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Rawal HC, Ali S, Mondal TK. Role of non-coding RNAs against salinity stress in Oryza species: Strategies and challenges in analyzing miRNAs, tRFs and circRNAs. Int J Biol Macromol 2023; 242:125172. [PMID: 37268077 DOI: 10.1016/j.ijbiomac.2023.125172] [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: 03/29/2023] [Revised: 05/03/2023] [Accepted: 05/24/2023] [Indexed: 06/04/2023]
Abstract
Salinity is an imbalanced concentration of mineral salts in the soil or water that causes yield loss in salt-sensitive crops. Rice plant is vulnerable to soil salinity stress at seedling and reproductive stages. Different non-coding RNAs (ncRNAs) post-transcriptionally regulate different sets of genes during different developmental stages under varying salinity tolerance levels. While microRNAs (miRNAs) are well known small endogenous ncRNAs, tRNA-derived RNA fragments (tRFs) are an emerging class of small ncRNAs derived from tRNA genes with a demonstrated regulatory role, like miRNAs, in humans but unexplored in plants. Circular RNA (circRNA), another ncRNA produced by back-splicing events, acts as target mimics by preventing miRNAs from binding with their target mRNAs, thereby reducing the miRNA's action upon its target. Same may hold true between circRNAs and tRFs. Hence, the work done on these ncRNAs was reviewed and no reports were found for circRNAs and tRFs under salinity stress in rice, either at seedling or reproductive stages. Even the reports on miRNAs are restricted to seedling stage only, in spite of severe effects on rice crop production due to salt stress during reproductive stage. Moreover, this review sheds light on strategies to predict and analyze these ncRNAs in an effective manner.
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Affiliation(s)
- Hukam Chand Rawal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India; School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Shakir Ali
- School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India; Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India.
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2
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Ryczek N, Łyś A, Makałowska I. The Functional Meaning of 5'UTR in Protein-Coding Genes. Int J Mol Sci 2023; 24:2976. [PMID: 36769304 PMCID: PMC9917990 DOI: 10.3390/ijms24032976] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
As it is well known, messenger RNA has many regulatory regions along its sequence length. One of them is the 5' untranslated region (5'UTR), which itself contains many regulatory elements such as upstream ORFs (uORFs), internal ribosome entry sites (IRESs), microRNA binding sites, and structural components involved in the regulation of mRNA stability, pre-mRNA splicing, and translation initiation. Activation of the alternative, more upstream transcription start site leads to an extension of 5'UTR. One of the consequences of 5'UTRs extension may be head-to-head gene overlap. This review describes elements in 5'UTR of protein-coding transcripts and the functional significance of protein-coding genes 5' overlap with implications for transcription, translation, and disease.
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Affiliation(s)
| | | | - Izabela Makałowska
- Institute of Human Biology and Evolution, Adam Mickiewicz University in Poznań, Uniwersytetu Ponańskiego 6, 61-614 Poznań, Poland
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3
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Mirdar Mansuri R, Azizi AH, Sadri AH, Shobbar ZS. Long non-coding RNAs as the regulatory hubs in rice response to salt stress. Sci Rep 2022; 12:21696. [PMID: 36522395 PMCID: PMC9755261 DOI: 10.1038/s41598-022-26133-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Salinity seriously constrains growth and fertility of rice worldwide. Long non-coding RNAs (lncRNAs) play crucial roles in plant abiotic stress response. However, salt responsive lncRNAs are poorly understood in rice. Herein, salt responsive lncRNAs (DE-lncRNAs) were identified in FL478 (salt tolerant) compared to its susceptible parent (IR29) using RNA-seq in root tissues at seedling stage. In FL478 and IR29, 8724 and 9235 transcripts with length of > 200 bp were nominated as potential lncRNAs, respectively. Rigorous filtering left four (in FL478) and nine (in IR29) DE-lncRNAs with only 2 DE-lncRNAs in common. ATAC-seq data showed that the genomic regions of all four lncRNAs in FL478 and 6/9 in IR29 are significantly accessible for transcription. Weighted correlation network analysis (WGCNA) revealed that lncRNA.2-FL was highly correlated with 173 mRNAs as trans-targets and a gene encoding pentatricopeptide repeat (PPR) protein was predicted as cis-target of lncRNA.2-FL. In silico mutagenesis analysis proposed the same transcription factor binding sites (TFBSs) in vicinity of the trans- and cis-regulatory target genes of lncRNA.2-FL, which significantly affect their transcription start site (TSS). This study provides new insights into involvement of the DE-lncRNAs in rice response to salt stress. Among them, lncRNA.2-FL may play a significant regulatory role in the salt stress tolerance of FL478.
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Affiliation(s)
- Raheleh Mirdar Mansuri
- grid.417749.80000 0004 0611 632XDepartment of Systems Biology, Agricultural Research, Education and Extension Organization (AREEO), Agricultural Biotechnology Research Institute of Iran (ABRII), PO Box 31535-1897, Karaj, Iran
| | - Amir-Hossein Azizi
- grid.417749.80000 0004 0611 632XDepartment of Systems Biology, Agricultural Research, Education and Extension Organization (AREEO), Agricultural Biotechnology Research Institute of Iran (ABRII), PO Box 31535-1897, Karaj, Iran
| | - Amir-Hossein Sadri
- grid.417749.80000 0004 0611 632XDepartment of Systems Biology, Agricultural Research, Education and Extension Organization (AREEO), Agricultural Biotechnology Research Institute of Iran (ABRII), PO Box 31535-1897, Karaj, Iran
| | - Zahra-Sadat Shobbar
- grid.417749.80000 0004 0611 632XDepartment of Systems Biology, Agricultural Research, Education and Extension Organization (AREEO), Agricultural Biotechnology Research Institute of Iran (ABRII), PO Box 31535-1897, Karaj, Iran
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4
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CCIVR facilitates comprehensive identification of cis-natural antisense transcripts with their structural characteristics and expression profiles. Sci Rep 2022; 12:15525. [PMID: 36109624 PMCID: PMC9477841 DOI: 10.1038/s41598-022-19782-5] [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: 06/14/2022] [Accepted: 09/05/2022] [Indexed: 11/23/2022] Open
Abstract
Cis-natural antisense transcripts (cis-NATs) are transcribed from the same genomic locus as their partner gene but from the opposite DNA strand and overlap with the partner gene transcript. Here, we developed a simple and convenient program termed CCIVR (comprehensive cis-NATs identifier via RNA-seq data) that comprehensively identifies all kinds of cis-NATs based on genome annotation with expression data obtained from RNA-seq. Using CCIVR with genome databases, we demonstrated total cis-NAT pairs from 11 model organisms. CCIVR analysis with RNA-seq data from parthenogenetic and androgenetic embryonic stem cells identified well-known imprinted cis-NAT pair, KCNQ1/KCNQ1OT1, ensuring the availability of CCIVR. Finally, CCIVR identified cis-NAT pairs that demonstrate inversely correlated expression upon TGFβ stimulation including cis-NATs that functionally repress their partner genes by introducing epigenetic alteration in the promoters of partner genes. Thus, CCIVR facilitates the investigation of structural characteristics and functions of cis-NATs in numerous processes in various species.
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Jin J, Ohama N, He X, Wu HW, Chua NH. Tissue-specific transcriptomic analysis uncovers potential roles of natural antisense transcripts in Arabidopsis heat stress response. FRONTIERS IN PLANT SCIENCE 2022; 13:997967. [PMID: 36160979 PMCID: PMC9498583 DOI: 10.3389/fpls.2022.997967] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/17/2022] [Indexed: 05/26/2023]
Abstract
Natural antisense transcripts (NATs) are an important class of non-coding ribonucleic acids (RNAs) that have been shown to regulate gene expression. Using strand-specific RNA sequencing, 36,317 NAT pairs were identified, and 5,536 were specifically expressed under heat stress. We found distinct expression patterns between vegetative and reproductive tissues for both coding genes and genes encoding NATs. Genes for heat-responsive NATs are associated with relatively high levels of H3K4me3 and low levels of H3K27me2/3. On the other hand, small RNAs are significantly enriched in sequence overlapping regions of NAT pairs, and a large number of heat-responsive NATs pairs serve as potential precursors of nat-siRNAs. Collectively, our results suggest epigenetic modifications and small RNAs play important roles in the regulation of NAT expression, and highlight the potential significance of heat-inducible NATs.
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Affiliation(s)
- Jingjing Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Naohiko Ohama
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Xiujing He
- West China Hospital, Sichuan University, Chengdu, China
| | - Hui-Wen Wu
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Nam-Hai Chua
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
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6
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Gelaw TA, Sanan-Mishra N. Non-Coding RNAs in Response to Drought Stress. Int J Mol Sci 2021; 22:12519. [PMID: 34830399 PMCID: PMC8621352 DOI: 10.3390/ijms222212519] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023] Open
Abstract
Drought stress causes changes in the morphological, physiological, biochemical and molecular characteristics of plants. The response to drought in different plants may vary from avoidance, tolerance and escape to recovery from stress. This response is genetically programmed and regulated in a very complex yet synchronized manner. The crucial genetic regulations mediated by non-coding RNAs (ncRNAs) have emerged as game-changers in modulating the plant responses to drought and other abiotic stresses. The ncRNAs interact with their targets to form potentially subtle regulatory networks that control multiple genes to determine the overall response of plants. Many long and small drought-responsive ncRNAs have been identified and characterized in different plant varieties. The miRNA-based research is better documented, while lncRNA and transposon-derived RNAs are relatively new, and their cellular role is beginning to be understood. In this review, we have compiled the information on the categorization of non-coding RNAs based on their biogenesis and function. We also discuss the available literature on the role of long and small non-coding RNAs in mitigating drought stress in plants.
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Affiliation(s)
- Temesgen Assefa Gelaw
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
- Department of Biotechnology, College of Natural and Computational Science, Debre Birhan University, Debre Birhan P.O. Box 445, Ethiopia
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
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7
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Xu YC, Zhang J, Zhang DY, Nan YH, Ge S, Guo YL. Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara). BMC Genomics 2021; 22:424. [PMID: 34103003 PMCID: PMC8188688 DOI: 10.1186/s12864-021-07754-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
Background Wild rice, including Oryza nivara and Oryza rufipogon, which are considered as the ancestors of Asian cultivated rice (Oryza sativa), possess high genetic diversity and serve as a crucial resource for breeding novel cultivars of cultivated rice. Although rice domestication related traits, such as seed shattering and plant architecture, have been intensively studied at the phenotypic and genomic levels, further investigation is needed to understand the molecular basis of phenotypic differences between cultivated and wild rice. Drought stress is one of the most severe abiotic stresses affecting rice growth and production. Adaptation to drought stress involves a cascade of genes and regulatory factors that form complex networks. O. nivara inhabits swampy areas with a seasonally dry climate, which is an ideal material to discover drought tolerance alleles. Long noncoding natural antisense transcripts (lncNATs), a class of long noncoding RNAs (lncRNAs), regulate the corresponding sense transcripts and play an important role in plant growth and development. However, the contribution of lncNATs to drought stress response in wild rice remains largely unknown. Results Here, we conducted strand-specific RNA sequencing (ssRNA-seq) analysis of Nipponbare (O. sativa) and two O. nivara accessions (BJ89 and BJ278) to determine the role of lncNATs in drought stress response in wild rice. A total of 1246 lncRNAs were identified, including 1091 coding–noncoding NAT pairs, of which 50 were expressed only in Nipponbare, and 77 were expressed only in BJ89 and/or BJ278. Of the 1091 coding–noncoding NAT pairs, 240 were differentially expressed between control and drought stress conditions. Among these 240 NAT pairs, 12 were detected only in Nipponbare, and 187 were detected uniquely in O. nivara. Furthermore, 10 of the 240 coding–noncoding NAT pairs were correlated with genes enriched in stress responsive GO terms; among these, nine pairs were uniquely found in O. nivara, and one pair was shared between O. nivara and Nipponbare. Conclusion We identified lncNATs associated with drought stress response in cultivated rice and O. nivara. These results will improve our understanding of the function of lncNATs in drought tolerance and accelerate rice breeding. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07754-4.
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Affiliation(s)
- Yong-Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dong-Yan Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying-Hui Nan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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8
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Bergalet J, Patel D, Legendre F, Lapointe C, Benoit Bouvrette LP, Chin A, Blanchette M, Kwon E, Lécuyer E. Inter-dependent Centrosomal Co-localization of the cen and ik2 cis-Natural Antisense mRNAs in Drosophila. Cell Rep 2021; 30:3339-3352.e6. [PMID: 32160541 DOI: 10.1016/j.celrep.2020.02.047] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 12/24/2019] [Accepted: 02/10/2020] [Indexed: 11/30/2022] Open
Abstract
Overlapping genes are prevalent in most genomes, but the extent to which this organization influences regulatory events operating at the post-transcriptional level remains unclear. Studying the cen and ik2 genes of Drosophila melanogaster, which are convergently transcribed as cis-natural antisense transcripts (cis-NATs) with overlapping 3' UTRs, we found that their encoded mRNAs strikingly co-localize to centrosomes. These transcripts physically interact in a 3' UTR-dependent manner, and the targeting of ik2 requires its 3' UTR sequence and the presence of cen mRNA, which serves as the main driver of centrosomal co-localization. The cen transcript undergoes localized translation in proximity to centrosomes, and its localization is perturbed by polysome-disrupting drugs. By interrogating global fractionation-sequencing datasets generated from Drosophila and human cellular models, we find that RNAs expressed as cis-NATs tend to co-localize to specific subcellular fractions. This work suggests that post-transcriptional interactions between RNAs with complementary sequences can dictate their localization fate in the cytoplasm.
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Affiliation(s)
- Julie Bergalet
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Dhara Patel
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de Biochimie et Médecine Moléculaire and Programme de Biologie Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Félix Legendre
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de Biochimie et Médecine Moléculaire and Programme de Biologie Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Catherine Lapointe
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Louis Philip Benoit Bouvrette
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de Biochimie et Médecine Moléculaire and Programme de Biologie Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Ashley Chin
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada; Division of Experimental Medicine, McGill University, Montréal, QC, Canada
| | | | - Eunjeong Kwon
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Eric Lécuyer
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de Biochimie et Médecine Moléculaire and Programme de Biologie Moléculaire, Université de Montréal, Montréal, QC, Canada; Division of Experimental Medicine, McGill University, Montréal, QC, Canada.
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9
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Jiang M, Chen H, Liu J, Du Q, Lu S, Liu C. Genome-wide identification and functional characterization of natural antisense transcripts in Salvia miltiorrhiza. Sci Rep 2021; 11:4769. [PMID: 33637790 PMCID: PMC7910453 DOI: 10.1038/s41598-021-83520-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 01/29/2021] [Indexed: 01/01/2023] Open
Abstract
Salvia miltiorrhiza is one of the most widely used traditional medicines. Natural antisense transcripts (NATs) are a class of long noncoding RNAs that can regulate gene expression. Here, we identified 812 NATs, including 168 cis-NATs and 644 trans-NATs from twelve root, flower, and leaf samples of S. miltiorrhiza using RNA-seq. The expression profiles for 41 of 50 NATs and their sense transcripts (STs) obtained from RNA-Seq were validated using qRT-PCR. The expression profiles of 17 NATs positively correlated with their STs. GO and KEGG pathway analyses mapped the STs for cis-NATs to pathways for biosynthesis of secondary metabolites. We characterized four NATs in detail, including NAT0001, NAT0002, NAT0004, and NAT00023. Their STs are kaurene synthase-like 1 and the homologs of UDP-glucose flavonoid 3-O-glucosyltransferase 6, UDP-glycosyltransferase 90A1, and beta-glucosidase 40, respectively. The first gene is involved in the biosynthesis of bioactive tanshinones, the next two are involved in anthocyanin biosynthesis, whereas the last is involved in phenylpropanoid biosynthesis. Besides, we found seven STs that are potential targets of miRNAs. And we found two miRNAs including miR156a and miR7208, might originate from NATs, NAT0112 and NAT0086. The results suggest that S. miltiorrhiza NATs might interact with STs, produce miRNAs, and be regulated by miRNAs. They potentially play significant regulatory roles in the biosynthesis of bioactive compounds.
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Affiliation(s)
- Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Jingting Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Qing Du
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China.,College of Pharmacy, Key Laboratory of Plant Resources of Qinghai-Tibet Plateau in Chemical Research, Qinghai Nationalities University, Xining, 810007, Qinghai, People's Republic of China
| | - Shanfa Lu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China.
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China.
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10
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Fonouni-Farde C, Ariel F, Crespi M. Plant Long Noncoding RNAs: New Players in the Field of Post-Transcriptional Regulations. Noncoding RNA 2021; 7:12. [PMID: 33671131 PMCID: PMC8005961 DOI: 10.3390/ncrna7010012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 02/08/2023] Open
Abstract
The first reference to the "C-value paradox" reported an apparent imbalance between organismal genome size and morphological complexity. Since then, next-generation sequencing has revolutionized genomic research and revealed that eukaryotic transcriptomes contain a large fraction of non-protein-coding components. Eukaryotic genomes are pervasively transcribed and noncoding regions give rise to a plethora of noncoding RNAs with undeniable biological functions. Among them, long noncoding RNAs (lncRNAs) seem to represent a new layer of gene expression regulation, participating in a wide range of molecular mechanisms at the transcriptional and post-transcriptional levels. In addition to their role in epigenetic regulation, plant lncRNAs have been associated with the degradation of complementary RNAs, the regulation of alternative splicing, protein sub-cellular localization, the promotion of translation and protein post-translational modifications. In this review, we report and integrate numerous and complex mechanisms through which long noncoding transcripts regulate post-transcriptional gene expression in plants.
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Affiliation(s)
- Camille Fonouni-Farde
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Bat 630, 91192 Gif sur Yvette, France;
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Bat 630, 91192 Gif sur Yvette, France
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe, Argentina;
| | - Martin Crespi
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Bat 630, 91192 Gif sur Yvette, France;
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Bat 630, 91192 Gif sur Yvette, France
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11
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Li Y, Li X, Yang J, He Y. Natural antisense transcripts of MIR398 genes suppress microR398 processing and attenuate plant thermotolerance. Nat Commun 2020; 11:5351. [PMID: 33093449 PMCID: PMC7582911 DOI: 10.1038/s41467-020-19186-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 09/30/2020] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) and natural antisense transcripts (NATs) control many biological processes and have been broadly applied for genetic manipulation of eukaryotic gene expression. Still unclear, however, are whether and how NATs regulate miRNA production. Here, we report that the cis-NATs of MIR398 genes repress the processing of their pri-miRNAs. Through genome-wide analysis of RNA sequencing data, we identify cis-NATs of MIRNA genes in Arabidopsis and Brassica. In Arabidopsis, MIR398b and MIR398c are coexpressed in vascular tissues with their antisense genes NAT398b and NAT398c, respectively. Knock down of NAT398b and NAT398c promotes miR398 processing, resulting in stronger plant thermotolerance owing to silencing of miR398-targeted genes; in contrast, their overexpression activates NAT398b and NAT398c, causing poorer thermotolerance due to the upregulation of miR398-targeted genes. Unexpectedly, overexpression of MIR398b and MIR398c activates NAT398b and NAT398c. Taken together, these results suggest that NAT398b/c repress miR398 biogenesis and attenuate plant thermotolerance via a regulatory loop. MiRNAs and natural antisense transcripts can both regulate gene expression and plant development. Here, the authors show that cis-NATs to MIR398 repress processing of pri-miR398 and that cis-NAT expression is downregulated at high temperatures, contributing to miR398 mediated thermotolerance responses.
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Affiliation(s)
- Yajie Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China.,University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiaorong Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China.,University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China.
| | - Yuke He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China.
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12
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Hamid R, Jacob F, Marashi H, Rathod V, Tomar RS. Uncloaking lncRNA-meditated gene expression as a potential regulator of CMS in cotton (Gossypium hirsutum L.). Genomics 2020; 112:3354-3364. [PMID: 32574832 DOI: 10.1016/j.ygeno.2020.06.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/03/2020] [Accepted: 06/17/2020] [Indexed: 02/01/2023]
Abstract
Cytoplasmic male sterility is a well-proven mechanism for cotton hybrid production. Long non-coding RNAs belong to a class of transcriptional regulators that function in multiple biological processes. The cDNA libraries from the flower buds of the cotton CGMS, it's restorer (Rf) and maintainer lines were sequenced using high throughput NGS technique. A total of 1531 lncRNAs showed significant differential expression patterns between these three lines. Functional analysis of the co-expression network of lncRNA-mRNA using gene ontology vouchsafes that, lncRNAs play a crucial role in cytoplasmic male sterility and fertility restoration through pollen development, INO80 complex, development of anther wall tapetum, chromatin remodeling, and histone modification. Additionally, 94 lncRNAs were identified as putative precursors of 49 miRNAs. qRT-PCR affirms the concordance of expression pattern to RNA-seq data. These findings divulge the lncRNA driven miRNA-mediated regulation of gene expression profiling superintended for a better understanding of the CMS mechanisms of cotton.
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Affiliation(s)
- Rasmieh Hamid
- Department of Biotechnology and Plant Breeding, Ferdowsi University of Mashhad, Iran.
| | - Feba Jacob
- Centre for plant biotechnology and molecular biology, Kerala agricultural university, Thrissur, India
| | - Hassan Marashi
- Department of Biotechnology and Plant Breeding, Ferdowsi University of Mashhad, Iran
| | - Visha Rathod
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India
| | - Rukam S Tomar
- Department of Biotechnology and Biochemistry, Junagadh Agricultural University, Junagadh, Gujarat, India
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13
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Baillo EH, Kimotho RN, Zhang Z, Xu P. Transcription Factors Associated with Abiotic and Biotic Stress Tolerance and Their Potential for Crops Improvement. Genes (Basel) 2019; 10:E771. [PMID: 31575043 PMCID: PMC6827364 DOI: 10.3390/genes10100771] [Citation(s) in RCA: 236] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/17/2019] [Accepted: 09/17/2019] [Indexed: 01/24/2023] Open
Abstract
In field conditions, crops are adversely affected by a wide range of abiotic stresses including drought, cold, salt, and heat, as well as biotic stresses including pests and pathogens. These stresses can have a marked effect on crop yield. The present and future effects of climate change necessitate the improvement of crop stress tolerance. Plants have evolved sophisticated stress response strategies, and genes that encode transcription factors (TFs) that are master regulators of stress-responsive genes are excellent candidates for crop improvement. Related examples in recent studies include TF gene modulation and overexpression approaches in crop species to enhance stress tolerance. However, much remains to be discovered about the diverse plant TFs. Of the >80 TF families, only a few, such as NAC, MYB, WRKY, bZIP, and ERF/DREB, with vital roles in abiotic and biotic stress responses have been intensively studied. Moreover, although significant progress has been made in deciphering the roles of TFs in important cereal crops, fewer TF genes have been elucidated in sorghum. As a model drought-tolerant crop, sorghum research warrants further focus. This review summarizes recent progress on major TF families associated with abiotic and biotic stress tolerance and their potential for crop improvement, particularly in sorghum. Other TF families and non-coding RNAs that regulate gene expression are discussed briefly. Despite the emphasis on sorghum, numerous examples from wheat, rice, maize, and barley are included. Collectively, the aim of this review is to illustrate the potential application of TF genes for stress tolerance improvement and the engineering of resistant crops, with an emphasis on sorghum.
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Affiliation(s)
- Elamin Hafiz Baillo
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
- Agricultural Research Corporation (ARC), Ministry of Agriculture, Gezira 21111, Sudan.
| | - Roy Njoroge Kimotho
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhengbin Zhang
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ping Xu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
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14
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Rai MI, Alam M, Lightfoot DA, Gurha P, Afzal AJ. Classification and experimental identification of plant long non-coding RNAs. Genomics 2019; 111:997-1005. [DOI: 10.1016/j.ygeno.2018.04.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/13/2018] [Accepted: 04/17/2018] [Indexed: 02/07/2023]
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15
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Datta R, Paul S. Long non-coding RNAs: Fine-tuning the developmental responses in plants. J Biosci 2019; 44:77. [PMID: 31502555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Plant developmental biology is associated with various gene regulatory pathways involved in different phases of their life cycle. In course of development, growth and differentiation of different organs in plants are regulated by specific sets of gene expression. With the advances in genomic and bioinformatic techniques, particularly high-throughput sequencing technology, many transcriptional units with no protein-coding potential have been discovered. Previously thought to be the dark matters of genome, long non-coding RNAs (lncRNAs) are gradually gaining importance as crucial players in gene regulation during different developmental phases. Some lncRNAs, showing complementarity to microRNAs (miRNAs), are used as endogenous target mimics of specific miRNA family. A number of lncRNAs can also act as natural antisense transcripts to attenuate the expression of coding genes. Although lncRNA-mediated regulations have extensively been studied in animals, plant lncRNA research is still in its initial phase. The present review highlights the regulatory mechanism and different physiological aspects of lncRNAs in plant development. In plants, lncRNAs are found to be associated with a number of plant developmental functions such as lateral root development, vernalization, photomorphogenesis, pollen development, fiber development and nodulation. Understanding these potent roles of lncRNAs in plant development can further provide novel tools for crop improvement programs in future.
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Affiliation(s)
- Riddhi Datta
- Department of Botany, Dr. A. P. J. Abdul Kalam Government College, New Town, Rajarhat, Kolkata 700 157, India
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16
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17
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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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18
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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.
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LncRNA expression profile and ceRNA analysis in tomato during flowering. PLoS One 2019; 14:e0210650. [PMID: 30653557 PMCID: PMC6336255 DOI: 10.1371/journal.pone.0210650] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 12/29/2018] [Indexed: 11/19/2022] Open
Abstract
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 lncRNAs during the flowering period of tomato are largely unknown. To explore the lncRNA profiles and functions during flowering in tomato, we performed strand-specific paired-end RNA sequencing of tomato leaves, flowers and roots, with three biological replicates. We identified 10919 lncRNAs including 248 novel lncRNAs, of which 65 novel lncRNAs were significantly differentially expressed (DE) in the flowers, leaves, and roots. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were carried out to identify the cis target gene of DE lncRNAs. The results showed that the lncRNAs might play an important role in the growth, development, and apoptosis of flowering tomato plant by regulating the formation of intima in flower tissues, binding to various molecules, influencing metabolic pathways, and inducing apoptosis. Moreover, we identified the interaction between 32, 78, and 397 kinds of miRNAs, lncRNAs, and mRNAs. The results suggest that the lncRNAs can regulate the expression of mRNA during flowering period in tomato by forming competitive endogenous RNA, and further regulate various biological metabolism pathways in tomato.
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20
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Abstract
Experimentally validated plant lncRNAs have been shown to regulate important agronomic traits such as phosphate starvation response, flowering time, and interaction with symbiotic organisms, making them of great interest in plant biology and in breeding. We developed a pipeline to annotate lncRNAs and applied it to 37 plant species and 6 algae, resulting in the annotation of more than 120,000 lncRNAs. To facilitate the study of lncRNAs for the plant research community, the information gathered is organized in the Green Non-Coding Database (GreeNC, http://greenc.sciencedesigners.com/) . This chapter contains a detailed explanation of the content of GreeNC and how to access both programmatically and with a web browser.
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21
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Shen E, Zhu X, Hua S, Chen H, Ye C, Zhou L, Liu Q, Zhu QH, Fan L, Chen X. Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus. BMC Genomics 2018; 19:745. [PMID: 30314449 PMCID: PMC6186049 DOI: 10.1186/s12864-018-5117-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 09/26/2018] [Indexed: 12/21/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) are transcripts longer than 200 bp that do not encode proteins but nonetheless have been shown to play important roles in various biological processes in plants. Brassica napus is an important seed oil crop worldwide and the target of many genetic improvement activities. To understand better the function of lncRNAs in regulating plant metabolic activities, we carried out a genome-wide lncRNA identification of lncRNAs in Brassica napus with a focus on lncRNAs involved in lipid metabolism. Twenty ribosomal RNA depleted strand specific RNA-seq (ssRNA-seq) datasets were generatred using RNAs isolated from B. napus seeds at four developmental stages. For comparison we also included 30 publically available RNA-seq datasets generated from poly(A) enriched mRNAs isolated from from various Brassica napus tissues in our analysis. Results A total of 8905 lncRNA loci were identified, including 7100 long intergenic noncoding RNA (lincRNA) loci and 1805 loci generating long noncoding natural antisense transcript (lncNAT). Many lncRNAs were identified only in the ssRNA-seq and poly(A) RNA-seq dataset, suggesting that B. napus has a large lncRNA repertoire and it is necessary to use libraries prepared from different tissues and developmental stages as well as different library preparation approaches to capture the whole spectrum of lncRNAs. Analysis of coexpression networks revealed that among the regulatory modules are networks containing lncRNAs and protein-coding genes related to oil biosynthesis indicating a possible role of lncRNAs in the control of lipid metabolism. One such example is that several lncRNAs are potential regulators of BnaC08g11970D that encodes oleosin1, a protein found in oil bodies and involved in seed lipid accumulation. We also observed that the expression levels of B. napus lncRNAs is positively correlated with their conservation levels. Conclusions We demonstrated that the B. napus genome has a large number of lncRNA and that these lncRNAs are expressed broadly across many developmental times and in different tissue types. We also provide evidence indicating that specific lncRNAs appear to be important regulators of lipid biosynthesis forming regulatory networks with transcripts involved in lipid biosynthesis. We also provide evidence that these lncRNAs are conserved in other species of the Brassicaceae family. Electronic supplementary material The online version of this article (10.1186/s12864-018-5117-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Shuijin Hua
- Institute of Crop and Utilization of Nuclear Technology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Hongyu Chen
- Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Chuyu Ye
- Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Longhua Zhou
- Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Qing Liu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Longjiang Fan
- Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xi Chen
- Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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22
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Karlik E, Gozukirmizi N. Expression analysis of lncRNA AK370814 involved in the barley vitamin B6 salvage pathway under salinity. Mol Biol Rep 2018; 45:1597-1609. [PMID: 30298351 DOI: 10.1007/s11033-018-4289-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 07/30/2018] [Indexed: 01/17/2023]
Abstract
Long non-coding RNAs (lncRNAs), which are longer than > 200 nt, perform various functions in a variety of important biological processes. The aim of this study is the investigation of relative expression levels of AK372815 putative pyridoxal reductase (PLR) gene and sense lncRNA AK370814 on four barley genotypes (Hasat, Beysehir 99, Konevi 98 and Tarm 92) in response to 150 mM salinity application during 3 days post-germination. Seeds were placed randomly in petri dishes containing (a) only H2O (control), (b) 150 mM NaCl, for 72 h. RNA isolation was carried out using TriPure® reagent from 150 mM salt-treated root and shoot samples. Relative expression levels of AK372815 PLR and sense lncRNA AK370814 were determined by qPCR. Results demonstrated that salinity affected the expression levels of both AK372815 PLR gene and sense lncRNA AK370814 during germination. Although expression levels of AK372815 PLR tended to be down-regulated under salinity, expression levels of sense lncRNA AK370814 were up-regulated. Another goal of this study is improvement of alternative approach to NGS technologies for determination of relative expression levels of sense lncRNAs under particular circumstances. This is the first report that demonstrates a relationship between lncRNA and vitamin B6 salvage pathway.
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Affiliation(s)
- Elif Karlik
- Department of Biotechnology, Istanbul University, 34134, Vezneciler, Istanbul, Turkey.
| | - Nermin Gozukirmizi
- Department of Molecular Biology and Genetics, Istanbul University, 34134, Vezneciler, Istanbul, Turkey.,Department of Molecular Biology and Genetics, İstinye University, 34010, Zeytinburnu, İstanbul, Turkey
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23
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Shin SY, Jeong JS, Lim JY, Kim T, Park JH, Kim JK, Shin C. Transcriptomic analyses of rice (Oryza sativa) genes and non-coding RNAs under nitrogen starvation using multiple omics technologies. BMC Genomics 2018; 19:532. [PMID: 30005603 PMCID: PMC6043990 DOI: 10.1186/s12864-018-4897-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 06/26/2018] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Nitrogen (N) is a key macronutrient essential for plant growth, and its availability has a strong influence on crop development. The application of synthetic N fertilizers on crops has increased substantially in recent decades; however, the applied N is not fully utilized due to the low N use efficiency of crops. To overcome this limitation, it is important to understand the genome-wide responses and functions of key genes and potential regulatory factors in N metabolism. RESULTS Here, we characterized changes in the rice (Oryza sativa) transcriptome, including genes, newly identified putative long non-coding RNAs (lncRNAs), and microRNAs (miRNAs) and their target mRNAs in response to N starvation using four different transcriptome approaches. Analysis of rice genes involved in N metabolism and/or transport using strand-specific RNA-Seq identified 2588 novel putative lncRNA encoding loci. Analysis of previously published RNA-Seq datasets revealed a group of N starvation-responsive lncRNAs showing differential expression under other abiotic stress conditions. Poly A-primed sequencing (2P-Seq) revealed alternatively polyadenylated isoforms of N starvation-responsive lncRNAs and provided precise 3' end information on the transcript models of these lncRNAs. Analysis of small RNA-Seq data identified N starvation-responsive miRNAs and down-regulation of miR169 family members, causing de-repression of NF-YA, as confirmed by strand-specific RNA-Seq and qRT-PCR. Moreover, we profiled the N starvation-responsive down-regulation of root-specific miRNA, osa-miR444a.4-3p, and Degradome sequencing confirmed MADS25 as a novel target gene. CONCLUSIONS In this study, we used a combination of multiple RNA-Seq analyses to extensively profile the expression of genes, newly identified lncRNAs, and microRNAs in N-starved rice roots and shoots. Data generated in this study provide an in-depth understanding of the regulatory pathways modulated by N starvation-responsive miRNAs. The results of comprehensive, large-scale data analysis provide valuable information on multiple aspects of the rice transcriptome, which may be useful in understanding the responses of rice plants to changes in the N supply status of soil.
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Affiliation(s)
- Sang-Yoon Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826 Republic of Korea
| | - Jin Seo Jeong
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang, 25354 Republic of Korea
- Present address: Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY 10065 USA
| | - Jae Yun Lim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
| | - Taewook Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
| | - June Hyun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
| | - Ju-Kon Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang, 25354 Republic of Korea
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826 Republic of Korea
- Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
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Johnson C, Conrad LJ, Patel R, Anderson S, Li C, Pereira A, Sundaresan V. Reproductive Long Intergenic Noncoding RNAs Exhibit Male Gamete Specificity and Polycomb Repressive Complex 2-Mediated Repression. PLANT PHYSIOLOGY 2018; 177:1198-1217. [PMID: 29844229 PMCID: PMC6053002 DOI: 10.1104/pp.17.01269] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 05/15/2018] [Indexed: 05/22/2023]
Abstract
Long noncoding RNAs (lncRNAs) have been characterized extensively in animals and are involved in several processes, including homeobox gene expression and X-chromosome inactivation. In comparison, there has been much less detailed characterization of plant lncRNAs, and the number of distinct lncRNAs encoded in plant genomes and their regulation by developmental and epigenetic mechanisms remain largely unknown. Here, we analyzed transcriptome data from Asian rice (Oryza sativa) and identified 6,309 long intergenic noncoding RNAs (lincRNAs), focusing on their expression in reproductive tissues and organs. Most O. sativa lincRNAs were expressed in a highly tissue-specific manner, with an unexpectedly high fraction specifically expressed in male gametes. Mutation of a component of the Polycomb Repressive Complex2 (PRC2) resulted in derepression of another large class of lincRNAs, whose expression is correlated with H3K27 trimethylation in developing panicles. Overlap with the sperm cell-specific lincRNAs suggests that epigenetic repression of lincRNAs in the panicles was partially relieved in the male germline. Expression of a subset of lincRNAs also showed modulation by drought in reproductive tissues. Comparison with other cereal genomes showed that the lincRNAs generally have low levels of conservation at both the sequence and structural levels. Use of a novelty detection support vector machine model enabled the detection of nucleotide sequence and structural homology in ∼10% and ∼4% of the lincRNAs in genomes of purple false brome (Brachypodium distachyon) and maize (Zea mays), respectively. This is the first study to report on a large number of lncRNAs that are targets of repression by PRC2 rather than mediating regulation via PRC2. That the vast majority of the lincRNAs reported here do not overlap with those of other rice studies indicates that these are a significant addition to the known lincRNAs in rice.
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Affiliation(s)
- Cameron Johnson
- Plant Biology Department, University of California, Davis, California 95616
| | - Liza J Conrad
- Plant Biology Department, University of California, Davis, California 95616
| | - Ravi Patel
- Plant Biology Department, University of California, Davis, California 95616
| | - Sarah Anderson
- Plant Biology Department, University of California, Davis, California 95616
| | - Chenxin Li
- Plant Biology Department, University of California, Davis, California 95616
| | - Andy Pereira
- Departments of Crop, Soil, and Environmental Sciences and Plant Pathology, University of Arkansas, Fayetteville, Arkansas 72701
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25
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Yuan Y, Chen S. Widespread antisense transcription of Populus genome under drought. Mol Genet Genomics 2018; 293:1017-1033. [PMID: 29876646 DOI: 10.1007/s00438-018-1456-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 05/31/2018] [Indexed: 12/18/2022]
Abstract
Antisense transcription is widespread in many genomes and plays important regulatory roles in gene expression. The objective of our study was to investigate the extent and functional relevance of antisense transcription in forest trees. We employed Populus, a model tree species, to probe the antisense transcriptional response of tree genome under drought, through stranded RNA-seq analysis. We detected nearly 48% of annotated Populus gene loci with antisense transcripts and 44% of them with co-transcription from both DNA strands. Global distribution of reads pattern across annotated gene regions uncovered that antisense transcription was enriched in untranslated regions while sense reads were predominantly mapped in coding exons. We further detected 1185 drought-responsive sense and antisense gene loci and identified a strong positive correlation between the expression of antisense and sense transcripts. Additionally, we assessed the antisense expression in introns and found a strong correlation between intronic expression and exonic expression, confirming antisense transcription of introns contributes to transcriptional activity of Populus genome under drought. Finally, we functionally characterized drought-responsive sense-antisense transcript pairs through gene ontology analysis and discovered that functional groups including transcription factors and histones were concordantly regulated at both sense and antisense transcriptional level. Overall, our study demonstrated the extensive occurrence of antisense transcripts of Populus genes under drought and provided insights into genome structure, regulation pattern and functional significance of drought-responsive antisense genes in forest trees. Datasets generated in this study serve as a foundation for future genetic analysis to improve our understanding of gene regulation by antisense transcription.
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Affiliation(s)
- Yinan Yuan
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.
| | - Su Chen
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
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26
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Qin P, Loraine AE, McCormick S. Cell-specific cis-natural antisense transcripts (cis-NATs) in the sperm and the pollen vegetative cells of Arabidopsis thaliana. F1000Res 2018; 7:93. [PMID: 29770209 PMCID: PMC5946162 DOI: 10.12688/f1000research.13311.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/16/2018] [Indexed: 11/20/2022] Open
Abstract
Background: cis-NATs
(cis-natural antisense transcripts
) are transcribed from opposite strands of adjacent genes and have been shown to regulate gene expression by generating small RNAs from the overlapping region. cis-NATs are important for plant development and resistance to pathogens and stress. Several genome-wide investigations identified a number of cis-NAT pairs, but these investigations predicted cis-NATS using expression data from bulk samples that included lots of cell types. Some cis-NAT pairs identified from those investigations might not be functional, because both transcripts of cis-NAT pairs need to be co-expressed in the same cell. Pollen only contains two cell types, two sperm and one vegetative cell, which makes cell-specific investigation of cis-NATs possible. Methods: We investigated potential protein-coding cis-NATs in pollen and sperm using pollen RNA-seq data and TAIR10 gene models using the Integrated Genome Browser. We then used sperm microarray data and sRNAs in sperm and pollen to determine possibly functional cis-NATs in the sperm or vegetative cell, respectively. Results: We identified 1471 potential protein-coding cis-NAT pairs, including 131 novel pairs that were not present in TAIR10 gene models. In pollen, 872 possibly functional pairs were identified. 72 and 56 pairs were potentially functional in sperm and vegetative cells, respectively. sRNAs were detected at 794 genes, belonging to 739 pairs. Conclusion: These potential candidates in sperm and the vegetative cell are tools for understanding gene expression mechanisms in pollen.
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Affiliation(s)
- Peng Qin
- Rice Research Institute, Sichuan Agricultural University, Chengdu Wenjiang, Sichuan, 611130, China.,U.S. Department of Agriculture/Agricultural Research Service and Department of Plant and Microbial Biology, University of California, Berkeley, Albany, CA, 94710, USA
| | - Ann E Loraine
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Sheila McCormick
- U.S. Department of Agriculture/Agricultural Research Service and Department of Plant and Microbial Biology, University of California, Berkeley, Albany, CA, 94710, USA
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27
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Liu X, Li D, Zhang D, Yin D, Zhao Y, Ji C, Zhao X, Li X, He Q, Chen R, Hu S, Zhu L. A novel antisense long noncoding RNA, TWISTED LEAF, maintains leaf blade flattening by regulating its associated sense R2R3-MYB gene in rice. THE NEW PHYTOLOGIST 2018; 218:774-788. [PMID: 29411384 DOI: 10.1111/nph.15023] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/25/2017] [Indexed: 05/20/2023]
Abstract
Natural antisense long noncoding RNAs (lncRNAs) are widespread in many organisms. However, their biological functions remain largely unknown, particularly in plants. We report the identification and characterization of an endogenous lncRNA, TWISTED LEAF (TL), which is transcribed from the opposite strand of the R2R3 MYB transcription factor gene locus, OsMYB60, in rice (Oryza sativa). TL and OsMYB60 were found to be coexpressed in many different tissues, and the expression level of TL was higher than that of OsMYB60. Downregulation of TL by RNA interference (RNAi) and overexpression of OsMYB60 resulted in twisted leaf blades in transgenic rice. The expression level of OsMYB60 was significantly increased in TL-RNAi transgenic plants. This suggests that TL may play a cis-regulatory role on OsMYB60 in leaf morphological development. We also determined that the antisense transcription suppressed the sense gene expression by mediating chromatin modifications. We further discovered that a C2H2 transcription factor, OsZFP7, is an OsMYB60 binding partner and involved in leaf development. Taken together, these findings reveal that the cis-natural antisense lncRNA plays a critical role in maintaining leaf blade flattening in rice. Our study uncovers a regulatory mechanism of lncRNA in plant leaf development.
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Affiliation(s)
- Xue Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dayong Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Donglei Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dedong Yin
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yi Zhao
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chengjun Ji
- Department of Ecology, Peking University, Beijing, 100871, China
| | - Xianfeng Zhao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaobing Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qun He
- State Key Laboratory of Agrobiotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Runsheng Chen
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Songnian Hu
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lihuang Zhu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
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28
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Karlik E, Gözükırmızı N. Evaluation of Barley lncRNAs Expression Analysis in Salinity Stress. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418020096] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Yuan J, Li J, Yang Y, Tan C, Zhu Y, Hu L, Qi Y, Lu ZJ. Stress-responsive regulation of long non-coding RNA polyadenylation in Oryza sativa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:814-827. [PMID: 29265542 DOI: 10.1111/tpj.13804] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 11/18/2017] [Accepted: 11/28/2017] [Indexed: 05/22/2023]
Abstract
Recently, long non-coding RNAs (lncRNAs) have been demonstrated to be involved in many biological processes of plants; however, a systematic study on transcriptional and, in particular, post-transcriptional regulation of stress-responsive lncRNAs in Oryza sativa (rice) is lacking. We sequenced three types of RNA libraries (poly(A)+, poly(A)- and nuclear RNAs) under four abiotic stresses (cold, heat, drought and salt). Based on an integrative bioinformatics approach and ~200 high-throughput data sets, ~170 of which have been published, we revealed over 7000 lncRNAs, nearly half of which were identified for the first time. Notably, we found that the majority of the ~500 poly(A) lncRNAs that were differentially expressed under stress were significantly downregulated, but approximately 25% were found to have upregulated non-poly(A) forms. Moreover, hundreds of lncRNAs with downregulated polyadenylation (DPA) tend to be highly conserved, show significant nuclear retention and are co-expressed with protein-coding genes that function under stress. Remarkably, these DPA lncRNAs are significantly enriched in quantitative trait loci (QTLs) for stress tolerance or development, suggesting their potential important roles in rice growth under various stresses. In particular, we observed substantially accumulated DPA lncRNAs in plants exposed to drought and salt, which is consistent with the severe reduction of RNA 3'-end processing factors under these conditions. Taken together, the results of this study reveal that polyadenylation and subcellular localization of many rice lncRNAs are likely to be regulated at the post-transcriptional level. Our findings strongly suggest that many upregulated/downregulated lncRNAs previously identified by traditional RNA-seq analyses need to be carefully reviewed to assess the influence of post-transcriptional modification.
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Affiliation(s)
- Jiapei Yuan
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jingrui Li
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yang Yang
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Chang Tan
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yumin Zhu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Long Hu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yijun Qi
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
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30
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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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31
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Oono Y, Yazawa T, Kanamori H, Sasaki H, Mori S, Matsumoto T. Genome-wide analysis of rice cis-natural antisense transcription under cadmium exposure using strand-specific RNA-Seq. BMC Genomics 2017; 18:761. [PMID: 28985711 PMCID: PMC6389181 DOI: 10.1186/s12864-017-4108-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 09/01/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The elucidation of novel transcripts and their expression in response to various stress conditions is necessary to understand the transcriptional network of plants as an adaptation to biotic and abiotic stresses. We performed strand-specific RNA-Seq (ssRNA-Seq) on rice exposed to cadmium (Cd) for 24 h and investigated the expression of cis-natural antisense transcripts (cis-NATs), a class of endogenous coding or non-protein-coding RNAs with sequence complementarity to the opposite strands of RAP transcripts. RESULTS Many RAP transcripts possessed cis-NATs and these cis-NATs were responsive to some extent. Cis-NATs were upregulated from 26, 266 and 409 RAP gene loci, while 2054, 2501 and 2825 RAP transcripts were upregulated from 38,123 RAP loci under high Cd exposure in roots at 1, 12 and 24 h, respectively. In addition, most of the upregulated cis-NATs showed little upregulation under ABA or cold treatment. A number of cis-NATs were upregulated from less than 35 RAP gene loci in different tissue and time-point combinations under low Cd exposure, suggesting that cis-NATs respond to environmental stress. Furthermore, 409 RAP transcripts with upregulated cis-NATs were classified into three groups based on the expression of the RAP transcripts from the opposite DNA strand, including 138 upregulated, 128 invariable, and 143 downregulated transcripts, although the responses of cis-NATs and RAP transcripts were not always correlated. CONCLUSIONS We have shown that the cis-NATs identified by ssRNA-Seq analysis are novel genes and that some of them are stress-specific and show different responses depending on the degree of stress and tissue. These results improve our understanding of the complete molecular mechanism of plant adaptation to Cd exposure.
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Affiliation(s)
- Youko Oono
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
| | - Takayuki Yazawa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Hiroyuki Kanamori
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Harumi Sasaki
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Satomi Mori
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Takashi Matsumoto
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.,Present address: Laboratory of Plant Molecular Breeding, Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8602, Japan
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32
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Banerjee S, Sirohi A, Ansari AA, Gill SS. Role of small RNAs in abiotic stress responses in plants. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2017.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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33
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Xu J, Wang Q, Freeling M, Zhang X, Xu Y, Mao Y, Tang X, Wu F, Lan H, Cao M, Rong T, Lisch D, Lu Y. Natural antisense transcripts are significantly involved in regulation of drought stress in maize. Nucleic Acids Res 2017; 45:5126-5141. [PMID: 28175341 PMCID: PMC5435991 DOI: 10.1093/nar/gkx085] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 01/30/2017] [Indexed: 01/02/2023] Open
Abstract
Natural antisense transcripts (NATs) are a prominent and complex class of regulatory RNAs. Using strand-specific RNA sequencing, we identified 1769 sense and antisense transcript pairs (NAT pairs) in two maize inbreds with different sensitivity to drought, as well as in two derivative recombination inbred lines (RILs). A significantly higher proportion of NATs relative to non-NATs are specifically expressed under water stress (WS). Surprisingly, expression of sense and antisense transcripts produced by NAT pairs is significantly correlated, particularly under WS. We found an unexpected large proportion of NATs with protein coding potential, as estimated by ribosome release scores. Small RNAs significantly accumulate within NAT pairs, with 21 nt smRNA particularly enriched in overlapping regions of these pairs of genes. The abundance of these smRNAs is significantly altered in the leafbladeless1 mutant, suggesting that these genes may be regulated by the tasiRNA pathway. Further, NATs are significantly hypomethylated and include fewer transposable element sequences relative to non-NAT genes. NAT gene regions also exhibit higher levels of H3K36me3, H3K9ac, and H3K4me3, but lower levels of H3K27me3, indicating that NAT gene pairs generally exhibit an open chromatin configuration. Finally, NAT pairs in 368 diverse maize inbreds and 19 segregating populations were specifically enriched for polymorphisms associated with drought tolerance. Taken together, the data highlight the potential impact of that small RNAs and histone modifications have in regulation of NAT expression, and the significance of NATs in response to WS.
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Affiliation(s)
- Jie Xu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China.,Department of Plant and Microbial Biology, University of California, Berkeley, CA 94703, USA
| | - Qi Wang
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Micheal Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94703, USA
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), El Batan 56130, Texcoco, Mexico
| | - Yunbi Xu
- International Maize and Wheat Improvement Center (CIMMYT), El Batan 56130, Texcoco, Mexico.,Institute of Crop Science, Chinese Academy of Agricultural Sciences, Haidian, Beijing 100081, China
| | - Yan Mao
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Xin Tang
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Hai Lan
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Moju Cao
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Tingzhao Rong
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
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34
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Identification and characterization of novel lncRNAs in Arabidopsis thaliana. Biochem Biophys Res Commun 2017; 488:348-354. [PMID: 28499866 DOI: 10.1016/j.bbrc.2017.05.051] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 05/09/2017] [Indexed: 11/24/2022]
Abstract
Long noncoding RNAs (lncRNAs) are important regulators of various biological processes, but few studies have identified lncRNAs in plants; genome-wide discovery of novel lncRNAs is thus required. We used deep strand-specific sequencing (ssRNA-seq) to obtain approximately 62 million reads from all developmental stages of Arabidopsis thaliana and identified 156 novel lncRNAs that we classified according to their localization. These novel identified lncRNAs showed low expression levels and sequence conservation. Bioinformatic analysis predicted potential target genes or cis-regulated genes of 91 antisense and 32 intergenic lncRNAs. Functional annotation of these potential targets and sequence motif analysis indicated that the lncRNAs participate in various biological processes underlying Arabidopsis growth and development. Seventeen of the lncRNAs were predicted targets of 22 miRNAs, and a network of interactions between ncRNAs and mRNAs was constructed. In addition, nine lncRNAs functioned as miRNA precursors. Finally, qRT-PCR revealed that novel lncRNAs have stage- and tissue-specific expression patterns in A. thaliana. Our study provides insight into the potential functions and regulatory interactions of novel Arabidopsis lncRNAs, and enhances our understanding of plant lncRNAs, which will facilitate functional research.
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35
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Present Scenario of Long Non-Coding RNAs in Plants. Noncoding RNA 2017; 3:ncrna3020016. [PMID: 29657289 PMCID: PMC5831932 DOI: 10.3390/ncrna3020016] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 03/03/2017] [Accepted: 03/20/2017] [Indexed: 12/13/2022] Open
Abstract
Small non-coding RNAs have been extensively studied in plants over the last decade. In contrast, genome-wide identification of plant long non-coding RNAs (lncRNAs) has recently gained momentum. LncRNAs are now being recognized as important players in gene regulation, and their potent regulatory roles are being studied comprehensively in eukaryotes. LncRNAs were first reported in humans in 1992. Since then, research in animals, particularly in humans, has rapidly progressed, and a vast amount of data has been generated, collected, and organized using computational approaches. Additionally, numerous studies have been conducted to understand the roles of these long RNA species in several diseases. However, the status of lncRNA investigation in plants lags behind that in animals (especially humans). Efforts are being made in this direction using computational tools and high-throughput sequencing technologies, such as the lncRNA microarray technique, RNA-sequencing (RNA-seq), RNA capture sequencing, (RNA CaptureSeq), etc. Given the current scenario, significant amounts of data have been produced regarding plant lncRNAs, and this amount is likely to increase in the subsequent years. In this review we have documented brief information about lncRNAs and their status of research in plants, along with the plant-specific resources/databases for information retrieval on lncRNAs.
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36
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Yuan J, Zhang Y, Dong J, Sun Y, Lim BL, Liu D, Lu ZJ. Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana. BMC Genomics 2016; 17:655. [PMID: 27538394 PMCID: PMC4991007 DOI: 10.1186/s12864-016-2929-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/12/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Previously, several long non-coding RNAs (lncRNAs) were characterized as regulators in phosphate (Pi) starvation responses. However, systematic studies of novel lncRNAs involved in the Pi starvation signaling pathways have not been reported. RESULTS Here, we used a genome-wide sequencing and bioinformatics approach to identify both poly(A) + and poly(A)- lncRNAs that responded to Pi starvation in Arabidopsis thaliana. We sequenced shoot and root transcriptomes of the Arabidopsis seedlings grown under Pi-sufficient and Pi-deficient conditions, and predicted 1212 novel lncRNAs, of which 78 were poly(A)- lncRNAs. By employing strand-specific RNA libraries, we discovered many novel antisense lncRNAs for the first time. We further defined 309 lncRNAs that were differentially expressed between P+ and P- conditions in either shoots or roots. Through Gene Ontology enrichment of the associated protein-coding genes (co-expressed or close on the genome), we found that many lncRNAs were adjacent or co-expressed with the genes involved in several Pi starvation related processes, including cell wall organization and photosynthesis. In total, we identified 104 potential lncRNA targets of PHR1, a key regulator for transcriptional response to Pi starvation. Moreover, we identified 16 candidate lncRNAs as potential targets of miR399, another key regulator of plant Pi homeostasis. CONCLUSIONS Altogether, our data provide a rich resource of candidate lncRNAs involved in the Pi starvation regulatory network.
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Affiliation(s)
- Jiapei Yuan
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Center for Synthetic and Systems Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Ye Zhang
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Center for Synthetic and Systems Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Jinsong Dong
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Center for Synthetic and Systems Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Yuzhe Sun
- School of Biological Sciences, the University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Boon L. Lim
- School of Biological Sciences, the University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Dong Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Center for Synthetic and Systems Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Center for Synthetic and Systems Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084 China
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37
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Joshi RK, Megha S, Basu U, Rahman MH, Kav NNV. Genome Wide Identification and Functional Prediction of Long Non-Coding RNAs Responsive to Sclerotinia sclerotiorum Infection in Brassica napus. PLoS One 2016; 11:e0158784. [PMID: 27388760 PMCID: PMC4936718 DOI: 10.1371/journal.pone.0158784] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/22/2016] [Indexed: 12/03/2022] Open
Abstract
Sclerotinia stem rot caused by Sclerotinia sclerotiorum affects canola production worldwide. Emerging evidence suggests that long non-coding RNAs (lncRNAs) play important roles in the regulation of gene expression in plants, in response to both abiotic and biotic stress. So far, identification of lncRNAs has been limited to a few model plant species, and their roles in mediating responses to biotic stresses are yet to be characterized in Brassica napus. The present study reports the identification of novel lncRNAs responsive to S. sclerotiorum infection in B. napus at two time points after infection (24 hpi and 48 hpi) using a stranded RNA-Sequencing technique and a detection pipeline for lncRNAs. Of the total 3,181 lncRNA candidates, 2,821 lncRNAs were intergenic, 111 were natural antisense transcripts, 76 possessed exonic overlap with the reference coding transcripts while the remaining 173 represented novel lnc- isoforms. Forty one lncRNAs were identified as the precursors for microRNAs (miRNAs) including miR156, miR169 and miR394, with significant roles in mediating plant responses to fungal phytopathogens. A total of 931 differentially expressed lncRNAs were identified in response to S. sclerotiorum infection and the expression of 12 such lncRNAs was further validated using qRT-PCR. B. napus antisense lncRNA, TCONS_00000966, having 90% overlap with a plant defensin gene, showed significant induction at both infection stages, suggesting its involvement in the transcriptional regulation of defense responsive genes under S. sclerotiorum infection. Additionally, nine lncRNAs showed overlap with cis-regulatory regions of differentially expressed genes of B. napus. Quantitative RT-PCR verification of a set of S. sclerotiorum responsive sense/antisense transcript pairs revealed contrasting expression patterns, supporting the hypothesis that steric clashes of transcriptional machinery may lead to inactivation of sense promoter. Our findings highlight the potential contributions of lncRNAs in regulating expression of plant genes that respond to biotic stress.
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Affiliation(s)
- Raj Kumar Joshi
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
- Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751003, India
| | - Swati Megha
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Urmila Basu
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Muhammad H. Rahman
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Nat N. V. Kav
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
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38
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Gurjar AKS, Panwar AS, Gupta R, Mantri SS. PmiRExAt: plant miRNA expression atlas database and web applications. Database (Oxford) 2016; 2016:baw060. [PMID: 27081157 PMCID: PMC4830907 DOI: 10.1093/database/baw060] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 03/14/2016] [Accepted: 03/22/2016] [Indexed: 11/22/2022]
Abstract
High-throughput small RNA (sRNA) sequencing technology enables an entirely new perspective for plant microRNA (miRNA) research and has immense potential to unravel regulatory networks. Novel insights gained through data mining in publically available rich resource of sRNA data will help in designing biotechnology-based approaches for crop improvement to enhance plant yield and nutritional value. Bioinformatics resources enabling meta-analysis of miRNA expression across multiple plant species are still evolving. Here, we report PmiRExAt, a new online database resource that caters plant miRNA expression atlas. The web-based repository comprises of miRNA expression profile and query tool for 1859 wheat, 2330 rice and 283 maize miRNA. The database interface offers open and easy access to miRNA expression profile and helps in identifying tissue preferential, differential and constitutively expressing miRNAs. A feature enabling expression study of conserved miRNA across multiple species is also implemented. Custom expression analysis feature enables expression analysis of novel miRNA in total 117 datasets. New sRNA dataset can also be uploaded for analysing miRNA expression profiles for 73 plant species. PmiRExAt application program interface, a simple object access protocol web service allows other programmers to remotely invoke the methods written for doing programmatic search operations on PmiRExAt database.Database URL:http://pmirexat.nabi.res.in.
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Affiliation(s)
- Anoop Kishor Singh Gurjar
- Computational Biology Laboratory, National Agri Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Abhijeet Singh Panwar
- HPC-Tech, Center for Development of Advance Computing (C-DAC), Pune, Maharashtra, India
| | - Rajinder Gupta
- Computational Biology Laboratory, National Agri Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Shrikant S Mantri
- Computational Biology Laboratory, National Agri Food Biotechnology Institute (NABI), Mohali, Punjab, India
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Kawahara Y, Oono Y, Wakimoto H, Ogata J, Kanamori H, Sasaki H, Mori S, Matsumoto T, Itoh T. TENOR: Database for Comprehensive mRNA-Seq Experiments in Rice. PLANT & CELL PHYSIOLOGY 2016; 57:e7. [PMID: 26578693 DOI: 10.1093/pcp/pcv179] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/06/2015] [Indexed: 05/18/2023]
Abstract
Here we present TENOR (Transcriptome ENcyclopedia Of Rice, http://tenor.dna.affrc.go.jp), a database that encompasses large-scale mRNA sequencing (mRNA-Seq) data obtained from rice under a wide variety of conditions. Since the elucidation of the ability of plants to adapt to various growing conditions is a key issue in plant sciences, it is of great interest to understand the regulatory networks of genes responsible for environmental changes. We used mRNA-Seq and performed a time-course transcriptome analysis of rice, Oryza sativa L. (cv. Nipponbare), under 10 abiotic stress conditions (high salinity; high and low phosphate; high, low and extremely low cadmium; drought; osmotic; cold; and flood) and two plant hormone treatment conditions (ABA and jasmonic acid). A large number of genes that were responsive to abiotic stresses and plant hormones were detected by differential expression analysis. Furthermore, several responsive genes were found to encode transcription factors that could control the transcriptional network of stress responses, but the timing of the induction of these genes was not uniform across conditions. A significant number of cis-regulatory elements were enriched in the promoter regions of the responsive genes and were shared among conditions. These data suggest that some key components of gene regulation networks are shared between different stress signaling pathways. All the resources (novel genes identified from mRNA-Seq data, expression profiles, co-expressed genes and cis-regulatory elements) can be searched for and are available in TENOR.
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Affiliation(s)
- Yoshihiro Kawahara
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Youko Oono
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Hironobu Wakimoto
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan Life Science Research Center, BITS. Co., Ltd., 5-201 Kandamatsunaga-cho, Chiyoda-ku, Tokyo, 101-0023 Japan
| | - Jun Ogata
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Hiroyuki Kanamori
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Harumi Sasaki
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Satomi Mori
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Takashi Matsumoto
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Takeshi Itoh
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
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Gurjar AKS, Panwar AS, Gupta R, Mantri SS. PmiRExAt: plant miRNA expression atlas database and web applications. Database (Oxford) 2016. [PMID: 27081157 DOI: 10.1093/database/baw1060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
High-throughput small RNA (sRNA) sequencing technology enables an entirely new perspective for plant microRNA (miRNA) research and has immense potential to unravel regulatory networks. Novel insights gained through data mining in publically available rich resource of sRNA data will help in designing biotechnology-based approaches for crop improvement to enhance plant yield and nutritional value. Bioinformatics resources enabling meta-analysis of miRNA expression across multiple plant species are still evolving. Here, we report PmiRExAt, a new online database resource that caters plant miRNA expression atlas. The web-based repository comprises of miRNA expression profile and query tool for 1859 wheat, 2330 rice and 283 maize miRNA. The database interface offers open and easy access to miRNA expression profile and helps in identifying tissue preferential, differential and constitutively expressing miRNAs. A feature enabling expression study of conserved miRNA across multiple species is also implemented. Custom expression analysis feature enables expression analysis of novel miRNA in total 117 datasets. New sRNA dataset can also be uploaded for analysing miRNA expression profiles for 73 plant species. PmiRExAt application program interface, a simple object access protocol web service allows other programmers to remotely invoke the methods written for doing programmatic search operations on PmiRExAt database.Database URL:http://pmirexat.nabi.res.in.
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Affiliation(s)
- Anoop Kishor Singh Gurjar
- Computational Biology Laboratory, National Agri Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Abhijeet Singh Panwar
- HPC-Tech, Center for Development of Advance Computing (C-DAC), Pune, Maharashtra, India
| | - Rajinder Gupta
- Computational Biology Laboratory, National Agri Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Shrikant S Mantri
- Computational Biology Laboratory, National Agri Food Biotechnology Institute (NABI), Mohali, Punjab, India
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Lu T, Cui L, Zhou Y, Zhu C, Fan D, Gong H, Zhao Q, Zhou C, Zhao Y, Lu D, Luo J, Wang Y, Tian Q, Feng Q, Huang T, Han B. Transcriptome-wide investigation of circular RNAs in rice. RNA (NEW YORK, N.Y.) 2015; 21:2076-87. [PMID: 26464523 PMCID: PMC4647462 DOI: 10.1261/rna.052282.115] [Citation(s) in RCA: 286] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 09/01/2015] [Indexed: 05/19/2023]
Abstract
Various stable circular RNAs (circRNAs) are newly identified to be the abundance of noncoding RNAs in Archaea, Caenorhabditis elegans, mice, and humans through high-throughput deep sequencing coupled with analysis of massive transcriptional data. CircRNAs play important roles in miRNA function and transcriptional controlling by acting as competing endogenous RNAs or positive regulators on their parent coding genes. However, little is known regarding circRNAs in plants. Here, we report 2354 rice circRNAs that were identified through deep sequencing and computational analysis of ssRNA-seq data. Among them, 1356 are exonic circRNAs. Some circRNAs exhibit tissue-specific expression. Rice circRNAs have a considerable number of isoforms, including alternative backsplicing and alternative splicing circularization patterns. Parental genes with multiple exons are preferentially circularized. Only 484 circRNAs have backsplices derived from known splice sites. In addition, only 92 circRNAs were found to be enriched for miniature inverted-repeat transposable elements (MITEs) in flanking sequences or to be complementary to at least 18-bp flanking intronic sequences, indicating that there are some other production mechanisms in addition to direct backsplicing in rice. Rice circRNAs have no significant enrichment for miRNA target sites. A transgenic study showed that overexpression of a circRNA construct could reduce the expression level of its parental gene in transgenic plants compared with empty-vector control plants. This suggested that circRNA and its linear form might act as a negative regulator of its parental gene. Overall, these analyses reveal the prevalence of circRNAs in rice and provide new biological insights into rice circRNAs.
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Affiliation(s)
- Tingting Lu
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Lingling Cui
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Yan Zhou
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Chuanrang Zhu
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Danlin Fan
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Hao Gong
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qiang Zhao
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Congcong Zhou
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Yan Zhao
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Danfeng Lu
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Jianghong Luo
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Yongchun Wang
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qilin Tian
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qi Feng
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Tao Huang
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Bin Han
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
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Paytuví Gallart A, Hermoso Pulido A, Anzar Martínez de Lagrán I, Sanseverino W, Aiese Cigliano R. GREENC: a Wiki-based database of plant lncRNAs. Nucleic Acids Res 2015; 44:D1161-6. [PMID: 26578586 PMCID: PMC4702861 DOI: 10.1093/nar/gkv1215] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/28/2015] [Indexed: 01/31/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are functional non-translated molecules greater than 200 nt. Their roles are diverse and they are usually involved in transcriptional regulation. LncRNAs still remain largely uninvestigated in plants with few exceptions. Experimentally validated plant lncRNAs have been shown to regulate important agronomic traits such as phosphate starvation response, flowering time and interaction with symbiotic organisms, making them of great interest in plant biology and in breeding. There is still a lack of lncRNAs in most sequenced plant species, and in those where they have been annotated, different methods have been used, so making the lncRNAs less useful in comparisons within and between species. We developed a pipeline to annotate lncRNAs and applied it to 37 plant species and six algae, resulting in the annotation of more than 120 000 lncRNAs. To facilitate the study of lncRNAs for the plant research community, the information gathered is organised in the Green Non-Coding Database (GreeNC, http://greenc.sciencedesigners.com/).
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Affiliation(s)
| | - Antonio Hermoso Pulido
- CRG Bioinformatics Facility, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain
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Sun Y, Xiao H. Identification of alternative splicing events by RNA sequencing in early growth tomato fruits. BMC Genomics 2015; 16:948. [PMID: 26573826 PMCID: PMC4647595 DOI: 10.1186/s12864-015-2128-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alternative splicing (AS) regulates multiple biological processes including flowering, circadian and stress response in plant. Although accumulating evidences indicate that AS is developmentally regulated, how AS responds to developmental cues is not well understood. Early fruit growth mainly characterized by active cell division and cell expansion contributes to the formation of fruit morphology and quality traits. Transcriptome profiling has revealed the coordinated complex regulation of gene expression in the process. High throughput RNA sequencing (RNA-seq) technology is advancing the genome-wide analysis of AS events in plant species, but the landscape of AS in early growth fruit is still not available for tomato (Solanum lycopersicum), a model plant for fleshy fruit development study. RESULTS Using RNA-seq, we surveyed the AS patterns in tomato seedlings, flowers and young developing fruits and found that 59.3 % of expressed multi-exon genes underwent AS in these tissues. The predominant type of AS events is intron retention, followed by alternative splice donor and acceptor, whereas exon skipping has the lowest frequency. Although the frequencies of AS events are similar among seedlings, flowers and early growth fruits, the fruits generated more splice variants per gene. Further comparison of gene expression in early growth fruits at 2, 5 and 10 days post anthesis revealed that 5206 multi-exon genes had at least one splice variants differentially expressed during early fruit development, whereas only 1059 out of them showed differential expression at gene level. We also identified 27 multi-exon genes showing differential splicing during early fruit growth. In addition, the study discovered 2507 new transcription regions (NTRs) unlinked to the annotated chromosomal regions, from where 956 putative protein coding transcripts and 1690 putative long non-coding RNAs were identified. CONCLUSIONS Our genome-wide analysis of AS events reveals a distinctive AS pattern in early growth tomato fruits. The landscape of AS obtained in this study will facilitate future investigation on transcriptome complexity and AS regulation during early fruit growth in tomato. The newly found NTRs will also be useful for updating the tomato genome annotation.
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Affiliation(s)
- Yuan Sun
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Han Xiao
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
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Potenza E, Racchi ML, Sterck L, Coller E, Asquini E, Tosatto SCE, Velasco R, Van de Peer Y, Cestaro A. Exploration of alternative splicing events in ten different grapevine cultivars. BMC Genomics 2015; 16:706. [PMID: 26380971 PMCID: PMC4574008 DOI: 10.1186/s12864-015-1922-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 09/11/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The complex dynamics of gene regulation in plants are still far from being fully understood. Among many factors involved, alternative splicing (AS) in particular is one of the least well documented. For many years, AS has been considered of less relevant in plants, especially when compared to animals, however, since the introduction of next generation sequencing techniques the number of plant genes believed to be alternatively spliced has increased exponentially. RESULTS Here, we performed a comprehensive high-throughput transcript sequencing of ten different grapevine cultivars, which resulted in the first high coverage atlas of the grape berry transcriptome. We also developed findAS, a software tool for the analysis of alternatively spliced junctions. We demonstrate that at least 44% of multi-exonic genes undergo AS and a large number of low abundance splice variants is present within the 131.622 splice junctions we have annotated from Pinot noir. CONCLUSIONS Our analysis shows that ~70% of AS events have relatively low expression levels, furthermore alternative splice sites seem to be enriched near the constitutive ones in some extent showing the noise of the splicing mechanisms. However, AS seems to be extensively conserved among the 10 cultivars.
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Affiliation(s)
- Emilio Potenza
- Fondazione Edmund Mach, Via E. Mach 1, 38010 S., Michele all'Adige, TN, Italy. .,Department of Agri-Food Production and Environmental Sciences, Università degli Studi di Firenze, Firenze, 50121, Italy. .,Department of Plant Systems Biology, VIB, Ghent, Belgium. .,Department of Biomedical Sciences, Università degli Studi di Padova, Padova, 35131, Italy.
| | - Milvia Luisa Racchi
- Department of Agri-Food Production and Environmental Sciences, Università degli Studi di Firenze, Firenze, 50121, Italy.
| | - Lieven Sterck
- Department of Plant Systems Biology, VIB, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
| | - Emanuela Coller
- Fondazione Edmund Mach, Via E. Mach 1, 38010 S., Michele all'Adige, TN, Italy.
| | - Elisa Asquini
- Fondazione Edmund Mach, Via E. Mach 1, 38010 S., Michele all'Adige, TN, Italy.
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, Università degli Studi di Padova, Padova, 35131, Italy.
| | - Riccardo Velasco
- Fondazione Edmund Mach, Via E. Mach 1, 38010 S., Michele all'Adige, TN, Italy.
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. .,Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria, South Africa.
| | - Alessandro Cestaro
- Fondazione Edmund Mach, Via E. Mach 1, 38010 S., Michele all'Adige, TN, Italy.
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Gago-Zachert S. Viroids, infectious long non-coding RNAs with autonomous replication. Virus Res 2015; 212:12-24. [PMID: 26319312 DOI: 10.1016/j.virusres.2015.08.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/20/2015] [Accepted: 08/22/2015] [Indexed: 10/23/2022]
Abstract
Transcriptome deep-sequencing studies performed during the last years confirmed that the vast majority of the RNAs transcribed in higher organisms correspond to several types of non-coding RNAs including long non-coding RNAs (lncRNAs). The study of lncRNAs and the identification of their functions, is still an emerging field in plants but the characterization of some of them indicate that they play an important role in crucial regulatory processes like flowering regulation, and responses to abiotic stress and plant hormones. A second group of lncRNAs present in plants is formed by viroids, exogenous infectious subviral plant pathogens well known since many years. Viroids are composed of circular RNA genomes without protein-coding capacity and subvert enzymatic activities of their hosts to complete its own biological cycle. Different aspects of viroid biology and viroid-host interactions have been elucidated in the last years and some of them are the main topic of this review together with the analysis of the state-of-the-art about the growing field of endogenous lncRNAs in plants.
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Affiliation(s)
- Selma Gago-Zachert
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany.
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46
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Functions of plants long non-coding RNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:155-62. [PMID: 26112461 DOI: 10.1016/j.bbagrm.2015.06.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/28/2015] [Accepted: 06/09/2015] [Indexed: 12/31/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been emerged as important players for various biological pathways, including dosage compensation, genomic imprinting, chromatin regulation, alternative splicing and nuclear organization. A large number of lncRNAs had already been identified by different approaches in plants, while the functions of only a few of them have been investigated. This review will summarize our current understanding of a wide range of plant lncRNAs functions, and highlight their roles in the regulation of diverse pathways in plants. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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The distribution and evolution of Arabidopsis thaliana cis natural antisense transcripts. BMC Genomics 2015; 16:444. [PMID: 26054753 PMCID: PMC4467840 DOI: 10.1186/s12864-015-1587-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/27/2015] [Indexed: 12/13/2022] Open
Abstract
Background Natural antisense transcripts (NATs) are regulatory RNAs that contain sequence complementary to other RNAs, these other RNAs usually being messenger RNAs. In eukaryotic genomes, cis-NATs overlap the gene they complement. Results Here, our goal is to analyze the distribution and evolutionary conservation of cis-NATs for a variety of available data sets for Arabidopsis thaliana, to gain insights into cis-NAT functional mechanisms and their significance. Cis-NATs derived from traditional sequencing are largely validated by other data sets, although different cis-NAT data sets have different prevalent cis-NAT topologies with respect to overlapping protein-coding genes. A. thaliana cis-NATs have substantial conservation (28-35% in the three substantive data sets analyzed) of expression in A. lyrata. We examined evolutionary sequence conservation at cis-NAT loci in Arabidopsis thaliana across nine sequenced Brassicaceae species (picked for optimal discernment of purifying selection), focussing on the parts of their sequences not overlapping protein-coding transcripts (dubbed ‘NOLPs’). We found significant NOLP sequence conservation for 28-34% NATs across different cis-NAT sets. This NAT NOLP sequence conservation versus A. lyrata is generally significantly correlated with conservation of expression. We discover a significant enrichment of transcription factor binding sites (as evidenced by CHIP-seq data) in NOLPs compared to randomly sampled near-gene NOLP-like DNA , that is linked to significant sequence conservation. Conversely, there is no such evidence for a general significant link between NOLPs and formation of small interfering RNAs (siRNAs), with the substantial majority of unique siRNAs arising from the overlapping portions of the cis-NATs. Conclusions In aggregate, our results suggest that many cis-NAT NOLPs function in the regulation of conserved promoter/regulatory elements that they ‘over-hang’. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1587-0) contains supplementary material, which is available to authorized users.
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Liu X, Hao L, Li D, Zhu L, Hu S. Long non-coding RNAs and their biological roles in plants. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:137-47. [PMID: 25936895 PMCID: PMC4563214 DOI: 10.1016/j.gpb.2015.02.003] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 12/31/2022]
Abstract
With the development of genomics and bioinformatics, especially the extensive applications of high-throughput sequencing technology, more transcriptional units with little or no protein-coding potential have been discovered. Such RNA molecules are called non-protein-coding RNAs (npcRNAs or ncRNAs). Among them, long npcRNAs or ncRNAs (lnpcRNAs or lncRNAs) represent diverse classes of transcripts longer than 200 nucleotides. In recent years, the lncRNAs have been considered as important regulators in many essential biological processes. In plants, although a large number of lncRNA transcripts have been predicted and identified in few species, our current knowledge of their biological functions is still limited. Here, we have summarized recent studies on their identification, characteristics, classification, bioinformatics, resources, and current exploration of their biological functions in plants.
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Affiliation(s)
- Xue Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lili Hao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dayong Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lihuang Zhu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
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Omidvar V, Fellner M. DNA methylation and transcriptomic changes in response to different lights and stresses in 7B-1 male-sterile tomato. PLoS One 2015; 10:e0121864. [PMID: 25849771 PMCID: PMC4388563 DOI: 10.1371/journal.pone.0121864] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/16/2015] [Indexed: 01/18/2023] Open
Abstract
We reported earlier that 7B-1 mutant in tomato (Solanum lycopersicum L., cv. Rutgers), an ABA overproducer, is defective in blue light (B) signaling leading to B-specific resistance to abiotic and biotic stresses. Using a methylation-sensitive amplified polymorphism (MSAP) assay, a number of genes were identified, which were differentially methylated between 7B-1 and its wild type (WT) seedlings in white (W), blue (B), red (R) lights and dark (D) or in response to exogenous ABA and mannitol-induced stresses. The genomic methylation level was almost similar in different lights between 7B-1 and WT seedlings, while significant differences were observed in response to stresses in D, but not B. Using a cDNA-AFLP assay, several transcripts were identified, which were differentially regulated between 7B-1 and WT by B or D or in response to stresses. Blue light receptors cryptochrome 1 and 2 (CRY1 and CRY2) and phototropin 1 and 2 (PHOT1 and PHOT2) were not affected by the 7B-1 mutation at the transcriptional level, instead the mutation had likely affected downstream components of the light signaling pathway. 5-azacytidine (5-azaC) induced DNA hypomethylation, inhibited stem elongation and differentially regulated the expression of a number of genes in 7B-1. In addition, it was shown that mir167 and mir390 were tightly linked to auxin signaling pathway in 5-azaC-treated 7B-1 seedlings via the regulation of auxin-response factor (ARF) transcripts. Our data showed that DNA methylation remodeling is an active epigenetic response to different lights and stresses in 7B-1 and WT, and highlighted the differences in epigenetic and transcriptional regulation of light and stress responses between 7B-1 and WT. Furthermore, it shed lights on the crosstalk between DNA hypomethylation and miRNA regulation of ARFs expression. This information could also be used as a benchmark for future studies of male-sterility in other crops.
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Affiliation(s)
- Vahid Omidvar
- Group of Molecular Physiology, Laboratory of Growth Regulators, Palacky University & Institute of Experimental Botany ASCR, Olomouc, Czech Republic
- * E-mail: (VO); (MF)
| | - Martin Fellner
- Group of Molecular Physiology, Laboratory of Growth Regulators, Palacky University & Institute of Experimental Botany ASCR, Olomouc, Czech Republic
- * E-mail: (VO); (MF)
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50
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Liu J, Wang H, Chua NH. Long noncoding RNA transcriptome of plants. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:319-28. [PMID: 25615265 DOI: 10.1111/pbi.12336] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/09/2014] [Accepted: 12/16/2014] [Indexed: 05/20/2023]
Abstract
Since their discovery more than two decades ago, animal long noncoding RNAs (lncRNAs) have emerged as important regulators of many biological processes. Recently, a large number of lncRNAs have also been identified in higher plants, and here, we review their identification, classification and known regulatory functions in various developmental events and stress responses. Knowledge gained from a deeper understanding of this special group of noncoding RNAs may lead to biotechnological improvement of crops. Some possible examples in this direction are discussed.
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Affiliation(s)
- Jun Liu
- Laboratory of Plant Molecular Biology, The Rockefeller University, New York, NY, USA
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