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Shimada A, Cahn J, Ernst E, Lynn J, Grimanelli D, Henderson I, Kakutani T, Martienssen RA. Retrotransposon addiction promotes centromere function via epigenetically activated small RNAs. NATURE PLANTS 2024; 10:1304-1316. [PMID: 39223305 PMCID: PMC11410651 DOI: 10.1038/s41477-024-01773-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 07/26/2024] [Indexed: 09/04/2024]
Abstract
Retrotransposons have invaded eukaryotic centromeres in cycles of repeat expansion and purging, but the function of centromeric retrotransposons has remained unclear. In Arabidopsis, centromeric ATHILA retrotransposons give rise to epigenetically activated short interfering RNAs in mutants in DECREASE IN DNA METHYLATION1 (DDM1). Here we show that mutants that lose both DDM1 and RNA-dependent RNA polymerase have pleiotropic developmental defects and mis-segregate chromosome 5 during mitosis. Fertility and segregation defects are epigenetically inherited with centromere 5, and can be rescued by directing artificial small RNAs to ATHILA5 retrotransposons that interrupt tandem satellite repeats. Epigenetically activated short interfering RNAs promote pericentromeric condensation, chromosome cohesion and chromosome segregation in mitosis. We propose that insertion of ATHILA silences centromeric transcription, while simultaneously making centromere function dependent on retrotransposon small RNAs in the absence of DDM1. Parallels are made with the fission yeast Schizosaccharomyces pombe, where chromosome cohesion depends on RNA interference, and with humans, where chromosome segregation depends on both RNA interference and HELLSDDM1.
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Affiliation(s)
- Atsushi Shimada
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, New York, NY, USA
| | - Jonathan Cahn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, New York, NY, USA
| | - Evan Ernst
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, New York, NY, USA
| | - Jason Lynn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, New York, NY, USA
| | | | - Ian Henderson
- Department of Plant Sciences, Cambridge University, Cambridge, UK
| | | | - Robert A Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, New York, NY, USA.
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2
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Xiao TW, Liu X, Fu N, Liu TJ, Wang ZF, Ge XJ, Huang HR. Chromosome-level genome assemblies of Musa ornata and Musa velutina provide insights into pericarp dehiscence and anthocyanin biosynthesis in banana. HORTICULTURE RESEARCH 2024; 11:uhae079. [PMID: 38766534 PMCID: PMC11101321 DOI: 10.1093/hr/uhae079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/08/2024] [Indexed: 05/22/2024]
Abstract
Musa ornata and Musa velutina are members of the Musaceae family and are indigenous to the South and Southeast Asia. They are very popular in the horticultural market, but the lack of genomic sequencing data and genetic studies has hampered efforts to improve their ornamental value. In this study, we generated the first chromosome-level genome assemblies for both species by utilizing Oxford Nanopore long reads and Hi-C reads. The genomes of M. ornata and M. velutina were assembled into 11 pseudochromosomes with genome sizes of 427.85 Mb and 478.10 Mb, respectively. Repetitive sequences comprised 46.70% and 50.91% of the total genomes for M. ornata and M. velutina, respectively. Differentially expressed gene (DEG) and Gene Ontology (GO) enrichment analyses indicated that upregulated genes in the mature pericarps of M. velutina were mainly associated with the saccharide metabolic processes, particularly at the cell wall and extracellular region. Furthermore, we identified polygalacturonase (PG) genes that exhibited higher expression level in mature pericarps of M. velutina compared to other tissues, potentially being accountable for pericarp dehiscence. This study also identified genes associated with anthocyanin biosynthesis pathway. Taken together, the chromosomal-level genome assemblies of M. ornata and M. velutina provide valuable insights into the mechanism of pericarp dehiscence and anthocyanin biosynthesis in banana, which will significantly contribute to future genetic and molecular breeding efforts.
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Affiliation(s)
- Tian-Wen Xiao
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
| | - Xin Liu
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Fu
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
| | - Zheng-Feng Wang
- South China National Botanical Garden, Guangzhou 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xue-Jun Ge
- South China National Botanical Garden, Guangzhou 510650, China
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Hui-Run Huang
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
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3
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Horvath R, Minadakis N, Bourgeois Y, Roulin AC. The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role. eLife 2024; 12:RP93284. [PMID: 38606833 PMCID: PMC11014726 DOI: 10.7554/elife.93284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024] Open
Abstract
Understanding how plants adapt to changing environments and the potential contribution of transposable elements (TEs) to this process is a key question in evolutionary genomics. While TEs have recently been put forward as active players in the context of adaptation, few studies have thoroughly investigated their precise role in plant evolution. Here, we used the wild Mediterranean grass Brachypodium distachyon as a model species to identify and quantify the forces acting on TEs during the adaptation of this species to various conditions, across its entire geographic range. Using sequencing data from more than 320 natural B. distachyon accessions and a suite of population genomics approaches, we reveal that putatively adaptive TE polymorphisms are rare in wild B. distachyon populations. After accounting for changes in past TE activity, we show that only a small proportion of TE polymorphisms evolved neutrally (<10%), while the vast majority of them are under moderate purifying selection regardless of their distance to genes. TE polymorphisms should not be ignored when conducting evolutionary studies, as they can be linked to adaptation. However, our study clearly shows that while they have a large potential to cause phenotypic variation in B. distachyon, they are not favored during evolution and adaptation over other types of mutations (such as point mutations) in this species.
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Affiliation(s)
- Robert Horvath
- Department of Plant and Microbial Biology, University of ZurichZurichSwitzerland
| | - Nikolaos Minadakis
- Department of Plant and Microbial Biology, University of ZurichZurichSwitzerland
| | - Yann Bourgeois
- DIADE, University of Montpellier, CIRAD, IRDMontpellierFrance
- University of PortsmouthPortsmouthUnited Kingdom
| | - Anne C Roulin
- Department of Plant and Microbial Biology, University of ZurichZurichSwitzerland
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4
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Suo A, Yang J, Mao C, Li W, Wu X, Xie W, Yang Z, Guo S, Zheng B, Zheng Y. Phased secondary small interfering RNAs in Camellia sinensis var. assamica. NAR Genom Bioinform 2023; 5:lqad103. [PMID: 38025046 PMCID: PMC10673657 DOI: 10.1093/nargab/lqad103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023] Open
Abstract
Phased secondary small interfering RNAs (phasiRNAs) in plants play important roles in regulating genome stability, plant development and stress adaption. Camellia sinensis var. assamica has immense economic, medicinal and cultural significance. However, there are still no studies of phasiRNAs and their putative functions in this valuable plant. We identified 476 and 43 PHAS loci which generated 4290 twenty one nucleotide (nt) and 264 twenty four nt phasiRNAs, respectively. Moreover, the analysis of degradome revealed more than 35000 potential targets for these phasiRNAs. We identified several conserved 21 nt phasiRNA generation pathways in tea plant, including miR390 → TAS3, miR482/miR2118 → NB-LRR, miR393 → F-box, miR828 → MYB/TAS4, and miR7122 → PPR in this study. Furthermore, we found that some transposase and plant mobile domain genes could generate phasiRNAs. Our results show that phasiRNAs target genes in the same family in cis- or trans-manners, and different members of the same gene family may generate the same phasiRNAs. The phasiRNAs, generated by transposase and plant mobile domain genes, and their targets, suggest that phasiRNAs may be involved in the inhibition of transposable elements in tea plant. To summarize, these results provide a comprehensive view of phasiRNAs in Camellia sinensis var. assamica.
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Affiliation(s)
- Angbaji Suo
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Jun Yang
- School of Criminal Investigation, Yunnan Police College, No. 249 North Jiaochang Road, 650223 Yunnan, China
| | - Chunyi Mao
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Wanran Li
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Xingwang Wu
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Wenping Xie
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Zhengan Yang
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Shiyong Guo
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, No. 220 Handan Road, 200433 Shanghai, China
| | - Yun Zheng
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
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5
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Shimada A, Cahn J, Ernst E, Lynn J, Grimanelli D, Henderson I, Kakutani T, Martienssen RA. Retrotransposon addiction promotes centromere function via epigenetically activated small RNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.02.551486. [PMID: 37577592 PMCID: PMC10418216 DOI: 10.1101/2023.08.02.551486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Retrotransposons have invaded eukaryotic centromeres in cycles of repeat expansion and purging, but the function of centromeric retrotransposons, if any, has remained unclear. In Arabidopsis, centromeric ATHILA retrotransposons give rise to epigenetically activated short interfering RNAs (easiRNAs) in mutants in DECREASE IN DNA METHYLATION1 (DDM1), which promote histone H3 lysine-9 di-methylation (H3K9me2). Here, we show that mutants which lose both DDM1 and RNA dependent RNA polymerase (RdRP) have pleiotropic developmental defects and mis-segregation of chromosome 5 during mitosis. Fertility defects are epigenetically inherited with the centromeric region of chromosome 5, and can be rescued by directing artificial small RNAs to a single family of ATHILA5 retrotransposons specifically embedded within this centromeric region. easiRNAs and H3K9me2 promote pericentromeric condensation, chromosome cohesion and proper chromosome segregation in mitosis. Insertion of ATHILA silences transcription, while simultaneously making centromere function dependent on retrotransposon small RNAs, promoting the selfish survival and spread of centromeric retrotransposons. Parallels are made with the fission yeast S. pombe, where chromosome segregation depends on RNAi, and with humans, where chromosome segregation depends on both RNAi and HELLSDDM1.
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Affiliation(s)
- Atsushi Shimada
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Jonathan Cahn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Evan Ernst
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Jason Lynn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Daniel Grimanelli
- Epigenetic Regulations and Seed Development, UMR232, Institut de Recherche pour le Développement (IRD), Université de Montpellier, 34394 Montpellier, France
| | - Ian Henderson
- Department of Plant Sciences, Cambridge University, Cambridge UK
| | - Tetsuji Kakutani
- Faculty of Science, The University of Tokyo, Bunkyo-ku, Hongo, Tokyo 113-0033, Japan
| | - Robert A. Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
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6
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Benson CW, Sheltra MR, Maughan PJ, Jellen EN, Robbins MD, Bushman BS, Patterson EL, Hall ND, Huff DR. Homoeologous evolution of the allotetraploid genome of Poa annua L. BMC Genomics 2023; 24:350. [PMID: 37365554 DOI: 10.1186/s12864-023-09456-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Poa annua (annual bluegrass) is an allotetraploid turfgrass, an agronomically significant weed, and one of the most widely dispersed plant species on earth. Here, we report the chromosome-scale genome assemblies of P. annua's diploid progenitors, P. infirma and P. supina, and use multi-omic analyses spanning all three species to better understand P. annua's evolutionary novelty. RESULTS We find that the diploids diverged from their common ancestor 5.5 - 6.3 million years ago and hybridized to form P. annua ≤ 50,000 years ago. The diploid genomes are similar in chromosome structure and most notably distinguished by the divergent evolutionary histories of their transposable elements, leading to a 1.7 × difference in genome size. In allotetraploid P. annua, we find biased movement of retrotransposons from the larger (A) subgenome to the smaller (B) subgenome. We show that P. annua's B subgenome is preferentially accumulating genes and that its genes are more highly expressed. Whole-genome resequencing of several additional P. annua accessions revealed large-scale chromosomal rearrangements characterized by extensive TE-downsizing and evidence to support the Genome Balance Hypothesis. CONCLUSIONS The divergent evolutions of the diploid progenitors played a central role in conferring onto P. annua its remarkable phenotypic plasticity. We find that plant genes (guided by selection and drift) and transposable elements (mostly guided by host immunity) each respond to polyploidy in unique ways and that P. annua uses whole-genome duplication to purge highly parasitized heterochromatic sequences. The findings and genomic resources presented here will enable the development of homoeolog-specific markers for accelerated weed science and turfgrass breeding.
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Affiliation(s)
- Christopher W Benson
- Department of Plant Science, Pennsylvania State University, University Park, PA, USA.
- Intercollegiate Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA, USA.
| | - Matthew R Sheltra
- Department of Plant Science, Pennsylvania State University, University Park, PA, USA
- Intercollegiate Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA, USA
| | - Peter J Maughan
- Department of Plant and Wildlife Sciences, Brigham Young University, Logan, UT, USA
| | - Eric N Jellen
- Department of Plant and Wildlife Sciences, Brigham Young University, Logan, UT, USA
| | | | | | - Eric L Patterson
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Nathan D Hall
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - David R Huff
- Department of Plant Science, Pennsylvania State University, University Park, PA, USA.
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7
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Sammarco I, Pieters J, Salony S, Toman I, Zolotarov G, Lafon Placette C. Epigenetic targeting of transposon relics: beating the dead horses of the genome? Epigenetics 2022; 17:1331-1344. [PMID: 36255200 PMCID: PMC9586680 DOI: 10.1080/15592294.2021.2022066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Transposable elements (TEs) have been seen as selfish genetic elements that can propagate in a host genome. Their propagation success is however hindered by a combination of mechanisms such as mutations, selection, and their epigenetic silencing by the host genome. As a result, most copies of TEs in a given genome are dead relics: their sequence is too degenerated to allow any transposition. Nevertheless, these TE relics often, but not always, remain epigenetically silenced, and if not to prevent transposition anymore, one can wonder the reason for this phenomenon. The mere self-perpetuating loop inherent to epigenetic silencing could alone explain that even when inactive, TE copies remain silenced. Beyond this process, nevertheless, antagonistic selective forces are likely to act on TE relic silencing. Especially, without the benefit of preventing transposition, TE relic silencing may prove deleterious to the host fitness, suggesting that the maintenance of TE relic silencing is the result of a fine, and perhaps case-by-case, evolutionary trade-off between beneficial and deleterious effects. Ultimately, the release of TE relics silencing may provide a 'safe' ground for adaptive epimutations to arise. In this review, we provide an overview of these questions in both plants and animals.
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Affiliation(s)
- Iris Sammarco
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic,Institute of Botany, Czech Academy of Sciences, Pruhonice, Czech Republic
| | - Janto Pieters
- Laboratory of Pollen Biology, Institute of Experimental Botany, Czech Academy of Science, Prague, Czech Republic,Department of Plant Experimental Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Susnata Salony
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Izabela Toman
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| | - Grygoriy Zolotarov
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Clément Lafon Placette
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic,CONTACT Clément Lafon Placette Department of Botany, Faculty of Science, Charles University, PragueCZ-128 01, Czech Republic
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8
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Gómez G, Marquez-Molins J, Martinez G, Pallas V. Plant epigenome alterations: an emergent player in viroid-host interactions. Virus Res 2022; 318:198844. [DOI: 10.1016/j.virusres.2022.198844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/31/2022] [Accepted: 06/05/2022] [Indexed: 10/18/2022]
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9
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Teresi SJ, Teresi MB, Edger PP. TE Density: a tool to investigate the biology of transposable elements. Mob DNA 2022; 13:11. [PMID: 35413944 PMCID: PMC9004194 DOI: 10.1186/s13100-022-00264-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are powerful creators of genotypic and phenotypic diversity due to their inherent mutagenic capabilities and in this way they serve as a deep reservoir of sequences for genomic variation. As agents of genetic disruption, a TE's potential to impact phenotype is partially a factor of its location in the genome. Previous research has shown TEs' ability to impact the expression of neighboring genes, however our understanding of this trend is hampered by the exceptional amount of diversity in the TE world, and a lack of publicly available computational methods that quantify the presence of TEs relative to genes. RESULTS Here, we have developed a tool to more easily quantify TE presence relative to genes through the use of only a gene and TE annotation, yielding a new metric we call TE Density. Briefly defined as the proportion of TE-occupied base-pairs relative to a window-size of the genome. This new pipeline reports TE density for each gene in the genome, for each type descriptor of TE (order and superfamily), and for multiple positions and distances relative to the gene (upstream, intragenic, and downstream) over sliding, user-defined windows. In this way, we overcome previous limitations to the study of TE-gene relationships by focusing on all TE types present in the genome, utilizing flexible genomic distances for measurement, and reporting a TE presence metric for every gene in the genome. CONCLUSIONS Together, this new tool opens up new avenues for studying TE-gene relationships, genome architecture, comparative genomics, and the tremendous diversity present of the TE world. TE Density is open-source and freely available at: https://github.com/sjteresi/TE_Density .
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Affiliation(s)
- Scott J Teresi
- Department of Horticulture, Michigan State University, East Lansing, Michigan, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, Michigan, USA
| | | | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, Michigan, USA.
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, Michigan, USA.
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10
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Kejnovsky E, Jedlicka P. Nucleic acids movement and its relation to genome dynamics of repetitive DNA: Is cellular and intercellular movement of DNA and RNA molecules related to the evolutionary dynamic genome components?: Is cellular and intercellular movement of DNA and RNA molecules related to the evolutionary dynamic genome components? Bioessays 2022; 44:e2100242. [PMID: 35112737 DOI: 10.1002/bies.202100242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 11/07/2022]
Abstract
There is growing evidence of evolutionary genome plasticity. The evolution of repetitive DNA elements, the major components of most eukaryotic genomes, involves the amplification of various classes of mobile genetic elements, the expansion of satellite DNA, the transfer of fragments or entire organellar genomes and may have connections with viruses. In addition to various repetitive DNA elements, a plethora of large and small RNAs migrate within and between cells during individual development as well as during evolution and contribute to changes of genome structure and function. Such migration of DNA and RNA molecules often results in horizontal gene transfer, thus shaping the whole genomic network of interconnected species. Here, we propose that a high evolutionary dynamism of repetitive genome components is often related to the migration/movement of DNA or RNA molecules. We speculate that the cytoplasm is probably an ideal compartment for such evolutionary experiments.
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Affiliation(s)
- Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Pavel Jedlicka
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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11
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Hu X, Persson Hodén K, Liao Z, Åsman A, Dixelius C. Phytophthora infestans Ago1-associated miRNA promotes potato late blight disease. THE NEW PHYTOLOGIST 2022; 233:443-457. [PMID: 34605025 DOI: 10.1111/nph.17758] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Phytophthora spp. cause serious damage to plants by exploiting a large number of effector proteins and small RNAs (sRNAs). Several reports have described modulation of host RNA biogenesis and defence gene expression. Here, we analysed Phytophthora infestans Argonaute (Ago) 1 associated small RNAs during potato leaf infection. Small RNAs were co-immunoprecipitated, deep sequenced and analysed against the P. infestans and potato genomes, followed by transcript analyses and transgenic assays on a predicted target. Extensive targeting of potato and pathogen-derived sRNAs to a range of mRNAs was observed, including 638 sequences coding for resistance (R) proteins in the host genome. The single miRNA encoded by P. infestans (miR8788) was found to target a potato alpha/beta hydrolase-type encoding gene (StABH1), a protein localized to the plasma membrane. Analyses of stable transgenic potato lines harbouring overexpressed StABH1 or artificial miRNA gene constructs demonstrated the importance of StABH1 during infection by P. infestans. miR8788 knock-down strains showed reduced growth on potato, and elevated StABH1 expression levels were observed when plants were inoculated with the two knock-down strains compared to the wild-type strain 88069. The findings of our study suggest that sRNA encoded by P. infestans can affect potato mRNA, thereby expanding our knowledge of the multifaceted strategies this species uses to facilitate infection.
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Affiliation(s)
- Xinyi Hu
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7080, S-75007, Uppsala, Sweden
| | - Kristian Persson Hodén
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7080, S-75007, Uppsala, Sweden
| | - Zhen Liao
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7080, S-75007, Uppsala, Sweden
| | - Anna Åsman
- Department of Molecular Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7015, S-75007, Uppsala, Sweden
| | - Christina Dixelius
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7080, S-75007, Uppsala, Sweden
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12
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Annacondia ML, Martinez G. Reprogramming of RNA silencing triggered by cucumber mosaic virus infection in Arabidopsis. Genome Biol 2021; 22:340. [PMID: 34911561 PMCID: PMC8672585 DOI: 10.1186/s13059-021-02564-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND RNA silencing has an important role mediating sequence-specific virus resistance in plants. The complex interaction of viruses with RNA silencing involves the loading of viral small interfering RNAs (vsiRNAs) into its host ARGONAUTE (AGO) proteins. As a side effect of their antiviral activity, vsiRNAs loading into AGO proteins can also mediate the silencing of endogenous genes. Here, we analyze at the genome-wide level both aspects of the interference of cucumber mosaic virus (CMV) with the RNA silencing machinery of Arabidopsis thaliana. RESULTS We observe CMV-derived vsiRNAs affect the levels of endogenous sRNA classes. Furthermore, we analyze the incorporation of vsiRNAs into AGO proteins with a described antiviral role and the viral suppressor of RNA silencing (VSR) 2b, by combining protein immunoprecipitation with sRNA high-throughput sequencing. Interestingly, vsiRNAs represent a substantial percentage of AGO-loaded sRNAs and displace other endogenous sRNAs. As a countermeasure, the VSR 2b loaded vsiRNAs and mRNA-derived siRNAs, which affect the expression of the genes they derive from. Additionally, we analyze how vsiRNAs incorporate into the endogenous RNA silencing pathways by exploring their target mRNAs using parallel analysis of RNA end (PARE) sequencing, which allow us to identify vsiRNA-targeted genes genome-wide. CONCLUSIONS This work exemplifies the complex relationship of RNA viruses with the endogenous RNA silencing machinery and the multiple aspects of virus resistance and virulence that this interaction induces.
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Affiliation(s)
- Maria Luz Annacondia
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - German Martinez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.
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13
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Lei Z, Kim EY, Cho J. Enrichment of Cytoplasmic RNA Granules from Arabidopsis Seedlings. Bio Protoc 2021; 11:e4212. [PMID: 34859127 DOI: 10.21769/bioprotoc.4212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 11/02/2022] Open
Abstract
RNA granules (RGs) are membraneless intracellular compartments that play important roles in the post-transcriptional control of gene expression. Stress granules (SGs) are a type of RGs that form under environmental challenges and/or internal cellular stresses. Stress treatments lead to strong mRNAs translational inhibition and storage in SGs until the normal growth conditions are restored. Intriguingly, we recently showed that plant stress granules are associated with siRNA bodies, where the RDR6-mediated and transposon-derived siRNA biogenesis occurs ( Kim et al., 2021 ). This protocol provides a technical workflow for the enrichment of cytoplasmic RGs from Arabidopsis seedlings. We used the DNA methylation-deficient ddm1 mutant in our study, but the method can be applied to any other plant samples with strong RG formation. The resulting RG fractions can be further tested for either RNAs or proteins using RNA-seq and mass spectrometry-based proteomics.
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Affiliation(s)
- Zhen Lei
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Eun Yu Kim
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jungnam Cho
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Chinese Academy of Sciences, Shanghai, China
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14
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Nicolau M, Picault N, Moissiard G. The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation. Cells 2021; 10:cells10112952. [PMID: 34831175 PMCID: PMC8616336 DOI: 10.3390/cells10112952] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/20/2021] [Accepted: 10/20/2021] [Indexed: 12/25/2022] Open
Abstract
Transposable elements (TEs) are self-replicating DNA elements that constitute major fractions of eukaryote genomes. Their ability to transpose can modify the genome structure with potentially deleterious effects. To repress TE activity, host cells have developed numerous strategies, including epigenetic pathways, such as DNA methylation or histone modifications. Although TE neo-insertions are mostly deleterious or neutral, they can become advantageous for the host under specific circumstances. The phenomenon leading to the appropriation of TE-derived sequences by the host is known as TE exaptation or co-option. TE exaptation can be of different natures, through the production of coding or non-coding DNA sequences with ultimately an adaptive benefit for the host. In this review, we first give new insights into the silencing pathways controlling TE activity. We then discuss a model to explain how, under specific environmental conditions, TEs are unleashed, leading to a TE burst and neo-insertions, with potential benefits for the host. Finally, we review our current knowledge of coding and non-coding TE exaptation by providing several examples in various organisms and describing a method to identify TE co-option events.
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Affiliation(s)
- Melody Nicolau
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Nathalie Picault
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Guillaume Moissiard
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
- Correspondence:
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15
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Ariel FD, Manavella PA. When junk DNA turns functional: transposon-derived non-coding RNAs in plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4132-4143. [PMID: 33606874 DOI: 10.1093/jxb/erab073] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/12/2021] [Indexed: 05/05/2023]
Abstract
Transposable elements (TEs) are major contributors to genome complexity in eukaryotes. TE mobilization may cause genome instability, although it can also drive genome diversity throughout evolution. TE transposition may influence the transcriptional activity of neighboring genes by modulating the epigenomic profile of the region or by altering the relative position of regulatory elements. Notably, TEs have emerged in the last few years as an important source of functional long and small non-coding RNAs. A plethora of small RNAs derived from TEs have been linked to the trans regulation of gene activity at the transcriptional and post-transcriptional levels. Furthermore, TE-derived long non-coding RNAs have been shown to modulate gene expression by interacting with protein partners, sequestering active small RNAs, and forming duplexes with DNA or other RNA molecules. In this review, we summarize our current knowledge of the functional and mechanistic paradigms of TE-derived long and small non-coding RNAs and discuss their role in plant development and evolution.
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Affiliation(s)
- Federico D Ariel
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
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16
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Wang D, Zheng Z, Li Y, Hu H, Wang Z, Du X, Zhang S, Zhu M, Dong L, Ren G, Yang Y. Which factors contribute most to genome size variation within angiosperms? Ecol Evol 2021; 11:2660-2668. [PMID: 33767827 PMCID: PMC7981209 DOI: 10.1002/ece3.7222] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 12/17/2020] [Accepted: 01/04/2021] [Indexed: 12/31/2022] Open
Abstract
Genome size varies greatly across the flowering plants and has played an important role in shaping their evolution. It has been reported that many factors correlate with the variation in genome size, but few studies have systematically explored this at the genomic level. Here, we scan genomic information for 74 species from 74 families in 38 orders covering the major groups of angiosperms (the taxonomic information was acquired from the latest Angiosperm Phylogeny Group (APG IV) system) to evaluate the correlation between genome size variation and different genome characteristics: polyploidization, different types of repeat sequence content, and the dynamics of long terminal repeat retrotransposons (LTRs). Surprisingly, we found that polyploidization shows no significant correlation with genome size, while LTR content demonstrates a significantly positive correlation. This may be due to genome instability after polyploidization, and since LTRs occupy most of the genome content, it may directly result in most of the genome variation. We found that the LTR insertion time is significantly negatively correlated with genome size, which may reflect the competition between insertion and deletion of LTRs in each genome, and that the old insertions are usually easy to recognize and eliminate. We also noticed that most of the LTR burst occurred within the last 3 million years, a timeframe consistent with the violent climate fluctuations in the Pleistocene. Our findings enhance our understanding of genome size evolution within angiosperms, and our methods offer immediate implications for corresponding research in other datasets.
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Affiliation(s)
- Dandan Wang
- State Key Laboratory of Grassland Agro‐EcosystemInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Zeyu Zheng
- State Key Laboratory of Grassland Agro‐EcosystemInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Ying Li
- State Key Laboratory of Grassland Agro‐EcosystemInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Hongyin Hu
- State Key Laboratory of Grassland Agro‐EcosystemInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Zhenyue Wang
- State Key Laboratory of Grassland Agro‐EcosystemInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Xin Du
- State Key Laboratory of Grassland Agro‐EcosystemInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Shangzhe Zhang
- State Key Laboratory of Grassland Agro‐EcosystemInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Mingjia Zhu
- State Key Laboratory of Grassland Agro‐EcosystemInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Longwei Dong
- State Key Laboratory of Grassland Agro‐EcosystemInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Guangpeng Ren
- State Key Laboratory of Grassland Agro‐EcosystemInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro‐EcosystemInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
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17
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Wu W, Li L, Zhao Y, Zhao Y, Jiang T, McCormick S, Zheng B. Heterochromatic silencing is reinforced by ARID1-mediated small RNA movement in Arabidopsis pollen. THE NEW PHYTOLOGIST 2021; 229:3269-3280. [PMID: 32783185 DOI: 10.1111/nph.16871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/27/2020] [Indexed: 06/11/2023]
Abstract
In the plant male germline, transposable elements (TEs) are reactivated in the companion vegetative nucleus, resulting in siRNA production and the intercellular movement of these siRNAs to reinforce TE silencing in sperm. However, the mechanism by which siRNA movement is regulated remains unexplored. Here we show that ARID1, a transcription factor which is constitutively expressed in the vegetative nucleus but dynamically accumulates in the generative cell (the progenitor of sperm) to promote the second pollen mitosis, mediates siRNA movement to reinforce heterochromatic silencing in the male germline. We looked for regulators involved in the accumulation of ARID1 in the generative cell, and found that AGO9, a germline-specific AGO in Arabidopsis, is required for the accumulation of ARID1 in the generative cell. Mutations in either ARID1 or AGO9 lead to the interruption of not only the second pollen mitosis but also the movement of siRNA from the vegetative nucleus to the male germline, resulting in the release of heterochromatic silencing in the male germline. Moreover, conditional knockdown of ARID1 in the generative cell causes reduced heterochromatic silencing in both bicellular and mature pollen. This study provides insights into how a spatiotemporal transcription factor coordinates heterochromatic silencing and male germline maturation.
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Affiliation(s)
- Wenye Wu
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lei Li
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yi Zhao
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Youshang Zhao
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ting Jiang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Sheila McCormick
- Department of Plant and Microbial Biology, UC-Berkeley, Albany, CA, 94710, USA
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
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18
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Ellison CE, Kagda MS, Cao W. Telomeric TART elements target the piRNA machinery in Drosophila. PLoS Biol 2020; 18:e3000689. [PMID: 33347429 PMCID: PMC7785250 DOI: 10.1371/journal.pbio.3000689] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 01/05/2021] [Accepted: 12/10/2020] [Indexed: 11/23/2022] Open
Abstract
Coevolution between transposable elements (TEs) and their hosts can be antagonistic, where TEs evolve to avoid silencing and the host responds by reestablishing TE suppression, or mutualistic, where TEs are co-opted to benefit their host. The TART-A TE functions as an important component of Drosophila telomeres but has also reportedly inserted into the Drosophila melanogaster nuclear export factor gene nxf2. We find that, rather than inserting into nxf2, TART-A has actually captured a portion of nxf2 sequence. We show that TART-A produces abundant Piwi-interacting small RNAs (piRNAs), some of which are antisense to the nxf2 transcript, and that the TART-like region of nxf2 is evolving rapidly. Furthermore, in D. melanogaster, TART-A is present at higher copy numbers, and nxf2 shows reduced expression, compared to the closely related species Drosophila simulans. We propose that capturing nxf2 sequence allowed TART-A to target the nxf2 gene for piRNA-mediated repression and that these 2 elements are engaged in antagonistic coevolution despite the fact that TART-A is serving a critical role for its host genome. Co-evolution between transposable elements (TEs) and their hosts can be antagonistic, where TEs evolve to avoid silencing and the host responds by re-establishing TE suppression, or mutualistic, where TEs are co-opted to benefit their host. This study shows that a specialized Drosophila retrotransposon that functions as a telomere has captured a portion of a host piRNA gene which may allow it to evade silencing.
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Affiliation(s)
- Christopher E. Ellison
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
- * E-mail:
| | - Meenakshi S. Kagda
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Weihuan Cao
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
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19
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Kirov I, Omarov M, Merkulov P, Dudnikov M, Gvaramiya S, Kolganova E, Komakhin R, Karlov G, Soloviev A. Genomic and Transcriptomic Survey Provides New Insight into the Organization and Transposition Activity of Highly Expressed LTR Retrotransposons of Sunflower ( Helianthus annuus L.). Int J Mol Sci 2020; 21:E9331. [PMID: 33297579 PMCID: PMC7730604 DOI: 10.3390/ijms21239331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 12/21/2022] Open
Abstract
LTR retrotransposons (RTEs) play a crucial role in plant genome evolution and adaptation. Although RTEs are generally silenced in somatic plant tissues under non-stressed conditions, some expressed RTEs (exRTEs) escape genome defense mechanisms. As our understanding of exRTE organization in plants is rudimentary, we systematically surveyed the genomic and transcriptomic organization and mobilome (transposition) activity of sunflower (Helianthus annuus L.) exRTEs. We identified 44 transcribed RTEs in the sunflower genome and demonstrated their distinct genomic features: more recent insertion time, longer open reading frame (ORF) length, and smaller distance to neighboring genes. We showed that GAG-encoding ORFs are present at significantly higher frequencies in exRTEs, compared with non-expressed RTEs. Most exRTEs exhibit variation in copy number among sunflower cultivars and one exRTE Gagarin produces extrachromosomal circular DNA in seedling, demonstrating recent and ongoing transposition activity. Nanopore direct RNA sequencing of full-length RTE RNA revealed complex patterns of alternative splicing in RTE RNAs, resulting in isoforms that carry ORFs for distinct RTE proteins. Together, our study demonstrates that tens of expressed sunflower RTEs with specific genomic organization shape the hidden layer of the transcriptome, pointing to the evolution of specific strategies that circumvent existing genome defense mechanisms.
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Affiliation(s)
- Ilya Kirov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
- Kurchatov Genomics Center of ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia
| | - Murad Omarov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
- Faculty of Computer Science, National Research University Higher School of Economics, Pokrovsky Boulvar 11, 109028 Moscow, Russia
| | - Pavel Merkulov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
| | - Maxim Dudnikov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
- Kurchatov Genomics Center of ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia
| | - Sofya Gvaramiya
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
| | - Elizaveta Kolganova
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
| | - Roman Komakhin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
| | - Gennady Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
| | - Alexander Soloviev
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
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20
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UNBRANCHED3 Expression and Inflorescence Development is Mediated by UNBRANCHED2 and the Distal Enhancer, KRN4, in Maize. PLoS Genet 2020; 16:e1008764. [PMID: 32330129 PMCID: PMC7202667 DOI: 10.1371/journal.pgen.1008764] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/06/2020] [Accepted: 04/07/2020] [Indexed: 12/22/2022] Open
Abstract
Enhancers are cis-acting DNA segments with the ability to increase target gene expression. They show high sensitivity to DNase and contain specific DNA elements in an open chromatin state that allows the binding of transcription factors (TFs). While numerous enhancers are annotated in the maize genome, few have been characterized genetically. KERNEL ROW NUMBER4 (KRN4), an intergenic quantitative trait locus for kernel row number, is assumed to be a cis-regulatory element of UNBRANCHED3 (UB3), a key inflorescence gene. However, the mechanism by which KRN4 controls UB3 expression remains unclear. Here, we found that KRN4 exhibits an open chromatin state, harboring sequences that showed high enhancer activity toward the 35S and UB3 promoters. KRN4 is bound by UB2-centered transcription complexes and interacts with the UB3 promoter by three duplex interactions to affect UB3 expression. Sequence variation at KRN4 enhances ub2 and ub3 mutant ear fasciation. Therefore, we suggest that KRN4 functions as a distal enhancer of the UB3 promoter via chromatin interactions and recruitment of UB2-centered transcription complexes for the fine-tuning of UB3 expression in meristems of ear inflorescences. These results provide evidence that an intergenic region helps to finely tune gene expression, providing a new perspective on the genetic control of quantitative traits.
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21
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Panda K, McCue AD, Slotkin RK. Arabidopsis RNA Polymerase IV generates 21-22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190417. [PMID: 32075560 DOI: 10.1098/rstb.2019.0417] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The plant-specific RNA Polymerase IV (Pol IV) transcribes heterochromatic regions, including many transposable elements (TEs), with the well-described role of generating 24 nucleotide (nt) small interfering RNAs (siRNAs). These siRNAs target DNA methylation back to TEs to reinforce the boundary between heterochromatin and euchromatin. In the male gametophytic phase of the plant life cycle, pollen, Pol IV switches to generating primarily 21-22 nt siRNAs, but the biogenesis and function of these siRNAs have been enigmatic. In contrast to being pollen-specific, we identified that Pol IV generates these 21-22 nt siRNAs in sporophytic tissues, likely from the same transcripts that are processed into the more abundant 24 nt siRNAs. The 21-22 nt forms are specifically generated by the combined activities of DICER proteins DCL2/DCL4 and can participate in RNA-directed DNA methylation. These 21-22 nt siRNAs are also loaded into ARGONAUTE1 (AGO1), which is known to function in post-transcriptional gene regulation. Like other plant siRNAs and microRNAs incorporated into AGO1, we find a signature of genic mRNA cleavage at the predicted target site of these siRNAs, suggesting that Pol IV-generated 21-22 nt siRNAs may function to regulate gene transcript abundance. Our data provide support for the existing model that in pollen Pol IV functions in gene regulation. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
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Affiliation(s)
- Kaushik Panda
- Donald Danforth Plant Science Center, St. Louis, MO 63132-2918, USA
| | - Andrea D McCue
- Donald Danforth Plant Science Center, St. Louis, MO 63132-2918, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210-1214, USA
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, MO 63132-2918, USA.,Division of Biological Sciences, University of Missouri, Columbia, MO 65211-7400, USA
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22
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Taochy C, Yu A, Bouché N, Bouteiller N, Elmayan T, Dressel U, Carroll BJ, Vaucheret H. Post-transcriptional gene silencing triggers dispensable DNA methylation in gene body in Arabidopsis. Nucleic Acids Res 2019; 47:9104-9114. [PMID: 31372641 PMCID: PMC6753489 DOI: 10.1093/nar/gkz636] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/27/2019] [Accepted: 07/26/2019] [Indexed: 11/14/2022] Open
Abstract
Spontaneous post-transcriptional silencing of sense transgenes (S-PTGS) is established in each generation and is accompanied by DNA methylation, but the pathway of PTGS-dependent DNA methylation is unknown and so is its role. Here we show that CHH and CHG methylation coincides spatially and temporally with RDR6-dependent products derived from the central and 3' regions of the coding sequence, and requires the components of the RNA-directed DNA methylation (RdDM) pathway NRPE1, DRD1 and DRM2, but not CLSY1, NRPD1, RDR2 or DCL3, suggesting that RDR6-dependent products, namely long dsRNAs and/or siRNAs, trigger PTGS-dependent DNA methylation. Nevertheless, none of these RdDM components are required to establish S-PTGS or produce a systemic silencing signal. Moreover, preventing de novo DNA methylation in non-silenced transgenic tissues grafted onto homologous silenced tissues does not inhibit the triggering of PTGS. Overall, these data indicate that gene body DNA methylation is a consequence, not a cause, of PTGS, and rule out the hypothesis that a PTGS-associated DNA methylation signal is transmitted independent of a PTGS signal.
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Affiliation(s)
- Christelle Taochy
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Agnès Yu
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Nicolas Bouché
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Nathalie Bouteiller
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Taline Elmayan
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Uwe Dressel
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
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23
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Abstract
Transposable elements (TEs) are mobile DNA sequences that colonize genomes and threaten genome integrity. As a result, several mechanisms appear to have emerged during eukaryotic evolution to suppress TE activity. However, TEs are ubiquitous and account for a prominent fraction of most eukaryotic genomes. We argue that the evolutionary success of TEs cannot be explained solely by evasion from host control mechanisms. Rather, some TEs have evolved commensal and even mutualistic strategies that mitigate the cost of their propagation. These coevolutionary processes promote the emergence of complex cellular activities, which in turn pave the way for cooption of TE sequences for organismal function.
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Affiliation(s)
- Rachel L Cosby
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Ni-Chen Chang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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24
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Bayless AM, Zapotocny RW, Han S, Grunwald DJ, Amundson KK, Bent AF. The rhg1-a ( Rhg1 low-copy) nematode resistance source harbors a copia-family retrotransposon within the Rhg1-encoded α-SNAP gene. PLANT DIRECT 2019; 3:e00164. [PMID: 31468029 PMCID: PMC6712407 DOI: 10.1002/pld3.164] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/13/2019] [Accepted: 08/02/2019] [Indexed: 05/14/2023]
Abstract
Soybean growers widely use the Resistance to Heterodera glycines 1 (Rhg1) locus to reduce yield losses caused by soybean cyst nematode (SCN). Rhg1 is a tandemly repeated four gene block. Two classes of SCN resistance-conferring Rhg1 haplotypes are recognized: rhg1-a ("Peking-type," low-copy number, three or fewer Rhg1 repeats) and rhg1-b ("PI 88788-type," high-copy number, four or more Rhg1 repeats). The rhg1-a and rhg1-b haplotypes encode α-SNAP (alpha-Soluble NSF Attachment Protein) variants α-SNAP Rhg1 LC and α-SNAP Rhg1 HC, respectively, with differing atypical C-terminal domains, that contribute to SCN resistance. Here we report that rhg1-a soybean accessions harbor a copia retrotransposon within their Rhg1 Glyma.18G022500 (α-SNAP-encoding) gene. We termed this retrotransposon "RAC," for Rhg1 alpha-SNAP copia. Soybean carries multiple RAC-like retrotransposon sequences. The Rhg1 RAC insertion is in the Glyma.18G022500 genes of all true rhg1-a haplotypes we tested and was not detected in any examined rhg1-b or Rhg1WT (single-copy) soybeans. RAC is an intact element residing within intron 1, anti-sense to the rhg1-a α-SNAP open reading frame. RAC has intrinsic promoter activities, but overt impacts of RAC on transgenic α-SNAP Rhg1 LC mRNA and protein abundance were not detected. From the native rhg1-a RAC+ genomic context, elevated α-SNAP Rhg1 LC protein abundance was observed in syncytium cells, as was previously observed for α-SNAP Rhg1 HC (whose rhg1-b does not carry RAC). Using a SoySNP50K SNP corresponding with RAC presence, just ~42% of USDA accessions bearing previously identified rhg1-a SoySNP50K SNP signatures harbor the RAC insertion. Subsequent analysis of several of these putative rhg1-a accessions lacking RAC revealed that none encoded α-SNAPRhg1LC, and thus, they are not rhg1-a. rhg1-a haplotypes are of rising interest, with Rhg4, for combating SCN populations that exhibit increased virulence against the widely used rhg1-b resistance. The present study reveals another unexpected structural feature of many Rhg1 loci, and a selectable feature that is predictive of rhg1-a haplotypes.
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Affiliation(s)
- Adam M. Bayless
- Department of Plant PathologyUniversity of Wisconsin – MadisonMadisonWIUSA
| | - Ryan W. Zapotocny
- Department of Plant PathologyUniversity of Wisconsin – MadisonMadisonWIUSA
| | - Shaojie Han
- Department of Plant PathologyUniversity of Wisconsin – MadisonMadisonWIUSA
| | | | - Kaela K. Amundson
- Department of Plant PathologyUniversity of Wisconsin – MadisonMadisonWIUSA
| | - Andrew F. Bent
- Department of Plant PathologyUniversity of Wisconsin – MadisonMadisonWIUSA
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25
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Valencia JD, Girgis HZ. LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo. BMC Genomics 2019; 20:450. [PMID: 31159720 PMCID: PMC6547461 DOI: 10.1186/s12864-019-5796-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/14/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Long terminal repeat retrotransposons are the most abundant transposons in plants. They play important roles in alternative splicing, recombination, gene regulation, and defense mechanisms. Large-scale sequencing projects for plant genomes are currently underway. Software tools are important for annotating long terminal repeat retrotransposons in these newly available genomes. However, the available tools are not very sensitive to known elements and perform inconsistently on different genomes. Some are hard to install or obsolete. They may struggle to process large plant genomes. None can be executed in parallel out of the box and very few have features to support visual review of new elements. To overcome these limitations, we developed LtrDetector, which uses techniques inspired by signal-processing. RESULTS We compared LtrDetector to LTR_Finder and LTRharvest, the two most successful predecessor tools, on six plant genomes. For each organism, we constructed a ground truth data set based on queries from a consensus sequence database. According to this evaluation, LtrDetector was the most sensitive tool, achieving 16-23% improvement in sensitivity over LTRharvest and 21% improvement over LTR_Finder. All three tools had low false positive rates, with LtrDetector achieving 98.2% precision, in between its two competitors. Overall, LtrDetector provides the best compromise between high sensitivity and low false positive rate while requiring moderate time and utilizing memory available on personal computers. CONCLUSIONS LtrDetector uses a novel methodology revolving around k-mer distributions, which allows it to produce high-quality results using relatively lightweight procedures. It is easy to install and use. It is not species specific, performing well using its default parameters on genomes of varying size and repeat content. It is automatically configured for parallel execution and runs efficiently on an ordinary personal computer. It includes a k-mer scores visualization tool to facilitate manual review of the identified elements. These features make LtrDetector an attractive tool for future annotation projects involving long terminal repeat retrotransposons.
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Affiliation(s)
- Joseph D Valencia
- The Bioinformatics Toolsmith Laboratory, Tandy School of Computer Science, University of Tulsa, 800 South Tucker Drive, Tulsa, 74104, OK, USA
| | - Hani Z Girgis
- The Bioinformatics Toolsmith Laboratory, Tandy School of Computer Science, University of Tulsa, 800 South Tucker Drive, Tulsa, 74104, OK, USA.
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26
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Cambiagno DA, Nota F, Zavallo D, Rius S, Casati P, Asurmendi S, Alvarez ME. Immune receptor genes and pericentromeric transposons as targets of common epigenetic regulatory elements. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:1178-1190. [PMID: 30238536 DOI: 10.1111/tpj.14098] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/24/2018] [Accepted: 09/03/2018] [Indexed: 05/04/2023]
Abstract
Pattern recognition receptors (PRR) and nucleotide-binding leucine-rich repeat proteins (NLR) are major components of the plant immune system responsible for pathogen detection. To date, the transcriptional regulation of PRR/NLR genes is poorly understood. Some PRR/NLR genes are affected by epigenetic changes of neighboring transposable elements (TEs) (cis regulation). We analyzed whether these genes can also respond to changes in the epigenetic marks of distal pericentromeric TEs (trans regulation). We found that Arabidopsis tissues infected with Pseudomonas syringae pv. tomato (Pst) initially induced the expression of pericentromeric TEs, and then repressed it by RNA-directed DNA methylation (RdDM). The latter response was accompanied by the accumulation of small RNAs (sRNAs) mapping to the TEs. Curiously these sRNAs also mapped to distal PRR/NLR genes, which were controlled by RdDM but remained induced in the infected tissues. Then, we used non-infected mom1 (Morpheus' molecule 1) mutants that expressed pericentromeric TEs to test if they lose repression of PRR/NLR genes. mom1 plants activated several PRR/NLR genes that were unlinked to MOM1-targeted TEs, and showed enhanced resistance to Pst. Remarkably, the increased defenses of mom1 were abolished when MOM1/RdDM-mediated pericentromeric TEs silencing was re-established. Therefore, common sRNAs could control PRR/NLR genes and distal pericentromeric TEs and preferentially silence TEs when they are activated.
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Affiliation(s)
- Damián A Cambiagno
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
- Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Córdoba, Argentina
| | - Florencia Nota
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
- Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Córdoba, Argentina
| | - Diego Zavallo
- Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Argentina
| | - Sebastián Rius
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Rosario, Argentina
| | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Rosario, Argentina
| | - Sebastián Asurmendi
- Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Argentina
- CONICET, Buenos Aires, Argentina
| | - María E Alvarez
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
- Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Córdoba, Argentina
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27
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Kooke R, Morgado L, Becker F, van Eekelen H, Hazarika R, Zheng Q, de Vos RCH, Johannes F, Keurentjes JJB. Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map. Genome Res 2018; 29:96-106. [PMID: 30504416 PMCID: PMC6314165 DOI: 10.1101/gr.232371.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 11/27/2018] [Indexed: 11/24/2022]
Abstract
Identifying the sources of natural variation underlying metabolic differences between plants will enable a better understanding of plant metabolism and provide insights into the regulatory networks that govern plant growth and morphology. So far, however, the contribution of epigenetic variation to metabolic diversity has been largely ignored. In the present study, we utilized a panel of Arabidopsis thaliana epigenetic recombinant inbred lines (epiRILs) to assess the impact of epigenetic variation on the metabolic composition. Thirty epigenetic QTL (QTLepi) were detected, which partly overlap with QTLepi linked to growth and morphology. In an effort to identify causal candidate genes in the QTLepi regions and their putative trans-targets, we performed in silico small RNA and qPCR analyses. Differentially expressed genes were further studied by phenotypic and metabolic analyses of knockout mutants. Three genes were detected that recapitulated the detected QTLepi effects, providing evidence for epigenetic regulation in cis and in trans. These results indicate that epigenetic mechanisms impact metabolic diversity, possibly via small RNAs, and thus aid in further disentangling the complex epigenotype-phenotype map.
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Affiliation(s)
- Rik Kooke
- Laboratory of Genetics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands.,Laboratory of Biometris, Wageningen University and Research, 6708 PB Wageningen, The Netherlands.,Centre for Biosystems Genomics, 6708 PB Wageningen, The Netherlands
| | - Lionel Morgado
- Groningen Bioinformatics Centre, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Frank Becker
- Laboratory of Genetics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Henriëtte van Eekelen
- Business Unit Bioscience, Wageningen Plant Research, 6708 PB Wageningen, The Netherlands
| | - Rashmi Hazarika
- Institute for Advanced Study, Technical University of Munich, 85748 Garching, Germany
| | - Qunfeng Zheng
- Business Unit Bioscience, Wageningen Plant Research, 6708 PB Wageningen, The Netherlands.,Tea Research Institute, Chinese Academy of Agricultural Sciences, 310008 Hangzhou, P.R. China
| | - Ric C H de Vos
- Centre for Biosystems Genomics, 6708 PB Wageningen, The Netherlands.,Business Unit Bioscience, Wageningen Plant Research, 6708 PB Wageningen, The Netherlands.,Netherlands Metabolomics Centre, 2333 CC Leiden, The Netherlands
| | - Frank Johannes
- Institute for Advanced Study, Technical University of Munich, 85748 Garching, Germany.,Population Epigenetics and Epigenomics, Department of Plant Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands.,Centre for Biosystems Genomics, 6708 PB Wageningen, The Netherlands
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28
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Peng T, Qiao M, Liu H, Teotia S, Zhang Z, Zhao Y, Wang B, Zhao D, Shi L, Zhang C, Le B, Rogers K, Gunasekara C, Duan H, Gu Y, Tian L, Nie J, Qi J, Meng F, Huang L, Chen Q, Wang Z, Tang J, Tang X, Lan T, Chen X, Wei H, Zhao Q, Tang G. A Resource for Inactivation of MicroRNAs Using Short Tandem Target Mimic Technology in Model and Crop Plants. MOLECULAR PLANT 2018; 11:1400-1417. [PMID: 30243763 DOI: 10.1016/j.molp.2018.09.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 08/01/2018] [Accepted: 09/06/2018] [Indexed: 05/04/2023]
Abstract
microRNAs (miRNAs) are endogenous small non-coding RNAs that bind to mRNAs and target them for cleavage and/or translational repression, leading to gene silencing. We previously developed short tandem target mimic (STTM) technology to deactivate endogenous miRNAs in Arabidopsis. Here, we created hundreds of STTMs that target both conserved and species-specific miRNAs in Arabidopsis, tomato, rice, and maize, providing a resource for the functional interrogation of miRNAs. We not only revealed the functions of several miRNAs in plant development, but also demonstrated that tissue-specific inactivation of a few miRNAs in rice leads to an increase in grain size without adversely affecting overall plant growth and development. RNA-seq and small RNA-seq analyses of STTM156/157 and STTM165/166 transgenic plants revealed the roles of these miRNAs in plant hormone biosynthesis and activation, secondary metabolism, and ion-channel activity-associated electrophysiology, demonstrating that STTM technology is an effective approach for studying miRNA functions. To facilitate the study and application of STTM transgenic plants and to provide a useful platform for storing and sharing of information about miRNA-regulated gene networks, we have established an online Genome Browser (https://blossom.ffr.mtu.edu/designindex2.php) to display the transcriptomic and miRNAomic changes in STTM-induced miRNA knockdown plants.
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Affiliation(s)
- Ting Peng
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Mengmeng Qiao
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Haiping Liu
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Sachin Teotia
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Zhanhui Zhang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Yafan Zhao
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China
| | - Bobo Wang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China
| | - Dongjie Zhao
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Lina Shi
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Cui Zhang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Brandon Le
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Kestrel Rogers
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Chathura Gunasekara
- School of Forest Resources and Environmental Science, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Haitang Duan
- Department of Computer Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Yiyou Gu
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Lei Tian
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Jinfu Nie
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, China; Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jian Qi
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, China
| | - Fanrong Meng
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Lan Huang
- College of Information and Electrical Engineering, China Agricultural University, Beijing 100083, China
| | - Qinghui Chen
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA; Department of Kinesiology and Integrative Physiology, Life Science and Technology Instituted, Michigan Technological University, Houghton, MI 49931, USA
| | - Zhenlin Wang
- Department of Computer Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Jinshan Tang
- School of Technology, Michigan Technological University, Houghton, MI 49931, USA
| | - Xiaoqing Tang
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Ting Lan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA; Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China.
| | - Hairong Wei
- School of Forest Resources and Environmental Science, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, P.R. China.
| | - Quanzhi Zhao
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China.
| | - Guiliang Tang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA; Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China; Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China.
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29
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Shaping Plant Adaptability, Genome Structure and Gene Expression through Transposable Element Epigenetic Control: Focus on Methylation. AGRONOMY-BASEL 2018. [DOI: 10.3390/agronomy8090180] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In plants, transposable elements (TEs) represent a large fraction of the genome, with potential to alter gene expression and produce genomic rearrangements. Epigenetic control of TEs is often used to stop unrestricted movement of TEs that would result in detrimental effects due to insertion in essential genes. The current review focuses on the effects of methylation on TEs and their genomic context, and how this type of epigenetic control affects plant adaptability when plants are faced with different stresses and changes. TEs mobilize in response to stress elicitors, including biotic and abiotic cues, but also developmental transitions and ‘genome shock’ events like polyploidization. These events transitionally lift TE repression, allowing TEs to move to new genomic locations. When TEs fall close to genes, silencing through methylation can spread to nearby genes, resulting in lower gene expression. The presence of TEs in gene promoter regions can also confer stress inducibility modulated through alternative methylation and demethylation of the TE. Bursts of transposition triggered by events of genomic shock can increase genome size and account for differences seen during polyploidization or species divergence. Finally, TEs have evolved several mechanisms to suppress their own repression, including the use of microRNAs to control genes that promote methylation. The interplay between silencing, transient TE activation, and purifying selection allows the genome to use TEs as a reservoir of potential beneficial modifications but also keeps TEs under control to stop uncontrolled detrimental transposition.
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30
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Montavon T, Kwon Y, Zimmermann A, Hammann P, Vincent T, Cognat V, Bergdoll M, Michel F, Dunoyer P. Characterization of DCL4 missense alleles provides insights into its ability to process distinct classes of dsRNA substrates. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:204-218. [PMID: 29682831 DOI: 10.1111/tpj.13941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/10/2018] [Accepted: 04/05/2018] [Indexed: 05/10/2023]
Abstract
In the model plant Arabidopsis thaliana, four Dicer-like proteins (DCL1-4) mediate the production of various classes of small RNAs (sRNAs). Among these four proteins, DCL4 is by far the most versatile RNaseIII-like enzyme, and previously identified dcl4 missense alleles were shown to uncouple the production of the various classes of DCL4-dependent sRNAs. Yet little is known about the molecular mechanism behind this uncoupling. Here, by studying the subcellular localization, interactome and binding to the sRNA precursors of three distinct dcl4 missense alleles, we simultaneously highlight the absolute requirement of a specific residue in the helicase domain for the efficient production of all DCL4-dependent sRNAs, and identify, within the PAZ domain, an important determinant of DCL4 versatility that is mandatory for the efficient processing of intramolecular fold-back double-stranded RNA (dsRNA) precursors, but that is dispensable for the production of small interfering RNAs (siRNAs) from RDR-dependent dsRNA susbtrates. This study not only provides insights into the DCL4 mode of action, but also delineates interesting tools to further study the complexity of RNA silencing pathways in plants, and possibly other organisms.
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Affiliation(s)
- Thomas Montavon
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, F-67000, Strasbourg, France
| | - Yerim Kwon
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, F-67000, Strasbourg, France
| | - Aude Zimmermann
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, F-67000, Strasbourg, France
| | - Philippe Hammann
- Institut de Biologie Moléculaire et Cellulaire du CNRS, FRC1589, Plateforme Protéomique Strasbourg - Esplanade, Université de Strasbourg, F-67000, Strasbourg, France
| | - Timothée Vincent
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, F-67000, Strasbourg, France
| | - Valérie Cognat
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, F-67000, Strasbourg, France
| | - Marc Bergdoll
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, F-67000, Strasbourg, France
| | - Fabrice Michel
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, F-67000, Strasbourg, France
| | - Patrice Dunoyer
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, F-67000, Strasbourg, France
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31
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Seifert F, Thiemann A, Schrag TA, Rybka D, Melchinger AE, Frisch M, Scholten S. Small RNA-based prediction of hybrid performance in maize. BMC Genomics 2018; 19:371. [PMID: 29783940 PMCID: PMC5963143 DOI: 10.1186/s12864-018-4708-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 04/22/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Small RNA (sRNA) sequences are known to have a broad impact on gene regulation by various mechanisms. Their performance for the prediction of hybrid traits has not yet been analyzed. Our objective was to analyze the relation of parental sRNA expression with the performance of their hybrids, to develop a sRNA-based prediction approach, and to compare it to more common SNP and mRNA transcript based predictions using a factorial mating scheme of a maize hybrid breeding program. RESULTS Correlation of genomic differences and messenger RNA (mRNA) or sRNA expression differences between parental lines with hybrid performance of their hybrids revealed that sRNAs showed an inverse relationship in contrast to the other two data types. We associated differences for SNPs, mRNA and sRNA expression between parental inbred lines with the performance of their hybrid combinations and developed two prediction approaches using distance measures based on associated markers. Cross-validations revealed parental differences in sRNA expression to be strong predictors for hybrid performance for grain yield in maize, comparable to genomic and mRNA data. The integration of both positively and negatively associated markers in the prediction approaches enhanced the prediction accurary. The associated sRNAs belong predominantly to the canonical size classes of 22- and 24-nt that show specific genomic mapping characteristics. CONCLUSION Expression profiles of sRNA are a promising alternative to SNPs or mRNA expression profiles for hybrid prediction, especially for plant species without reference genome or transcriptome information. The characteristics of the sRNAs we identified suggest that association studies based on breeding populations facilitate the identification of sRNAs involved in hybrid performance.
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Affiliation(s)
- Felix Seifert
- Developmental Biology, Biocenter Klein Flottbek, University of Hamburg, 22609 Hamburg, Germany
| | - Alexander Thiemann
- Developmental Biology, Biocenter Klein Flottbek, University of Hamburg, 22609 Hamburg, Germany
| | - Tobias A. Schrag
- Institute for Plant Breeding, Seed Science and Population Genetics, Quantitative Genetics and Genomics of Crops, University of Hohenheim, Fruwirthstrasse 21, 70599 Stuttgart, Germany
| | - Dominika Rybka
- Developmental Biology, Biocenter Klein Flottbek, University of Hamburg, 22609 Hamburg, Germany
| | - Albrecht E. Melchinger
- Institute for Plant Breeding, Seed Science and Population Genetics, Quantitative Genetics and Genomics of Crops, University of Hohenheim, Fruwirthstrasse 21, 70599 Stuttgart, Germany
| | - Matthias Frisch
- Institute of Agronomy and Plant Breeding II, Justus Liebig University, 35392 Giessen, Germany
| | - Stefan Scholten
- Developmental Biology, Biocenter Klein Flottbek, University of Hamburg, 22609 Hamburg, Germany
- Institute for Plant Breeding, Seed Science and Population Genetics, Quantitative Genetics and Genomics of Crops, University of Hohenheim, Fruwirthstrasse 21, 70599 Stuttgart, Germany
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32
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Towards annotating the plant epigenome: the Arabidopsis thaliana small RNA locus map. Sci Rep 2018; 8:6338. [PMID: 29679055 PMCID: PMC5910406 DOI: 10.1038/s41598-018-24515-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/05/2018] [Indexed: 01/18/2023] Open
Abstract
Based on 98 public and internal small RNA high throughput sequencing libraries, we mapped small RNAs to the genome of the model organism Arabidopsis thaliana and defined loci based on their expression using an empirical Bayesian approach. The resulting loci were subsequently classified based on their genetic and epigenetic context as well as their expression properties. We present the results of this classification, which broadly conforms to previously reported divisions between transcriptional and post-transcriptional gene silencing small RNAs, and to PolIV and PolV dependencies. However, we are able to demonstrate the existence of further subdivisions in the small RNA population of functional significance. Moreover, we present a framework for similar analyses of small RNA populations in all species.
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33
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Morgado L, Preite V, Oplaat C, Anava S, Ferreira de Carvalho J, Rechavi O, Johannes F, Verhoeven KJF. Small RNAs Reflect Grandparental Environments in Apomictic Dandelion. Mol Biol Evol 2018; 34:2035-2040. [PMID: 28472380 PMCID: PMC5850771 DOI: 10.1093/molbev/msx150] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Plants can show long-term effects of environmental stresses and in some cases a stress “memory” has been reported to persist across generations, potentially mediated by epigenetic mechanisms. However, few documented cases exist of transgenerational effects that persist for multiple generations and it remains unclear if or how epigenetic mechanisms are involved. Here, we show that the composition of small regulatory RNAs in apomictic dandelion lineages reveals a footprint of drought stress and salicylic acid treatment experienced two generations ago. Overall proportions of 21 and 24 nt RNA pools were shifted due to grandparental treatments. While individual genes did not show strong up- or downregulation of associated sRNAs, the subset of genes that showed the strongest shifts in sRNA abundance was significantly enriched for several GO terms including stress-specific functions. This suggests that a stress-induced signal was transmitted across multiple unexposed generations leading to persistent changes in epigenetic gene regulation.
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Affiliation(s)
- Lionel Morgado
- Groningen Bioinformatics Centre, University of Groningen, AG Groningen, The Netherlands
| | - Veronica Preite
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Carla Oplaat
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Sarit Anava
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Julie Ferreira de Carvalho
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Frank Johannes
- Population Epigenetics and Epigenomics, Technical University of Munich, Freising, Germany.,Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Koen J F Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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34
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Seifert F, Thiemann A, Grant-Downton R, Edelmann S, Rybka D, Schrag TA, Frisch M, Dickinson HG, Melchinger AE, Scholten S. Parental Expression Variation of Small RNAs Is Negatively Correlated with Grain Yield Heterosis in a Maize Breeding Population. FRONTIERS IN PLANT SCIENCE 2018; 9:13. [PMID: 29441076 PMCID: PMC5797689 DOI: 10.3389/fpls.2018.00013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 01/04/2018] [Indexed: 05/26/2023]
Abstract
Heterosis refers to a quantitative phenomenon in which F1 hybrid trait values exceed the mean of the parental values in a positive direction. Generally, it is dependent on a high degree of heterozygosity, which is maintained in hybrid breeding by developing parental lines in separate, genetically distinct heterotic groups. The mobility of small RNAs (sRNAs) that mediate epigenetic regulation of gene expression renders them promising candidates for modulating the action of combined diverse genomes in trans-and evidence already indicates their contribution to transgressive phenotypes. By sequencing small RNA libraries of a panel of 21 maize parental inbred lines we found a low overlap of 35% between the sRNA populations from both distinct heterotic groups. Surprisingly, in contrast to genetic or gene expression variation, parental sRNA expression variation is negatively correlated with grain yield (GY) heterosis. Among 0.595 million expressed sRNAs, we identified 9,767, predominantly 22- and 24-nt long sRNAs, which showed an association of their differential expression between parental lines and GY heterosis of the respective hybrids. Of these sRNAs, 3,485 or 6,282 showed an association with high or low GY heterosis, respectively, thus the low heterosis associated group prevailing at 64%. The heterosis associated sRNAs map more frequently to genes that show differential expression between parental lines than reference sets. Together these findings suggest that trans-chromosomal actions of sRNAs in hybrids might add up to a negative contribution in heterosis formation, mediated by unfavorable gene expression regulation. We further revealed an exclusive accumulation of 22-nt sRNAs that are associated with low GY heterosis in pericentromeric genomic regions. That recombinational suppression led to this enrichment is indicated by its close correlation with low recombination rates. The existence of this enrichment, which we hypothesize resulted from the separated breeding of inbred lines within heterotic groups, may have implications for hybrid breeding strategies addressing the recombinational constraints characteristic of complex crop genomes.
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Affiliation(s)
- Felix Seifert
- Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | | | | | - Susanne Edelmann
- Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Dominika Rybka
- Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Tobias A. Schrag
- Institute for Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Matthias Frisch
- Institute of Agronomy and Plant Breeding II, Justus-Liebig University, Giessen, Germany
| | - Hugh G. Dickinson
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Albrecht E. Melchinger
- Institute for Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Stefan Scholten
- Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
- Institute for Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
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35
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Cho J. Transposon-Derived Non-coding RNAs and Their Function in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:600. [PMID: 29774045 PMCID: PMC5943564 DOI: 10.3389/fpls.2018.00600] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/16/2018] [Indexed: 05/03/2023]
Abstract
Transposable elements (TEs) are often regarded as harmful genomic factors and indeed they are strongly suppressed by the epigenetic silencing mechanisms. On the other hand, the mobilization of TEs brings about variability of genome and transcriptome which are essential in the survival and evolution of the host species. The vast majority of such controlling TEs influence the neighboring genes in cis by either promoting or repressing the transcriptional activities. Although TEs are highly repetitive in the genomes and transcribed in specific stress conditions or developmental stages, the trans-acting regulatory roles of TE-derived RNAs have been rarely studied. It was only recently that TEs were investigated for their regulatory roles as a form of RNA. Particularly in plants, TEs are ample source of small RNAs such as small interfering (si) RNAs and micro (mi) RNAs. Those TE-derived small RNAs have potentials to affect non-TE transcripts by sequence complementarity, thereby generating novel gene regulatory networks including stress resistance and hybridization barrier. Apart from the small RNAs, a number of long non-coding RNAs (lncRNAs) are originated from TEs in plants. For example, a retrotransposon-derived lncRNA expressed in rice root acts as a decoy RNA or miRNA target mimic which negatively controls miRNA171. The post-transcriptional suppression of miRNA171 in roots ensures the stabilization of the target transcripts encoding SCARECROW-LIKE transcription factors, the key regulators of root development. In this review article, the recent discoveries of the regulatory roles of TE-derived RNAs in plants will be highlighted.
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36
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Huang SSC, Ecker JR. Piecing together cis-regulatory networks: insights from epigenomics studies in plants. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 10:e1411. [PMID: 29194997 DOI: 10.1002/wsbm.1411] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 12/20/2022]
Abstract
5-Methylcytosine, a chemical modification of DNA, is a covalent modification found in the genomes of both plants and animals. Epigenetic inheritance of phenotypes mediated by DNA methylation is well established in plants. Most of the known mechanisms of establishing, maintaining and modifying DNA methylation have been worked out in the reference plant Arabidopsis thaliana. Major functions of DNA methylation in plants include regulation of gene expression and silencing of transposable elements (TEs) and repetitive sequences, both of which have parallels in mammalian biology, involve interaction with the transcriptional machinery, and may have profound effects on the regulatory networks in the cell. Methylome and transcriptome dynamics have been investigated in development and environmental responses in Arabidopsis and agriculturally and ecologically important plants, revealing the interdependent relationship among genomic context, methylation patterns, and expression of TE and protein coding genes. Analyses of methylome variation among plant natural populations and species have begun to quantify the extent of genetic control of methylome variation vs. true epimutation, and model the evolutionary forces driving methylome evolution in both short and long time scales. The ability of DNA methylation to positively or negatively modulate binding affinity of transcription factors (TFs) provides a natural link from genome sequence and methylation changes to transcription. Technologies that allow systematic determination of methylation sensitivities of TFs, in native genomic and methylation context without confounding factors such as histone modifications, will provide baseline datasets for building cell-type- and individual-specific regulatory networks that underlie the establishment and inheritance of complex traits. This article is categorized under: Laboratory Methods and Technologies > Genetic/Genomic Methods Biological Mechanisms > Regulatory Biology.
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Affiliation(s)
- Shao-Shan C Huang
- Genomic Analysis Laboratory and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA
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37
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Montavon T, Kwon Y, Zimmermann A, Hammann P, Vincent T, Cognat V, Michel F, Dunoyer P. A specific dsRNA-binding protein complex selectively sequesters endogenous inverted-repeat siRNA precursors and inhibits their processing. Nucleic Acids Res 2017; 45:1330-1344. [PMID: 28180322 PMCID: PMC5388410 DOI: 10.1093/nar/gkw1264] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 12/01/2016] [Accepted: 12/06/2016] [Indexed: 01/03/2023] Open
Abstract
In plants, several dsRNA-binding proteins (DRBs) have been shown to play important roles in various RNA silencing pathways, mostly by promoting the efficiency and/or accuracy of Dicer-like proteins (DCL)-mediated small RNA production. Among the DRBs encoded by the Arabidopsis genome, we recently identified DRB7.2 whose function in RNA silencing was unknown. Here, we show that DRB7.2 is specifically involved in siRNA production from endogenous inverted-repeat (endoIR) loci. This function requires its interacting partner DRB4, the main cofactor of DCL4 and is achieved through specific sequestration of endoIR dsRNA precursors, thereby repressing their access and processing by the siRNA-generating DCLs. The present study also provides multiple lines of evidence showing that DRB4 is partitioned into, at least, two distinct cellular pools fulfilling different functions, through mutually exclusive binding with either DCL4 or DRB7.2. Collectively, these findings revealed that plants have evolved a specific DRB complex that modulates selectively the production of endoIR-siRNAs. The existence of such a complex and its implication regarding the still elusive biological function of plant endoIR-siRNA will be discussed.
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Affiliation(s)
- Thomas Montavon
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000 Strasbourg, France
| | - Yerim Kwon
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000 Strasbourg, France
| | - Aude Zimmermann
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000 Strasbourg, France
| | - Philippe Hammann
- Université de Strasbourg, CNRS, IBMC FRC1589, Plateforme Protéomique Strasbourg - Esplanade, F-67000 Strasbourg, France
| | - Timothée Vincent
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000 Strasbourg, France
| | - Valérie Cognat
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000 Strasbourg, France
| | - Fabrice Michel
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000 Strasbourg, France
| | - Patrice Dunoyer
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000 Strasbourg, France
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38
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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.
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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
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39
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Cho J, Paszkowski J. Regulation of rice root development by a retrotransposon acting as a microRNA sponge. eLife 2017; 6:e30038. [PMID: 28847366 PMCID: PMC5599236 DOI: 10.7554/elife.30038] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/21/2017] [Indexed: 12/19/2022] Open
Abstract
It is well documented that transposable elements (TEs) can regulate the expression of neighbouring genes. However, their ability to act in trans and influence ectopic loci has been reported rarely. We searched in rice transcriptomes for tissue-specific expression of TEs and found them to be regulated developmentally. They often shared sequence homology with co-expressed genes and contained potential microRNA-binding sites, which suggested possible contributions to gene regulation. In fact, we have identified a retrotransposon that is highly transcribed in roots and whose spliced transcript constitutes a target mimic for miR171. miR171 destabilizes mRNAs encoding the root-specific family of SCARECROW-Like transcription factors. We demonstrate that retrotransposon-derived transcripts act as decoys for miR171, triggering its degradation and thus results in the root-specific accumulation of SCARECROW-Like mRNAs. Such transposon-mediated post-transcriptional control of miR171 levels is conserved in diverse rice species.
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Affiliation(s)
- Jungnam Cho
- The Sainsbury Laboratory, University of CambridgeCambridgeUnited Kingdom
| | - Jerzy Paszkowski
- The Sainsbury Laboratory, University of CambridgeCambridgeUnited Kingdom
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40
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Cho J, Paszkowski J. Regulation of rice root development by a retrotransposon acting as a microRNA sponge. eLife 2017; 6:30038. [PMID: 28847366 DOI: 10.7554/elife.30038.054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/21/2017] [Indexed: 05/23/2023] Open
Abstract
It is well documented that transposable elements (TEs) can regulate the expression of neighbouring genes. However, their ability to act in trans and influence ectopic loci has been reported rarely. We searched in rice transcriptomes for tissue-specific expression of TEs and found them to be regulated developmentally. They often shared sequence homology with co-expressed genes and contained potential microRNA-binding sites, which suggested possible contributions to gene regulation. In fact, we have identified a retrotransposon that is highly transcribed in roots and whose spliced transcript constitutes a target mimic for miR171. miR171 destabilizes mRNAs encoding the root-specific family of SCARECROW-Like transcription factors. We demonstrate that retrotransposon-derived transcripts act as decoys for miR171, triggering its degradation and thus results in the root-specific accumulation of SCARECROW-Like mRNAs. Such transposon-mediated post-transcriptional control of miR171 levels is conserved in diverse rice species.
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Affiliation(s)
- Jungnam Cho
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Jerzy Paszkowski
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
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41
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Abstract
LTR retrotransposons are the most abundant group of transposable elements (TEs) in plants. These elements can fall inside or close to genes, and therefore influence their expression and evolution. This review aims to examine how LTR retrotransposons, especially Ty1-copia elements, mediate gene regulation and evolution. Various stimuli, including polyploidization and biotic and abiotic elicitors, result in the transcription and movement of these retrotransposons, and can facilitate adaptation. The presence of cis-regulatory motifs in the LTRs are central to their stress-mediated responses and are shared with host stress-responsive genes, showing a complex evolutionary history in which TEs provide new regulatory units to genes. The presence of retrotransposon remnants in genes that are necessary for normal gene function, demonstrates the importance of exaptation and co-option, and is also a consequence of the abundance of these elements in plant genomes. Furthermore, insertions of LTR retrotransposons in and around genes provide potential for alternative splicing, epigenetic control, transduction, duplication and recombination. These characteristics can become an active part of the evolution of gene families as in the case of resistance genes (R-genes). The character of TEs as exclusively selfish is now being re-evaluated. Since genome-wide reprogramming via TEs is a long evolutionary process, the changes we can examine are case-specific and their fitness advantage may not be evident until TE-derived motifs and domains have been completely co-opted and fixed. Nevertheless, the presence of LTR retrotransposons inside genes and as part of gene promoter regions is consistent with their roles as engines of plant genome evolution.
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42
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Bousios A, Gaut BS, Darzentas N. Considerations and complications of mapping small RNA high-throughput data to transposable elements. Mob DNA 2017; 8:3. [PMID: 28228849 PMCID: PMC5311732 DOI: 10.1186/s13100-017-0086-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 01/31/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND High-throughput sequencing (HTS) has revolutionized the way in which epigenetic research is conducted. When coupled with fully-sequenced genomes, millions of small RNA (sRNA) reads are mapped to regions of interest and the results scrutinized for clues about epigenetic mechanisms. However, this approach requires careful consideration in regards to experimental design, especially when one investigates repetitive parts of genomes such as transposable elements (TEs), or when such genomes are large, as is often the case in plants. RESULTS Here, in an attempt to shed light on complications of mapping sRNAs to TEs, we focus on the 2,300 Mb maize genome, 85% of which is derived from TEs, and scrutinize methodological strategies that are commonly employed in TE studies. These include choices for the reference dataset, the normalization of multiply mapping sRNAs, and the selection among sRNA metrics. We further examine how these choices influence the relationship between sRNAs and the critical feature of TE age, and contrast their effect on low copy genomic regions and other popular HTS data. CONCLUSIONS Based on our analyses, we share a series of take-home messages that may help with the design, implementation, and interpretation of high-throughput TE epigenetic studies specifically, but our conclusions may also apply to any work that involves analysis of HTS data.
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Affiliation(s)
- Alexandros Bousios
- School of Life Sciences, University of Sussex, Brighton, East Sussex BN1 9RH UK
| | - Brandon S. Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697 USA
| | - Nikos Darzentas
- Central European Institute of Technology, Masaryk University, Brno, 62500 Czech Republic
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43
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Abstract
A significant part of eukaryotic genomes is formed by transposable elements (TEs) containing not only genes but also regulatory sequences. Some of the regulatory sequences located within TEs can form secondary structures like hairpins or three-stranded (triplex DNA) and four-stranded (quadruplex DNA) conformations. This review focuses on recent evidence showing that G-quadruplex-forming sequences in particular are often present in specific parts of TEs in plants and humans. We discuss the potential role of these structures in the TE life cycle as well as the impact of G-quadruplexes on replication, transcription, translation, chromatin status, and recombination. The aim of this review is to emphasize that TEs may serve as vehicles for the genomic spread of G-quadruplexes. These non-canonical DNA structures and their conformational switches may constitute another regulatory system that, together with small and long non-coding RNA molecules and proteins, contribute to the complex cellular network resulting in the large diversity of eukaryotes.
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44
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Hirsch CD, Springer NM. Transposable element influences on gene expression in plants. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:157-165. [PMID: 27235540 DOI: 10.1016/j.bbagrm.2016.05.010] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 01/29/2023]
Abstract
Transposable elements (TEs) comprise a major portion of many plant genomes and bursts of TE movements cause novel genomic variation within species. In order to maintain proper gene function, plant genomes have evolved a variety of mechanisms to tolerate the presence of TEs within or near genes. Here, we review our understanding of the interactions between TEs and gene expression in plants by assessing three ways that transposons can influence gene expression. First, there is growing evidence that TE insertions within introns or untranslated regions of genes are often tolerated and have minimal impact on expression level or splicing. However, there are examples in which TE insertions within genes can result in aberrant or novel transcripts. Second, TEs can provide novel alternative promoters, which can lead to new expression patterns or original coding potential of an alternate transcript. Third, TE insertions near genes can influence regulation of gene expression through a variety of mechanisms. For example, TEs may provide novel cis-acting regulatory sites behaving as enhancers or insert within existing enhancers to influence transcript production. Alternatively, TEs may change chromatin modifications in regions near genes, which in turn can influence gene expression levels. Together, the interactions of genes and TEs provide abundant evidence for the role of TEs in changing basic functions within plant genomes beyond acting as latent genomic elements or as simple insertional mutagens. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Nathan M Springer
- Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA.
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45
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Clavel M, Pélissier T, Montavon T, Tschopp MA, Pouch-Pélissier MN, Descombin J, Jean V, Dunoyer P, Bousquet-Antonelli C, Deragon JM. Evolutionary history of double-stranded RNA binding proteins in plants: identification of new cofactors involved in easiRNA biogenesis. PLANT MOLECULAR BIOLOGY 2016; 91:131-47. [PMID: 26858002 DOI: 10.1007/s11103-016-0448-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 02/03/2016] [Indexed: 05/27/2023]
Abstract
In this work, we retrace the evolutionary history of plant double-stranded RNA binding proteins (DRBs), a group of non-catalytic factors containing one or more double-stranded RNA binding motif (dsRBM) that play important roles in small RNA biogenesis and functions. Using a phylogenetic approach, we show that multiple dsRBM DRBs are systematically composed of two different types of dsRBMs evolving under different constraints and likely fulfilling complementary functions. In vascular plants, four distinct clades of multiple dsRBM DRBs are always present with the exception of Brassicaceae species, that do not possess member of the newly identified clade we named DRB6. We also identified a second new and highly conserved DRB family (we named DRB7) whose members possess a single dsRBM that shows concerted evolution with the most C-terminal dsRBM domain of the Dicer-like 4 (DCL4) proteins. Using a BiFC approach, we observed that Arabidopsis thaliana DRB7.2 (AtDRB7.2) can directly interact with AtDRB4 but not with AtDCL4 and we provide evidence that both AtDRB7.2 and AtDRB4 participate in the epigenetically activated siRNAs pathway.
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Affiliation(s)
- Marion Clavel
- UMR5096 LGDP, Université de Perpignan Via Domitia, 58 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Thierry Pélissier
- UMR 6293 CNRS - INSERM U1103 - GreD, Clermont Université, 24 avenue des Landais, B.P. 80026, 63171, Aubière Cedex, France
| | - Thomas Montavon
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, Strasbourg Cedex, France
| | - Marie-Aude Tschopp
- Department of Biology LFW D17/D18, ETH Zürich, Universitätsstrasse 2, 8092, Zurich, Switzerland
| | - Marie-Noëlle Pouch-Pélissier
- UMR 6293 CNRS - INSERM U1103 - GreD, Clermont Université, 24 avenue des Landais, B.P. 80026, 63171, Aubière Cedex, France
| | - Julie Descombin
- UMR5096 LGDP, Université de Perpignan Via Domitia, 58 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Viviane Jean
- UMR5096 LGDP, Université de Perpignan Via Domitia, 58 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Patrice Dunoyer
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, Strasbourg Cedex, France
| | - Cécile Bousquet-Antonelli
- UMR5096 LGDP, Université de Perpignan Via Domitia, 58 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Jean-Marc Deragon
- UMR5096 LGDP, Université de Perpignan Via Domitia, 58 Avenue Paul Alduy, 66860, Perpignan Cedex, France.
- CNRS UMR5096 LGDP, Perpignan Cedex, France.
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46
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Lunardon A, Forestan C, Farinati S, Axtell MJ, Varotto S. Genome-Wide Characterization of Maize Small RNA Loci and Their Regulation in the required to maintain repression6-1 (rmr6-1) Mutant and Long-Term Abiotic Stresses. PLANT PHYSIOLOGY 2016; 170:1535-48. [PMID: 26747286 PMCID: PMC4775107 DOI: 10.1104/pp.15.01205] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 01/04/2016] [Indexed: 05/03/2023]
Abstract
Endogenous small RNAs (sRNAs) contribute to gene regulation and genome homeostasis, but their activities and functions are incompletely known. The maize genome has a high number of transposable elements (TEs; almost 85%), some of which spawn abundant sRNAs. We performed sRNA and total RNA sequencing from control and abiotically stressed B73 wild-type plants and rmr6-1 mutants. RMR6 encodes the largest subunit of the RNA polymerase IV complex and is responsible for accumulation of most 24-nucleotide (nt) small interfering RNAs (siRNAs). We identified novel MIRNA loci and verified miR399 target conservation in maize. RMR6-dependent 23-24 nt siRNA loci were specifically enriched in the upstream region of the most highly expressed genes. Most genes misregulated in rmr6-1 did not show a significant correlation with loss of flanking siRNAs, but we identified one gene supporting existing models of direct gene regulation by TE-derived siRNAs. Long-term drought correlated with changes of miRNA and sRNA accumulation, in particular inducing down-regulation of a set of sRNA loci in the wild-typeleaf.
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Affiliation(s)
- Alice Lunardon
- Department of Agronomy, Animals, Food, Natural Resources and Environment, University of Padova, Agripolis Viale dell'Università 16, 35020 Legnaro PD Italy (A.L., C.F., S.F., S.V.); andDepartment of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802 (A.L., M.J.A.)
| | - Cristian Forestan
- Department of Agronomy, Animals, Food, Natural Resources and Environment, University of Padova, Agripolis Viale dell'Università 16, 35020 Legnaro PD Italy (A.L., C.F., S.F., S.V.); andDepartment of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802 (A.L., M.J.A.)
| | - Silvia Farinati
- Department of Agronomy, Animals, Food, Natural Resources and Environment, University of Padova, Agripolis Viale dell'Università 16, 35020 Legnaro PD Italy (A.L., C.F., S.F., S.V.); andDepartment of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802 (A.L., M.J.A.)
| | - Michael J Axtell
- Department of Agronomy, Animals, Food, Natural Resources and Environment, University of Padova, Agripolis Viale dell'Università 16, 35020 Legnaro PD Italy (A.L., C.F., S.F., S.V.); andDepartment of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802 (A.L., M.J.A.)
| | - Serena Varotto
- Department of Agronomy, Animals, Food, Natural Resources and Environment, University of Padova, Agripolis Viale dell'Università 16, 35020 Legnaro PD Italy (A.L., C.F., S.F., S.V.); andDepartment of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802 (A.L., M.J.A.)
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47
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Springer NM, Lisch D, Li Q. Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes. THE PLANT CELL 2016; 28:314-25. [PMID: 26869701 PMCID: PMC4790878 DOI: 10.1105/tpc.15.00911] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/10/2016] [Indexed: 05/02/2023]
Abstract
Flowering plants have strikingly distinct genomes, although they contain a similar suite of expressed genes. The diversity of genome structures and organization is largely due to variation in transposable elements (TEs) and whole-genome duplication (WGD) events. We review evidence that chromatin modifications and epigenetic regulation are intimately associated with TEs and likely play a role in mediating the effects of WGDs. We hypothesize that the current structure of a genome is the result of various TE bursts and WGDs and it is likely that the silencing mechanisms and the chromatin structure of a genome have been shaped by these events. This suggests that the specific mechanisms targeting chromatin modifications and epigenomic patterns may vary among different species. Many crop species have likely evolved chromatin-based mechanisms to tolerate silenced TEs near actively expressed genes. These interactions of heterochromatin and euchromatin are likely to have important roles in modulating gene expression and variability within species.
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Affiliation(s)
- Nathan M Springer
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Qing Li
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108
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48
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Zhao D, Ferguson AA, Jiang N. What makes up plant genomes: The vanishing line between transposable elements and genes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:366-80. [PMID: 26709091 DOI: 10.1016/j.bbagrm.2015.12.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 12/09/2015] [Accepted: 12/11/2015] [Indexed: 02/07/2023]
Abstract
The ultimate source of evolution is mutation. As the largest component in plant genomes, transposable elements (TEs) create numerous types of mutations that cannot be mimicked by other genetic mechanisms. When TEs insert into genomic sequences, they influence the expression of nearby genes as well as genes unlinked to the insertion. TEs can duplicate, mobilize, and recombine normal genes or gene fragments, with the potential to generate new genes or modify the structure of existing genes. TEs also donate their transposase coding regions for cellular functions in a process called TE domestication. Despite the host defense against TE activity, a subset of TEs survived and thrived through discreet selection of transposition activity, target site, element size, and the internal sequence. Finally, TEs have established strategies to reduce the efficacy of host defense system by increasing the cost of silencing TEs. This review discusses the recent progress in the area of plant TEs with a focus on the interaction between TEs and genes.
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Affiliation(s)
- Dongyan Zhao
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824, USA
| | - Ann A Ferguson
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824, USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824, USA.
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49
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Dodsworth S, Leitch AR, Leitch IJ. Genome size diversity in angiosperms and its influence on gene space. Curr Opin Genet Dev 2015; 35:73-8. [PMID: 26605684 DOI: 10.1016/j.gde.2015.10.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 10/28/2015] [Accepted: 10/28/2015] [Indexed: 01/02/2023]
Abstract
Genome size varies c. 2400-fold in angiosperms (flowering plants), although the range of genome size is skewed towards small genomes, with a mean genome size of 1C=5.7Gb. One of the most crucial factors governing genome size in angiosperms is the relative amount and activity of repetitive elements. Recently, there have been new insights into how these repeats, previously discarded as 'junk' DNA, can have a significant impact on gene space (i.e. the part of the genome comprising all the genes and gene-related DNA). Here we review these new findings and explore in what ways genome size itself plays a role in influencing how repeats impact genome dynamics and gene space, including gene expression.
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Affiliation(s)
- Steven Dodsworth
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Ilia J Leitch
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK.
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50
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Fultz D, Choudury SG, Slotkin RK. Silencing of active transposable elements in plants. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:67-76. [PMID: 26164237 DOI: 10.1016/j.pbi.2015.05.027] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/20/2015] [Accepted: 05/22/2015] [Indexed: 05/04/2023]
Abstract
In plant genomes the vast majority of transposable elements (TEs) are found in a transcriptionally silenced state that is epigenetically propagated from generation to generation. Although the mechanism of this maintenance of silencing has been well studied, it is now clear that the pathways responsible for maintaining TEs in a silenced state differ from the pathways responsible for initially targeting the TE for silencing. Recently, attention in this field has focused on investigating the molecular mechanisms that initiate and establish TE silencing. Here we review the current models of how TEs are triggered for silencing, the data supporting each model, and the key future questions in this fast moving field.
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Affiliation(s)
- Dalen Fultz
- Department of Molecular Genetics, The Ohio State University, United States
| | - Sarah G Choudury
- Department of Molecular Genetics, The Ohio State University, United States
| | - R Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, United States; Center for RNA Biology, The Ohio State University, United States.
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