1
|
Wang Y, Cao L, Liu M, Yan P, Niu F, Dong S, Ma F, Lan D, Zhang X, Hu J, Xin X, Yang J, Luo X. Alternative splicing of lncRNA LAIR fine-tunes the regulation of neighboring yield-related gene LRK1 expression in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1751-1766. [PMID: 38943483 DOI: 10.1111/tpj.16882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 07/01/2024]
Abstract
The diversity in alternative splicing of long noncoding RNAs (lncRNAs) poses a challenge for functional annotation of lncRNAs. Moreover, little is known on the effects of alternatively spliced lncRNAs on crop yield. In this study, we cloned nine isoforms resulting from the alternative splicing of the lncRNA LAIR in rice. The LAIR isoforms are generated via alternative 5'/3' splice sites and different combinations of specific introns. All LAIR isoforms activate the expression of the neighboring LRK1 gene and enhance yield-related rice traits. In addition, there are slight differences in the binding ability of LAIR isoforms to the epigenetic modification-related proteins OsMOF and OsWDR5, which affect the enrichment of H4K16ac and H3K4me3 at the LRK1 locus, and consequently fine-tune the regulation of LRK1 expression and yield-related traits. These differences in binding may be caused by polymorphic changes to the RNA secondary structure resulting from alternative splicing. It was also observed that the composition of LAIR isoforms was sensitive to abiotic stress. These findings suggest that the alternative splicing of LAIR leads to the formation of a functional transcript population that precisely regulates yield-related gene expression, which may be relevant for phenotypic polymorphism-based crop breeding under changing environmental conditions.
Collapse
Affiliation(s)
- Ying Wang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Research Center for Ecological Science and Technology, Fudan Zhangjiang Institute, Shanghai, 201203, China
- National Science Park of Fudan University, Shanghai, 200433, China
| | - Liming Cao
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Mingyu Liu
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Peiwen Yan
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Fuan Niu
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Shiqing Dong
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai'an, 223300, China
| | - Fuying Ma
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Dengyong Lan
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xinwei Zhang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jian Hu
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xiaoyun Xin
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jinshui Yang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xiaojin Luo
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| |
Collapse
|
2
|
Li X, Liu Q, Liu J. Long Non-Coding RNAs: Discoveries, Mechanisms, and Research Strategies in Seeds. Genes (Basel) 2023; 14:2214. [PMID: 38137035 PMCID: PMC10742540 DOI: 10.3390/genes14122214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Seeds provide nutrients for the embryo and allow for dormancy in stressed environments to better adapt the plant to its environment. In addition, seeds are an essential source of food for human survival and are the basis for the formation of food production and quality. Therefore, the research on the genetic mechanism of seed development and germination will provide a theoretical basis and technical support for the improvement of crop yield and quality. Recent studies have shown that long non-coding RNAs (lncRNAs) occupy a pivotal position in seed development and germination. In this review, we describe the key processes in seed biology and examine discoveries and insights made in seed lncRNA, with emphasis on lncRNAs that regulate seed biology through multiple mechanisms. Given that thousands of lncRNAs are present in the seed transcriptome, characterization has lagged far behind identification. We provide an overview of research strategies and approaches including some exciting new techniques that may uncover the function of lncRNAs in seed. Finally, we discuss the challenges facing the field and the opening questions. All in all, we hope to provide a clear perspective on discoveries of seed lncRNA by linking discoveries, mechanisms, and technologies.
Collapse
Affiliation(s)
| | | | - Jun Liu
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (X.L.); (Q.L.)
| |
Collapse
|
3
|
Pinky, Jain R, Yadav A, Sharma R, Dhaka N. Emerging roles of long non-coding RNAs in regulating agriculturally important seed traits. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108019. [PMID: 37714026 DOI: 10.1016/j.plaphy.2023.108019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/26/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023]
Abstract
Seeds have enormous economic importance as source of calories, nutrition, edible oil, and biofuels. Therefore, seed traits like seed size and shape, weight, micronutrient content, oil content, quality, post-harvest sprouting, etc., are some of the main targets in crop improvement. Designing the strategies for their improvement benefits heavily from understanding the regulatory aspects of seed development. Recent studies indicate that long non-coding RNAs (lncRNAs) are one of the important regulators of seed development. They played a significant role in crop domestication by influencing seed traits. LncRNAs are conventionally defined as non-coding RNAs greater than 200 bp in length but lacking protein coding potential. Here we highlight the emerging pieces of evidence of lncRNA-mediated regulation of seed development through diverse mechanisms, for instance, by acting as target mimics or precursors of regulatory small RNAs or through chromatin remodeling and post-transcriptional repression. We also enumerate the insights from high-throughput transcriptomic studies from developing seeds of cereal, oilseed, biofuel, and pulse crops. We highlight the lncRNA candidates and lncRNA-mediated regulatory networks regulating seed development and related agronomic traits. Further, we discuss the potential of lncRNAs for improvement of agriculturally important seed traits through marker-assisted breeding and/or transgenic approaches.
Collapse
Affiliation(s)
- Pinky
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - Rubi Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Abhinandan Yadav
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - Rita Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Namrata Dhaka
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India.
| |
Collapse
|
4
|
Babaei S, Singh MB, Bhalla PL. Role of long non-coding RNAs in rice reproductive development. FRONTIERS IN PLANT SCIENCE 2022; 13:1040366. [PMID: 36457537 PMCID: PMC9705774 DOI: 10.3389/fpls.2022.1040366] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/28/2022] [Indexed: 05/13/2023]
Abstract
Rice is a staple crop, feeding over half of the global population. The future demand of population growth and climate change requires substantial rice improvement. Recent advances in rice genomics have highlighted the vital role of the non-coding part of the genome. The protein-coding regions account for only a tiny portion of the eukaryotic genome, and most of the genomic regions transcribe copious amounts of non-coding RNAs. Of these, the long non-coding RNAs, including linear non-coding RNAs (lncRNAs) and circular non-coding RNAs (circRNAs), have been shown to play critical roles in various developmental processes by regulating the expression of genes and functions of proteins at transcriptional, post-transcriptional and post-translational levels. With the advances in next-generation sequencing technologies, a substantial number of long non-coding RNAs have been found to be expressed in plant reproductive organs in a cell- and tissue-specific manner suggesting their reproductive development-related functions. Accumulating evidence points towards the critical role of these non-coding RNAs in flowering, anther, and pollen development, ovule and seed development and photoperiod and temperature regulation of male fertility. In this mini review, we provide a brief overview of the role of the linear and circular long non-coding RNAs in rice reproductive development and control of fertility and crop yield.
Collapse
Affiliation(s)
| | | | - Prem L. Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
| |
Collapse
|
5
|
PLncWX: A Machine-Learning Algorithm for Plant lncRNA Identification Based on WOA-XGBoost. J CHEM-NY 2021. [DOI: 10.1155/2021/6256021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are a class of RNAs longer than 200 nt and cannot encode the protein. Studies have shown that lncRNAs can regulate gene expression at the epigenetic, transcriptional, and posttranscriptional levels, which are not only closely related to the occurrence, development, and prevention of human diseases, but also can regulate plant flowering and participate in plant abiotic stress responses such as drought and salt. Therefore, how to accurately and efficiently identify lncRNAs is still an essential job of relevant researches. There have been a large number of identification tools based on machine-learning and deep learning algorithms, mostly using human and mouse gene sequences as training sets, seldom plants, and only using one or one class of feature selection methods after feature extraction. We developed an identification model containing dicot, monocot, algae, moss, and fern. After comparing 20 feature selection methods (seven filter and thirteen wrapper methods) combined with seven classifiers, respectively, considering the correlation between features and model redundancy at the same time, we found that the WOA-XGBoost-based model had better performance with 91.55%, 96.78%, and 91.68% of accuracy, AUC, and F1_score. Meanwhile, the number of elements in the feature subset was reduced to 23, which effectively improved the prediction accuracy and modeling efficiency.
Collapse
|
6
|
Cheng C, Liu F, Tian N, Mensah RA, Sun X, Liu J, Wu J, Wang B, Li D, Lai Z. Identification and characterization of early Fusarium wilt responsive mRNAs and long non-coding RNAs in banana root using high-throughput sequencing. Sci Rep 2021; 11:16363. [PMID: 34381122 PMCID: PMC8358008 DOI: 10.1038/s41598-021-95832-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 07/29/2021] [Indexed: 12/03/2022] Open
Abstract
Fusarium wilt disease, caused by Fusarium oxysporum f.sp. cubense (Foc), has been recognized as the most devastating disease to banana. The regulatory role of long non-coding RNAs (lncRNAs) in plant defense has been verified in many plant species. However, the understanding of their role during early FocTR4 (Foc tropical race 4) infection stage is very limited. In this study, lncRNA sequencing was used to reveal banana root transcriptome profile changes during early FocTR4 infection stages. Quantitative real time PCR (qRT-PCR) was performed to confirm the expression of eight differentially expressed (DE) lncRNAs (DELs) and their predicted target genes (DETs), and three DE genes (DEGs). Totally, 12,109 lncRNAs, 36,519 mRNAs and 2642 novel genes were obtained, of which 1398 (including 78 DELs, 1220 DE known genes and 100 DE novel genes) were identified as FocTR4 responsive DE transcripts. Gene function analysis revealed that most DEGs were involved in biosynthesis of secondary metabolites, plant–pathogen interaction, plant hormone signal transduction, phenylalanine metabolism, phenylpropanoid biosynthesis, alpha-linolenic acid metabolism and so on. Coincidently, many DETs have been identified as DEGs in previous transcriptome studies. Moreover, many DETs were found to be involved in ribosome, oxidative phosphorylation, lipoic acid metabolism, ubiquitin mediated proteolysis, N-glycan biosynthesis, protein processing in endoplasmic reticulum and DNA damage response pathways. QRT-PCR result showed the expression patterns of the selected transcripts were mostly consistent with our lncRNA sequencing data. Our present study showed the regulatory role of lncRNAs on known biotic and abiotic stress responsive genes and some new-found FocTR4 responsive genes, which can provide new insights into FocTR4-induced changes in the banana root transcriptome during the early pathogen infection stage.
Collapse
Affiliation(s)
- Chunzhen Cheng
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,College of Horticulture, Shanxi Agricultural University, Taigu, 030801, China.
| | - Fan Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Na Tian
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Raphael Anue Mensah
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xueli Sun
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiapeng Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Junwei Wu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Bin Wang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dan Li
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
7
|
Han Y, Zhu L, Li L, Wang Y, Zhao M, Wang K, Sun C, Chen J, Liu L, Chen P, Lei J, Wang Y, Zhang M. Characteristics of RNA alternative splicing and its potential roles in ginsenoside biosynthesis in a single plant of ginseng, Panax ginseng C.A. Meyer. Mol Genet Genomics 2021; 296:971-983. [PMID: 34008042 DOI: 10.1007/s00438-021-01792-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 04/22/2021] [Indexed: 11/26/2022]
Abstract
RNA alternative splicing (AS) is prevalent in higher organisms and plays a paramount role in biology; therefore, it is crucial to have comprehensive knowledge on AS to understand biology. However, knowledge is limited about how AS activates in a single plant and functions in a biological process. Ginseng is one of the most widely used medicinal herbs that is abundant in a number of medicinal bioactive components, especially ginsenosides. In this study, we sequenced the transcripts of 14 organs from a 4-year-old ginseng plant and quantified their ginsenoside contents. We identified AS genes by analyzing their transcripts with the ginseng genome and verified their AS events by PCR. The plant had a total of 13,863 AS genes subjected to 30,801 AS events with five mechanisms: skipped exon, retained intron, alternative 5'splice site, alternative 3' splice site, and mutually exclusive exon. The genes that were more conserved, had more exons, and/or expressed across organs were more likely to be subjected to AS. AS genes were enriched in over 500 GO terms in the plant even though the number of AS gene-enriched GO terms varied across organs. At least 24 AS genes were found to be involved in ginsenoside biosynthesis. These AS genes were significantly up-enriched and more likely to form a co-expression network, thus suggesting the functions of AS and correlations of the AS genes in the process. This study provides comprehensive insights into the molecular characteristics and biological functions of AS in a single plant; thus, helping better understand biology.
Collapse
Affiliation(s)
- Yilai Han
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Lei Zhu
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Li Li
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Yanfang Wang
- Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, 130118, Jilin, China
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China
- Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China
- Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Chunyu Sun
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China
- Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Jing Chen
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Lingyu Liu
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Ping Chen
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Jun Lei
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China.
- Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, 130118, Jilin, China.
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China.
- Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, 130118, Jilin, China.
| |
Collapse
|
8
|
Kay MK, Zhang J, Choudhury M. Screening for alternative splicing of lncRNA Dleu2 in the mouse liver cell line AML-12. Biomed Rep 2021; 14:50. [PMID: 33859821 DOI: 10.3892/br.2021.1426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/19/2021] [Indexed: 11/05/2022] Open
Abstract
The long non coding RNA deleted in leukemia 2 gene (Dleu2) has recently been demonstrated to be an active player in the progression of several types of cancer, including hepatocellular carcinoma. Dleu2 may serve a role in modulating the downstream effects-mediated by alternative splicing of its multiple exons. However, the proportional expression of these alternative splicing populations of the Dleu2 exons is currently unknown. To determine how Dleu2 could be affected by alternative splicing, a series of alternative splicing primer sets were designed to investigate which transcripts were preferentially activated when Dleu2 was targeted for downregulation or upregulation. A specific Dleu2 small interfering RNA that targeted an exon upstream of the tumor suppressor microRNA site significantly knocked down Dleu2 expression across all the primer sets used, which targeted 13 different alternative splicing transcripts over 5 different promoter sites in the mouse liver cell line, AML-12. Similarly, 50 µM Resveratrol led to significant upregulation of Dleu2 in 11 alternative splicing transcripts. These results show that Dleu2 is capable of successful modulation across alternative splicing transcripts that can be screened, and also that Resveratrol can be a potential nutraceutical, which may potentially lead to novel approaches in the use of lncRNA Dleu2 for diagnostics and regulation.
Collapse
Affiliation(s)
- Matthew Krivacka Kay
- Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas, TX 77843, USA
| | - Jian Zhang
- Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas, TX 77843, USA
| | - Mahua Choudhury
- Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas, TX 77843, USA
| |
Collapse
|
9
|
Khemka NK, Singh U, Dwivedi AK, Jain M. Machine Learning-Based Annotation of Long Noncoding RNAs Using PLncPRO. Methods Mol Biol 2021; 2107:253-260. [PMID: 31893451 DOI: 10.1007/978-1-0716-0235-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Long noncoding RNAs (lncRNAs) are noncoding RNAs with transcript length more than 200 nucleotides. Although poorly conserved, lncRNAs are expressed across diverse species, including plants and animals, and are known to be involved in regulation of various biological processes. To understand their biological significance, we first need to identify the lncRNAs accurately. However, distinguishing lncRNAs from coding transcripts is still a challenging task. Here, we describe a machine learning-based approach to accurately identify the plant lncRNAs. We describe the usage of plant long noncoding RNA prediction by random forests (PLncPRO), which employs machine learning-based random forest algorithm to recognize the lncRNAs from the set of given transcript sequences. Stepwise instructions have been provided to use PLncPRO to annotate the lncRNA sequences.
Collapse
Affiliation(s)
- Niraj K Khemka
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Urminder Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Anuj K Dwivedi
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
| |
Collapse
|
10
|
Feng S, Fang H, Liu X, Dong Y, Wang Q, Yang KQ. Genome-wide identification and characterization of long non-coding RNAs conferring resistance to Colletotrichum gloeosporioides in walnut (Juglans regia). BMC Genomics 2021; 22:15. [PMID: 33407106 PMCID: PMC7789297 DOI: 10.1186/s12864-020-07310-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/07/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Walnut anthracnose caused by Colletotrichum gloeosporioides (Penz.) Penz. and Sacc. is an important walnut production problem in China. Although the long non-coding RNAs (lncRNAs) are important for plant disease resistance, the molecular mechanisms underlying resistance to C. gloeosporioides in walnut remain poorly understood. RESULTS The anthracnose-resistant F26 fruits from the B26 clone and the anthracnose-susceptible F423 fruits from the 4-23 clone of walnut were used as the test materials. Specifically, we performed a comparative transcriptome analysis of F26 and F423 fruit bracts to identify differentially expressed LncRNAs (DELs) at five time-points (tissues at 0 hpi, pathological tissues at 24 hpi, 48 hpi, 72 hpi, and distal uninoculated tissues at 120 hpi). Compared with F423, a total of 14,525 DELs were identified, including 10,645 upregulated lncRNAs and 3846 downregulated lncRNAs in F26. The number of upregulated lncRNAs in F26 compared to in F423 was significantly higher at the early stages of C. gloeosporioides infection. A total of 5 modules related to disease resistance were screened by WGCNA and the target genes of lncRNAs were obtained. Bioinformatic analysis showed that the target genes of upregulated lncRNAs were enriched in immune-related processes during the infection of C. gloeosporioides, such as activation of innate immune response, defense response to bacterium, incompatible interaction and immune system process, and enriched in plant hormone signal transduction, phenylpropanoid biosynthesis and other pathways. And 124 known target genes for 96 hub lncRNAs were predicted, including 10 known resistance genes. The expression of 5 lncRNAs and 5 target genes was confirmed by qPCR, which was consistent with the RNA-seq data. CONCLUSIONS The results of this study provide the basis for future functional characterizations of lncRNAs regarding the C. gloeosporioides resistance of walnut fruit bracts.
Collapse
Affiliation(s)
- Shan Feng
- College of Forestry, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
| | - Hongcheng Fang
- College of Forestry, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Tai'an, 271018, Shandong Province, China
- Shandong Taishan Forest Ecosystem Research Station, Tai'an, 271018, Shandong Province, China
| | - Xia Liu
- College of Forestry, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
- Department of Science and Technology, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, China
| | - Yuhui Dong
- College of Forestry, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
| | - Qingpeng Wang
- College of Forestry, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
| | - Ke Qiang Yang
- College of Forestry, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China.
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Tai'an, 271018, Shandong Province, China.
- Shandong Taishan Forest Ecosystem Research Station, Tai'an, 271018, Shandong Province, China.
| |
Collapse
|
11
|
Xu B, Meng Y, Jin Y. RNA structures in alternative splicing and back-splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1626. [PMID: 32929887 DOI: 10.1002/wrna.1626] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/14/2020] [Accepted: 08/22/2020] [Indexed: 12/12/2022]
Abstract
Alternative splicing greatly expands the transcriptomic and proteomic diversities related to physiological and developmental processes in higher eukaryotes. Splicing of long noncoding RNAs, and back- and trans- splicing further expanded the regulatory repertoire of alternative splicing. RNA structures were shown to play an important role in regulating alternative splicing and back-splicing. Application of novel sequencing technologies made it possible to identify genome-wide RNA structures and interaction networks, which might provide new insights into RNA splicing regulation in vitro to in vivo. The emerging transcription-folding-splicing paradigm is changing our understanding of RNA alternative splicing regulation. Here, we review the insights into the roles and mechanisms of RNA structures in alternative splicing and back-splicing, as well as how disruption of these structures affects alternative splicing and then leads to human diseases. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
Collapse
Affiliation(s)
- Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, Hangzhou, China
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, China
| |
Collapse
|
12
|
Lu Y, Zhou DX, Zhao Y. Understanding epigenomics based on the rice model. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1345-1363. [PMID: 31897514 DOI: 10.1007/s00122-019-03518-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/18/2019] [Indexed: 05/26/2023]
Abstract
The purpose of this paper provides a comprehensive overview of the recent researches on rice epigenomics, including DNA methylation, histone modifications, noncoding RNAs, and three-dimensional genomics. The challenges and perspectives for future research in rice are discussed. Rice as a model plant for epigenomic studies has much progressed current understanding of epigenetics in plants. Recent results on rice epigenome profiling and three-dimensional chromatin structure studies reveal specific features and implication in gene regulation during rice plant development and adaptation to environmental changes. Results on rice chromatin regulator functions shed light on mechanisms of establishment, recognition, and resetting of epigenomic information in plants. Cloning of several rice epialleles associated with important agronomic traits highlights importance of epigenomic variation in rice plant growth, fitness, and yield. In this review, we summarize and analyze recent advances in rice epigenomics and discuss challenges and directions for future research in the field.
Collapse
Affiliation(s)
- Yue Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Institute of Plant Science of Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University Paris-Saclay, 91405, Orsay, France
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
13
|
Robinson EK, Covarrubias S, Carpenter S. The how and why of lncRNA function: An innate immune perspective. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194419. [PMID: 31487549 PMCID: PMC7185634 DOI: 10.1016/j.bbagrm.2019.194419] [Citation(s) in RCA: 181] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/21/2019] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing has provided a more complete picture of the composition of the human transcriptome indicating that much of the "blueprint" is a vastness of poorly understood non-protein-coding transcripts. This includes a newly identified class of genes called long noncoding RNAs (lncRNAs). The lack of sequence conservation for lncRNAs across species meant that their biological importance was initially met with some skepticism. LncRNAs mediate their functions through interactions with proteins, RNA, DNA, or a combination of these. Their functions can often be dictated by their localization, sequence, and/or secondary structure. Here we provide a review of the approaches typically adopted to study the complexity of these genes with an emphasis on recent discoveries within the innate immune field. Finally, we discuss the challenges, as well as the emergence of new technologies that will continue to move this field forward and provide greater insight into the biological importance of this class of genes. This article is part of a Special Issue entitled: ncRNA in control of gene expression edited by Kotb Abdelmohsen.
Collapse
Affiliation(s)
- Elektra K Robinson
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Sergio Covarrubias
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America.
| |
Collapse
|
14
|
Price DC, Goodenough UW, Roth R, Lee JH, Kariyawasam T, Mutwil M, Ferrari C, Facchinelli F, Ball SG, Cenci U, Chan CX, Wagner NE, Yoon HS, Weber APM, Bhattacharya D. Analysis of an improved Cyanophora paradoxa genome assembly. DNA Res 2020; 26:287-299. [PMID: 31098614 PMCID: PMC6704402 DOI: 10.1093/dnares/dsz009] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 03/30/2019] [Indexed: 12/12/2022] Open
Abstract
Glaucophyta are members of the Archaeplastida, the founding group of photosynthetic eukaryotes that also includes red algae (Rhodophyta), green algae, and plants (Viridiplantae). Here we present a high-quality assembly, built using long-read sequences, of the ca. 100 Mb nuclear genome of the model glaucophyte Cyanophora paradoxa. We also conducted a quick-freeze deep-etch electron microscopy (QFDEEM) analysis of C. paradoxa cells to investigate glaucophyte morphology in comparison to other organisms. Using the genome data, we generated a resolved 115-taxon eukaryotic tree of life that includes a well-supported, monophyletic Archaeplastida. Analysis of muroplast peptidoglycan (PG) ultrastructure using QFDEEM shows that PG is most dense at the cleavage-furrow. Analysis of the chlamydial contribution to glaucophytes and other Archaeplastida shows that these foreign sequences likely played a key role in anaerobic glycolysis in primordial algae to alleviate ATP starvation under night-time hypoxia. The robust genome assembly of C. paradoxa significantly advances knowledge about this model species and provides a reference for exploring the panoply of traits associated with the anciently diverged glaucophyte lineage.
Collapse
Affiliation(s)
- Dana C Price
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | | | - Robyn Roth
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, USA
| | - Jae-Hyeok Lee
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | | | - Marek Mutwil
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.,School of Biological Sciences, Nanyang Technological University, Singapore
| | - Camilla Ferrari
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Fabio Facchinelli
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, D-40225 Düsseldorf, Germany
| | - Steven G Ball
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS-USTL, Université des Sciences et Technologies de Lille, Villeneuve d'Ascq Cedex, France
| | - Ugo Cenci
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS-USTL, Université des Sciences et Technologies de Lille, Villeneuve d'Ascq Cedex, France
| | - Cheong Xin Chan
- Institute for Molecular Bioscience and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Nicole E Wagner
- Department of Biochemistry and Microbiology, Rutgers, Rutgers University, New Brunswick, NJ, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Andreas P M Weber
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, D-40225 Düsseldorf, Germany
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers, Rutgers University, New Brunswick, NJ, USA
| |
Collapse
|
15
|
Tu Z, Shen Y, Wen S, Zong Y, Li H. Alternative Splicing Enhances the Transcriptome Complexity of Liriodendron chinense. FRONTIERS IN PLANT SCIENCE 2020; 11:578100. [PMID: 33072153 PMCID: PMC7539066 DOI: 10.3389/fpls.2020.578100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/04/2020] [Indexed: 05/11/2023]
Abstract
Alternative splicing (AS) plays pivotal roles in regulating plant growth and development, flowering, biological rhythms, signal transduction, and stress responses. However, no studies on AS have been performed in Liriodendron chinense, a deciduous tree species that has high economic and ecological value. In this study, we used multiple tools and algorithms to analyze transcriptome data derived from seven tissues via hybrid sequencing. Although only 17.56% (8,503/48,408) of genes in L. chinense were alternatively spliced, these AS genes occurred in 37,844 AS events. Among these events, intron retention was the most frequent AS event, producing 1,656 PTC-containing and 3,310 non-PTC-containing transcripts. Moreover, 183 long noncoding RNAs (lncRNAs) also underwent AS events. Furthermore, weighted gene coexpression network analysis (WGCNA) revealed that there were great differences in the activities of transcription and post-transcriptional regulation between pistils and leaves, and AS had an impact on many physiological and biochemical processes in L. chinense, such as photosynthesis, sphingolipid metabolism, fatty acid biosynthesis and metabolism. Moreover, our analysis showed that the features of genes may affect AS, as AS genes and non-AS genes had differences in the exon/intron length, transcript length, and number of exons/introns. In addition, the structure of AS genes may impact the frequencies and types of AS because AS genes with more exons or introns tended to exhibit more AS events, and shorter introns tended to be retained, whereas shorter exons tended to be skipped. Furthermore, eight AS genes were verified, and the results were consistent with our analysis. Overall, this study reveals that AS and gene interaction are mutual-on one hand, AS can affect gene expression and translation, while on the other hand, the structural characteristics of the gene can also affect AS. This work is the first to comprehensively report on AS in L. chinense, and it can provide a reference for further research on AS in L. chinense.
Collapse
Affiliation(s)
- Zhonghua Tu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yufang Shen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Shaoying Wen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yaxian Zong
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Huogen Li
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- *Correspondence: Huogen Li,
| |
Collapse
|
16
|
Wang Y, Zhang H, Li Q, Jin J, Chen H, Zou Y, Huang X, Ding Y. Genome-Wide Identification of lncRNAs Involved in Fertility Transition in the Photo-Thermosensitive Genic Male Sterile Rice Line Wuxiang S. FRONTIERS IN PLANT SCIENCE 2020; 11:580050. [PMID: 33519839 PMCID: PMC7840536 DOI: 10.3389/fpls.2020.580050] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 12/22/2020] [Indexed: 05/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) act as universal regulators of various biological processes, but no genome-wide screening of lncRNAs involved in the fertility transition of the photo-thermosensitive genic male sterile (PTGMS) rice line has been reported. Here, we performed strand-specific RNA sequencing at three developmental stages of a novel PTGMS line Wuxiang S (WXS). A total of 3,948 lncRNAs were identified; 622 of these were detected as differentially expressed lncRNAs (DE-lncRNAs) between male-sterile WXS (WXS-S) and male-fertile WXS (WXS-F). A large proportion of lncRNAs differentially expressed at the stage of pollen mother cells meiosis, suggested that it may be the most critical stage for fertility transition of WXS. Furthermore, functional annotation of the cis- and trans- targets of DE-lncRNAs showed that 150 targets corresponding to 141 DE-lncRNAs were identified as involved in anther and pollen development. Moreover, computational analysis predicted 97 lncRNAs as precursors for 72 miRNAs, and 94 DE-lncRNAs as potential endogenous target mimics (eTMs) for 150 miRNAs. Finally, using the dual luciferase reporter assays, we demonstrated that two lncRNAs act as eTMs to regulate the expression of the SPL and GRF genes by competing for the shared osa-miR156 and osa-miR396, respectively. These genomic characteristics, differential expression, and interaction of lncRNAs with miRNAs and mRNAs contribute to our understanding of the roles of lncRNAs during the fertility transition in PTGMS rice lines.
Collapse
Affiliation(s)
- Ying Wang
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hongyuan Zhang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Qian Li
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jing Jin
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hao Chen
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yu Zou
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xingguo Huang
- Wuhan Wuda Tianyuau Bio-Tech Co., Ltd., Wuhan, China
| | - Yi Ding
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, China
- *Correspondence: Yi Ding,
| |
Collapse
|
17
|
Téllez-Robledo B, Manzano C, Saez A, Navarro-Neila S, Silva-Navas J, de Lorenzo L, González-García MP, Toribio R, Hunt AG, Baigorri R, Casimiro I, Brady SM, Castellano MM, Del Pozo JC. The polyadenylation factor FIP1 is important for plant development and root responses to abiotic stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:1203-1219. [PMID: 31111599 DOI: 10.1111/tpj.14416] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/03/2019] [Accepted: 05/14/2019] [Indexed: 05/28/2023]
Abstract
Root development and its response to environmental changes is crucial for whole plant adaptation. These responses include changes in transcript levels. Here, we show that the alternative polyadenylation (APA) of mRNA is important for root development and responses. Mutations in FIP1, a component of polyadenylation machinery, affects plant development, cell division and elongation, and response to different abiotic stresses. Salt treatment increases the amount of poly(A) site usage within the coding region and 5' untranslated regions (5'-UTRs), and the lack of FIP1 activity reduces the poly(A) site usage within these non-canonical sites. Gene ontology analyses of transcripts displaying APA in response to salt show an enrichment in ABA signaling, and in the response to stresses such as salt or cadmium (Cd), among others. Root growth assays show that fip1-2 is more tolerant to salt but is hypersensitive to ABA or Cd. Our data indicate that FIP1-mediated alternative polyadenylation is important for plant development and stress responses.
Collapse
Affiliation(s)
- Barbara Téllez-Robledo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Concepcion Manzano
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Angela Saez
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
- DTD, Timac Agro Spain, Lodosa, 31580, Navarra, Spain
| | - Sara Navarro-Neila
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Javier Silva-Navas
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Laura de Lorenzo
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
| | - Mary-Paz González-García
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - René Toribio
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Arthur G Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
| | | | - Ilda Casimiro
- Facultad de Ciencias, Department de Anatomía, Biología Celular y Zoología, Universidad de Extremadura, 06006, Badajoz, Spain
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - M Mar Castellano
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - J Carlos Del Pozo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| |
Collapse
|
18
|
Yang Z, Yang Z, Yang C, Wang Z, Chen D, Xie Y, Wu Y. Identification and genetic analysis of alternative splicing of long non-coding RNAs in tomato initial flowering stage. Genomics 2019; 112:897-907. [PMID: 31175976 DOI: 10.1016/j.ygeno.2019.06.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/19/2019] [Accepted: 06/04/2019] [Indexed: 01/07/2023]
Abstract
Alternative splicing (AS) is a key modulator of development in many eukaryotic organisms. Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs that play essential regulatory roles in various developmental processes and stress responses. However, the functions of AS lncRNAs during the initial flowering of tomato are largely unknown. This study was designed to investigate the AS pattern of lncRNAs in tomato flower, leaf, and root tissues at the initial flowering stage. Using RNA-Seq, we found that 72.55% of lncRNAs underwent AS in these tissues, yielding a total of 16,995 AS events. Among them, the main type of AS event is alternative first exon (AFE), followed by retained intron (RI). We performed candidate target genes analysis on tissue-specific AS lncRNA, and the results indicated that the candidate target genes of these lncRNAs may be involved in the regulation of circadian rhythm, plant immunity, cellulose synthesis and phosphate-containing compound metabolic process. Moreover, a total of 73,085 putative SNPs and 15,679 InDels were detected, and the potential relationship between the AS of lncRNAs and interesting SNP and InDel loci, as well as their numbers, revealed their effects on tomato genetic diversity and genomic stability. Our data provide new insights into the complexity of the transcriptome and the regulation of AS.
Collapse
Affiliation(s)
- Zhenchao Yang
- College of Horticulture, College of Life Sciences, College of Science, Northwest A&F University, Yangling, Shaan Xi, China
| | - Zhao Yang
- College of Horticulture, College of Life Sciences, College of Science, Northwest A&F University, Yangling, Shaan Xi, China
| | - Chengcheng Yang
- College of Horticulture, College of Life Sciences, College of Science, Northwest A&F University, Yangling, Shaan Xi, China
| | - Zhengyan Wang
- College of Horticulture, College of Life Sciences, College of Science, Northwest A&F University, Yangling, Shaan Xi, China
| | - Danyan Chen
- College of Horticulture, College of Life Sciences, College of Science, Northwest A&F University, Yangling, Shaan Xi, China
| | - Yingge Xie
- College of Horticulture, College of Life Sciences, College of Science, Northwest A&F University, Yangling, Shaan Xi, China.
| | - Yongjun Wu
- College of Horticulture, College of Life Sciences, College of Science, Northwest A&F University, Yangling, Shaan Xi, China.
| |
Collapse
|
19
|
Cui J, Jiang N, Meng J, Yang G, Liu W, Zhou X, Ma N, Hou X, Luan Y. LncRNA33732-respiratory burst oxidase module associated with WRKY1 in tomato- Phytophthora infestans interactions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:933-946. [PMID: 30472748 DOI: 10.1111/tpj.14173] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 11/10/2018] [Accepted: 11/15/2018] [Indexed: 05/09/2023]
Abstract
Our previous studies indicated that tomato WRKY1 transcription factor acts as a positive regulator during tomato resistance to Phytophthora infestans. However, the molecular mechanism of WRKY1-mediated resistance regulation remains unclear. Here, we used a comparative transcriptome analysis between wild-type and WRKY1-overexpressing tomato plants to identify differentially expressed genes (DEGs) and long non-coding RNAs (DELs), and we examined long non-coding RNA (lncRNA)-gene networks. The promoter sequences of the upregulated DEGs and DELs were analyzed. Among 1073 DEGs and 199 DELs, 1 kb 5'-upstream regions of 59 DEGs and 22 DELs contain the W-box, the target sequence of the WRKY1. The results of promoter-β-glucuronidase (GUS) fusion and yeast one-hybrid assay showed that lncRNA33732 was activated by WRKY1 through sequence-specific interactions with the W-box element in its promoter. The overexpression and silencing analysis of lncRNA33732 in tomato showed that lncRNA33732 acts as a positive regulator and enhanced tomato resistance to P. infestans by induction of the expression of respiratory burst oxidase (RBOH) and increase in the accumulation of H2 O2 . When the expression of RBOH gene was inhibited in tomato plants, H2 O2 accumulation decreased and resistance were impaired. These findings suggest that lncRNA33732 activated by WRKY1 induces RBOH expression to increase H2 O2 accumulation in early defense reaction of tomato to P. infestans attack. Our results provide insights into the WRKY1-lncRNA33732-RBOH module involved in the regulation of H2 O2 accumulation and resistance to P. infestans, as well as provide candidates to enhance broad-spectrum resistance to pathogens in tomato.
Collapse
Affiliation(s)
- Jun Cui
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Ning Jiang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Guanglei Yang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Weiwei Liu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Xiaoxu Zhou
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Ning Ma
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Xinxin Hou
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Yushi Luan
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| |
Collapse
|
20
|
Wu J, Liu C, Liu Z, Li S, Li D, Liu S, Huang X, Liu S, Yukawa Y. Pol III-Dependent Cabbage BoNR8 Long ncRNA Affects Seed Germination and Growth in Arabidopsis. PLANT & CELL PHYSIOLOGY 2019; 60:421-435. [PMID: 30462304 DOI: 10.1093/pcp/pcy220] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/02/2018] [Indexed: 05/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) are non-protein-coding transcripts longer than 200 nt that are distributed widely in organisms and play many physiological roles. The BoNR8 lncRNA is a 272 nt long transcript yielded by RNA polymerase III in cabbage that was identified as the closest homolog of the AtR8 lncRNA in Arabidopsis. The BoNR8 lncRNA was expressed extensively in the epidermal tissue in the root elongation zone of germinated seeds, and its accumulation was induced by abiotic stresses, auxins and ABA. To investigate the correlation between the BoNR8 lncRNA and germination, BoNR8-overexpressing Arabidopsis plants (BoNR8-AtOX) were prepared. Three independent BoNR8-AtOX lines showed less primary root elongation, incomplete silique development and decreased germination rates. The germination efficiencies were affected strongly by ABA and slightly by salt stress, and ABA-related gene expression was changed in the BoNR8-AtOX lines.
Collapse
Affiliation(s)
- Juan Wu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, PR, Harbin, China
| | - Chunxiao Liu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
| | - Ziguang Liu
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, PR, Harbin, China
| | - Shuang Li
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
| | - Dandan Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
| | - Shengyi Liu
- Mudanjiang Medical University, Mudanjiang, Heilongjiang, China
| | - Xiaoqing Huang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
| | - ShenKui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A and F University, Lin'an, Hangzhou, China
| | - Yasushi Yukawa
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
| |
Collapse
|
21
|
Abstract
Long non-coding RNAs (lncRNAs) exert a multitude of functions in regulating numerous biological processes. Recent studies have uncovered a growing number of lncRNAs within the plant genome. These molecules show striking tissue-specific expression patterns, suggesting that they exert regulatory functions in the growth and development processes of plants. Plant reproductive development is tightly regulated by both environmental and endogenous factors. As plant reproductive development is a crucial aspect of crop breeding, lncRNAs that modulate reproductive development are now particularly worth regarding. Here, we summarize findings that implicate lncRNAs in the control of plant reproductive development, especially in flowering control. Additionally, we elaborate on the regulation mechanisms of lncRNAs, tools for research on their function and mechanism, and potential directions of future research.
Collapse
|
22
|
Jiang H, Jia Z, Liu S, Zhao B, Li W, Jin B, Wang L. Identification and characterization of long non-coding RNAs involved in embryo development of Ginkgo biloba. PLANT SIGNALING & BEHAVIOR 2019; 14:1674606. [PMID: 31595821 PMCID: PMC6866700 DOI: 10.1080/15592324.2019.1674606] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Long non-coding RNAs (lncRNAs) are important regulatory factors for plant growth and development. Despite this, little is known about the regulatory interactions of lncRNAs with mRNA during embryo development. Here, we used a bioinformatics genome-wide approach to identify lncRNAs involved in embryo development of Ginkgo biloba, based on RNA sequencing datasets from G. biloba embryos during early, middle, late developmental stages. In total, 2326 lncRNAs were identified in the G. biloba embryos, of which 1307 and 1019 could be classified as long intergenic non-coding RNAs and antisense lncRNAs, respectively. Among them, a total of 657 differentially expressed lncRNAs were identified in the different developmental stages of the G. biloba embryos. Based on the functional annotation of potential target genes of lncRNAs, 50, 33, and 76 lncRNAs were predicted to target genes involved in plant hormone signal transduction, plant hormone biosynthesis, and circadian rhythm regulation, respectively. A lncRNA (17)-miRNA (25)-PCgene (52) network was constructed for the G. biloba embryo. Three lncRNAs (lnc000823, lnc002072, lnc000866) were predicted as target mimics of miR159, which targeted two transcription factors with variety of functions, Gb_11536 (MYB33) and Gb_23921 (MYB101). The data generated in this study provide a better understanding of the roles of lncRNAs in embryo development of G. biloba and plants in general.
Collapse
Affiliation(s)
- Huiru Jiang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Zhichao Jia
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Sian Liu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Beibei Zhao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Weixing Li
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Biao Jin
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Li Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
- CONTACT Li Wang College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| |
Collapse
|
23
|
Kumar A, Pathak RK, Gayen A, Gupta S, Singh M, Lata C, Sharma H, Roy JK, Gupta SM. Systems biology of seeds: decoding the secret of biochemical seed factories for nutritional security. 3 Biotech 2018; 8:460. [PMID: 30370201 PMCID: PMC6200710 DOI: 10.1007/s13205-018-1483-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/16/2018] [Indexed: 11/28/2022] Open
Abstract
Seeds serve as biochemical factories of nutrition, processing, bio-energy and storage related important bio-molecules and act as a delivery system to transmit the genetic information to the next generation. The research pertaining towards delineating the complex system of regulation of genes and pathways related to seed biology and nutrient partitioning is still under infancy. To understand these, it is important to know the genes and pathway(s) involved in the homeostasis of bio-molecules. In recent past with the advent and advancement of modern tools of genomics and genetic engineering, multi-layered 'omics' approaches and high-throughput platforms are being used to discern the genes and proteins involved in various metabolic, and signaling pathways and their regulations for understanding the molecular genetics of biosynthesis and homeostasis of bio-molecules. This can be possible by exploring systems biology approaches via the integration of omics data for understanding the intricacy of seed development and nutrient partitioning. These information can be exploited for the improvement of biologically important chemicals for large-scale production of nutrients and nutraceuticals through pathway engineering and biotechnology. This review article thus describes different omics tools and other branches that are merged to build the most attractive area of research towards establishing the seeds as biochemical factories for human health and nutrition.
Collapse
Affiliation(s)
- Anil Kumar
- Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh 284003 India
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Rajesh Kumar Pathak
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Department of Biotechnology, G. B. Pant Institute of Engineering and Technology, Pauri Garhwal, Uttarakhand 246194 India
| | - Aranyadip Gayen
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Supriya Gupta
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Manoj Singh
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Charu Lata
- Council of Scientific and Industrial Research-National Botanical Research Institute, Lucknow, India
| | - Himanshu Sharma
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
| | - Joy Kumar Roy
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
| | - Sanjay Mohan Gupta
- Molecular Biology and Genetic Engineering Laboratory, Defence Institute of Bio-Energy Research (DIBER), DRDO, Haldwani, 263139 India
| |
Collapse
|