1
|
Shi X, Yang H, Birchler JA. MicroRNAs play regulatory roles in genomic balance. Bioessays 2023; 45:e2200187. [PMID: 36470594 DOI: 10.1002/bies.202200187] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022]
Abstract
Classic genetics studies found that genomic imbalance caused by changing the dosage of part of the genome (aneuploidy) has more detrimental effects than altering the dosage of the whole genome (ploidy). Previous analysis revealed global modulation of gene expression triggered by aneuploidy across various species, including maize (Zea mays), Arabidopsis, yeast, mammals, etc. Plant microRNAs (miRNAs) are a class of 20- to 24-nt endogenous small noncoding RNAs that carry out post-transcriptional gene expression regulation. That miRNAs and their putative targets are preferentially retained as duplicates after whole-genome duplication, as are many transcription factors and signaling components, indicates miRNAs are likely to be dosage-sensitive and potentially involved in genomic balance networks. This review addresses the following questions regarding the role of miRNAs in genomic imbalance. (1) How do aneuploidy and polyploidy impact the expression of miRNAs? (2) Do miRNAs play a regulatory role in modulating the expression of their targets under genomic imbalance?
Collapse
Affiliation(s)
- Xiaowen Shi
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.,Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| | - Hua Yang
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| |
Collapse
|
2
|
Papolu PK, Ramakrishnan M, Mullasseri S, Kalendar R, Wei Q, Zou L, Ahmad Z, Vinod KK, Yang P, Zhou M. Retrotransposons: How the continuous evolutionary front shapes plant genomes for response to heat stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1064847. [PMID: 36570931 PMCID: PMC9780303 DOI: 10.3389/fpls.2022.1064847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/21/2022] [Indexed: 05/28/2023]
Abstract
Long terminal repeat retrotransposons (LTR retrotransposons) are the most abundant group of mobile genetic elements in eukaryotic genomes and are essential in organizing genomic architecture and phenotypic variations. The diverse families of retrotransposons are related to retroviruses. As retrotransposable elements are dispersed and ubiquitous, their "copy-out and paste-in" life cycle of replicative transposition leads to new genome insertions without the excision of the original element. The overall structure of retrotransposons and the domains responsible for the various phases of their replication is highly conserved in all eukaryotes. The two major superfamilies of LTR retrotransposons, Ty1/Copia and Ty3/Gypsy, are distinguished and dispersed across the chromosomes of higher plants. Members of these superfamilies can increase in copy number and are often activated by various biotic and abiotic stresses due to retrotransposition bursts. LTR retrotransposons are important drivers of species diversity and exhibit great variety in structure, size, and mechanisms of transposition, making them important putative actors in genome evolution. Additionally, LTR retrotransposons influence the gene expression patterns of adjacent genes by modulating potential small interfering RNA (siRNA) and RNA-directed DNA methylation (RdDM) pathways. Furthermore, comparative and evolutionary analysis of the most important crop genome sequences and advanced technologies have elucidated the epigenetics and structural and functional modifications driven by LTR retrotransposon during speciation. However, mechanistic insights into LTR retrotransposons remain obscure in plant development due to a lack of advancement in high throughput technologies. In this review, we focus on the key role of LTR retrotransposons response in plants during heat stress, the role of centromeric LTR retrotransposons, and the role of LTR retrotransposon markers in genome expression and evolution.
Collapse
Affiliation(s)
- Pradeep K. Papolu
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Muthusamy Ramakrishnan
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Sileesh Mullasseri
- Department of Zoology, St. Albert’s College (Autonomous), Kochi, Kerala, India
| | - Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, Biocenter 3, University of Helsinki, Helsinki, Finland
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Long−Hai Zou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Zishan Ahmad
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | | | - Ping Yang
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, Zhejiang, China
| |
Collapse
|
3
|
Oliver C, Annacondia ML, Wang Z, Jullien PE, Slotkin RK, Köhler C, Martinez G. The miRNome function transitions from regulating developmental genes to transposable elements during pollen maturation. THE PLANT CELL 2022; 34:784-801. [PMID: 34755870 PMCID: PMC8824631 DOI: 10.1093/plcell/koab280] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Animal and plant microRNAs (miRNAs) are essential for the spatio-temporal regulation of development. Together with this role, plant miRNAs have been proposed to target transposable elements (TEs) and stimulate the production of epigenetically active small interfering RNAs. This activity is evident in the plant male gamete containing structure, the male gametophyte or pollen grain. How the dual role of plant miRNAs, regulating both genes and TEs, is integrated during pollen development and which mRNAs are regulated by miRNAs in this cell type at a genome-wide scale are unknown. Here, we provide a detailed analysis of miRNA dynamics and activity during pollen development in Arabidopsis thaliana using small RNA and degradome parallel analysis of RNA end high-throughput sequencing. Furthermore, we uncover miRNAs loaded into the two main active Argonaute (AGO) proteins in the uninuclear and mature pollen grain, AGO1 and AGO5. Our results indicate that the developmental progression from microspore to mature pollen grain is characterized by a transition from miRNAs targeting developmental genes to miRNAs regulating TE activity.
Collapse
Affiliation(s)
- Cecilia Oliver
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Maria Luz Annacondia
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Zhenxing Wang
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
- College of Horticulture and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs and Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Nanjing Agricultural University, Nanjing 210095, China
| | - Pauline E Jullien
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Division of Biological Sciences, University of Missouri Columbia, Columbia, Missouri 65201, USA
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | | |
Collapse
|
4
|
Oberlin S, Rajeswaran R, Trasser M, Barragán-Borrero V, Schon MA, Plotnikova A, Loncsek L, Nodine MD, Marí-Ordóñez A, Voinnet O. Innate, translation-dependent silencing of an invasive transposon in Arabidopsis. EMBO Rep 2021; 23:e53400. [PMID: 34931432 PMCID: PMC8892269 DOI: 10.15252/embr.202153400] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 11/25/2022] Open
Abstract
Co‐evolution between hosts’ and parasites’ genomes shapes diverse pathways of acquired immunity based on silencing small (s)RNAs. In plants, sRNAs cause heterochromatinization, sequence degeneration, and, ultimately, loss of autonomy of most transposable elements (TEs). Recognition of newly invasive plant TEs, by contrast, involves an innate antiviral‐like silencing response. To investigate this response’s activation, we studied the single‐copy element EVADÉ (EVD), one of few representatives of the large Ty1/Copia family able to proliferate in Arabidopsis when epigenetically reactivated. In Ty1/Copia elements, a short subgenomic mRNA (shGAG) provides the necessary excess of structural GAG protein over the catalytic components encoded by the full‐length genomic flGAG‐POL. We show here that the predominant cytosolic distribution of shGAG strongly favors its translation over mostly nuclear flGAG‐POL. During this process, an unusually intense ribosomal stalling event coincides with mRNA breakage yielding unconventional 5’OH RNA fragments that evade RNA quality control. The starting point of sRNA production by RNA‐DEPENDENT‐RNA‐POLYMERASE‐6 (RDR6), exclusively on shGAG, occurs precisely at this breakage point. This hitherto‐unrecognized “translation‐dependent silencing” (TdS) is independent of codon usage or GC content and is not observed on TE remnants populating the Arabidopsis genome, consistent with their poor association, if any, with polysomes. We propose that TdS forms a primal defense against EVD de novo invasions that underlies its associated sRNA pattern.
Collapse
Affiliation(s)
- Stefan Oberlin
- Department of Biology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Rajendran Rajeswaran
- Department of Biology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Marieke Trasser
- Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Verónica Barragán-Borrero
- Department of Biology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland.,Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, Austria
| | - Michael A Schon
- Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexandra Plotnikova
- Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, Austria
| | - Lukas Loncsek
- Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, Austria
| | - Michael D Nodine
- Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, Austria.,Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands
| | - Arturo Marí-Ordóñez
- Department of Biology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland.,Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, Austria
| | - Olivier Voinnet
- Department of Biology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| |
Collapse
|
5
|
Ma X, Liu C, Cao X. Plant transfer RNA-derived fragments: Biogenesis and functions. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1399-1409. [PMID: 34114725 DOI: 10.1111/jipb.13143] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/10/2021] [Indexed: 06/12/2023]
Abstract
Processing of mature transfer RNAs (tRNAs) produces complex populations of tRNA-derived fragments (tRFs). Emerging evidence shows that tRFs have important functions in bacteria, animals, and plants. Here, we review recent advances in understanding plant tRFs, focusing on their biological and cellular functions, such as regulating stress responses, mediating plant-pathogen interactions, and modulating post-transcriptional gene silencing and translation. We also review sequencing strategies and bioinformatics resources for studying tRFs in plants. Finally, we discuss future directions for plant tRF research, which will expand our knowledge of plant non-coding RNAs.
Collapse
Affiliation(s)
- Xuan Ma
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Chunyan Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Molecular Plant Sciences, the Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
6
|
Alves CS, Nogueira FTS. Plant Small RNA World Growing Bigger: tRNA-Derived Fragments, Longstanding Players in Regulatory Processes. Front Mol Biosci 2021; 8:638911. [PMID: 34164429 PMCID: PMC8215267 DOI: 10.3389/fmolb.2021.638911] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/24/2021] [Indexed: 11/13/2022] Open
Abstract
In the past 2 decades, the discovery of a new class of small RNAs, known as tRNA-derived fragments (tRFs), shed light on a new layer of regulation implicated in many biological processes. tRFs originate from mature tRNAs and are classified according to the tRNA regions that they derive from, namely 3′tRF, 5′tRF, and tRF-halves. Additionally, another tRF subgroup deriving from tRNA precursors has been reported, the 3′U tRFs. tRF length ranges from 17 to 26 nt for the 3′and 5′tRFs, and from 30 to 40 nt for tRF-halves. tRF biogenesis is still not yet elucidated, although there is strong evidence that Dicer (and DICER-LIKE) proteins, as well as other RNases such as Angiogenin in mammal and RNS proteins family in plants, are responsible for processing specific tRFs. In plants, the abundance of those molecules varies among tissues, developmental stages, and environmental conditions. More recently, several studies have contributed to elucidate the role that these intriguing molecules may play in all organisms. Among the recent discoveries, tRFs were found to be involved in distinctive regulatory layers, such as transcription and translation regulation, RNA degradation, ribosome biogenesis, stress response, regulatory signaling in plant nodulation, and genome protection against transposable elements. Although tRF biology is still poorly understood, the field has blossomed in the past few years, and this review summarizes the most recent developments in the tRF field in plants.
Collapse
Affiliation(s)
- Cristiane S Alves
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Fabio T S Nogueira
- Laboratório de Genética Molecular do Desenvolvimento Vegetal, Departamento de Ciências Biológicas, ESALQ/USP, Piracicaba, Brazil
| |
Collapse
|
7
|
Ángel Martín-Rodríguez J, Ariani A, Leija A, Elizondo A, Fuentes SI, Ramirez M, Gepts P, Hernández G, Formey D. Phaseolus vulgaris MIR1511 genotypic variations differentially regulate plant tolerance to aluminum toxicity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1521-1533. [PMID: 33300202 DOI: 10.1111/tpj.15129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/20/2020] [Accepted: 12/03/2020] [Indexed: 05/28/2023]
Abstract
The common-bean (Phaseolus vulgaris), a widely consumed legume, originated in Mesoamerica and expanded to South America, resulting in the development of two geographically distinct gene pools. Poor soil condition, including metal toxicity, are often constraints to common-bean crop production. Several P. vulgaris miRNAs, including miR1511, respond to metal toxicity. The MIR1511 gene sequence from the two P. vulgaris model sequenced genotypes revealed that, as opposed to BAT93 (Mesoamerican), the G19833 (Andean) accession displays a 58-bp deletion, comprising the mature and star miR1511 sequences. Genotyping-By-Sequencing data analysis from 87 non-admixed Phaseolus genotypes, comprising different Phaseolus species and P. vulgaris populations, revealed that all the P. vulgaris Andean genotypes and part of the Mesoamerican (MW1) genotypes analyzed displayed a truncated MIR1511 gene. The geographic origin of genotypes with a complete versus truncated MIR1511 showed a distinct distribution. The P. vulgaris ALS3 (Aluminum Sensitive Protein 3) gene, known to be important for aluminum detoxification in several plants, was experimentally validated as the miR1511 target. Roots from BAT93 plants showed decreased miR1511 and increased ALS3 transcript levels at early stages under aluminum toxicity (AlT), while G19833 plants, lacking mature miR1511, showed higher and earlier ALS3 response. Root architecture analyses evidenced higher tolerance of G19833 plants to AlT. However, G19833 plants engineered for miR1511 overexpression showed lower ALS3 transcript level and increased sensitivity to AlT. Absence of miR1511 in Andean genotypes, resulting in a diminished ALS3 transcript degradation, appears to be an evolutionary advantage to high Al levels in soils with increased drought conditions.
Collapse
Affiliation(s)
| | - Andrea Ariani
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA, USA
| | - Alfonso Leija
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Armando Elizondo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Sara I Fuentes
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mario Ramirez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA, USA
| | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Damien Formey
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| |
Collapse
|
8
|
Analysis of tRNA-derived RNA fragments (tRFs) in Cryptococcus spp.: RNAi-independent generation and possible compensatory effects in a RNAi-deficient genotype. Fungal Biol 2021; 125:389-399. [PMID: 33910680 DOI: 10.1016/j.funbio.2020.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 11/30/2020] [Accepted: 12/18/2020] [Indexed: 01/03/2023]
Abstract
Small RNAs (sRNAs) are key factors in the regulation of gene expression. Recently, a new class of regulatory sRNAs derived from tRNAs was described, the tRNA-derived RNA fragments (tRFs). Such RNAs range in length from 14 to 30 nucleotides and are produced from both mature and primary tRNA transcripts, with very specific cleavage sites along the tRNA sequence. Although several mechanisms have been proposed for how tRFs mediate regulation of gene expression, the exact mechanism of tRF biogenesis and its dependency upon the RNAi pathway remain unclear. Cryptococcus gattii and Cryptococcus neoformans are basidiomycetous yeasts and important human pathogens. While C. neoformans is RNAi proficient, C. gattii VGII has lost essential RNAi genes. Here, we sought to identify the tRF production profile in C. gattii VGII and C. neoformans in order to assess the RNAi-dependency of tRF production in these fungal species. We developed a RNA-sequencing-based tRF prediction workflow designed to improve the currently available prediction tools. Using this methodology, we were able to identify tRFs in both organisms. Despite the loss of the RNAi pathway, C. gattii VGII displayed a number of identified tRFs that did not differ significantly from those observed in C. neoformans. The analysis of predicted tRF targets revealed that a higher number of targets was found for C. gattii VGII tRFs compared to C. neoformans tRFs. These results support the idea that tRFs are at least partially independent of the canonical RNAi machinery, raising questions about possible compensatory roles of alternative regulatory RNAs in the absence of a functional RNAi pathway.
Collapse
|
9
|
Small RNA Function in Plants: From Chromatin to the Next Generation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:133-140. [PMID: 32518093 DOI: 10.1101/sqb.2019.84.040394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Small RNA molecules can target a particular virus, gene, or transposable element (TE) with a high degree of specificity. Their ability to move from cell to cell and recognize targets in trans also allows building networks capable of regulating a large number of related targets at once. In the case of epigenetic silencing, small RNA may use the widespread distribution of TEs in eukaryotic genomes to coordinate many loci across developmental and generational time. Here, we discuss the intriguing role of plant small RNA in targeting transposons and repeats in pollen and seeds. Epigenetic reprogramming in the germline and early seed development provides a mechanism to control genome dosage, imprinted gene expression, and incompatible hybridizations via the "triploid block."
Collapse
|
10
|
Ianiri G, Fang YF, Dahlmann TA, Clancey SA, Janbon G, Kück U, Heitman J. Mating-Type-Specific Ribosomal Proteins Control Aspects of Sexual Reproduction in Cryptococcus neoformans. Genetics 2020; 214:635-649. [PMID: 31882399 PMCID: PMC7054023 DOI: 10.1534/genetics.119.302740] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/21/2019] [Indexed: 12/31/2022] Open
Abstract
The MAT locus of Cryptococcus neoformans has a bipolar organization characterized by an unusually large structure, spanning over 100 kb. MAT genes have been characterized by functional genetics as being involved in sexual reproduction and virulence. However, classical gene replacement failed to achieve mutants for five MAT genes (RPL22, RPO41, MYO2, PRT1, and RPL39), indicating that they are likely essential. In the present study, targeted gene replacement was performed in a diploid strain for both the α and a alleles of the ribosomal genes RPL22 and RPL39 Mendelian analysis of the progeny confirmed that both RPL22 and RPL39 are essential for viability. Ectopic integration of the RPL22 allele of opposite MAT identity in the heterozygous RPL22a/rpl22αΔ or RPL22α/rpl22aΔ mutant strains failed to complement their essential phenotype. Evidence suggests that this is due to differential expression of the RPL22 genes, and an RNAi-dependent mechanism that contributes to control RPL22a expression. Furthermore, via CRISPR/Cas9 technology, the RPL22 alleles were exchanged in haploid MATα and MATa strains of C. neoformans These RPL22 exchange strains displayed morphological and genetic defects during bilateral mating. These results contribute to elucidating functions of C. neoformans essential mating type genes that may constitute a type of imprinting system to promote inheritance of nuclei of both mating types.
Collapse
Affiliation(s)
- Giuseppe Ianiri
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Yufeng Francis Fang
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Tim A Dahlmann
- Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Shelly Applen Clancey
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Guilhem Janbon
- Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Institut Pasteur, 75015 Paris, France
| | - Ulrich Kück
- Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| |
Collapse
|
11
|
Carbone F, Bruno L, Perrotta G, Bitonti MB, Muzzalupo I, Chiappetta A. Identification of miRNAs involved in fruit ripening by deep sequencing of Olea europaea L. transcriptome. PLoS One 2019; 14:e0221460. [PMID: 31437230 PMCID: PMC6705801 DOI: 10.1371/journal.pone.0221460] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/08/2019] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The ripening process of olive fruits is associated with chemical and/or enzymatic specific transformations, making them particularly attractive to animals and humans. In olive drupes, including 'Cassanese' ones, ripening is usually accompanied by progressive chromatic change, resulting in a final red-brown colourization of both epidermis and mesocarp. This event has an exception in the 'Leucocarpa', in which we observed the destabilization in the equilibrium between the chlorophyll metabolism and that of the other pigments, particularly the anthocyanins, whose switch-off during maturation promotes the white colouration of the fruits. Recently, transcription profiling of 'Leucocarpa' and 'Cassanese' olives along ripening, performed through an Illumina RNA-seq approach, has provided useful insights on genes functions involved in fruit maturation such as those related to the biosynthesis of flavonoids and anthocyanins. METHODOLOGY To assess expression alterations of genes involved in flavonoids and anthocyanins biosynthetic pathways during ripening, possibly caused by small nuclear RNA (snRNA) in olive drupes, snRNA libraries from 'Leucocarpa' and 'Cassanese' were constructed with RNAs extracted at 100 and 130 Days After Flowering (DAF) and sequenced by an Illumina approach. 130 conserved microRNAs (miRNA) in the Viridiplantae belonging to 14 miRNA families were identified. Regarding the 130 conserved miRNAs, approximately the 48% were identified in all libraries, 5 and 18 miRNAs were shared between the "Cassanese" (C100, C130) and "Leucocarpa" (L100, L130) libraries, respectively. CONCLUSION For the remaining reads not-matching with known miRNAs in the Viridiplantae, we combined secondary structure and minimum free energy to discover novel olive miRNAs. Based on these analyses, 492 sequences were considered as putative novel miRNAs. The putative target genes of identified miRNA were computationally predicted by alignment with the olive drupe transcripts obtained from the same samples. A total of 218 transcripts were predicted as targets of 130 known and 492 putative novel miRNAs. Interestingly, some identified target genes are involved in negative regulation of anthocyanin metabolic process. Quantification of the expression pattern of three miRNA and their target transcripts by qRT-PCR assay confirmed the results of Illumina sequencing.
Collapse
Affiliation(s)
- Fabrizio Carbone
- Department of Biology, Ecology and Earth Science, University of Calabria, Arcavacata Rende (CS) IT
| | - Leonardo Bruno
- Research Centre for Olive, Citrus and Tree Fruit—Council for Agricultural Research and Economics, Rende (CS) IT
| | | | - Maria B. Bitonti
- Research Centre for Olive, Citrus and Tree Fruit—Council for Agricultural Research and Economics, Rende (CS) IT
| | - Innocenzo Muzzalupo
- Department of Biology, Ecology and Earth Science, University of Calabria, Arcavacata Rende (CS) IT
| | - Adriana Chiappetta
- Research Centre for Olive, Citrus and Tree Fruit—Council for Agricultural Research and Economics, Rende (CS) IT
| |
Collapse
|
12
|
Wang Y, Zhang F, Cui W, Chen K, Zhao R, Zhang Z. The FvPHR1 transcription factor control phosphate homeostasis by transcriptionally regulating miR399a in woodland strawberry. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 280:258-268. [PMID: 30824004 DOI: 10.1016/j.plantsci.2018.12.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 12/19/2018] [Accepted: 12/24/2018] [Indexed: 05/26/2023]
Abstract
Plants have evolved phosphate (Pi) starvation response to adapt the low-Pi environment. The regulation of adaptive responses to phosphorus deficiency by the PHR1-miR399-PHO2 module has been well studied in Arabidopsis thaliana but not in strawberry. Transcription factor PHR1 as the central regulator in the Pi starvation signaling has been revealed in a few plant species. However, the function of PHR1 homologues in strawberry is still unknown. In this study, a total of 13 MYB-CC genes were identified in the woodland strawberry (Fragaria vesca) genome and the FvPHR1 gene was characterized. FvPHR1 contains MYB domain and coiled-coil (CC) domain and is localized in the nucleus. FvPHR1 also exhibits trans-activation ability. Furthermore, the P content in leaves of FvPHR1-overexpressing woodland strawberries was significantly increased by 1.38-fold to 1.78-fold compared with that in the wild type. FvPHR1 was also demonstrated to directly bind to the FvMIR399a promoter and positively regulate the expression of FvmiR399a in woodland strawberry. These results showed that PHR1-miR399 module is involved in the regulation of phosphate-signaling pathway and phosphate homeostasis in woodland strawberry.
Collapse
Affiliation(s)
- Yan Wang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Feng Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Weixu Cui
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Keqin Chen
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Rui Zhao
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhihong Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China.
| |
Collapse
|
13
|
Pooggin MM. Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization. Front Microbiol 2018; 9:2779. [PMID: 30524398 PMCID: PMC6256188 DOI: 10.3389/fmicb.2018.02779] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/30/2018] [Indexed: 11/13/2022] Open
Abstract
RNA interference (RNAi)-based antiviral defense generates small interfering RNAs that represent the entire genome sequences of both RNA and DNA viruses as well as viroids and viral satellites. Therefore, deep sequencing and bioinformatics analysis of small RNA population (small RNA-ome) allows not only for universal virus detection and genome reconstruction but also for complete virome reconstruction in mixed infections. Viral infections (like other stress factors) can also perturb the RNAi and gene silencing pathways regulating endogenous gene expression and repressing transposons and host genome-integrated endogenous viral elements which can potentially be released from the genome and contribute to disease. This review describes the application of small RNA-omics for virus detection, virome reconstruction and antiviral defense characterization in cultivated and non-cultivated plants. Reviewing available evidence from a large and ever growing number of studies of naturally or experimentally infected hosts revealed that all families of land plant viruses, their satellites and viroids spawn characteristic small RNAs which can be assembled into contigs of sufficient length for virus, satellite or viroid identification and for exhaustive reconstruction of complex viromes. Moreover, the small RNA size, polarity and hotspot profiles reflect virome interactions with the plant RNAi machinery and allow to distinguish between silent endogenous viral elements and their replicating episomal counterparts. Models for the biogenesis and functions of small interfering RNAs derived from all types of RNA and DNA viruses, satellites and viroids as well as endogenous viral elements are presented and discussed.
Collapse
Affiliation(s)
- Mikhail M. Pooggin
- Institut National de la Recherche Agronomique, UMR BGPI, Montpellier, France
| |
Collapse
|
14
|
Chen Y, Chen Y, Shi C, Huang Z, Zhang Y, Li S, Li Y, Ye J, Yu C, Li Z, Zhang X, Wang J, Yang H, Fang L, Chen Q. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience 2018; 7:1-6. [PMID: 29220494 PMCID: PMC5788068 DOI: 10.1093/gigascience/gix120] [Citation(s) in RCA: 950] [Impact Index Per Article: 158.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 11/22/2017] [Indexed: 12/15/2022] Open
Abstract
Quality control (QC) and preprocessing are essential steps for sequencing data analysis to ensure the accuracy of results. However, existing tools cannot provide a satisfying solution with integrated comprehensive functions, proper architectures, and highly scalable acceleration. In this article, we demonstrate SOAPnuke as a tool with abundant functions for a “QC-Preprocess-QC” workflow and MapReduce acceleration framework. Four modules with different preprocessing functions are designed for processing datasets from genomic, small RNA, Digital Gene Expression, and metagenomic experiments, respectively. As a workflow-like tool, SOAPnuke centralizes processing functions into 1 executable and predefines their order to avoid the necessity of reformatting different files when switching tools. Furthermore, the MapReduce framework enables large scalability to distribute all the processing works to an entire compute cluster. We conducted a benchmarking where SOAPnuke and other tools are used to preprocess a ∼30× NA12878 dataset published by GIAB. The standalone operation of SOAPnuke struck a balance between resource occupancy and performance. When accelerated on 16 working nodes with MapReduce, SOAPnuke achieved ∼5.7 times the fastest speed of other tools.
Collapse
Affiliation(s)
| | | | - Chunmei Shi
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou 350001.,Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou 350014.,Department of Stem Cell Research Institute, Fujian Medical University Stem Cell Research Institute, Fuzhou 350000
| | | | - Yong Zhang
- BGI-Shenzhen, Shenzhen 518083.,Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha 410073
| | - Shengkang Li
- BGI-Shenzhen, Shenzhen 518083.,Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha 410073
| | - Yan Li
- BGI-Shenzhen, Shenzhen 518083
| | - Jia Ye
- BGI-Shenzhen, Shenzhen 518083
| | - Chang Yu
- Intel China Ltd., Shanghai 200336
| | - Zhuo Li
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou 510120.,Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | | | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Lin Fang
- BGI-Shenzhen, Shenzhen 518083.,Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha 410073
| | - Qiang Chen
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou 350001.,Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou 350014.,Department of Stem Cell Research Institute, Fujian Medical University Stem Cell Research Institute, Fuzhou 350000
| |
Collapse
|
15
|
Schorn AJ, Martienssen R. Tie-Break: Host and Retrotransposons Play tRNA. Trends Cell Biol 2018; 28:793-806. [PMID: 29934075 DOI: 10.1016/j.tcb.2018.05.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/08/2018] [Accepted: 05/23/2018] [Indexed: 11/28/2022]
Abstract
tRNA fragments (tRFs) are a class of small, regulatory RNAs with diverse functions. 3'-Derived tRFs perfectly match long terminal repeat (LTR)-retroelements which use the 3'-end of tRNAs to prime reverse transcription. Recent work has shown that tRFs target LTR-retroviruses and -transposons for the RNA interference (RNAi) pathway and also inhibit mobility by blocking reverse transcription. The highly conserved tRNA primer binding site (PBS) in LTR-retroelements is a unique target for 3'-tRFs to recognize and block abundant but diverse LTR-retrotransposons that become transcriptionally active during epigenetic reprogramming in development and disease. 3'-tRFs are processed from full-length tRNAs under so far unknown conditions and potentially protect many cell types. tRFs appear to be an ancient link between RNAi, transposons, and genome stability.
Collapse
Affiliation(s)
- Andrea J Schorn
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Rob Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| |
Collapse
|
16
|
Ujino-Ihara T, Ueno S, Uchiyama K, Futamura N. Comprehensive analysis of small RNAs expressed in developing male strobili of Cryptomeria japonica. PLoS One 2018. [PMID: 29529051 PMCID: PMC5846777 DOI: 10.1371/journal.pone.0193665] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Deep sequencing of small RNAs (sRNAs) in developing male strobili of second-generation offspring originating from a nuclear genic male sterile tree of Cryptomeria japonica were performed to characterize sRNA populations in the male strobili at early pollen developmental stages. Comparing to sequences of microRNA (miRNA) families of plant species and sRNAs expressed in the reproductive organs of representative vascular plants, 37 conserved miRNA families were detected, of which eight were ubiquitously expressed in the reproductive organs of land plant species. In contrast, miR1083 was common in male reproductive organs of gymnosperm species but absent in angiosperm species. In addition to conserved miRNAs, 199 novel miRNAs candidates were predicted. The expression patterns of the obtained sRNAs were further investigated to detect the differentially expressed (DE) sRNAs between genic male sterile and fertile individuals. A total of 969 DE sRNAs were obtained and only three known miRNA families were included among them. These results suggest that both conserved and species-specific sRNAs contribute to the development of male strobili in C. japonica.
Collapse
Affiliation(s)
- Tokuko Ujino-Ihara
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan
- * E-mail:
| | - Saneyoshi Ueno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan
| | - Kentaro Uchiyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan
| | - Norihiro Futamura
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan
| |
Collapse
|
17
|
Borges F, Parent JS, van Ex F, Wolff P, Martínez G, Köhler C, Martienssen RA. Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis. Nat Genet 2018; 50:186-192. [PMID: 29335544 PMCID: PMC5805582 DOI: 10.1038/s41588-017-0032-5] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 12/15/2017] [Indexed: 01/08/2023]
Abstract
Chromosome dosage has substantial effects on reproductive isolation and speciation in both plants and animals, but the underlying mechanisms are largely obscure 1 . Transposable elements in animals can regulate hybridity through maternal small RNA 2 , whereas small RNAs in plants have been postulated to regulate dosage response via neighboring imprinted genes3,4. Here we show that a highly conserved microRNA in plants, miR845, targets the tRNAMet primer-binding site (PBS) of long terminal repeat (LTR) retrotransposons in Arabidopsis pollen, and triggers the accumulation of 21-22-nucleotide (nt) small RNAs in a dose-dependent fashion via RNA polymerase IV. We show that these epigenetically activated small interfering RNAs (easiRNAs) mediate hybridization barriers between diploid seed parents and tetraploid pollen parents (the 'triploid block'), and that natural variation for miR845 may account for 'endosperm balance' allowing the formation of triploid seeds. Targeting of the PBS with small RNA is a common mechanism for transposon control in mammals and plants, and provides a uniquely sensitive means to monitor chromosome dosage and imprinting in the developing seed.
Collapse
Affiliation(s)
- Filipe Borges
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jean-Sébastien Parent
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Frédéric van Ex
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Bayer CropScience NV, Ghent, Belgium
| | - Philip Wolff
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala, Sweden
- John Innes Centre, Norwich, UK
| | - German Martínez
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala, Sweden
| | - Robert A Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| |
Collapse
|
18
|
A multi-omics study of the grapevine-downy mildew (Plasmopara viticola) pathosystem unveils a complex protein coding- and noncoding-based arms race during infection. Sci Rep 2018; 8:757. [PMID: 29335535 PMCID: PMC5768699 DOI: 10.1038/s41598-018-19158-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/15/2017] [Indexed: 12/16/2022] Open
Abstract
Fungicides are applied intensively to prevent downy mildew infections of grapevines (Vitis vinifera) with high impact on the environment. In order to develop alternative strategies we sequenced the genome of the oomycete pathogen Plasmopara viticola causing this disease. We show that it derives from a Phytophthora-like ancestor that switched to obligate biotrophy by losing genes involved in nitrogen metabolism and γ-Aminobutyric acid catabolism. By combining multiple omics approaches we characterized the pathosystem and identified a RxLR effector that trigger an immune response in the wild species V. riparia. This effector is an ideal marker to screen novel grape resistant varieties. Our study reveals an unprecedented bidirectional noncoding RNA-based mechanism that, in one direction might be fundamental for P. viticola to proficiently infect its host, and in the other might reduce the effects of the infection on the plant.
Collapse
|
19
|
Martinez G, Choudury SG, Slotkin RK. tRNA-derived small RNAs target transposable element transcripts. Nucleic Acids Res 2017; 45:5142-5152. [PMID: 28335016 PMCID: PMC5605234 DOI: 10.1093/nar/gkx103] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/06/2017] [Indexed: 12/19/2022] Open
Abstract
tRNA-derived RNA fragments (tRFs) are 18–26 nucleotide small RNAs that are not random degradation products, but are rather specifically cleaved from mature tRNA transcripts. Abundant in stressed or viral-infected cells, the function and potential targets of tRFs are not known. We identified that in the unstressed wild-type male gamete containing pollen of flowering plants, and analogous reproductive structure in non-flowering plant species, tRFs accumulate to high levels. In the reference plant Arabidopsis thaliana, tRFs are processed by Dicer-like 1 and incorporated into Argonaute1 (AGO1), akin to a microRNA. We utilized the fact that many plant small RNAs direct cleavage of their target transcripts to demonstrate that the tRF–AGO1 complex acts to specifically target and cleave endogenous transposable element (TE) mRNAs produced from transcriptionally active TEs. The data presented here demonstrate that tRFs are bona-fide regulatory microRNA-like small RNAs involved in the regulation of genome stability through the targeting of TE transcripts.
Collapse
Affiliation(s)
- German Martinez
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, Columbus, 43210 OH, USA.,Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, 75007 Uppsala, Sweden
| | - Sarah G Choudury
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, Columbus, 43210 OH, USA.,Molecular, Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, 43210 OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, 43210 OH, USA
| | - R Keith Slotkin
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, Columbus, 43210 OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, 43210 OH, USA
| |
Collapse
|
20
|
Yue J, Lu X, Zhang H, Ge J, Gao X, Liu Y. Identification of Conserved and Novel MicroRNAs in Blueberry. FRONTIERS IN PLANT SCIENCE 2017; 8:1155. [PMID: 28713413 PMCID: PMC5492659 DOI: 10.3389/fpls.2017.01155] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 06/15/2017] [Indexed: 05/21/2023]
Abstract
MicroRNAs (miRNAs) are a class of small endogenous RNAs that play important regulatory roles in cells by negatively affecting gene expression at both transcriptional and post-transcriptional levels. There have been extensive studies aiming to identify miRNAs and to elucidate their functions in various plant species. In the present study, we employed the high-throughput sequencing technology to profile miRNAs in blueberry fruits. A total of 9,992,446 small RNA tags with sizes ranged from 18 to 30 nt were obtained, indicating that blueberry fruits have a large and diverse small RNA population. Bioinformatic analysis identified 412 conserved miRNAs belonging to 29 families, and 35 predicted novel miRNAs that are likely to be unique to blueberries. Among them, expression profiles of five conserved miRNAs were validated by stem loop qRT-PCR. Furthermore, the potential target genes of conserved and novel miRNAs were predicted and subjected to Gene Ontology (GO) annotation. Enrichment analysis of the GO-represented biological processes and molecular functions revealed that these target genes were potentially involved in a wide range of metabolic pathways and developmental processes. Particularly, anthocyanin biosynthesis has been predicted to be directly or indirectly regulated by diverse miRNA families. This study is the first report on genome-wide miRNA profile analysis in blueberry and it provides a useful resource for further elucidation of the functional roles of miRNAs during fruit development and ripening.
Collapse
Affiliation(s)
- Junyang Yue
- School of Tea and Food Science, Anhui Agricultural UniversityHefei, China
- College of Food Science and Engineering, Hefei University of TechnologyHefei, China
| | - Xiaohui Lu
- School of Tea and Food Science, Anhui Agricultural UniversityHefei, China
| | - Huan Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of ChinaHefei, China
| | - Jiao Ge
- School of Tea and Food Science, Anhui Agricultural UniversityHefei, China
| | - Xueling Gao
- School of Tea and Food Science, Anhui Agricultural UniversityHefei, China
- *Correspondence: Xueling Gao, Yongsheng Liu,
| | - Yongsheng Liu
- School of Tea and Food Science, Anhui Agricultural UniversityHefei, China
- College of Food Science and Engineering, Hefei University of TechnologyHefei, China
- *Correspondence: Xueling Gao, Yongsheng Liu,
| |
Collapse
|