high nutritional value and excellent flavor. Although pollen plays an important role in the double fertilization and subsequent fruit production of this species, little is known about its pollen tube transcriptome. In this study, we identified 16,409 transcripts using single-molecule sequencing. After filtering 292 transposable elements, we conducted further analyses including mRNA classification, gene function prediction, alternative splicing (AS) analysis, and long noncoding RNA (lncRNA) identification to gain insight into the pollen transcriptome. The filtered transcripts could be matched with 3,438 coding region sequences from the sweet cherry genome. GO and KEGG analyses revealed complex biological processes during pollen tube elongation. A total of 2043 AS events were predicted, 7 of which were identified in different organs, such as the leaf, pistil and pollen tube. Using BLASTnt and the Coding-Potential Assessment Tool (CPAT), we distinguished a total of 284 lncRNAs, among which 154 qualified as natural antisense transcripts (NATs). As the NATs could be the reverse complements of coding mRNA sequences, they might bind to coding sequences. Antisense transfection assays showed that the NATs could regulate the expression levels of their complementary sequences and even affect the growth conditions of pollen tubes. In summary, this research characterizes the transcripts of P. avium pollen and lays the foundation for elucidating the physiological and biochemical mechanisms underlying sexual reproduction in the male gametes of this species.
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Affiliation(s)
- Yang Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, China
| | - Chuanbao Wu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, China
| | - Chunsheng Liu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, China
| | - Jie Yu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, China
| | - Xuwei Duan
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Wenqi Fan
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, China
| | - Jing Wang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Xiaoming Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Guohua Yan
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Tianzhong Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, China
| | - Kaichun Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
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Challa GS, Li W. De novo assembly of wheat root transcriptomes and transcriptional signature of longitudinal differentiation. PLoS One 2018; 13:e0205582. [PMID: 30395610 PMCID: PMC6218025 DOI: 10.1371/journal.pone.0205582] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 09/27/2018] [Indexed: 01/14/2023] Open
Abstract
Hidden underground, root systems constitute an important part of the plant for its development, nourishment and sensing the soil environment around it, but we know very little about its genetic regulation in crop plants like wheat. In the present study, we de novo assembled the root transcriptomes in reference cultivar Chinese Spring from RNA-seq reads generated by the 454-GS-FLX and HiSeq platforms. The FLX reads were assembled into 24,986 transcripts with completeness of 54.84%, and the HiSeq reads were assembled into 91,543 high-confidence protein-coding transcripts, 2,404 low-confidence protein-coding transcripts, and 13,181 non-coding transcripts with the completeness of >90%. Combining the FLX and HiSeq assemblies, we assembled a root transcriptome of 92,335 ORF-containing transcripts. Approximately 7% of the coding transcripts and ~2% non-coding transcripts are not present in the current wheat genome assembly. Functional annotation of both assemblies showed similar gene ontology patterns and that ~7% coding and >5% non-coding transcripts are root-specific. Transcription quantification identified 1,728 differentially expressed transcripts between root tips and maturation zone, and functional annotation of these transcripts captured a transcriptional signature of longitudinal development of wheat root. With the transcriptomic resources developed, this study provided the first view of wheat root transcriptome under different developmental zones and laid a foundation for molecular studies of wheat root development and growth using a reverse genetic approach.
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Affiliation(s)
- Ghana Shyam Challa
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, United States of America
| | - Wanlong Li
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, United States of America
- Department of Plant Science, South Dakota State University, Brookings, SD, United States of America
- * E-mail:
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128
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Lin Y, Jiang L, Chen Q, Li Y, Zhang Y, Luo Y, Zhang Y, Sun B, Wang X, Tang H. Comparative Transcriptome Profiling Analysis of Red- and White-Fleshed Strawberry (Fragaria�ananassa) Provides New Insight into the Regulation of the Anthocyanin Pathway. PLANT & CELL PHYSIOLOGY 2018; 59:1844-1859. [PMID: 29800352 DOI: 10.1093/pcp/pcy098] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/14/2018] [Indexed: 05/07/2023]
Abstract
Anthocyanins are water-soluble pigments in plants. They confer both economic and healthy profits for humans. To gain a deeper insight into the regulation of anthocyanin biosynthesis in octoploid strawberry (Fragaria�ananassa; Fa), a widely consumed economically important fruit, we performed comparative transcriptomic analysis of red- and white-fleshed strawberry cultivars in two ripening stages. In total, 365,455 non-redundant transcripts were assembled from the RNA sequencing (RNAseq) data. Of this collection, 377 were annotated as putative anthocyanin-related transcripts. Differential expression analysis revealed that 57 anthocyanin biosynthesis transcripts were down-regulated, and 89 transcription factors (TFs) were either down- or up-regulated under anthocyanin deficiency. Additionally, amongst the 50,601 putative long non-coding RNAs (lncRNAs) identified here, 68 lncRNAs were differentially expressed and co-expressed with differentially expressed anthocyanin-related mRNAs; 2,070 co-expressing lncRNA-mRNA pairs were generated. Expression profile analysis revealed that it was the limited expression of FaF3'H (flavonoid 3'-hydroxylase) that blocked the cyanidin 3-glucoside accumulation in the two investigated strawberry cultivars. This was further supported by a transient overexpression experiment with FaMYB10. The down-regulated lncRNAs might participate in anthocyanin regulation by acting as targets for microRNAs (miRNAs). The level of competitive intensity in miRNA and lncRNA for the same mRNA targets was probably lower in the white-fleshed strawberries, which can release the repression effect of the mRNAs in red-fleshed strawberry as a result. This study for the first time presents lncRNAs related to anthocyanins in strawberries, provides new insights into the anthocyanin regulatory network and also lays the foundation for identifying new anthocyanin regulators in strawberry.
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Affiliation(s)
- Yuanxiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Leiyu Jiang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yali Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yunting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
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129
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Wu HW, Deng S, Xu H, Mao HZ, Liu J, Niu QW, Wang H, Chua NH. A noncoding RNA transcribed from the AGAMOUS (AG) second intron binds to CURLY LEAF and represses AG expression in leaves. THE NEW PHYTOLOGIST 2018; 219:1480-1491. [PMID: 29862530 DOI: 10.1111/nph.15231] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/23/2018] [Indexed: 05/25/2023]
Abstract
Dispersed H3K27 trimethylation (H3K27me3) of the AGAMOUS (AG) genomic locus is mediated by CURLY LEAF (CLF), a component of the Polycomb Repressive Complex (PRC) 2. Previous reports have shown that the AG second intron, which confers AG tissue-specific expression, harbors sequences targeted by several positive and negative regulators. Using RACE reverse transcription polymerase chain reaction, we found that the AG intron 2 encodes several noncoding RNAs. RNAi experiment showed that incRNA4 is needed for CLF repressive activity. AG-incRNA4RNAi lines showed increased leaf AG mRNA levels associated with a decrease of H3K27me3 levels; these plants displayed AG overexpression phenotypes. Genetic and biochemical analyses demonstrated that the AG-incRNA4 can associate with CLF to repress AG expression in leaf tissues through H3K27me3-mediated repression and to autoregulate its own expression level. The mechanism of AG-incRNA4-mediated repression may be relevant to investigations on tissue-specific expression of Arabidopsis MADS-box genes.
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MESH Headings
- AGAMOUS Protein, Arabidopsis/genetics
- AGAMOUS Protein, Arabidopsis/metabolism
- Arabidopsis/genetics
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Co-Repressor Proteins/metabolism
- Flowers/genetics
- Gene Expression Regulation, Plant
- Glucuronidase/metabolism
- Histones/metabolism
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Introns/genetics
- Organ Specificity/genetics
- Plant Leaves/genetics
- Plants, Genetically Modified
- Promoter Regions, Genetic/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- Seedlings/genetics
- Transcription, Genetic
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Affiliation(s)
- Hui-Wen Wu
- Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, 10065-6399, USA
- Temasek Life Sciences Laboratory, Singapore City, 117604, Singapore
| | - Shulin Deng
- Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, 10065-6399, USA
- Temasek Life Sciences Laboratory, Singapore City, 117604, Singapore
| | - Haiying Xu
- Temasek Life Sciences Laboratory, Singapore City, 117604, Singapore
| | - Hui-Zhu Mao
- Temasek Life Sciences Laboratory, Singapore City, 117604, Singapore
| | - Jun Liu
- Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, 10065-6399, USA
| | - Qi-Wen Niu
- Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, 10065-6399, USA
| | - Huan Wang
- Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, 10065-6399, USA
| | - Nam-Hai Chua
- Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, 10065-6399, USA
- Temasek Life Sciences Laboratory, Singapore City, 117604, Singapore
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Wani SH, Tripathi P, Zaid A, Challa GS, Kumar A, Kumar V, Upadhyay J, Joshi R, Bhatt M. Transcriptional regulation of osmotic stress tolerance in wheat (Triticum aestivum L.). PLANT MOLECULAR BIOLOGY 2018; 97:469-487. [PMID: 30109563 DOI: 10.1007/s11103-018-0761-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/31/2018] [Indexed: 05/24/2023]
Abstract
The current review provides an updated, new insights into the regulation of transcription mediated underlying mechanisms of wheat plants to osmotic stress perturbations. Osmotic stress tolerance mechanisms being complex are governed by multiple factors at physiological, biochemical and at the molecular level, hence approaches like "OMICS" that can underpin mechanisms behind osmotic tolerance in wheat is of paramount importance. The transcription factors (TFs) are a class of molecular proteins, which are involved in regulation, modulation and orchestrating the responses of plants to a variety of environmental stresses. Recent reports have provided novel insights on the role of TFs in osmotic stress tolerance via direct molecular links. However, our knowledge on the regulatory role TFs during osmotic stress tolerance in wheat remains limited. The present review in its first part sheds light on the importance of studying the role of osmotic stress tolerance in wheat plants and second aims to decipher molecular mechanisms of TFs belonging to several classes, including DREB, NAC, MYB, WRKY and bHLH, which have been reported to engage in osmotic stress mediated gene expression in wheat and third part covers the systems biology approaches to understand the transcriptional regulation of osmotic stress and the role of long non-coding RNAs in response to osmotic stress with special emphasis on wheat. The current concept may lead to an understanding in molecular regulation and signalling interaction of TFs under osmotic stress to clarify challenges and problems for devising potential strategies to improve complex regulatory events involved in plant tolerance to osmotic stress adaptive pathways in wheat.
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Affiliation(s)
- Shabir H Wani
- Mountain Research Centre for Field Crops, Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K, 192101, India.
| | - Prateek Tripathi
- Department of Cell & Molecular Biology, The Scripps Research Institute, Jolla, CA, 92037, USA
| | - Abbu Zaid
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202002, India
| | - Ghana S Challa
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA
| | - Anuj Kumar
- Advance Centre for Computational and Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Dehradun, Uttarakhand, 248007, India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule, Pune University, Pune, India
| | - Jyoti Upadhyay
- Department of Pharmaceutical Sciences, Kumaun University, Campus Bhimtal, Bhimtal, Uttarakhand, 293136, India
| | - Rohit Joshi
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Manoj Bhatt
- Guru Gobind Singh Indraprastha University, New Delhi, India
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131
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Genome-wide identification and characterization of mRNAs and lncRNAs involved in cold stress in the wild banana (Musa itinerans). PLoS One 2018; 13:e0200002. [PMID: 29985922 PMCID: PMC6037364 DOI: 10.1371/journal.pone.0200002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 06/18/2018] [Indexed: 12/19/2022] Open
Abstract
Cold stress seriously affects banana growth, yield and fruit quality. Long noncoding RNAs (lncRNAs) have been demonstrated as key regulators of biotic and abiotic stress in plants, but the identification and prediction of cold responsive mRNAs and lncRNAs in wild banana remains unexplored. In present study, a cold resistant wild banana line from China was used to profile the cold-responsive mRNAs and lncRNAs by RNA-seq under cold stress conditions, i.e. 13°C (critical growth temperature), 4°C (chilling temperature), 0°C (freezing temperature) and normal growing condition, i.e. 28°C (control group). A total of 12,462 lncRNAs were identified in cold-stressed wild banana. In mRNA, much more alternative splicing events occurred in wild banana under the cold stress conditions compared with that in the normal growing condition. The GO analysis of differential expression genes (DEGs) showed the biochemical processes and membrane related genes responded positively to the cold stress. The KEGG pathway enrichment analysis of the DEGs showed that the pathways of photosynthesis, photosynthesis–antenna proteins, circadian rhythm–plant, glutathione metabolism, starch and sucrose metabolism, cutin/suberine/biosynthesis were altered or affected by the cold stress conditions. Our analyses of the generated transcriptome and lncRNAs provide new insights into regulating expression of genes and lncRNAs that respond to cold stress in the wild banana.
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Wang Y, Gao L, Li J, Zhu B, Zhu H, Luo Y, Wang Q, Zuo J. Analysis of long-non-coding RNAs associated with ethylene in tomato. Gene 2018; 674:151-160. [PMID: 29958947 DOI: 10.1016/j.gene.2018.06.089] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 06/06/2018] [Accepted: 06/25/2018] [Indexed: 11/18/2022]
Abstract
Long-Non-Coding RNAs (LncRNAs) are a class of non-coding endogenous RNAs contributing to numerous biological processes. LeERF1 is a tomato ethylene response factor (ERF) near the end of the ethylene signal transduction pathway. To identify lncRNAs in tomato and elucidate their roles in ethylene signaling, deep sequencing was deployed in over-expression and repression LeERF1 transgenic and control tomato fruits. A total of 397 lncRNAs were identified, including 169 tomato lncRNAs that had not previously been identified. Among these, 12 were differentially expressed between the transgenic and control tomato fruits. Numerous lncRNA target genes were identified including many associated with ethylene signaling including auxin response factors and auxin-induced proteins, F-box proteins, ERFs and MADS-box proteins. In addition, two lncRNAs were found to be the precursor of three miRNAs and four lncRNAs could be targeted by five miRNAs. We propose a regulatory model highlighting the relationships between lncRNAs and their targets involved in ethylene signal transduction which establishes a foundation for addressing the role of LncRNAs in ethylene response.
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Affiliation(s)
- Yunxiang Wang
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China; Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Lipu Gao
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jian Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048,China
| | - Benzhong Zhu
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Hongliang Zhu
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunbo Luo
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Qing Wang
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
| | - Jinhua Zuo
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China; Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, NY 14853, USA.
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Wang J, Lin J, Kan J, Wang H, Li X, Yang Q, Li H, Chang Y. Genome-Wide Identification and Functional Prediction of Novel Drought-Responsive lncRNAs in Pyrus betulifolia. Genes (Basel) 2018; 9:E311. [PMID: 29925818 PMCID: PMC6027255 DOI: 10.3390/genes9060311] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/14/2018] [Accepted: 06/14/2018] [Indexed: 11/17/2022] Open
Abstract
Increasing evidence shows that long noncoding RNAs (lncRNAs) play important roles in developmental regulation and many other biological processes in plants. However, identification of lncRNAs in Pyrus betulifolia is limited compared with studies of functional gene expression. Using high-throughput sequencing technology, the transcriptome of P. betulifolia under drought stress was analyzed to identify lncRNAs. A total of 14,478 lncRNAs were identified, of which 251 were found to be drought-responsive. The putative target genes of these differentially expressed lncRNAs were significantly enriched in metabolic processes, organic substance metabolic processes, macromolecule metabolic processes, and heterocyclic compound binding. Real-time quantitative polymerase chain reaction validation suggested that the results of the RNA sequencing data analysis were reliable. This study will provide genetic resources for pear breeding and provide reference to other pomological studies.
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Affiliation(s)
- Jinxing Wang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Jing Lin
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Jialiang Kan
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Hong Wang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Xiaogang Li
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Qingsong Yang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Hui Li
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Youhong Chang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
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Zuo C, Blow M, Sreedasyam A, Kuo RC, Ramamoorthy GK, Torres-Jerez I, Li G, Wang M, Dilworth D, Barry K, Udvardi M, Schmutz J, Tang Y, Xu Y. Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:170. [PMID: 29951114 PMCID: PMC6009963 DOI: 10.1186/s13068-018-1167-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/08/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Switchgrass (Panicum virgatum L.) is an important bioenergy crop widely used for lignocellulosic research. While extensive transcriptomic analyses have been conducted on this species using short read-based sequencing techniques, very little has been reliably derived regarding alternatively spliced (AS) transcripts. RESULTS We present an analysis of transcriptomes of six switchgrass tissue types pooled together, sequenced using Pacific Biosciences (PacBio) single-molecular long-read technology. Our analysis identified 105,419 unique transcripts covering 43,570 known genes and 8795 previously unknown genes. 45,168 are novel transcripts of known genes. A total of 60,096 AS transcripts are identified, 45,628 being novel. We have also predicted 1549 transcripts of genes involved in cell wall construction and remodeling, 639 being novel transcripts of known cell wall genes. Most of the predicted transcripts are validated against Illumina-based short reads. Specifically, 96% of the splice junction sites in all the unique transcripts are validated by at least five Illumina reads. Comparisons between genes derived from our identified transcripts and the current genome annotation revealed that among the gene set predicted by both analyses, 16,640 have different exon-intron structures. CONCLUSIONS Overall, substantial amount of new information is derived from the PacBio RNA data regarding both the transcriptome and the genome of switchgrass.
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Affiliation(s)
- Chunman Zuo
- College of Computer Science and Technology, Jilin University, Changchun, China
- Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA USA
- BESC BioEnergy Research Center, Oak Ridge National Lab, Oak Ridge, TN USA
| | - Matthew Blow
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | | | - Rita C. Kuo
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | | | | | - Guifen Li
- Noble Research Institute, LLC, Ardmore, OK USA
| | - Mei Wang
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - David Dilworth
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | | | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Yuhong Tang
- BESC BioEnergy Research Center, Oak Ridge National Lab, Oak Ridge, TN USA
- Noble Research Institute, LLC, Ardmore, OK USA
| | - Ying Xu
- College of Computer Science and Technology, Jilin University, Changchun, China
- Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA USA
- BESC BioEnergy Research Center, Oak Ridge National Lab, Oak Ridge, TN USA
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135
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Genome-wide analysis of long non-coding RNAs affecting roots development at an early stage in the rice response to cadmium stress. BMC Genomics 2018; 19:460. [PMID: 29902991 PMCID: PMC6002989 DOI: 10.1186/s12864-018-4807-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 05/21/2018] [Indexed: 11/16/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) have been found to play a vital role in several gene regulatory networks involved in the various biological processes in plants related to stress response. However, systematic analyses of lncRNAs expressed in rice Cadmium (Cd) stress are seldom studied. Thus, we presented the characterization and expression of lncRNAs in rice root development at an early stage in response to Cd stress. Results The lncRNA deep sequencing revealed differentially expressed lncRNAs among Cd stress and normal condition. In the Cd stress group, 69 lncRNAs were up-regulated and 75 lncRNAs were down-regulated. Furthermore, 386 matched lncRNA-mRNA pairs were detected for 120 differentially expressed lncRNAs and 362 differentially expressed genes in cis, and target gene-related pathway analyses exhibited significant variations in cysteine and methionine metabolism pathway-related genes. For the genes in trans, overall, 28,276 interaction relationships for 144 lncRNAs and differentially expressed protein-coding genes were detected. The pathway analyses found that secondary metabolites, such as phenylpropanoids and phenylalanine, and photosynthesis pathway-related genes were significantly altered by Cd stress. All of these results indicate that lncRNAs may regulate genes of cysteine-rich peptide metabolism in cis, as well as secondary metabolites and photosynthesis in trans, to activate various physiological and biochemical reactions to respond to excessive Cd. Conclusion The present study could provide a valuable resource for lncRNA studies in response to Cd treatment in rice. It also expands our knowledge about lncRNA biological function and contributes to the annotation of the rice genome. Electronic supplementary material The online version of this article (10.1186/s12864-018-4807-6) contains supplementary material, which is available to authorized users.
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Albihlal WS, Obomighie I, Blein T, Persad R, Chernukhin I, Crespi M, Bechtold U, Mullineaux PM. Arabidopsis HEAT SHOCK TRANSCRIPTION FACTORA1b regulates multiple developmental genes under benign and stress conditions. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2847-2862. [PMID: 29697803 PMCID: PMC5961379 DOI: 10.1093/jxb/ery142] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 04/05/2018] [Indexed: 05/22/2023]
Abstract
In Arabidopsis thaliana, HEAT SHOCK TRANSCRIPTION FACTORA1b (HSFA1b) controls resistance to environmental stress and is a determinant of reproductive fitness by influencing seed yield. To understand how HSFA1b achieves this, we surveyed its genome-wide targets (ChIP-seq) and its impact on the transcriptome (RNA-seq) under non-stress (NS), heat stress (HS) in the wild type, and in HSFA1b-overexpressing plants under NS. A total of 952 differentially expressed HSFA1b-targeted genes were identified, of which at least 85 are development associated and were bound predominantly under NS. A further 1780 genes were differentially expressed but not bound by HSFA1b, of which 281 were classified as having development-associated functions. These genes are indirectly regulated through a hierarchical network of 27 transcription factors (TFs). Furthermore, we identified 480 natural antisense non-coding RNA (cisNAT) genes bound by HSFA1b, defining a further mode of indirect regulation. Finally, HSFA1b-targeted genomic features not only harboured heat shock elements, but also MADS box, LEAFY, and G-Box promoter motifs. This revealed that HSFA1b is one of eight TFs that target a common group of stress defence and developmental genes. We propose that HSFA1b transduces environmental cues to many stress tolerance and developmental genes to allow plants to adjust their growth and development continually in a varying environment.
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Affiliation(s)
- Waleed S Albihlal
- Department of Microbial & Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Irabonosi Obomighie
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, UK
| | - Thomas Blein
- Institute of Plant Sciences-Paris-Saclay, Gif-sur-Yvette Cedex, France
| | - Ramona Persad
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, UK
| | - Igor Chernukhin
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Martin Crespi
- Institute of Plant Sciences-Paris-Saclay, Gif-sur-Yvette Cedex, France
| | - Ulrike Bechtold
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, UK
| | - Philip M Mullineaux
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, UK
- Correspondence:
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137
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Wang M, Zhao W, Gao L, Zhao L. Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening. BMC PLANT BIOLOGY 2018; 18:75. [PMID: 29728060 PMCID: PMC5935960 DOI: 10.1186/s12870-018-1300-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 04/30/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are involved in multiple biological processes in both mammals and plants. There is growing evidence that they are associated with development; but their expression and regulation during fruit ripening in the model plant tomato (Solanum lycopersicum) has yet to be described. RESULTS Following integration of 134 RNA-seq data sets, we identified 79,322 putative lncRNAs, consisting of 70,635 lincRNAs, 8085 antisense non-coding RNAs (ancRNAs) and 602 sense lncRNAs (slncRNAs). lncRNAs had specific features that are distinct from mRNAs, including tissue-specificity, and shorter and fewer exons. Notably, more than 5000 of the novel lincRNAs were found to be expressed across the mature green (MG), breaker (BR) and breaker plus 7 days (BR + 7) developmental stages. The differently expressed lincRNAs had different DNA methylation profiles from the mRNAs. CONCLUSIONS Integrating transcriptome datasets and genome-wide screening enabled the identification of a comprehensive set of tomato lncRNAs. Here, we found that the lncRNAs DNA methylation profiles were different from those of mRNAs. This will help future investigation of lncRNA function, especially for the dissection of the molecular mechanisms involved in the regulation of fruit development.
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MESH Headings
- DNA Methylation
- Fruit/genetics
- Fruit/growth & development
- Gene Expression Regulation, Developmental/genetics
- Gene Expression Regulation, Developmental/physiology
- Gene Expression Regulation, Plant/genetics
- Gene Expression Regulation, Plant/physiology
- Genome, Plant/genetics
- Genome, Plant/physiology
- Solanum lycopersicum/genetics
- Solanum lycopersicum/growth & development
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/physiology
- RNA, Messenger/genetics
- RNA, Messenger/physiology
- Transcriptome
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Affiliation(s)
- Minghui Wang
- BRC Bioinformatics Facility Cornell University, Ithaca, 14850 USA
| | - Weihua Zhao
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
- Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Lei Gao
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
- Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Lingxia Zhao
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
- Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
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138
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Zhang C, Tang G, Peng X, Sun F, Liu S, Xi Y. Long non-coding RNAs of switchgrass (Panicum virgatum L.) in multiple dehydration stresses. BMC PLANT BIOLOGY 2018; 18:79. [PMID: 29728055 PMCID: PMC5936019 DOI: 10.1186/s12870-018-1288-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 04/22/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play important roles in plant growth and stress responses. Studies of lncRNAs in non-model plants are quite limited, especially those investigating multiple dehydration stresses. In this study, we identified novel lncRNAs and analyzed their functions in dehydration stress memory in switchgrass, an excellent biofuel feedstock and soil-conserving plant in the Gramineae family. RESULTS We analyzed genome-wide transcriptional profiles of leaves of 5-week-old switchgrass plantlets grown via tissue culture after primary and secondary dehydration stresses (D1 and D2) and identified 16,551 novel lncRNAs, including 4554 annotated lncRNAs (targeting 3574 genes), and 11,997 unknown lncRNAs. Gene ontology and pathway enrichment analysis of annotated genes showed that the differentially expressed lncRNAs were related to abscisic acid (ABA) and ethylene (ETH) biosynthesis and signal transduction, and to starch and sucrose metabolism. The upregulated lncRNAs and genes were related to ABA synthesis and its signal transduction, and to trehalose synthesis. Meanwhile, lncRNAs and genes related to ETH biosynthesis and signal transduction were suppressed. LncRNAs and genes involved in ABA metabolism were verified using quantitative real-time PCR, and the endogenous ABA content was determined via high performance liquid chromatography mass spectrometry (HPLC-MS). These results showed that ABA accumulated significantly during dehydration stress, especially in D2. Furthermore, we identified 307 dehydration stress memory lncRNAs, and the ratios of different memory types in switchgrass were similar to those in Arabidopsis and maize. CONCLUSIONS The molecular responses of switchgrass lncRNAs to multiple dehydration stresses were researched systematically, revealing novel information about their transcriptional regulatory behavior. This study provides new insights into the response mechanism to dehydration stress in plants. The lncRNAs and pathways identified in this study provide valuable information for genetic modification of switchgrass and other crops.
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Affiliation(s)
- Chao Zhang
- College of Agronomy, Northwest A & F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Wheat Biology and Genetic Breeding, Ministry of Agriculture, Yangling, 712100 Shaanxi China
| | - Gaijuan Tang
- College of Plant Protection, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Xi Peng
- College of Agronomy, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Fengli Sun
- College of Agronomy, Northwest A & F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Wheat Biology and Genetic Breeding, Ministry of Agriculture, Yangling, 712100 Shaanxi China
| | - Shudong Liu
- College of Agronomy, Northwest A & F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Wheat Biology and Genetic Breeding, Ministry of Agriculture, Yangling, 712100 Shaanxi China
| | - Yajun Xi
- College of Agronomy, Northwest A & F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Wheat Biology and Genetic Breeding, Ministry of Agriculture, Yangling, 712100 Shaanxi China
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139
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Zhou J, Shi YY. A Bipartite Network and Resource Transfer-Based Approach to Infer lncRNA-Environmental Factor Associations. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:753-759. [PMID: 28436883 DOI: 10.1109/tcbb.2017.2695187] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Phenotypes and diseases are often determined by the complex interactions between genetic factors and environmental factors (EFs). However, compared with protein-coding genes and microRNAs, there is a paucity of computational methods for understanding the associations between long non-coding RNAs (lncRNAs) and EFs. In this study, we focused on the associations between lncRNA and EFs. By using the common miRNA partners of any pair of lncRNA and EF, based on the competing endogenous RNA (ceRNA) hypothesis and the technique of resources transfer within the experimentally-supported lncRNA-miRNA and miRNA-EF association bipartite networks, we propose an algorithm for predicting new lncRNA-EF associations. Results show that, compared with another recently-proposed method, our approach is capable of predicting more credible lncRNA-EF associations. These results support the validity of our approach to predict biologically significant associations, which could lead to a better understanding of the molecular processes.
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140
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Huanca-Mamani W, Arias-Carrasco R, Cárdenas-Ninasivincha S, Rojas-Herrera M, Sepúlveda-Hermosilla G, Caris-Maldonado JC, Bastías E, Maracaja-Coutinho V. Long Non-Coding RNAs Responsive to Salt and Boron Stress in the Hyper-Arid Lluteño Maize from Atacama Desert. Genes (Basel) 2018; 9:genes9030170. [PMID: 29558449 PMCID: PMC5867891 DOI: 10.3390/genes9030170] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/02/2018] [Accepted: 03/08/2018] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been defined as transcripts longer than 200 nucleotides, which lack significant protein coding potential and possess critical roles in diverse cellular processes. Long non-coding RNAs have recently been functionally characterized in plant stress-response mechanisms. In the present study, we perform a comprehensive identification of lncRNAs in response to combined stress induced by salinity and excess of boron in the Lluteño maize, a tolerant maize landrace from Atacama Desert, Chile. We use deep RNA sequencing to identify a set of 48,345 different lncRNAs, of which 28,012 (58.1%) are conserved with other maize (B73, Mo17 or Palomero), with the remaining 41.9% belonging to potentially Lluteño exclusive lncRNA transcripts. According to B73 maize reference genome sequence, most Lluteño lncRNAs correspond to intergenic transcripts. Interestingly, Lluteño lncRNAs presents an unusual overall higher expression compared to protein coding genes under exposure to stressed conditions. In total, we identified 1710 putatively responsive to the combined stressed conditions of salt and boron exposure. We also identified a set of 848 stress responsive potential trans natural antisense transcripts (trans-NAT) lncRNAs, which seems to be regulating genes associated with regulation of transcription, response to stress, response to abiotic stimulus and participating of the nicotianamine metabolic process. Reverse transcription-quantitative PCR (RT-qPCR) experiments were performed in a subset of lncRNAs, validating their existence and expression patterns. Our results suggest that a diverse set of maize lncRNAs from leaves and roots is responsive to combined salt and boron stress, being the first effort to identify lncRNAs from a maize landrace adapted to extreme conditions such as the Atacama Desert. The information generated is a starting point to understand the genomic adaptabilities suffered by this maize to surpass this extremely stressed environment.
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Affiliation(s)
- Wilson Huanca-Mamani
- Departamento de Producción Agrícola, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica 1000000, Chile.
| | - Raúl Arias-Carrasco
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile.
| | | | - Marcelo Rojas-Herrera
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile.
| | | | - José Carlos Caris-Maldonado
- Departamento de Producción Agrícola, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica 1000000, Chile.
- Departamento de Bioquímica y Biologia Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380494, Chile.
| | - Elizabeth Bastías
- Departamento de Producción Agrícola, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica 1000000, Chile.
| | - Vinicius Maracaja-Coutinho
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile.
- Departamento de Bioquímica y Biologia Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380494, Chile.
- Instituto Vandique, João Pessoa 58000-000, Brazil.
- Beagle Bioinformatics, Santiago 7500554, Chile.
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141
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Deng F, Zhang X, Wang W, Yuan R, Shen F. Identification of Gossypium hirsutum long non-coding RNAs (lncRNAs) under salt stress. BMC PLANT BIOLOGY 2018; 18:23. [PMID: 29370759 PMCID: PMC5785843 DOI: 10.1186/s12870-018-1238-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 01/17/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) represent a class of riboregulators that either directly act in long form or are processed into shorter microRNAs (miRNAs) and small interfering RNAs. Long noncoding RNAs (lncRNAs) are arbitrarily defined as RNA genes larger than 200 nt in length that have no apparent coding potential. lncRNAs have emerged as playing important roles in various biological regulatory processes and are expressed in a more tissue-specific manner than mRNA. Emerging evidence shows that lncRNAs participate in stress-responsive regulation. RESULTS In this study, in order to develop a comprehensive catalogue of lncRNAs in upland cotton under salt stress, we performed whole-transcriptome strand-specific RNA sequencing for three-leaf stage cotton seedlings treated with salt stress (S_NaCl) and controls (S_CK). In total we identified 1117 unique lncRNAs in this study and 44 differentially expressed RNAs were identified as potential non-coding RNAs. For the differentially expressed lncRNAs that were identified as intergenic lncRNAs (lincRNA), we analysed the gene ontology enrichment of cis targets and found that cis target protein-coding genes were mainly enriched in stress-related categories. Real-time quantitative PCR confirmed that all selected lincRNAs responsive to salt stress. We found lnc_388 was likely as regulator of Gh_A09G1182. And lnc_883 may participate in regulating tolerance to salt stress by modulating the expression of Gh_D03G0339 MS_channel. We then predicted the target mimics for miRNA in Gossypium. six miRNAs were identified, and the result of RT-qPCR with lncRNA and miRNA suggested that lnc_973 and lnc_253 may regulate the expression of ghr-miR399 and ghr-156e as a target mimic under salt stress. CONCLUSIONS We identified 44 lincRNAs that were differentially expressed under salt stress. These lincRNAs may target protein-coding genes via cis-acting regulation. We also discovered that specifically-expressed lincRNAs under salt stress may act as endogenous target mimics for conserved miRNAs. These findings extend the current view on lincRNAs as ubiquitous regulators under stress stress.
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Affiliation(s)
- Fenni Deng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong People’s Republic of China
| | - Xiaopei Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong People’s Republic of China
| | - Wei Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong People’s Republic of China
| | - Rui Yuan
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong People’s Republic of China
| | - Fafu Shen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong People’s Republic of China
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142
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Cho J. Transposon-Derived Non-coding RNAs and Their Function in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:600. [PMID: 29774045 PMCID: PMC5943564 DOI: 10.3389/fpls.2018.00600] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/16/2018] [Indexed: 05/03/2023]
Abstract
Transposable elements (TEs) are often regarded as harmful genomic factors and indeed they are strongly suppressed by the epigenetic silencing mechanisms. On the other hand, the mobilization of TEs brings about variability of genome and transcriptome which are essential in the survival and evolution of the host species. The vast majority of such controlling TEs influence the neighboring genes in cis by either promoting or repressing the transcriptional activities. Although TEs are highly repetitive in the genomes and transcribed in specific stress conditions or developmental stages, the trans-acting regulatory roles of TE-derived RNAs have been rarely studied. It was only recently that TEs were investigated for their regulatory roles as a form of RNA. Particularly in plants, TEs are ample source of small RNAs such as small interfering (si) RNAs and micro (mi) RNAs. Those TE-derived small RNAs have potentials to affect non-TE transcripts by sequence complementarity, thereby generating novel gene regulatory networks including stress resistance and hybridization barrier. Apart from the small RNAs, a number of long non-coding RNAs (lncRNAs) are originated from TEs in plants. For example, a retrotransposon-derived lncRNA expressed in rice root acts as a decoy RNA or miRNA target mimic which negatively controls miRNA171. The post-transcriptional suppression of miRNA171 in roots ensures the stabilization of the target transcripts encoding SCARECROW-LIKE transcription factors, the key regulators of root development. In this review article, the recent discoveries of the regulatory roles of TE-derived RNAs in plants will be highlighted.
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143
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Ma K, Shi W, Xu M, Liu J, Zhang F. Genome-Wide Identification and Characterization of Long Non-Coding RNA in Wheat Roots in Response to Ca 2+ Channel Blocker. FRONTIERS IN PLANT SCIENCE 2018; 9:244. [PMID: 29559983 PMCID: PMC5845709 DOI: 10.3389/fpls.2018.00244] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 02/12/2018] [Indexed: 05/12/2023]
Abstract
It remains unclear whether plant lncRNAs are responsive to Ca2+-channel blocking. When using the Ca2+-channel blocker, LaCl3, to treat germinated wheat seeds for 24 h, we found that both root length and mitosis were inhibited in the LaCl3-treated groups. The effect of the Ca2+-channel blocker was verified in three ways: a [Ca2+]cyt decrease detected using Fluo-3/AM staining, a decrease in the Ca content measured using inductively coupled plasma mass spectrometry, and an inhibition of Ca2+ influx detected using Non-invasive Micro-test Technology. Genome-wide high throughput RNA-seq and bioinformatical methods were used to identify lncRNAs, and found 177 differentially expressed lncRNAs that might be in responsive to Ca2+-channel blocking. Among these, 108 were up-regulated and 69 were down-regulated. The validity of identified lncRNAs data from RNA-seq was verified using qPCR. GO and KEGG analysis indicated that a number of lncRNAs might be involved in diverse biological processes upon Ca2+-channel blocking. Further GO analysis showed that 23 lncRNAs might play roles as transcription factor (TF); Moreover, eight lncRNAs might participate in cell cycle regulation, and their relative expressions were detected using qPCR. This study also provides diverse data on wheat lncRNAs that can deepen our understanding of the function and regulatory mechanism of Ca2+-channel blocking in plants.
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Affiliation(s)
- Keshi Ma
- College of Life Sciences, Capital Normal University, Beijing, China
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Wenshuo Shi
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Mengyue Xu
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Jiaxi Liu
- College of Life Sciences, Capital Normal University, Beijing, China
- *Correspondence: Jiaxi Liu
| | - Feixiong Zhang
- College of Life Sciences, Capital Normal University, Beijing, China
- Feixiong Zhang
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Zhang SR, Wang H, Wang Z, Ren Y, Niu L, Liu J, Liu B. Photoperiodism dynamics during the domestication and improvement of soybean. SCIENCE CHINA. LIFE SCIENCES 2017; 60:1416-1427. [PMID: 28942538 DOI: 10.1007/s11427-016-9154-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 07/25/2017] [Indexed: 10/18/2022]
Abstract
Soybean (Glycine max) is a facultative short-day plant with a sensitive photoperiod perception and reaction system, which allows it to adjust its physiological state and gene regulatory networks to seasonal and diurnal changes in environmental conditions. In the past few decades, soybean cultivation has spread from East Asia to areas throughout the world. Biologists and breeders must now confront the challenge of understanding the molecular mechanism of soybean photoperiodism and improving agronomic traits to enable this important crop to adapt to geographical and environmental changes. In this review, we summarize the genetic regulatory network underlying photoperiodic responses in soybean. Genomic and genetic studies have revealed that the circadian clock, in conjunction with the light perception pathways, regulates photoperiodic flowering. Here, we provide an annotated list of 844 candidate flowering genes in soybean, with their putative biological functions. Many photoperiod-related genes have been intensively selected during domestication and crop improvement. Finally, we describe recent progress in engineering photoperiod-responsive genes for improving agronomic traits to enhance geographic adaptation in soybean, as well as future prospects for research on soybean photoperiodic responses.
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Affiliation(s)
- Sheng-Rui Zhang
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhongyu Wang
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yao Ren
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Lifang Niu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jun Liu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Bin Liu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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145
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Štorchová H. The Role of Non-Coding RNAs in Cytoplasmic Male Sterility in Flowering Plants. Int J Mol Sci 2017; 18:E2429. [PMID: 29144434 PMCID: PMC5713397 DOI: 10.3390/ijms18112429] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 11/17/2022] Open
Abstract
The interactions between mitochondria and nucleus substantially influence plant development, stress response and morphological features. The prominent example of a mitochondrial-nuclear interaction is cytoplasmic male sterility (CMS), when plants produce aborted anthers or inviable pollen. The genes responsible for CMS are located in mitochondrial genome, but their expression is controlled by nuclear genes, called fertility restorers. Recent explosion of high-throughput sequencing methods enabled to study transcriptomic alterations in the level of non-coding RNAs under CMS biogenesis. We summarize current knowledge of the role of nucleus encoded regulatory non-coding RNAs (long non-coding RNA, microRNA as well as small interfering RNA) in CMS. We also focus on the emerging data of non-coding RNAs encoded by mitochondrial genome and their possible involvement in mitochondrial-nuclear interactions and CMS development.
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Affiliation(s)
- Helena Štorchová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic.
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146
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Deng P, Liu S, Nie X, Weining S, Wu L. Conservation analysis of long non-coding RNAs in plants. SCIENCE CHINA-LIFE SCIENCES 2017; 61:190-198. [PMID: 29101587 DOI: 10.1007/s11427-017-9174-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 07/20/2017] [Indexed: 11/26/2022]
Abstract
Long non-coding RNAs (lncRNAs) are gene regulators that have vital roles in development and adaptation to the environment in eukaryotes. However, the structural and evolutionary analyses of plant lncRNAs are limited. In this study, we performed an analysis of lncRNAs in five monocot and five dicot species. Our results showed that plant lncRNA genes were generally shorter and had fewer exons than protein-coding genes. The numbers of lncRNAs were positively correlated with the numbers of protein-coding genes in different plant species, despite a high range of variation. Sequence conservation analysis showed that the majority of lncRNAs had high sequence conservation at the intra-species and sub-species levels, reminiscent of protein-coding genes. At the inter-species level, a subset of lncRNAs were highly diverged at the nucleotide level, but conserved by position. Interestingly, we found that plant lncRNAs have identical splicing signals, and those which can form precursors or targets of miRNAs have a conservative identity in different species. We also revealed that most of the lowly expressed lncRNAs were tissue-specific, while those highly conserved were constitutively transcribed. Meanwhile, we characterized a subset of rice lncRNAs that were co-expressed with their adjacent protein-coding genes, suggesting they may play cis-regulatory roles. These results will contribute to understanding the biological significance and evolution of lncRNAs in plants.
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Affiliation(s)
- Pingchuan Deng
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shu Liu
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, China
| | - Song Weining
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, China
| | - Liang Wu
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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147
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Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation. Proc Natl Acad Sci U S A 2017; 114:E10018-E10027. [PMID: 29087317 PMCID: PMC5699049 DOI: 10.1073/pnas.1708433114] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Noncoding RNAs are an underexplored reservoir of regulatory molecules in eukaryotes. We analyzed the environmental response of roots to phosphorus (Pi) nutrition to understand how a change in availability of an essential element is managed. Pi availability influenced translational regulation mediated by small upstream ORFs on protein-coding mRNAs. Discovery, classification, and evaluation of long noncoding RNAs (lncRNAs) associated with translating ribosomes uncovered diverse new examples of translational regulation. These included Pi-regulated small peptide synthesis, ribosome-coupled phased small interfering RNA production, and the translational regulation of natural antisense RNAs and other regulatory RNAs. This study demonstrates that translational control contributes to the stability and activity of regulatory RNAs, providing an avenue for manipulation of traits. Eukaryotic transcriptomes contain a major non–protein-coding component that includes precursors of small RNAs as well as long noncoding RNA (lncRNAs). Here, we utilized the mapping of ribosome footprints on RNAs to explore translational regulation of coding and noncoding RNAs in roots of Arabidopsis thaliana shifted from replete to deficient phosphorous (Pi) nutrition. Homodirectional changes in steady-state mRNA abundance and translation were observed for all but 265 annotated protein-coding genes. Of the translationally regulated mRNAs, 30% had one or more upstream ORF (uORF) that influenced the number of ribosomes on the principal protein-coding region. Nearly one-half of the 2,382 lncRNAs detected had ribosome footprints, including 56 with significantly altered translation under Pi-limited nutrition. The prediction of translated small ORFs (sORFs) by quantitation of translation termination and peptidic analysis identified lncRNAs that produce peptides, including several deeply evolutionarily conserved and significantly Pi-regulated lncRNAs. Furthermore, we discovered that natural antisense transcripts (NATs) frequently have actively translated sORFs, including five with low-Pi up-regulation that correlated with enhanced translation of the sense protein-coding mRNA. The data also confirmed translation of miRNA target mimics and lncRNAs that produce trans-acting or phased small-interfering RNA (tasiRNA/phasiRNAs). Mutational analyses of the positionally conserved sORF of TAS3a linked its translation with tasiRNA biogenesis. Altogether, this systematic analysis of ribosome-associated mRNAs and lncRNAs demonstrates that nutrient availability and translational regulation controls protein and small peptide-encoding mRNAs as well as a diverse cadre of regulatory RNAs.
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148
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Arabidopsis noncoding RNA modulates seedling greening during deetiolation. SCIENCE CHINA-LIFE SCIENCES 2017; 61:199-203. [DOI: 10.1007/s11427-017-9187-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/16/2017] [Indexed: 01/21/2023]
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149
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Wang J, Meng X, Dobrovolskaya OB, Orlov YL, Chen M. Non-coding RNAs and Their Roles in Stress Response in Plants. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:301-312. [PMID: 29017967 PMCID: PMC5673675 DOI: 10.1016/j.gpb.2017.01.007] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 01/04/2017] [Accepted: 01/26/2017] [Indexed: 02/04/2023]
Abstract
Eukaryotic genomes encode thousands of non-coding RNAs (ncRNAs), which play crucial roles in transcriptional and post-transcriptional regulation of gene expression. Accumulating evidence indicates that ncRNAs, especially microRNAs (miRNAs) and long ncRNAs (lncRNAs), have emerged as key regulatory molecules in plant stress responses. In this review, we have summarized the current progress on the understanding of plant miRNA and lncRNA identification, characteristics, bioinformatics tools, and resources, and provided examples of mechanisms of miRNA- and lncRNA-mediated plant stress tolerance.
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Affiliation(s)
- Jingjing Wang
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xianwen Meng
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Oxana B Dobrovolskaya
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Yuriy L Orlov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Ming Chen
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China.
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150
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Wang Z, Liu Y, Li L, Li D, Zhang Q, Guo Y, Wang S, Zhong C, Huang H. Whole transcriptome sequencing of Pseudomonas syringae pv. actinidiae-infected kiwifruit plants reveals species-specific interaction between long non-coding RNA and coding genes. Sci Rep 2017; 7:4910. [PMID: 28687784 PMCID: PMC5501815 DOI: 10.1038/s41598-017-05377-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 05/30/2017] [Indexed: 12/31/2022] Open
Abstract
An outbreak of kiwifruit bacterial canker disease caused by Pseudomonas syringae pv. actinidiae (Psa) beginning in 2008 caused disaster to the kiwifruit industry. However the mechanisms of interaction between kiwifruit and Psa are unknown. Long noncoding RNAs (lncRNAs) are known to regulate many biological processes, but comprehensive repertoires of kiwifruit lncRNAs and their effects on the interaction between kiwifruit and Psa are unknown. Here, based on in-depth transcriptomic analysis of four kiwifruit materials at three stages of infection with Psa, we identified 14,845 transcripts from 12,280 loci as putative lncRNAs. Hierarchical clustering analysis of differentially-expressed transcripts reveals that both protein-coding and lncRNA transcripts are expressed species-specifically. Comparing differentially-expressed transcripts from different species, variations in pattern-triggered immunity (PTI) were the main causes of species-specific responses to infection by Psa. Using weighted gene co-expression network analysis, we identified species-specific expressed key lncRNAs which were closely related to plant immune response and signal transduction. Our results illustrate that different kiwifruit species employ multiple different plant immunity layers to fight against Psa infection, which causes distinct responses. We also discovered that lncRNAs might affect kiwifruit responses to Psa infection, indicating that both protein-coding regions and noncoding regions can affect kiwifruit response to Psa infection.
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Affiliation(s)
- Zupeng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, Guangdong, 510650, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yifei Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China. .,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, Guangdong, 510650, China.
| | - Li Li
- Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Dawei Li
- Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Qiong Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Yangtao Guo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, Guangdong, 510650, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuaibin Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, Guangdong, 510650, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Caihong Zhong
- Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Hongwen Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China. .,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, Guangdong, 510650, China. .,Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
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