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Mueth NA, Hulbert SH. Small RNAs target native and cross-kingdom transcripts on both sides of the wheat stripe rust interaction. Genomics 2022; 114:110526. [PMID: 36427746 DOI: 10.1016/j.ygeno.2022.110526] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/08/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022]
Abstract
The wheat stripe rust fungus (Puccinia striiformis f.sp. tritici) threatens global wheat production. Small RNAs (sRNAs) modulate plant defense induction, and RNA exchange between host and microbe causes cross-kingdom gene silencing, but few examples are known in rust fungi. This study combined sRNA, parallel analysis of RNA ends, and gene expression data to discover sRNA-target pairs on each side of the interaction. Specific wheat 24 nt sRNAs were suppressed, while particular 35 nt fragments were strongly induced upon infection. Wheat sRNAs cleaved fungal transcripts coding for a ribosomal protein and a glycosyl hydrolase effector. Fungal microRNA-like and phased 21 nt sRNAs originated from long inverted repeats near protein coding genes. Fungal sRNAs targeted native transcripts: transposons and kinases; and cross-kingdom transcripts: a wheat nucleotide-binding domain leucine-rich repeat receptor (NLR) and multiple defense-related transcription factor families. This work sheds light on host-microbe coevolution and delivers prospects for developing pathogen control biotechnology.
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Affiliation(s)
- Nicholas A Mueth
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, USA; Department of Plant Pathology, Washington State University, Pullman, WA, USA.
| | - Scot H Hulbert
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, USA; Department of Plant Pathology, Washington State University, Pullman, WA, USA
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2
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Cervantes-Pérez SA, Yong-Villalobos L, Florez-Zapata NMV, Oropeza-Aburto A, Rico-Reséndiz F, Amasende-Morales I, Lan T, Martínez O, Vielle-Calzada JP, Albert VA, Herrera-Estrella L. Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba. Sci Rep 2021; 11:15725. [PMID: 34344949 PMCID: PMC8333044 DOI: 10.1038/s41598-021-95054-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 07/20/2021] [Indexed: 12/27/2022] Open
Abstract
The most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), a conserved mechanism that involves the role of noncoding RNAs to control the expansion of the noncoding genome. Genome-wide DNA methylation levels have been reported to correlate with genome size. However, little is known about the catalog of noncoding RNAs and the impact on DNA methylation in small plant genomes with reduced noncoding regions. Because of the small length of intergenic regions in the compact genome of the carnivorous plant Utricularia gibba, we investigated its repertoire of noncoding RNA and DNA methylation landscape. Here, we report that, compared to other angiosperms, U. gibba has an unusual distribution of small RNAs and reduced global DNA methylation levels. DNA methylation was determined using a novel strategy based on long-read DNA sequencing with the Pacific Bioscience platform and confirmed by whole-genome bisulfite sequencing. Moreover, some key genes involved in the RdDM pathway may not represented by compensatory paralogs or comprise truncated proteins, for example, U. gibba DICER-LIKE 3 (DCL3), encoding a DICER endonuclease that produces 24-nt small-interfering RNAs, has lost key domains required for complete function. Our results unveil that a truncated DCL3 correlates with a decreased proportion of 24-nt small-interfering RNAs, low DNA methylation levels, and developmental abnormalities during female gametogenesis in U. gibba. Alterations in female gametogenesis are reminiscent of RdDM mutant phenotypes in Arabidopsis thaliana. It would be interesting to further study the biological implications of the DCL3 truncation in U. gibba, as it could represent an initial step in the evolution of RdDM pathway in compact genomes.
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Affiliation(s)
- Sergio Alan Cervantes-Pérez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, Guanajuato, Mexico
| | - Lenin Yong-Villalobos
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, Guanajuato, Mexico.,Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Department, Texas Tech University, Lubbock, TX, 79409, USA
| | - Nathalia M V Florez-Zapata
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, Guanajuato, Mexico.,Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Avenida Paseo Bolívar (Circunvalar) #16-20, Bogotá, DC, 111311, Colombia
| | - Araceli Oropeza-Aburto
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, Guanajuato, Mexico
| | - Félix Rico-Reséndiz
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, Guanajuato, Mexico
| | - Itzel Amasende-Morales
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, Guanajuato, Mexico
| | - Tianying Lan
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Octavio Martínez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, Guanajuato, Mexico
| | - Jean Philippe Vielle-Calzada
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, Guanajuato, Mexico
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA.,School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, Guanajuato, Mexico. .,Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Department, Texas Tech University, Lubbock, TX, 79409, USA.
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3
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Jia W, Lin K, Lou T, Feng J, Lv S, Jiang P, Yi Z, Zhang X, Wang D, Guo Z, Tang Y, Qiu R, Li Y. Comparative analysis of sRNAs, degradome and transcriptomics in sweet sorghum reveals the regulatory roles of miRNAs in Cd accumulation and tolerance. PLANTA 2021; 254:16. [PMID: 34185181 DOI: 10.1007/s00425-021-03669-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Abstract
Key miRNAs including sbi-miR169p/q, sbi-miR171g/j, sbi-miR172a/c/d, sbi-miR172e, sbi-miR319a/b, sbi-miR396a/b, miR408, sbi-miR5384, sbi-miR5565e and nov_23 were identified to function in the regulation of Cd accumulation and tolerance. As an energy plant, sweet sorghum shows great potential in the phytoremediation of Cd-contaminated soils. However, few studies have focused on the regulatory roles of miRNAs and their targets under Cd stress. In this study, comparative analysis of sRNAs, degradome and transcriptomics was conducted in high-Cd accumulation (H18) and low-Cd accumulation (L69) genotypes of sweet sorghum. A total of 38 conserved and 23 novel miRNAs with differential expressions were identified under Cd stress or between H18 and L69, and 114 target genes of 41 miRNAs were validated. Furthermore, 25 miRNA-mRNA pairs exhibited negatively correlated expression profiles and sbi-miR172e together with its target might participate in the distinct Cd tolerance between H18 and L69 as well as sbi-miR172a/c/d. Additionally, two groups of them: miR169p/q-nov_23 and miR408 were focused through the co-expression analysis, which might be involved in Cd uptake and tolerance by regulating their targets associated with transmembrane transportation, cytoskeleton activity, cell wall construction and ROS (reactive oxygen species) homeostasis. Further experiments exhibited that cell wall components of H18 and L69 were different when exposed to cadmium, which might be regulated by miR169p/q, miR171g/j, miR319a/b, miR396a/b, miR5384 and miR5565e through their targets. Through this study, we aim to reveal the potential miRNAs involved in sweet sorghum in response to Cd stress and provide references for developing high-Cd accumulation or high Cd-resistant germplasm of sweet sorghum that can be used in phytoremediation.
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Affiliation(s)
- Weitao Jia
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, People's Republic of China
| | - Kangqi Lin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Tengxue Lou
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Juanjuan Feng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
| | - Sulian Lv
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
| | - Ping Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
| | - Ze Yi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xuan Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Duoliya Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zijing Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yetao Tang
- Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China
| | - Rongliang Qiu
- Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China
| | - Yinxin Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China.
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Sanan-Mishra N, Abdul Kader Jailani A, Mandal B, Mukherjee SK. Secondary siRNAs in Plants: Biosynthesis, Various Functions, and Applications in Virology. FRONTIERS IN PLANT SCIENCE 2021; 12:610283. [PMID: 33737942 PMCID: PMC7960677 DOI: 10.3389/fpls.2021.610283] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/18/2021] [Indexed: 05/13/2023]
Abstract
The major components of RNA silencing include both transitive and systemic small RNAs, which are technically called secondary sRNAs. Double-stranded RNAs trigger systemic silencing pathways to negatively regulate gene expression. The secondary siRNAs generated as a result of transitive silencing also play a substantial role in gene silencing especially in antiviral defense. In this review, we first describe the discovery and pathways of transitivity with emphasis on RNA-dependent RNA polymerases followed by description on the short range and systemic spread of silencing. We also provide an in-depth view on the various size classes of secondary siRNAs and their different roles in RNA silencing including their categorization based on their biogenesis. The other regulatory roles of secondary siRNAs in transgene silencing, virus-induced gene silencing, transitivity, and trans-species transfer have also been detailed. The possible implications and applications of systemic silencing and the different gene silencing tools developed are also described. The details on mobility and roles of secondary siRNAs derived from viral genome in plant defense against the respective viruses are presented. This entails the description of other compatible plant-virus interactions and the corresponding small RNAs that determine recovery from disease symptoms, exclusion of viruses from shoot meristems, and natural resistance. The last section presents an overview on the usefulness of RNA silencing for management of viral infections in crop plants.
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Affiliation(s)
- Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - A. Abdul Kader Jailani
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Advanced Center for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Bikash Mandal
- Advanced Center for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Sunil K. Mukherjee
- Advanced Center for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Sunil K. Mukherjee,
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5
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Liu Y, El-Kassaby YA. Landscape of Fluid Sets of Hairpin-Derived 21-/24-nt-Long Small RNAs at Seed Set Uncovers Special Epigenetic Features in Picea glauca. Genome Biol Evol 2017; 9:82-92. [PMID: 28082604 PMCID: PMC5381586 DOI: 10.1093/gbe/evw283] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2016] [Indexed: 12/23/2022] Open
Abstract
Conifers’ exceptionally large genome (20–30 Gb) is scattered with 60% retrotransposon (RT) components and we have little knowledge on their origin and evolutionary implications. RTs may impede the expression of flanking genes and provide sources of the formation of novel small RNA (sRNAs) populations to constrain events of transposon (TE) proliferation/transposition. Here we show a declining expression of 24-nt-long sRNAs and low expression levels of their key processing gene, pgRTL2 (RNASE THREE LIKE 2) at seed set in Picea glauca. The sRNAs in 24-nt size class are significantly less enriched in type and read number than 21-nt sRNAs and have not been documented in other species. The architecture of MIR loci generating highly expressed 24-/21-nt sRNAs is featured by long terminal repeat—retrotransposons (LTR-RTs) in families of Ty3/Gypsy and Ty1/Copia elements. This implies that the production of sRNAs may be predominantly originated from TE fragments on chromosomes. Furthermore, a large proportion of highly expressed 24-nt sRNAs does not have predictable targets against unique genes in Picea, suggestive of their potential pathway in DNA methylation modifications on, for instance, TEs. Additionally, the classification of computationally predicted sRNAs suggests that 24-nt sRNA targets may bear particular functions in metabolic processes while 21-nt sRNAs target genes involved in many different biological processes. This study, therefore, directs our attention to a possible extrapolation that lacking of 24-nt sRNAs at the late conifer seed developmental phase may result in less constraints in TE activities, thus contributing to the massive expansion of genome size.
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Affiliation(s)
- Yang Liu
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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6
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Liu Y, El-Kassaby YA. Regulatory crosstalk between microRNAs and hormone signalling cascades controls the variation on seed dormancy phenotype at Arabidopsis thaliana seed set. PLANT CELL REPORTS 2017; 36:705-717. [PMID: 28197719 DOI: 10.1007/s00299-017-2111-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/26/2017] [Indexed: 05/05/2023]
Abstract
We employed an Illumina sequencing approach to identify candidate microRNA cohorts that may greatly contribute to seed dormancy modulation and to construct a microRNA-gene regulatory network in hormone signalling cascades. MicroRNAs (miRNAs) are important signalling molecules and regulate many developmental programs of plants. Some miRNAs have been integrated into gene regulatory networks (GRNs) and coordinate developmental plasticity, but few study systematically investigated how phenotypical variations are regulated through differential expression of miRNA tags in GRNs during seed set. Using 'top-down' analyses (i.e., identify miRNAs associated with known phenotypical variations), we chose two Arabidopsis ecotypes (Cvi-0 and Col-0) with contrasting seed dormancy and sequenced miRNA reads in the first ten phases at seed set. We computationally predicted target genes of miRNAs and implemented statistical analyses for normalized relative expression of top abundant miRNA cohorts between the two ecotypes. We especially focused on miRNA cohorts targeting mRNAs encoding transcription factors in hormone signalling cascades. We report, with high confidence hits, that a cohort of 14 miRNAs (miR-156b, -159b, -160, -161*, -319a, -390a, -396, -773a, -779, -842, -852, -859, -1886*, and a novel sequence in miR8172 family) may greatly contribute to seed dormancy modulation, of which seven are involved in hormone signalling cascades. Moreover, their expression patterns indicated that 5 ± 1 days after flowering (at embryogenesis-to-maturation transition) is a critical phase at seed set. This study reinforces the notion that miRNAs that regulate seed dormancy modulation and provides a novel paradigm of studying the correlation between genotypes (miRNAs) and phenotypes.
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Affiliation(s)
- Yang Liu
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
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7
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Flórez-Zapata NMV, Reyes-Valdés MH, Martínez O. Long non-coding RNAs are major contributors to transcriptome changes in sunflower meiocytes with different recombination rates. BMC Genomics 2016; 17:490. [PMID: 27401977 PMCID: PMC4940957 DOI: 10.1186/s12864-016-2776-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/25/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Meiosis is a form of specialized cell division that marks the transition from diploid meiocyte to haploid gamete, and provides an opportunity for genetic reassortment through recombination. Experimental data indicates that, relative to their wild ancestors, cultivated sunflower varieties show a higher recombination rate during meiosis. To better understand the molecular basis for this difference, we compared gene expression in male sunflower meiocytes in prophase I isolated from a domesticated line, a wild relative, and a F1 hybrid of the two. RESULTS Of the genes that showed differential expression between the wild and domesticated genotypes, 63.62 % could not be identified as protein-coding genes, and of these genes, 70.98 % passed stringent filters to be classified as long non-coding RNAs (lncRNAs). Compared to the sunflower somatic transcriptome, meiocytes express a higher proportion of lncRNAs, and the majority of genes with exclusive expression in meiocytes were lncRNAs. Around 40 % of the lncRNAs showed sequence similarity with small RNAs (sRNA), while 1.53 % were predicted to be sunflower natural antisense transcripts (NATs), and 9.18 % contained transposable elements (TE). We identified 6895 lncRNAs that are exclusively expressed in meiocytes, these lncRNAs appear to have higher conservation, a greater degree of differential expression, a higher proportion of sRNA similarity, and higher TE content relative to lncRNAs that are also expressed in the somatic transcriptome. CONCLUSIONS lncRNAs play important roles in plant meiosis and may participate in chromatin modification processes, although other regulatory functions cannot be excluded. lncRNAs could also be related to the different recombination rates seen for domesticated and wild sunflowers.
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Affiliation(s)
- Nathalia M V Flórez-Zapata
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO)/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), 36821, Irapuato, Guanajuato, México
| | - M Humberto Reyes-Valdés
- Department of Plant Breeding, Universidad Autónoma Agraria Antonio Narro, Buenavista, 25315, Saltillo, Coahuila, México
| | - Octavio Martínez
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO)/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), 36821, Irapuato, Guanajuato, México.
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8
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Yu D, Meng Y, Zuo Z, Xue J, Wang H. NATpipe: an integrative pipeline for systematical discovery of natural antisense transcripts (NATs) and phase-distributed nat-siRNAs from de novo assembled transcriptomes. Sci Rep 2016; 6:21666. [PMID: 26858106 PMCID: PMC4746697 DOI: 10.1038/srep21666] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 01/28/2016] [Indexed: 12/12/2022] Open
Abstract
Nat-siRNAs (small interfering RNAs originated from natural antisense transcripts) are a class of functional small RNA (sRNA) species discovered in both plants and animals. These siRNAs are highly enriched within the annealed regions of the NAT (natural antisense transcript) pairs. To date, great research efforts have been taken for systematical identification of the NATs in various organisms. However, developing a freely available and easy-to-use program for NAT prediction is strongly demanded by researchers. Here, we proposed an integrative pipeline named NATpipe for systematical discovery of NATs from de novo assembled transcriptomes. By utilizing sRNA sequencing data, the pipeline also allowed users to search for phase-distributed nat-siRNAs within the perfectly annealed regions of the NAT pairs. Additionally, more reliable nat-siRNA loci could be identified based on degradome sequencing data. A case study on the non-model plant Dendrobium officinale was performed to illustrate the utility of NATpipe. Finally, we hope that NATpipe would be a useful tool for NAT prediction, nat-siRNA discovery, and related functional studies. NATpipe is available at www.bioinfolab.cn/NATpipe/NATpipe.zip.
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Affiliation(s)
- Dongliang Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.,Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Ziwei Zuo
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.,Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Jie Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.,Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.,Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
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9
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Pappas MDCR, Pappas GJ, Grattapaglia D. Genome-wide discovery and validation of Eucalyptus small RNAs reveals variable patterns of conservation and diversity across species of Myrtaceae. BMC Genomics 2015; 16:1113. [PMID: 26714854 PMCID: PMC4696225 DOI: 10.1186/s12864-015-2322-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 12/15/2015] [Indexed: 11/17/2022] Open
Abstract
Background Micro RNAs are a class of small non coding RNAs of 20–24 nucleotides transcribed as single stranded precursors from MIR gene loci. Initially described as post-transcriptional regulators involved in development, two decades ago, miRNAs have been proven to regulate a wide range of processes in plants such as germination, morphology and responses to biotic and abiotic stress. Despite wide conservation in plants, a number of miRNAs are lineage specific. We describe the first genome wide survey of Eucalyptus miRNAs based on high throughput sequencing. Results In addition to discovering small RNA sequences, MIR loci were mapped onto the reference genome and interspecific variability investigated. Sequencing was carried out for the two most world widely planted species, E. grandis and E. globulus. To maximize discovery, E. grandis samples were from BRASUZ1, the same tree whose genome provided the reference sequence. Interspecific analysis reinforces the variability in small RNA repertoire even between closely related species. Characterization of Eucalyptus small RNA sequences showed 95 orthologous to conserved miRNAs and 193 novel miRNAs. In silico target prediction confirmed 163 novel miRNAs and degradome sequencing experimentally confirmed several hundred targets. Experimental evidence based on the exclusive expression of a set of small RNAs across 16 species within Myrtaceae further highlighted variable patterns of conservation and diversity of these regulatory elements. Conclusions The description of miRNAs in Eucalyptus contributes to scientific knowledge of this vast genre, which is the most widely planted hardwood crop in the tropical and subtropical world, adding another important element to the annotation of Eucalyptus grandis reference genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2322-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Dario Grattapaglia
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil. .,Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil.
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10
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Wang M, Wu B, Chen C, Lu S. Identification of mRNA-like non-coding RNAs and validation of a mighty one named MAR in Panax ginseng. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:256-70. [PMID: 25040236 DOI: 10.1111/jipb.12239] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 07/03/2014] [Indexed: 05/11/2023]
Abstract
Increasing evidence suggests that long non-coding RNAs (lncRNAs) play significant roles in plants. However, little is known about lncRNAs in Panax ginseng C. A. Meyer, an economically significant medicinal plant species. A total of 3,688 mRNA-like non-coding RNAs (mlncRNAs), a class of lncRNAs, were identified in P. ginseng. Approximately 40% of the identified mlncRNAs were processed into small RNAs, implying their regulatory roles via small RNA-mediated mechanisms. Eleven miRNA-generating mlncRNAs also produced siRNAs, suggesting the coordinated production of miRNAs and siRNAs in P. ginseng. The mlncRNA-derived small RNAs might be 21-, 22-, or 24-nt phased and could be generated from both or only one strand of mlncRNAs, or from super long hairpin structures. A full-length mlncRNA, termed MAR (multiple-function-associated mlncRNA), was cloned. It generated the most abundant siRNAs. The MAR siRNAs were predominantly 24-nt and some of them were distributed in a phased pattern. A total of 228 targets were predicted for 71 MAR siRNAs. Degradome sequencing validated 68 predicted targets involved in diverse metabolic pathways, suggesting the significance of MAR in P. ginseng. Consistently, MAR was detected in all tissues analyzed and responded to methyl jasmonate (MeJA) treatment. It sheds light on the function of mlncRNAs in plants.
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MESH Headings
- Base Sequence
- Cloning, Molecular
- DNA, Complementary/genetics
- Gene Expression Regulation, Plant
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Molecular Sequence Data
- Nucleic Acid Conformation
- Open Reading Frames/genetics
- Panax/genetics
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Untranslated/chemistry
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- Reproducibility of Results
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Affiliation(s)
- Meizhen Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
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11
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Zhang Y, Yan C, Kuang H. GC content fluctuation around plant small RNA-generating sites. FEBS Lett 2014; 588:764-9. [PMID: 24462689 DOI: 10.1016/j.febslet.2014.01.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 01/05/2014] [Accepted: 01/10/2014] [Indexed: 10/25/2022]
Abstract
GC content of small RNA-generating sites and their flanking sequences in Arabidopsis thaliana and rice was systematically analyzed in silico. High GC content fluctuation (GCF) is observed at the borders of sRNA sites, while the GCF within sRNA sites is low. Furthermore, the GC content along sequences of some miniature inverted-repeat transposable element (MITE) families coincides with the abundance of MITE-derived small RNAs. The GCF within tasiRNA clusters is negatively correlated with its phasing score. We conclude that high GC content and low GCF could increase the expression of small RNA. Our results provide further insights on small RNA expression, which may be applied to improve the silencing efficiency of RNAi and virus-induced gene silencing.
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Affiliation(s)
- Yu Zhang
- Key Laboratory of Horticulture Biology, Ministry of Education, Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Chenghuan Yan
- Key Laboratory of Horticulture Biology, Ministry of Education, Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Hanhui Kuang
- Key Laboratory of Horticulture Biology, Ministry of Education, Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, PR China.
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12
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Zhang X, Lii Y, Wu Z, Polishko A, Zhang H, Chinnusamy V, Lonardi S, Zhu JK, Liu R, Jin H. Mechanisms of small RNA generation from cis-NATs in response to environmental and developmental cues. MOLECULAR PLANT 2013; 6:704-15. [PMID: 23505223 PMCID: PMC3660955 DOI: 10.1093/mp/sst051] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 02/28/2013] [Indexed: 05/18/2023]
Abstract
A large proportion of eukaryotic genomes is transcribed from both positive and negative strands of DNA and thus may generate overlapping sense and antisense transcripts. Some of these so-called natural antisense transcripts (NATs) are possibly co-regulated. When the overlapping sense and antisense transcripts are expressed at the same time in the same cell in response to various developmental and environmental cues; they may form double-stranded RNAs, which could be recognized by the small RNA biogenesis machinery and processed into small interfering RNAs (siRNAs). cis-NAT-derived siRNAs (nat-siRNAs) are present in plants, animals, and fungi. In plants, the presence of nat-siRNAs is supported not only by Northern blot and genetic analyses, but also by the fact that there is an overall sixfold enrichment of siRNAs in the overlapping regions of cis-NATs and 19%-29% of the siRNA-generating cis-NATs in plants give rise to siRNAs only in their overlapping regions. Silencing mediated by nat-siRNAs is one of the mechanisms for regulating the expression of the cis-NATs. This review focuses on challenging issues related to the biogenesis mechanisms as well as regulation and detection of nat-siRNAs. The advantages and limitations of new technologies for detecting cis-NATs, including direct RNA sequencing and strand-specific RNA sequencing, are also discussed.
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Affiliation(s)
- Xiaoming Zhang
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Yifan Lii
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Zhigang Wu
- Department of Botany and Plant Sciences and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Anton Polishko
- Computer Science and Engineering, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Huiming Zhang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Stefano Lonardi
- Computer Science and Engineering, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Jian-Kang Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
- Shanghai Center for Plant Stress Biology and Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- To whom correspondence should be addressed. H.J. E-mail , tel. +1-951-827-7995. R.L. E-mail . J.-k.Z. E-mail
| | - Renyi Liu
- Department of Botany and Plant Sciences and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- To whom correspondence should be addressed. H.J. E-mail , tel. +1-951-827-7995. R.L. E-mail . J.-k.Z. E-mail
| | - Hailing Jin
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- To whom correspondence should be addressed. H.J. E-mail , tel. +1-951-827-7995. R.L. E-mail . J.-k.Z. E-mail
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13
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Zheng H, Qiyan J, Zhiyong N, Hui Z. Prediction and identification of natural antisense transcripts and their small RNAs in soybean (Glycine max). BMC Genomics 2013; 14:280. [PMID: 23617936 PMCID: PMC3643859 DOI: 10.1186/1471-2164-14-280] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 04/20/2013] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Natural antisense transcripts (NATs) are a class of RNAs that contain a sequence complementary to other transcripts. NATs occur widely in eukaryotes and play critical roles in post-transcriptional regulation. Soybean NAT sequences are predicted in the PlantNATsDB, but detailed analyses of these NATs remain to be performed. RESULTS A total of 26,216 NATs, including 994 cis-NATs and 25,222 trans-NATs, were predicted in soybean. Each sense transcript had 1-177 antisense transcripts. We identified 21 trans-NATs using RT-PCR amplification. Additionally, we identified 179 cis-NATs and 6,629 trans-NATs that gave rise to small RNAs; these were enriched in the NAT overlapping region. The most abundant small RNAs were 21, 22, and 24 nt in length. The generation of small RNAs was biased to one stand of the NATs, and the degradation of NATs was biased. High-throughput sequencing of the degradome allowed for the global identification of NAT small interfering RNAs (nat-siRNAs) targets. 446 target genes for 165 of these nat-siRNAs were identified. The nat-siRNA target could be one transcript of a given NAT, or from other gene transcripts. We identified five NAT transcripts containing a hairpin structure that is characteristic of pre-miRNA. We identified a total of 86 microRNA (miRNA) targets that had antisense transcripts in soybean. CONCLUSIONS We globally identified nat-siRNAs, and the targets of nat-siRNAs in soybean. It is likely that the cis-NATs, trans-NATs, nat-siRNAs, miRNAs, and miRNA targets form complex regulatory networks.
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Affiliation(s)
- Hu Zheng
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiang Qiyan
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ni Zhiyong
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhang Hui
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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14
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Zhai L, Liu Z, Zou X, Jiang Y, Qiu F, Zheng Y, Zhang Z. Genome-wide identification and analysis of microRNA responding to long-term waterlogging in crown roots of maize seedlings. PHYSIOLOGIA PLANTARUM 2013; 147:181-93. [PMID: 22607471 DOI: 10.1111/j.1399-3054.2012.01653.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
MicroRNAs (miRNAs) are critical post-transcriptional modulators of gene expression involving in plant responses to abiotic stress. However, the regulation of miRNA in the morphological response to waterlogging is poorly understood in maize. In this study, we detected miRNAs and their targets that expressed in waterlogged crown roots of maize seedlings in two inbred lines (Hz32 and Mo17) by RNA sequencing. A total of 61 mature miRNAs were found including 36 known maize (zma) miRNAs and 25 potential novel miRNA candidates. Comparison of miRNA expression in both waterlogged and control crown roots revealed 32 waterlogging-responsive miRNAs, most were consistently downregulated under waterlogging in the two inbred lines. We identified the miRNA targets through degradome sequencing. Many known miRNA targets involving in transcription regulation and reactive oxygen species elimination were found in the degradome libraries, and 17 targets of 10 newly detected miRNAs were identified as well. Moreover, the miRNA-mediated pathways that respond to waterlogging and regulate the induction of crown roots were discussed. This study is a comprehensive survey of responsive miRNAs in waterlogged maize crown roots. The results will help to understand the miRNA expression in response to waterlogging and miRNA-mediated regulation of morphological adaptation to waterlogging in maize.
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Affiliation(s)
- Lihong Zhai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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15
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Meng Y, Shao C, Wang H, Ma X, Chen M. Construction of gene regulatory networks mediated by vegetative and reproductive stage-specific small RNAs in rice (Oryza sativa). THE NEW PHYTOLOGIST 2013; 197:441-453. [PMID: 23121287 DOI: 10.1111/nph.12018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 09/24/2012] [Indexed: 05/16/2023]
Abstract
Although huge amounts of high-throughput sequencing (HTS) data are available, limited systematic analyses have been performed by integrating these valuable resources. Based on small RNA (sRNA), RNA and degradome HTS data, the sRNAs specifically expressed at vegetative and reproductive stages were identified separately in rice. Two distinct groups of sRNA HTS data, which were prepared during the vegetative and the reproductive stages, were utilized to extract stage-specific sRNAs. Degradome sequencing data were employed for sRNA target validation. RNA sequencing data were used to construct expression-based, sRNA-mediated networks. As a result, 26 microRNAs and 413 sRNAs were specifically expressed at the vegetative stage, and 79 microRNAs and 539 sRNAs were specifically expressed at the reproductive stage. In addition to the microRNAs, numerous stage-specific sRNAs enriched in ARGONAUTE1 showed great potential to perform cleavage-based repression on the targets. Several stage-specific sRNAs were indicated to result from the wobble effect of Dicer-like 1-mediated processing of microRNA precursors. The expression patterns of the sRNA targets, and the stage-specific cleavage signals strongly indicated the reliability of the constructed networks. A set of rice stage-specific sRNAs along with the regulatory cascades, which have great potential in regulating specific developmental stages, were provided for further investigation.
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Affiliation(s)
- Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Chaogang Shao
- College of Life Sciences, Huzhou Teachers College, Huzhou, 313000, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Xiaoxia Ma
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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16
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Chen D, Yuan C, Zhang J, Zhang Z, Bai L, Meng Y, Chen LL, Chen M. PlantNATsDB: a comprehensive database of plant natural antisense transcripts. Nucleic Acids Res 2011; 40:D1187-93. [PMID: 22058132 PMCID: PMC3245084 DOI: 10.1093/nar/gkr823] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Natural antisense transcripts (NATs), as one type of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and pathological processes. Although their important biological functions have been reported widely, a comprehensive database is lacking up to now. Consequently, we constructed a plant NAT database (PlantNATsDB) involving approximately 2 million NAT pairs in 69 plant species. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. PlantNATsDB provides various user-friendly web interfaces to facilitate the presentation of NATs and an integrated, graphical network browser to display the complex networks formed by different NATs. Moreover, a ‘Gene Set Analysis’ module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs. The PlantNATsDB is freely available at http://bis.zju.edu.cn/pnatdb/.
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Affiliation(s)
- Dijun Chen
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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17
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Chen D, Meng Y, Yuan C, Bai L, Huang D, Lv S, Wu P, Chen LL, Chen M. Plant siRNAs from introns mediate DNA methylation of host genes. RNA (NEW YORK, N.Y.) 2011; 17:1012-24. [PMID: 21518803 PMCID: PMC3096033 DOI: 10.1261/rna.2589011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Small RNAs (sRNAs), largely known as microRNAs (miRNAs) and short interfering RNAs (siRNAs), emerged as the critical components of genetic and epigenetic regulation in eukaryotic genomes. In animals, a sizable portion of miRNAs reside within the introns of protein-coding genes, designated as mirtron genes. Recently, high-throughput sequencing (HTS) revealed a huge amount of sRNAs that derived from introns in plants, such as the monocot rice (Oryza sativa). However, the biogenesis and the biological functions of this kind of sRNAs remain elusive. Here, we performed a genome-scale survey of intron-derived sRNAs in rice based on HTS data. Several introns were found to have great potential to form internal hairpin structures, and the short hairpins could generate miRNAs while the larger ones could produce siRNAs. Furthermore, 22 introns, termed "sirtrons," were identified from the rice protein-coding genes. The single-stranded sirtrons produced a diverse set of siRNAs from long hairpin structures. These sirtron-derived siRNAs are dominantly 21 nt, 22 nt, and 24 nt in length, whose production relied on DCL4, DCL2, and DCL3, respectively. We also observed a strong tendency for the sirtron-derived siRNAs to be coexpressed with their host genes. Finally, the 24-nt siRNAs incorporated with Argonaute 4 (AGO4) could direct DNA methylation on their host genes. In this regard, homeostatic self-regulation between intron-derived siRNAs and their host genes was proposed.
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MESH Headings
- DNA Methylation
- Gene Expression Regulation, Plant
- Genes, Plant
- Genome, Plant
- Introns/genetics
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Models, Biological
- Nucleic Acid Conformation
- Oryza/genetics
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Interfering/chemistry
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
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Affiliation(s)
- Dijun Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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18
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Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, Bonawitz ND, Chapple C, Cheng C, Correa LGG, Dacre M, DeBarry J, Dreyer I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T, Gramzow L, Gutensohn M, Harholt J, Hattori M, Heyl A, Hirai T, Hiwatashi Y, Ishikawa M, Iwata M, Karol KG, Koehler B, Kolukisaoglu U, Kubo M, Kurata T, Lalonde S, Li K, Li Y, Litt A, Lyons E, Manning G, Maruyama T, Michael TP, Mikami K, Miyazaki S, Morinaga SI, Murata T, Mueller-Roeber B, Nelson DR, Obara M, Oguri Y, Olmstead RG, Onodera N, Petersen BL, Pils B, Prigge M, Rensing SA, Riaño-Pachón DM, Roberts AW, Sato Y, Scheller HV, Schulz B, Schulz C, Shakirov EV, Shibagaki N, Shinohara N, Shippen DE, Sørensen I, Sotooka R, Sugimoto N, Sugita M, Sumikawa N, Tanurdzic M, Theissen G, Ulvskov P, Wakazuki S, Weng JK, Willats WWGT, Wipf D, Wolf PG, Yang L, Zimmer AD, Zhu Q, Mitros T, Hellsten U, Loqué D, Otillar R, Salamov A, Schmutz J, Shapiro H, Lindquist E, Lucas S, Rokhsar D, Grigoriev IV. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 2011; 332:960-3. [PMID: 21551031 PMCID: PMC3166216 DOI: 10.1126/science.1203810] [Citation(s) in RCA: 591] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.
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Affiliation(s)
- Jo Ann Banks
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.
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19
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Rosas-Cárdenas FDF, Durán-Figueroa N, Vielle-Calzada JP, Cruz-Hernández A, Marsch-Martínez N, de Folter S. A simple and efficient method for isolating small RNAs from different plant species. PLANT METHODS 2011; 7:4. [PMID: 21349188 PMCID: PMC3056851 DOI: 10.1186/1746-4811-7-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 02/24/2011] [Indexed: 05/13/2023]
Abstract
BACKGROUND Small RNAs emerged over the last decade as key regulators in diverse biological processes in eukaryotic organisms. To identify and study small RNAs, good and efficient protocols are necessary to isolate them, which sometimes may be challenging due to the composition of specific tissues of certain plant species. Here we describe a simple and efficient method to isolate small RNAs from different plant species. RESULTS We developed a simple and efficient method to isolate small RNAs from different plant species by first comparing different total RNA extraction protocols, followed by streamlining the best one, finally resulting in a small RNA extraction method that has no need of first total RNA extraction and is not based on the commercially available TRIzol® Reagent or columns. This small RNA extraction method not only works well for plant tissues with high polysaccharide content, like cactus, agave, banana, and tomato, but also for plant species like Arabidopsis or tobacco. Furthermore, the obtained small RNA samples were successfully used in northern blot assays. CONCLUSION Here we provide a simple and efficient method to isolate small RNAs from different plant species, such as cactus, agave, banana, tomato, Arabidopsis, and tobacco, and the small RNAs from this simplified and low cost method is suitable for downstream handling like northern blot assays.
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Affiliation(s)
- Flor de Fátima Rosas-Cárdenas
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), CINVESTAV-IPN, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821 Irapuato, Guanajuato, México
| | - Noé Durán-Figueroa
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), CINVESTAV-IPN, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821 Irapuato, Guanajuato, México
| | - Jean-Philippe Vielle-Calzada
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), CINVESTAV-IPN, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821 Irapuato, Guanajuato, México
| | - Andrés Cruz-Hernández
- Facultad de Ciencias Naturales-Biología, Universidad Autónoma de Querétaro, CP 76360 Juriquilla, Querétaro, México
| | - Nayelli Marsch-Martínez
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), CINVESTAV-IPN, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821 Irapuato, Guanajuato, México
| | - Stefan de Folter
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), CINVESTAV-IPN, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821 Irapuato, Guanajuato, México
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