1
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Kramer MC, Swanson R, Slotkin RK. Reading banned regions of genomes. Nat Plants 2024; 10:7-8. [PMID: 38225351 DOI: 10.1038/s41477-023-01600-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Affiliation(s)
| | - Ryan Swanson
- Donald Danforth Plant Science Center, St Louis, MO, USA
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St Louis, MO, USA.
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA.
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2
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Bélanger S, Kramer MC, Payne HA, Hui AY, Slotkin RK, Meyers BC, Staub JM. Plastid dsRNA transgenes trigger phased small RNA-based gene silencing of nuclear-encoded genes. Plant Cell 2023; 35:3398-3412. [PMID: 37309669 PMCID: PMC10473229 DOI: 10.1093/plcell/koad165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 05/16/2023] [Accepted: 06/12/2023] [Indexed: 06/14/2023]
Abstract
Plastid transformation technology has been widely used to express traits of potential commercial importance, though the technology has been limited to traits that function while sequestered in the organelle. Prior research indicates that plastid contents can escape from the organelle, suggesting a possible mechanism for engineering plastid transgenes to function in other cellular locations. To test this hypothesis, we created tobacco (Nicotiana tabacum cv. Petit Havana) plastid transformants that express a fragment of the nuclear-encoded Phytoene desaturase (PDS) gene capable of catalyzing post-transcriptional gene silencing if RNA escapes into the cytoplasm. We found multiple lines of direct evidence that plastid-encoded PDS transgenes affect nuclear PDS gene silencing: knockdown of the nuclear-encoded PDS mRNA and/or its apparent translational inhibition, biogenesis of 21-nucleotide (nt) phased small interfering RNAs (phasiRNAs), and pigment-deficient plants. Furthermore, plastid-expressed dsRNA with no cognate nuclear-encoded pairing partner also produced abundant 21-nt phasiRNAs in the cytoplasm, demonstrating that a nuclear-encoded template is not required for siRNA biogenesis. Our results indicate that RNA escape from plastids to the cytoplasm occurs generally, with functional consequences that include entry into the gene silencing pathway. Furthermore, we uncover a method to produce plastid-encoded traits with functions outside of the organelle and open additional fields of study in plastid development, compartmentalization, and small RNA biogenesis.
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Affiliation(s)
- Sébastien Bélanger
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132, USA
| | - Marianne C Kramer
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132, USA
| | - Hayden A Payne
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132, USA
| | - Alice Y Hui
- Plastomics Inc, 1100 Corporate Square Drive, St. Louis, MO 63132, USA
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132, USA
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Jeffrey M Staub
- Plastomics Inc, 1100 Corporate Square Drive, St. Louis, MO 63132, USA
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3
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Zhang P, Mbodj A, Soundiramourtty A, Llauro C, Ghesquière A, Ingouff M, Keith Slotkin R, Pontvianne F, Catoni M, Mirouze M. Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants. Nat Commun 2023; 14:5236. [PMID: 37640706 PMCID: PMC10462705 DOI: 10.1038/s41467-023-41023-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
Abundant extrachromosomal circular DNA (eccDNA) is associated with transposable element (TE) activity. However, how the eccDNA compartment is controlled by epigenetic regulations and what is its impact on the genome is understudied. Here, using long reads, we sequence both the eccDNA compartment and the genome of Arabidopsis thaliana mutant plants affected in DNA methylation and post-transcriptional gene silencing. We detect a high load of TE-derived eccDNA with truncated and chimeric forms. On the genomic side, on top of truncated and full length TE neo-insertions, we detect complex structural variations (SVs) notably at a disease resistance cluster being a natural hotspot of SV. Finally, we serendipitously identify large tandem duplications in hypomethylated plants, suggesting that SVs could have been overlooked in epigenetic mutants. We propose that a high eccDNA load may alter DNA repair pathways leading to genome instability and the accumulation of SVs, at least in plants.
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Affiliation(s)
- Panpan Zhang
- Institut de Recherche pour le Développement (IRD), Laboratory of Plant Genome and Development, Perpignan, France
- EMR269 MANGO (CNRS/IRD/UPVD), Laboratory of Plant Genome and Development, Perpignan, France
- University of Montpellier, Montpellier, France
| | - Assane Mbodj
- Institut de Recherche pour le Développement (IRD), Laboratory of Plant Genome and Development, Perpignan, France
- EMR269 MANGO (CNRS/IRD/UPVD), Laboratory of Plant Genome and Development, Perpignan, France
| | - Abirami Soundiramourtty
- EMR269 MANGO (CNRS/IRD/UPVD), Laboratory of Plant Genome and Development, Perpignan, France
- University of Perpignan, Perpignan, France
| | - Christel Llauro
- EMR269 MANGO (CNRS/IRD/UPVD), Laboratory of Plant Genome and Development, Perpignan, France
- Centre National de la Recherche Scientifique (CNRS), Laboratory of Plant Genome and Development, Perpignan, France
| | - Alain Ghesquière
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - Mathieu Ingouff
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Frédéric Pontvianne
- Centre National de la Recherche Scientifique (CNRS), Laboratory of Plant Genome and Development, Perpignan, France
| | - Marco Catoni
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Marie Mirouze
- Institut de Recherche pour le Développement (IRD), Laboratory of Plant Genome and Development, Perpignan, France.
- EMR269 MANGO (CNRS/IRD/UPVD), Laboratory of Plant Genome and Development, Perpignan, France.
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4
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Panda K, Mohanasundaram B, Gutierrez J, McLain L, Castillo SE, Sheng H, Casto A, Gratacós G, Chakrabarti A, Fahlgren N, Pandey S, Gehan MA, Slotkin RK. The plant response to high CO 2 levels is heritable and orchestrated by DNA methylation. New Phytol 2023; 238:2427-2439. [PMID: 36918471 DOI: 10.1111/nph.18876] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 03/07/2023] [Indexed: 05/19/2023]
Abstract
Plant responses to abiotic environmental challenges are known to have lasting effects on the plant beyond the initial stress exposure. Some of these lasting effects are transgenerational, affecting the next generation. The plant response to elevated carbon dioxide (CO2 ) levels has been well studied. However, these investigations are typically limited to plants grown for a single generation in a high CO2 environment while transgenerational studies are rare. We aimed to determine transgenerational growth responses in plants after exposure to high CO2 by investigating the direct progeny when returned to baseline CO2 levels. We found that both the flowering plant Arabidopsis thaliana and seedless nonvascular plant Physcomitrium patens continue to display accelerated growth rates in the progeny of plants exposed to high CO2 . We used the model species Arabidopsis to dissect the molecular mechanism and found that DNA methylation pathways are necessary for heritability of this growth response. More specifically, the pathway of RNA-directed DNA methylation is required to initiate methylation and the proteins CMT2 and CMT3 are needed for the transgenerational propagation of this DNA methylation to the progeny plants. Together, these two DNA methylation pathways establish and then maintain a cellular memory to high CO2 exposure.
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Affiliation(s)
- Kaushik Panda
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | | | - Jorge Gutierrez
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Lauren McLain
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | | | - Hudanyun Sheng
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Anna Casto
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Gustavo Gratacós
- Department of Computer Science & Engineering, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Ayan Chakrabarti
- Department of Computer Science & Engineering, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Noah Fahlgren
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Sona Pandey
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Malia A Gehan
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
- Division of Biological Sciences, University of Missouri, MO, 65211, Columbia, USA
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5
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Renken K, Mendoza SM, Diaz S, Slotkin RK, Hancock CN. Pol V produced RNA facilitates transposable element excision site repair in Arabidopsis. MicroPubl Biol 2023; 2023:10.17912/micropub.biology.000793. [PMID: 37273575 PMCID: PMC10236241 DOI: 10.17912/micropub.biology.000793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 06/06/2023]
Abstract
The plant-specific RNA Polymerase V (Pol V) plays a key role in gene silencing, but its role in repair of double stranded DNA breaks is unclear. Excision of the transposable element mPing creates double stranded breaks that are repaired by NHEJ. We measured mPing excision site repair in multiple DNA methylation mutants including pol V using an mPing : GFP reporter. Two independent mutant alleles of pol V showed less GFP expression, indicating that the Pol V protein plays a role in excision site repair. Sequence analysis of the pol V excision sites indicated an elevated rate of large deletions consistent with less efficient repair. These results clarify the role of Pol V, but not other RNA-directed DNA methylation proteins (Pol IV) or maintenance DNA methylation pathways ( MET1 ), in the repair of double-strand DNA breaks.
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Affiliation(s)
- Kaili Renken
- Biology and Geology, University of South Carolina Aiken, Aiken, South Carolina, United States
| | - Sarah M. Mendoza
- Biology and Geology, University of South Carolina Aiken, Aiken, South Carolina, United States
| | - Stephanie Diaz
- Biology and Geology, University of South Carolina Aiken, Aiken, South Carolina, United States
- Cardiovascular Disease Initiative, Bayer and Broad Institute of MIT and Harvard
| | - R. Keith Slotkin
- Donald Danforth Plant Science Center, St Louis, Missouri, United States
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States
| | - C. Nathan Hancock
- Biology and Geology, University of South Carolina Aiken, Aiken, South Carolina, United States
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6
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Edwards SA, Slotkin RK. Broken up but still living together: how ARGONAUTE's retention of cleaved fragments explains its role during chromatin modification. Genes Dev 2023; 37:69-71. [PMID: 36754778 PMCID: PMC10069453 DOI: 10.1101/gad.350424.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Throughout the eukaryotic kingdoms, small RNAs direct chromatin modification. ARGONAUTE proteins sit at the nexus of this process, linking the small RNA information to the programming of chromatin. ARGONAUTE proteins physically incorporate the small RNAs as guides to target specific regions of the genome. In this issue of Genes & Development, Wang and colleagues (pp. 103-118) add substantial new detail to the processes of ARGONAUTE RNA loading, preference, cleavage, and retention, which together accomplish RNA-directed chromatin modification. They show that after catalytic cleavage by the plant ARGONAUTE protein AGO4, the cleaved fragment remains bound. This happens during two distinct RNA cleavage reactions performed by AGO4: first for a passenger RNA strand of the siRNA duplex, and second for a nascent transcript at the target DNA locus. Cleaved fragment retention of the nascent transcript explains how the protein complex accumulates to high levels at the target locus, amplifying chromatin modification.
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Affiliation(s)
- Seth A Edwards
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA;
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
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7
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Liu P, Cuerda-Gil D, Shahid S, Slotkin RK. The Epigenetic Control of the Transposable Element Life Cycle in Plant Genomes and Beyond. Annu Rev Genet 2022; 56:63-87. [DOI: 10.1146/annurev-genet-072920-015534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Within the life cycle of a living organism, another life cycle exists for the selfish genome inhabitants, which are called transposable elements (TEs). These mobile sequences invade, duplicate, amplify, and diversify within a genome, increasing the genome's size and generating new mutations. Cells act to defend their genome, but rather than permanently destroying TEs, they use chromatin-level repression and epigenetic inheritance to silence TE activity. This level of silencing is ephemeral and reversible, leading to a dynamic equilibrium between TE suppression and reactivation within a host genome. The coexistence of the TE and host genome can also lead to the domestication of the TE to serve in host genome evolution and function. In this review, we describe the life cycle of a TE, with emphasis on how epigenetic regulation is harnessed to control TEs for host genome stability and innovation.
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Affiliation(s)
- Peng Liu
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - Diego Cuerda-Gil
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
- Graduate Program in the Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Saima Shahid
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - R. Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
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8
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Cuerda-Gil D, Hung YH, Panda K, Slotkin RK. A plant tethering system for the functional study of protein-RNA interactions in vivo. Plant Methods 2022; 18:75. [PMID: 35658900 PMCID: PMC9166424 DOI: 10.1186/s13007-022-00907-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
The sorting of RNA transcripts dictates their ultimate post-transcriptional fates, such as translation, decay or degradation by RNA interference (RNAi). This sorting of RNAs into distinct fates is mediated by their interaction with RNA-binding proteins. While hundreds of RNA binding proteins have been identified, which act to sort RNAs into different pathways is largely unknown. Particularly in plants, this is due to the lack of reliable protein-RNA artificial tethering tools necessary to determine the mechanism of protein action on an RNA in vivo. Here we generated a protein-RNA tethering system which functions on an endogenous Arabidopsis RNA that is tracked by the quantitative flowering time phenotype. Unlike other protein-RNA tethering systems that have been attempted in plants, our system circumvents the inadvertent triggering of RNAi. We successfully in vivo tethered a protein epitope, deadenylase protein and translation factor to the target RNA, which function to tag, decay and boost protein production, respectively. We demonstrated that our tethering system (1) is sufficient to engineer the downstream fate of an RNA, (2) enables the determination of any protein's function upon recruitment to an RNA, and (3) can be used to discover new interactions with RNA-binding proteins.
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Affiliation(s)
- Diego Cuerda-Gil
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Yu-Hung Hung
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Kaushik Panda
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA.
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9
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Oliver C, Annacondia ML, Wang Z, Jullien PE, Slotkin RK, Köhler C, Martinez G. The miRNome function transitions from regulating developmental genes to transposable elements during pollen maturation. Plant Cell 2022; 34:784-801. [PMID: 34755870 PMCID: PMC8824631 DOI: 10.1093/plcell/koab280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Animal and plant microRNAs (miRNAs) are essential for the spatio-temporal regulation of development. Together with this role, plant miRNAs have been proposed to target transposable elements (TEs) and stimulate the production of epigenetically active small interfering RNAs. This activity is evident in the plant male gamete containing structure, the male gametophyte or pollen grain. How the dual role of plant miRNAs, regulating both genes and TEs, is integrated during pollen development and which mRNAs are regulated by miRNAs in this cell type at a genome-wide scale are unknown. Here, we provide a detailed analysis of miRNA dynamics and activity during pollen development in Arabidopsis thaliana using small RNA and degradome parallel analysis of RNA end high-throughput sequencing. Furthermore, we uncover miRNAs loaded into the two main active Argonaute (AGO) proteins in the uninuclear and mature pollen grain, AGO1 and AGO5. Our results indicate that the developmental progression from microspore to mature pollen grain is characterized by a transition from miRNAs targeting developmental genes to miRNAs regulating TE activity.
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Affiliation(s)
- Cecilia Oliver
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Maria Luz Annacondia
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Zhenxing Wang
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
- College of Horticulture and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs and Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Nanjing Agricultural University, Nanjing 210095, China
| | - Pauline E Jullien
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Division of Biological Sciences, University of Missouri Columbia, Columbia, Missouri 65201, USA
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
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10
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Sigman MJ, Panda K, Kirchner R, McLain LL, Payne H, Peasari JR, Husbands AY, Slotkin RK, McCue AD. An siRNA-guided ARGONAUTE protein directs RNA polymerase V to initiate DNA methylation. Nat Plants 2021; 7:1461-1474. [PMID: 34750500 PMCID: PMC8592841 DOI: 10.1038/s41477-021-01008-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 09/09/2021] [Indexed: 05/03/2023]
Abstract
In mammals and plants, cytosine DNA methylation is essential for the epigenetic repression of transposable elements and foreign DNA. In plants, DNA methylation is guided by small interfering RNAs (siRNAs) in a self-reinforcing cycle termed RNA-directed DNA methylation (RdDM). RdDM requires the specialized RNA polymerase V (Pol V), and the key unanswered question is how Pol V is first recruited to new target sites without pre-existing DNA methylation. We find that Pol V follows and is dependent on the recruitment of an AGO4-clade ARGONAUTE protein, and any siRNA can guide the ARGONAUTE protein to the new target locus independent of pre-existing DNA methylation. These findings reject long-standing models of RdDM initiation and instead demonstrate that siRNA-guided ARGONAUTE targeting is necessary, sufficient and first to target Pol V recruitment and trigger the cycle of RdDM at a transcribed target locus, thereby establishing epigenetic silencing.
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Affiliation(s)
- Meredith J Sigman
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Kaushik Panda
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Rachel Kirchner
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
- Medical Scientist Training Program, University of Wisconsin, Madison, WI, USA
| | | | - Hayden Payne
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- Graduate Program in the School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - John Reddy Peasari
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- Bioinformatics and Computational Biology Program, Saint Louis University, St. Louis, MO, USA
| | - Aman Y Husbands
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA.
| | - Andrea D McCue
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
- Donald Danforth Plant Science Center, St. Louis, MO, USA
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11
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Hung YH, Slotkin RK. The initiation of RNA interference (RNAi) in plants. Curr Opin Plant Biol 2021; 61:102014. [PMID: 33657510 DOI: 10.1016/j.pbi.2021.102014] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/19/2021] [Accepted: 01/24/2021] [Indexed: 05/15/2023]
Abstract
When an mRNA enters into the RNA degradation pathway called RNA interference (RNAi), it is cleaved into small interfering RNAs (siRNAs) that then target complementary mRNAs for destruction. The consequence of entry into RNAi is mRNA degradation, post-transcriptional silencing and in some cases transcriptional silencing. RNAi functions as a defense against transposable element and virus activity, and in plants, RNAi additionally plays a role in development by regulating some genes. However, it is unknown how specific transcripts are selected for RNAi, and how most genic mRNAs steer clear. This Current Opinion article explores the key question of how RNAs are selected for entry into RNAi, and proposes models that enable the cell to distinguish between transcripts to translate versus destroy.
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Affiliation(s)
- Yu-Hung Hung
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA; Division of Biological Sciences, University of Missouri-Columbia, 65211, USA.
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12
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Annacondia ML, Markovic D, Reig-Valiente JL, Scaltsoyiannes V, Pieterse CMJ, Ninkovic V, Slotkin RK, Martinez G. Aphid feeding induces the relaxation of epigenetic control and the associated regulation of the defense response in Arabidopsis. New Phytol 2021; 230:1185-1200. [PMID: 33475147 DOI: 10.1111/nph.17226] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/14/2021] [Indexed: 05/23/2023]
Abstract
Environmentally induced changes in the epigenome help individuals to quickly adapt to fluctuations in the conditions of their habitats. We explored those changes in Arabidopsis thaliana plants subjected to multiple biotic and abiotic stresses, and identified transposable element (TE) activation in plants infested with the green peach aphid, Myzus persicae. We performed a genome-wide analysis mRNA expression, small RNA accumulation and DNA methylation Our results demonstrate that aphid feeding induces loss of methylation of hundreds of loci, mainly TEs. This loss of methylation has the potential to regulate gene expression and we found evidence that it is involved in the control of plant immunity genes. Accordingly, mutant plants deficient in DNA and H3K9 methylation (kyp) showed increased resistance to M. persicae infestation. Collectively, our results show that changes in DNA methylation play a significant role in the regulation of the plant transcriptional response and induction of defense response against aphid feeding.
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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, 75007, Sweden
| | - Dimitrije Markovic
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
- Faculty of Agriculture, University of Banja Luka, Banja Luka, 78000, Bosnia and Herzegovina
| | - Juan Luis Reig-Valiente
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
| | - Vassilis Scaltsoyiannes
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
- Institut de Biologie de Moléculaire des Plantes, UPR 2357 du CNRS, Strasbourg University, Strasbourg, 67000, France
| | - Corné M J Pieterse
- Department of Biology, Science4Life, Utrecht University, Utrecht, 3584 CS, the Netherlands
| | - Velemir Ninkovic
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO, 65021, USA
| | - German Martinez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
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13
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Antunez-Sanchez J, Naish M, Ramirez-Prado JS, Ohno S, Huang Y, Dawson A, Opassathian K, Manza-Mianza D, Ariel F, Raynaud C, Wibowo A, Daron J, Ueda M, Latrasse D, Slotkin RK, Weigel D, Benhamed M, Gutierrez-Marcos J. A new role for histone demethylases in the maintenance of plant genome integrity. eLife 2020. [PMID: 33107825 DOI: 10.7554/elife.58533.sa2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
Histone modifications deposited by the Polycomb repressive complex 2 (PRC2) play a critical role in the control of growth, development, and adaptation to environmental fluctuations of most multicellular eukaryotes. The catalytic activity of PRC2 is counteracted by Jumonji-type (JMJ) histone demethylases, which shapes the genomic distribution of H3K27me3. Here, we show that two JMJ histone demethylases in Arabidopsis, EARLY FLOWERING 6 (ELF6) and RELATIVE OF EARLY FLOWERING 6 (REF6), play distinct roles in H3K27me3 and H3K27me1 homeostasis. We show that failure to reset these chromatin marks during sexual reproduction results in the transgenerational inheritance of histone marks, which cause a loss of DNA methylation at heterochromatic loci and transposon activation. Thus, Jumonji-type histone demethylases play a dual role in plants by helping to maintain transcriptional states through development and safeguard genome integrity during sexual reproduction.
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Affiliation(s)
| | - Matthew Naish
- School of Life Science, University of Warwick, Coventry, United Kingdom
| | | | - Sho Ohno
- School of Life Science, University of Warwick, Coventry, United Kingdom
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Ying Huang
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Alexander Dawson
- School of Life Science, University of Warwick, Coventry, United Kingdom
| | | | - Deborah Manza-Mianza
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Federico Ariel
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Cecile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Anjar Wibowo
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Josquin Daron
- Department of Molecular Genetics, The Ohio State University, Columbus, United States
| | - Minako Ueda
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, United States
- Division of Biological Sciences, University of Missouri, Columbia, United States
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), F-75006, Paris, France
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14
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Antunez-Sanchez J, Naish M, Ramirez-Prado JS, Ohno S, Huang Y, Dawson A, Opassathian K, Manza-Mianza D, Ariel F, Raynaud C, Wibowo A, Daron J, Ueda M, Latrasse D, Slotkin RK, Weigel D, Benhamed M, Gutierrez-Marcos J. A new role for histone demethylases in the maintenance of plant genome integrity. eLife 2020; 9:e58533. [PMID: 33107825 PMCID: PMC7671693 DOI: 10.7554/elife.58533] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 10/26/2020] [Indexed: 12/16/2022] Open
Abstract
Histone modifications deposited by the Polycomb repressive complex 2 (PRC2) play a critical role in the control of growth, development, and adaptation to environmental fluctuations of most multicellular eukaryotes. The catalytic activity of PRC2 is counteracted by Jumonji-type (JMJ) histone demethylases, which shapes the genomic distribution of H3K27me3. Here, we show that two JMJ histone demethylases in Arabidopsis, EARLY FLOWERING 6 (ELF6) and RELATIVE OF EARLY FLOWERING 6 (REF6), play distinct roles in H3K27me3 and H3K27me1 homeostasis. We show that failure to reset these chromatin marks during sexual reproduction results in the transgenerational inheritance of histone marks, which cause a loss of DNA methylation at heterochromatic loci and transposon activation. Thus, Jumonji-type histone demethylases play a dual role in plants by helping to maintain transcriptional states through development and safeguard genome integrity during sexual reproduction.
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Affiliation(s)
| | - Matthew Naish
- School of Life Science, University of WarwickCoventryUnited Kingdom
| | | | - Sho Ohno
- School of Life Science, University of WarwickCoventryUnited Kingdom
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-kuKyotoJapan
| | - Ying Huang
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2)OrsayFrance
| | - Alexander Dawson
- School of Life Science, University of WarwickCoventryUnited Kingdom
| | | | - Deborah Manza-Mianza
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2)OrsayFrance
| | - Federico Ariel
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2)OrsayFrance
| | - Cecile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2)OrsayFrance
| | - Anjar Wibowo
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | - Josquin Daron
- Department of Molecular Genetics, The Ohio State UniversityColumbusUnited States
| | - Minako Ueda
- Institute of Transformative Bio-Molecules, Nagoya UniversityNagoyaJapan
- Division of Biological Science, Graduate School of Science, Nagoya UniversityNagoyaJapan
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2)OrsayFrance
| | - R Keith Slotkin
- Donald Danforth Plant Science CenterSt. LouisUnited States
- Division of Biological Sciences, University of MissouriColumbiaUnited States
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2)OrsayFrance
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), F-75006ParisFrance
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15
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Lai Y, Lu XM, Daron J, Pan S, Wang J, Wang W, Tsuchiya T, Holub E, McDowell JM, Slotkin RK, Le Roch KG, Eulgem T. The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression. PLoS Genet 2020; 16:e1008993. [PMID: 32925902 PMCID: PMC7529245 DOI: 10.1371/journal.pgen.1008993] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/01/2020] [Accepted: 07/14/2020] [Indexed: 12/19/2022] Open
Abstract
Plant NLR-type receptors serve as sensitive triggers of host immunity. Their expression has to be well-balanced, due to their interference with various cellular processes and dose-dependency of their defense-inducing activity. A genetic “arms race” with fast-evolving pathogenic microbes requires plants to constantly innovate their NLR repertoires. We previously showed that insertion of the COPIA-R7 retrotransposon into RPP7 co-opted the epigenetic transposon silencing signal H3K9me2 to a new function promoting expression of this Arabidopsis thaliana NLR gene. Recruitment of the histone binding protein EDM2 to COPIA-R7-associated H3K9me2 is required for optimal expression of RPP7. By profiling of genome-wide effects of EDM2, we now uncovered additional examples illustrating effects of transposons on NLR gene expression, strongly suggesting that these mobile elements can play critical roles in the rapid evolution of plant NLR genes by providing the “raw material” for gene expression mechanisms. We further found EDM2 to have a global role in NLR expression control. Besides serving as a positive regulator of RPP7 and a small number of other NLR genes, EDM2 acts as a suppressor of a multitude of additional NLR genes. We speculate that the dual functionality of EDM2 in NLR expression control arose from the need to compensate for fitness penalties caused by high expression of some NLR genes by suppression of others. Moreover, we are providing new insights into functional relationships of EDM2 with its interaction partner, the RNA binding protein EDM3/AIPP1, and its target gene IBM1, encoding an H3K9-demethylase. We previously found the Arabidopsis thaliana PHD-finger protein EDM2 to serve as a chromatin-associated factor controlling expression of the NLR-type immune receptor gene RPP7. EDM2 binds to the transposon-silencing signal H3K9me2 and affects levels of this epigenetic mark at various loci. By genome-wide profiling of transcript- and H3K9me2-levels we now found EDM2 to have a broader role in controlling NLR gene expression. In order to mitigate fitness costs caused by its promoting effects on RPP7 expression and that of several other NLR genes, EDM2 seems to suppress expression of many additional members of this gene family. This observation is in line with multiple reports demonstrating the need for balanced expression of NLRs, which can substantially reduce overall plant fitness, but need to be present at certain minimal levels to confer sufficient immune protection. Our previous results demonstrated that the influence of EDM2 on RPP7 expression was co-opted to this immune receptor gene by the insertion of an EDM2-controlled transposon. Here, we are providing additional examples for transposon-associated effects on NLR gene expression, suggesting that these mobile elements play an important role for NLR genes by equipping members of this rapidly evolving gene family with regulatory mechanisms needed for balanced expression.
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Affiliation(s)
- Yan Lai
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
- College of Life Sciences, Fujian Agricultural and Forestry University, Fuzhou, Fujian, China
| | - Xueqing Maggie Lu
- Center for Infectious Disease and Vector Research, Institute of Integrative Genome Biology, Department of Molecular, Cell and Systems Biology, University of California at Riverside, Riverside, CA, United States of America
| | - Josquin Daron
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Songqin Pan
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
| | - Jianqiang Wang
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
| | - Wei Wang
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, United States of America
| | - Tokuji Tsuchiya
- College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Eric Holub
- School of Life Sciences, University of Warwick, Wellesbourne campus, United Kingdom
| | - John M. McDowell
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, United States of America
| | - R. Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Karine G. Le Roch
- Center for Infectious Disease and Vector Research, Institute of Integrative Genome Biology, Department of Molecular, Cell and Systems Biology, University of California at Riverside, Riverside, CA, United States of America
- * E-mail: (KGLR); (TE)
| | - Thomas Eulgem
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
- * E-mail: (KGLR); (TE)
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16
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Panda K, Slotkin RK. Long-Read cDNA Sequencing Enables a "Gene-Like" Transcript Annotation of Transposable Elements. Plant Cell 2020; 32:2687-2698. [PMID: 32647069 PMCID: PMC7474280 DOI: 10.1105/tpc.20.00115] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/11/2020] [Accepted: 06/25/2020] [Indexed: 05/05/2023]
Abstract
Transcript-based annotations of genes facilitate both genome-wide analyses and detailed single-locus research. In contrast, transposable element (TE) annotations are rudimentary, consisting of information only on TE location and type. The repetitiveness and limited annotation of TEs prevent the ability to distinguish between potentially functional expressed elements and degraded copies. To improve genome-wide TE bioinformatics, we performed long-read sequencing of cDNAs from Arabidopsis (Arabidopsis thaliana) lines deficient in multiple layers of TE repression. These uniquely mapping transcripts were used to identify the set of TEs able to generate polyadenylated RNAs and create a new transcript-based annotation of TEs that we have layered upon the existing high-quality community standard annotation. We used this annotation to reduce the bioinformatic complexity associated with multimapping reads from short-read RNA sequencing experiments, and we show that this improvement is expanded in a TE-rich genome such as maize (Zea mays). Our TE annotation also enables the testing of specific standing hypotheses in the TE field. We demonstrate that inaccurate TE splicing does not trigger small RNA production, and the cell more strongly targets DNA methylation to TEs that have the potential to make mRNAs. This work provides a transcript-based TE annotation for Arabidopsis and maize, which serves as a blueprint to reduce the bioinformatic complexity associated with repetitive TEs in any organism.
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Affiliation(s)
- Kaushik Panda
- Donald Danforth Plant Science Center, St. Louis, 63132 Missouri
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, 63132 Missouri
- Division of Biological Sciences, University of Missouri, Columbia, 63132 Missouri
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17
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Yates-Stewart AD, Daron J, Wijeratne S, Shahid S, Edgington HA, Slotkin RK, Michel A. Soybean aphids adapted to host-plant resistance by down regulating putative effectors and up regulating transposable elements. Insect Biochem Mol Biol 2020; 121:103363. [PMID: 32201218 DOI: 10.1016/j.ibmb.2020.103363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 03/06/2020] [Accepted: 03/15/2020] [Indexed: 06/10/2023]
Abstract
In agricultural systems, crops equipped with host-plant resistance (HPR) have enhanced protection against pests, and are used as a safe and sustainable tool in pest management. In soybean, HPR can control the soybean aphid (Aphis glycines), but certain aphid populations have overcome this resistance (i.e., virulence). The molecular mechanisms underlying aphid virulence to HPR are unknown, but likely involve effector proteins that are secreted by aphids to modulate plant defenses. Another mechanism to facilitate adaptation is through the activity of transposable elements, which can become activated by stress. In this study, we performed RNA sequencing of virulent and avirulent soybean aphids fed susceptible or resistant (Rag1 + Rag2) soybean. Our goal was to better understand the molecular mechanisms underlying soybean aphid virulence. Our data showed that virulent aphids mostly down regulate putative effector genes relative to avirulent aphids, especially when aphids were fed susceptible soybean. Decreased expression of effectors may help evade HPR plant defenses. Virulent aphids also transcriptionally up regulate a diverse set of transposable elements and nearby genes, which is consistent with stress adaptation. Our work demonstrates two mechanisms of pest adaptation to resistance, and identifies effector gene targets for future functional testing.
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Affiliation(s)
| | - Josquin Daron
- CNRS, Centre National de la Recherche Scientifique, Montpellier, France
| | - Saranga Wijeratne
- The Ohio State University, Molecular and Cellular Imaging Center, OARDC, Wooster, OH, USA
| | - Saima Shahid
- Donald Danforth Plant Science Center, St, Louis, MO, USA
| | - Hilary A Edgington
- The Ohio State University, Department of Entomology, CFAES Wooster Campus, Wooster, OH, USA
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St, Louis, MO, USA; Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Andy Michel
- The Ohio State University, Center for Applied Plant Sciences, Wooster, OH, USA; The Ohio State University, Department of Entomology, CFAES Wooster Campus, Wooster, OH, USA.
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18
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Warman C, Panda K, Vejlupkova Z, Hokin S, Unger-Wallace E, Cole RA, Chettoor AM, Jiang D, Vollbrecht E, Evans MMS, Slotkin RK, Fowler JE. High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements. PLoS Genet 2020; 16:e1008462. [PMID: 32236090 PMCID: PMC7112179 DOI: 10.1371/journal.pgen.1008462] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/27/2020] [Indexed: 12/20/2022] Open
Abstract
In flowering plants, gene expression in the haploid male gametophyte (pollen) is essential for sperm delivery and double fertilization. Pollen also undergoes dynamic epigenetic regulation of expression from transposable elements (TEs), but how this process interacts with gene expression is not clearly understood. To explore relationships among these processes, we quantified transcript levels in four male reproductive stages of maize (tassel primordia, microspores, mature pollen, and sperm cells) via RNA-seq. We found that, in contrast with vegetative cell-limited TE expression in Arabidopsis pollen, TE transcripts in maize accumulate as early as the microspore stage and are also present in sperm cells. Intriguingly, coordinate expression was observed between highly expressed protein-coding genes and their neighboring TEs, specifically in mature pollen and sperm cells. To investigate a potential relationship between elevated gene transcript level and pollen function, we measured the fitness cost (male-specific transmission defect) of GFP-tagged coding sequence insertion mutations in over 50 genes identified as highly expressed in the pollen vegetative cell, sperm cell, or seedling (as a sporophytic control). Insertions in seedling genes or sperm cell genes (with one exception) exhibited no difference from the expected 1:1 transmission ratio. In contrast, insertions in over 20% of vegetative cell genes were associated with significant reductions in fitness, showing a positive correlation of transcript level with non-Mendelian segregation when mutant. Insertions in maize gamete expressed2 (Zm gex2), the sole sperm cell gene with measured contributions to fitness, also triggered seed defects when crossed as a male, indicating a conserved role in double fertilization, given the similar phenotype previously demonstrated for the Arabidopsis ortholog GEX2. Overall, our study demonstrates a developmentally programmed and coordinated transcriptional activation of TEs and genes in pollen, and further identifies maize pollen as a model in which transcriptomic data have predictive value for quantitative phenotypes.
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Affiliation(s)
- Cedar Warman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Kaushik Panda
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Zuzana Vejlupkova
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Sam Hokin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America
| | - Erica Unger-Wallace
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
| | - Rex A. Cole
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Antony M. Chettoor
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America
| | - Duo Jiang
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
| | - Erik Vollbrecht
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
- Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa, United States of America
- Interdepartmental Genetics, Iowa State University, Ames, Iowa, United States of America
| | - Matthew M. S. Evans
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America
| | - R. Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - John E. Fowler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
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19
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Shahid S, Slotkin RK. The current revolution in transposable element biology enabled by long reads. Curr Opin Plant Biol 2020; 54:49-56. [PMID: 32007731 DOI: 10.1016/j.pbi.2019.12.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
Technological advancement in DNA sequencing read-length has drastically changed the quality and completeness of decoded genomes. The aim of this article is not to describe the different technologies of long-read sequencing, or the widely appreciated power of this technology in genome sequencing, assembly, and gene annotation. Instead, in this article, we provide our opinion that with the exception of genome production, transposable element biology is the most radically altered field as a consequence of the advent of long-read sequencing technology. We review how long-reads have been used to answer key questions in transposable element biology, and how in the future long-reads will help elucidate the function of the repetitive fraction of genomes.
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Affiliation(s)
- Saima Shahid
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, MO, USA; Division of Biological Sciences, University of Missouri, Columbia, MO, USA.
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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Ji L, Mathioni SM, Johnson S, Tucker D, Bewick AJ, Do Kim K, Daron J, Slotkin RK, Jackson SA, Parrott WA, Meyers BC, Schmitz RJ. Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean. Plant Cell 2019; 31:2315-2331. [PMID: 31439802 PMCID: PMC6790092 DOI: 10.1105/tpc.19.00255] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/29/2019] [Accepted: 08/19/2019] [Indexed: 05/06/2023]
Abstract
Somatic embryogenesis is an important tissue culture technique that sometimes leads to phenotypic variation via genetic and/or epigenetic changes. To understand the genomic and epigenomic impacts of somatic embryogenesis, we characterized soybean (Glycine max) epigenomes sampled from embryos at 10 different stages ranging from 6 weeks to 13 years of continuous culture. We identified genome-wide increases in DNA methylation from cultured samples, especially at CHH sites. The hypermethylation almost exclusively occurred in regions previously possessing non-CG methylation and was accompanied by increases in the expression of genes encoding the RNA-directed DNA methylation (RdDM) machinery. The epigenomic changes were similar between somatic and zygotic embryogenesis. Following the initial global wave of hypermethylation, rare decay events of maintenance methylation were observed, and the extent of the decay increased with time in culture. These losses in DNA methylation were accompanied by downregulation of genes encoding the RdDM machinery and transcriptome reprogramming reminiscent of transcriptomes during late-stage seed development. These results reveal a process for reinforcing already silenced regions to maintain genome integrity during somatic embryogenesis over the short term, which eventually decays at certain loci over longer time scales.
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Affiliation(s)
- Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602
| | | | - Sarah Johnson
- Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia 30602
| | - Donna Tucker
- Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia 30602
| | - Adam J Bewick
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Josquin Daron
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Wayne A Parrott
- Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia 30602
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 63132
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia 30602
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22
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Zhang Y, Ramming A, Heinke L, Altschmied L, Slotkin RK, Becker JD, Kappel C, Lenhard M. The poly(A) polymerase PAPS1 interacts with the RNA-directed DNA-methylation pathway in sporophyte and pollen development. Plant J 2019; 99:655-672. [PMID: 31009115 DOI: 10.1111/tpj.14348] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 03/21/2019] [Accepted: 04/08/2019] [Indexed: 05/28/2023]
Abstract
RNA-based processes play key roles in the regulation of eukaryotic gene expression. This includes both the processing of pre-mRNAs into mature mRNAs ready for translation and RNA-based silencing processes, such as RNA-directed DNA methylation (RdDM). Polyadenylation of pre-mRNAs is one important step in their processing and is carried out by three functionally specialized canonical nuclear poly(A) polymerases in Arabidopsis thaliana. Null mutations in one of these, termed PAPS1, result in a male gametophytic defect. Using a fluorescence-labelling strategy, we have characterized this defect in more detail using RNA and small-RNA sequencing. In addition to global defects in the expression of pollen-differentiation genes, paps1 null-mutant pollen shows a strong overaccumulation of transposable element (TE) transcripts, yet a depletion of 21- and particularly 24-nucleotide-long short interfering RNAs (siRNAs) and microRNAs (miRNAs) targeting the corresponding TEs. Double-mutant analyses support a specific functional interaction between PAPS1 and components of the RdDM pathway, as evident from strong synergistic phenotypes in mutant combinations involving paps1, but not paps2 paps4, mutations. In particular, the double-mutant of paps1 and rna-dependent rna polymerase 6 (rdr6) shows a synergistic developmental phenotype disrupting the formation of the transmitting tract in the female gynoecium. Thus, our findings in A. thaliana uncover a potentially general link between canonical poly(A) polymerases as components of mRNA processing and RdDM, reflecting an analogous interaction in fission yeast.
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Affiliation(s)
- Yunming Zhang
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Anna Ramming
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Lisa Heinke
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Lothar Altschmied
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstrasse 3, D-06466 Seeland, OT, Gatersleben, Germany
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jörg D Becker
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Michael Lenhard
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
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23
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Choudury SG, Shahid S, Cuerda-Gil D, Panda K, Cullen A, Ashraf Q, Sigman MJ, McCue AD, Slotkin RK. The RNA Export Factor ALY1 Enables Genome-Wide RNA-Directed DNA Methylation. Plant Cell 2019; 31:759-774. [PMID: 30814259 PMCID: PMC6501602 DOI: 10.1105/tpc.18.00624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 01/23/2019] [Accepted: 02/22/2019] [Indexed: 05/07/2023]
Abstract
RNA-directed DNA methylation (RdDM) is a set of mechanisms by which transcriptionally repressive DNA and histone methylation are targeted to viruses, transposable elements, and some transgenes. We identified an Arabidopsis (Arabidopsis thaliana) mutant in which all forms of RdDM are deficient, leading to transcriptional activation of some transposable elements and the inability to initiate transgene silencing. The corresponding gene, ALY1, encodes an RNA binding nuclear export protein. Arabidopsis ALY proteins function together to export many messenger RNAs (mRNAs), but we found that ALY1 is unique among this family for its ability to enable RdDM. Through the identification of ALY1 direct targets via RNA immunoprecipitation sequencing, coupled with mRNA sequencing of nuclear and cytoplasmic fractions, we identified mRNAs of known RdDM factors that fail to efficiently export from the nucleus in aly1 mutants. We found that loss of RdDM in aly1 is a result of deficient nuclear export of the ARGONAUTE6 mRNA and subsequent decreases in ARGONAUTE6 protein, a key effector of RdDM. One aly1 allele was more severe due to an additional loss of RNA Polymerase V function, which is also necessary for RdDM. Together, our data reconcile the broad role of ALY1 in mRNA export with the specific loss of RdDM through the activities of ARGONAUTE6 and RNA Polymerase V.
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Affiliation(s)
- Sarah G Choudury
- Molecular, Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, Ohio 43210
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Saima Shahid
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Diego Cuerda-Gil
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Kaushik Panda
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Alissa Cullen
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Quratulayn Ashraf
- Molecular, Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, Ohio 43210
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Meredith J Sigman
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Andrea D McCue
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - R Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
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24
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Jupe F, Rivkin AC, Michael TP, Zander M, Motley ST, Sandoval JP, Slotkin RK, Chen H, Castanon R, Nery JR, Ecker JR. The complex architecture and epigenomic impact of plant T-DNA insertions. PLoS Genet 2019; 15:e1007819. [PMID: 30657772 PMCID: PMC6338467 DOI: 10.1371/journal.pgen.1007819] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/07/2018] [Indexed: 12/17/2022] Open
Abstract
The bacterium Agrobacterium tumefaciens has been the workhorse in plant genome engineering. Customized replacement of native tumor-inducing (Ti) plasmid elements enabled insertion of a sequence of interest called Transfer-DNA (T-DNA) into any plant genome. Although these transfer mechanisms are well understood, detailed understanding of structure and epigenomic status of insertion events was limited by current technologies. Here we applied two single-molecule technologies and analyzed Arabidopsis thaliana lines from three widely used T-DNA insertion collections (SALK, SAIL and WISC). Optical maps for four randomly selected T-DNA lines revealed between one and seven insertions/rearrangements, and the length of individual insertions from 27 to 236 kilobases. De novo nanopore sequencing-based assemblies for two segregating lines partially resolved T-DNA structures and revealed multiple translocations and exchange of chromosome arm ends. For the current TAIR10 reference genome, nanopore contigs corrected 83% of non-centromeric misassemblies. The unprecedented contiguous nucleotide-level resolution enabled an in-depth study of the epigenome at T-DNA insertion sites. SALK_059379 line T-DNA insertions were enriched for 24nt small interfering RNAs (siRNA) and dense cytosine DNA methylation, resulting in transgene silencing via the RNA-directed DNA methylation pathway. In contrast, SAIL_232 line T-DNA insertions are predominantly targeted by 21/22nt siRNAs, with DNA methylation and silencing limited to a reporter, but not the resistance gene. Additionally, we profiled the H3K4me3, H3K27me3 and H2A.Z chromatin environments around T-DNA insertions using ChIP-seq in SALK_059379, SAIL_232 and five additional T-DNA lines. We discovered various effect s ranging from complete loss of chromatin marks to the de novo incorporation of H2A.Z and trimethylation of H3K4 and H3K27 around the T-DNA integration sites. This study provides new insights into the structural impact of inserting foreign fragments into plant genomes and demonstrates the utility of state-of-the-art long-range sequencing technologies to rapidly identify unanticipated genomic changes. Our routine ability to add or alter genes in plant genomes using transgenesis has proven to be a game changer to plant sciences. Transgenics not only enables the study of gene function but also allows the development of modern crop plants without the unwanted genetic baggage coming from natural crossing. A major tool to create transgenics is the Agrobacterium system which naturally shuttles and integrates pieces of foreign DNA into its host genome. While the position and number of integrations was relatively easy to track, molecular tools never allowed to see the integrated piece of DNA within a single “picture”. Here we have utilized state-of-the-art DNA sequencing technology to capture the size and structure of multiple DNA insertion events in a plant genome. We discovered that insertion of the anticipated DNA fragment occurred as multiple concatenated full and partial fragments that led in some cases to intra- and interchromosomal rearrangements. Our analysis of the epigenetic landscapes showed variable effects from silencing of the integrated foreign DNA to alterations of chromatin marks and thus chromatin structure and functionality.
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Affiliation(s)
- Florian Jupe
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - Angeline C. Rivkin
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - Todd P. Michael
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Mark Zander
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | | | - Justin P. Sandoval
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - R. Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, MO, United States of America
| | - Huaming Chen
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - Rosa Castanon
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - Joseph R. Nery
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - Joseph R. Ecker
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States of America
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, United States of America
- * E-mail:
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25
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Abstract
In the course of analyzing whole-genome data, it is common practice to mask or filter out repetitive regions of a genome, such as transposable elements and endogenous retroviruses, in order to focus only on genes and thus simplify the results. This Commentary is a plea from one member of the Mobile DNA community to all gene-centric researchers: please do not ignore the repetitive fraction of the genome. Please stop narrowing your findings by only analyzing a minority of the genome, and instead broaden your analyses to include the rich biology of repetitive and mobile DNA. In this article, I present four arguments supporting a case for retaining repetitive DNA in your genome-wide analysis.
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Affiliation(s)
- R Keith Slotkin
- Department of Molecular Genetics and Center for Applied Plant Sciences, The Ohio State University, 500 Aronoff Laboratory, 318 West 12th Ave, Columbus, Ohio 43210 USA
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26
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Martinez G, Wolff P, Wang Z, Moreno-Romero J, Santos-González J, Conze LL, DeFraia C, Slotkin RK, Köhler C. Paternal easiRNAs regulate parental genome dosage in Arabidopsis. Nat Genet 2018; 50:193-198. [PMID: 29335548 DOI: 10.1038/s41588-017-0033-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 12/15/2017] [Indexed: 01/22/2023]
Abstract
The regulation of parental genome dosage is of fundamental importance in animals and plants, as exemplified by X-chromosome inactivation and dosage compensation. The 'triploid block' is a classic example of dosage regulation in plants that establishes a reproductive barrier between species differing in chromosome number1,2. This barrier acts in the embryo-nourishing endosperm tissue and induces the abortion of hybrid seeds through a yet unknown mechanism 3 . Here we show that depletion of paternal epigenetically activated small interfering RNAs (easiRNAs) bypasses the triploid block in response to increased paternal ploidy in Arabidopsis thaliana. Paternal loss of the plant-specific RNA polymerase IV suppressed easiRNA formation and rescued triploid seeds by restoring small-RNA-directed DNA methylation at transposable elements (TEs), correlating with reduced expression of paternally expressed imprinted genes (PEGs). Our data suggest that easiRNAs form a quantitative signal for paternal chromosome number and that their balanced dosage is required for post-fertilization genome stability and seed viability.
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Affiliation(s)
- German Martinez
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Linnean Center for Plant Biology, Uppsala, Sweden
| | - Philip Wolff
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Linnean Center for Plant Biology, Uppsala, Sweden.,John Innes Centre, Norwich, UK
| | - Zhenxing Wang
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Linnean Center for Plant Biology, Uppsala, Sweden
| | - Jordi Moreno-Romero
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Linnean Center for Plant Biology, Uppsala, Sweden.,Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Juan Santos-González
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Linnean Center for Plant Biology, Uppsala, Sweden
| | - Lei Liu Conze
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Linnean Center for Plant Biology, Uppsala, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Christopher DeFraia
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Biological Sciences, Ferris State University, Big Rapids, MI, USA
| | - R Keith Slotkin
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden. .,Linnean Center for Plant Biology, Uppsala, Sweden.
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27
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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: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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28
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Daron J, Slotkin RK. EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels. Genome Biol 2017; 18:91. [PMID: 28499400 PMCID: PMC5429532 DOI: 10.1186/s13059-017-1232-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/05/2017] [Indexed: 11/15/2022] Open
Abstract
The genome-wide investigation of DNA methylation levels has been limited to reference transposable element positions. The methylation analysis of non-reference and mobile transposable elements has only recently been performed, but required both genome resequencing and MethylC-seq datasets. We have created epiTEome, a program that detects both new transposable element insertion sites and their methylation states from a single MethylC-seq dataset. EpiTEome outperforms other split-read insertion site detection programs, even while functioning on bisulfite-converted reads. EpiTEome characterizes the previously discarded fraction of DNA methylation at sites of new insertions, enabling future investigation into the epigenetic regulation of non-reference and transposed elements.
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Affiliation(s)
- Josquin Daron
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - R Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA.
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29
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Fultz D, Slotkin RK. Exogenous Transposable Elements Circumvent Identity-Based Silencing, Permitting the Dissection of Expression-Dependent Silencing. Plant Cell 2017; 29:360-376. [PMID: 28193737 PMCID: PMC5354191 DOI: 10.1105/tpc.16.00718] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 12/19/2016] [Accepted: 02/10/2017] [Indexed: 05/09/2023]
Abstract
The propagation of epigenetic marks has received a great deal of attention, yet the initiation of epigenetic silencing of a new transgene, virus, or transposable element (TE) remains enigmatic. The overlapping and simultaneous function of multiple silencing mechanisms has obscured this area of investigation. Here, we revealed two broad mechanisms that can initiate silencing independently: identity-based and expression-dependent silencing. We found that identity-based silencing is targeted by 21- to 22-nucleotide or 24-nucleotide small interfering RNAs (siRNAs) generated from previously silenced regions of the genome. By transforming exogenous TEs into Arabidopsis thaliana, we circumvented identity-based silencing, allowing us to isolate and investigate the molecular mechanism of expression-dependent silencing. We found that several siRNA-generating mechanisms all trigger de novo expression-dependent RNA-directed DNA methylation (RdDM) through RNA Polymerase V. In addition, while full-length TEs quickly progress beyond RdDM to heterochromatin formation and the final maintenance methylation state, TE fragments stall at the RdDM phase. Lastly, we found that transformation into a mutant genotype followed by introgression into the wild type does not result in the same level of silencing as direct transformation into the wild type. This demonstrates that the plant genotype during a narrow window of time at TE insertion (or transgene transformation) is key for establishing the transgenerational extent of epigenetic silencing.
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Affiliation(s)
- Dalen Fultz
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, Ohio 43210
| | - R Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
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30
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Cuerda-Gil D, Slotkin RK. Corrigendum: Non-canonical RNA-directed DNA methylation. Nat Plants 2016; 3:16211. [PMID: 27941819 DOI: 10.1038/nplants.2016.211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
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31
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Abstract
Small RNA-directed DNA methylation (RdDM) has been extensively studied in plants, resulting in a deep understanding of a major 'canonical RdDM' mechanism. However, current models of canonical RdDM cannot explain how this self-perpetuating mechanism is initiated. Recent investigations into the initiation of epigenetic silencing have determined that there are several alternative 'non-canonical RdDM' pathways that function through distinct mechanisms to modify chromatin. This Review aims to illustrate the diversity of non-canonical RdDM mechanisms described to date, recognize common themes within this dizzying array of interconnected pathways, and identify the key unanswered questions remaining in this field.
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Affiliation(s)
- Diego Cuerda-Gil
- Department of Molecular Genetics, The Ohio State University, 500 Aronoff Laboratory, 318 West Twelfth Avenue, Columbus, Ohio 43210, USA
| | - R Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, 500 Aronoff Laboratory, 318 West Twelfth Avenue, Columbus, Ohio 43210, USA
- Center for RNA Biology, The Ohio State University, 105 Biological Sciences Building, 484 West Twelfth Avenue, Columbus, Ohio 43210, USA
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32
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Gautheret D, Taube JH, Mani SA, Santulli G, Cuerda-Gil D, Slotkin RK, Zhang B, Wang Y, Salzman DW, Weidhaas JB. Erratum: The Non-Coding RNA Journal Club: Highlights on Recent Papers-4. Non-Coding RNA 2016, 2, 9. Noncoding RNA 2016; 2:E10. [PMID: 29657269 PMCID: PMC5831929 DOI: 10.3390/ncrna2040010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 09/28/2016] [Indexed: 11/30/2022] Open
Abstract
Please note that in the published editorial [1], affiliations 1, and 8 contained errors.[...].
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Affiliation(s)
- Daniel Gautheret
- Institute for Integrative Biology of the Cell CNRS, CEA, Universite Paris-Sud. 91198 Gif sur Yvette, France.
| | - Joseph H Taube
- Department of Biology, Baylor University, Waco, Texas, USA.
| | - Sendurai A Mani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
- Metastasis Research Center, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
| | - Gaetano Santulli
- College of Physicians & Surgeons, Columbia University Medical Center, 1150 St Nicholas Avenue, New York, NY 10032, USA.
| | - Diego Cuerda-Gil
- Department of Molecular Genetics, Ohio State University, 570 Aronoff Laboratory, 318 West 12th Avenue, Columbus, OH 43210, USA.
| | - R Keith Slotkin
- Department of Molecular Genetics, Ohio State University, 570 Aronoff Laboratory, 318 West 12th Avenue, Columbus, OH 43210, USA.
| | - Bo Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yanli Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - David W Salzman
- Department of Radiation Oncology, UCLA David Geffen School of Medicine, Professor, Director, Translational Research, Los Angeles, California 90024, USA.
| | - Joanne B Weidhaas
- Department of Radiation Oncology, UCLA David Geffen School of Medicine, Professor, Director, Translational Research, Los Angeles, California 90024, USA.
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33
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Panda K, Ji L, Neumann DA, Daron J, Schmitz RJ, Slotkin RK. Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation. Genome Biol 2016; 17:170. [PMID: 27506905 PMCID: PMC4977677 DOI: 10.1186/s13059-016-1032-y] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 07/26/2016] [Indexed: 01/06/2023] Open
Abstract
Background Chromatin modifications such as DNA methylation are targeted to transposable elements by small RNAs in a process termed RNA-directed DNA methylation (RdDM). In plants, canonical RdDM functions through RNA polymerase IV to reinforce pre-existing transposable element silencing. Recent investigations have identified a “non-canonical” form of RdDM dependent on RNA polymerase II expression to initiate and re-establish silencing of active transposable elements. This expression-dependent RdDM mechanism functions through RNAi degradation of transposable element mRNAs into small RNAs guided by the RNA-dependent RNA polymerase 6 (RDR6) protein and is therefore referred to as RDR6-RdDM. Results We performed whole-genome MethylC-seq in 20 mutants that distinguish RdDM mechanisms when transposable elements are either transcriptionally silent or active. We identified a new mechanism of expression-dependent RdDM, which functions through DICER-LIKE3 (DCL3) but bypasses the requirement of both RNA polymerase IV and RDR6 (termed DCL3-RdDM). We found that RNA polymerase II expression-dependent forms of RdDM function on over 20 % of transcribed transposable elements, including the majority of full-length elements with all of the domains required for autonomous transposition. Lastly, we find that RDR6-RdDM preferentially targets long transposable elements due to the specificity of primary small RNAs to cleave full-length mRNAs. Conclusions Expression-dependent forms of RdDM function to critically target DNA methylation to full-length and transcriptionally active transposable elements, suggesting that these pathways are key to suppressing mobilization. This targeting specificity is initiated on the mRNA cleavage-level, yet manifested as chromatin-level silencing that in plants is epigenetically inherited from generation to generation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1032-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kaushik Panda
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | | | - Josquin Daron
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | | | - R Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA.
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34
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Abstract
A report on the Plant Epigenetics: From Genotype to Phenotype Keystone Symposium held in Taos, New Mexico, USA, 15–19 February, 2016.
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Affiliation(s)
- R Keith Slotkin
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, Columbus, Ohio, 43210, USA.
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35
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Martínez G, Panda K, Köhler C, Slotkin RK. Silencing in sperm cells is directed by RNA movement from the surrounding nurse cell. Nat Plants 2016; 2:16030. [PMID: 27249563 DOI: 10.1038/nplants.2016.30] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 02/04/2016] [Indexed: 05/23/2023]
Abstract
Plant small interfering RNAs (siRNAs) communicate from cell to cell and travel long distances through the vasculature. However, siRNA movement into germ cells has remained controversial, and has gained interest because the terminally differentiated pollen vegetative nurse cell surrounding the sperm cells undergoes a programmed heterochromatin decondensation and transcriptional reactivation of transposable elements (TEs). Transcription of TEs leads to their post-transcriptional degradation into siRNAs, and it has been proposed that the purpose of this TE reactivation is to generate and load TE siRNAs into the sperm cells. Here, we identify the molecular pathway of TE siRNA production in the pollen grain and demonstrate that siRNAs produced from pollen vegetative cell transcripts can silence TE reporters in the sperm cells. Our data demonstrates that TE siRNAs act non-cell-autonomously, inhibiting TE activity in the germ cells and potentially the next generation.
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Affiliation(s)
- Germán Martínez
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, 500 Aronoff Laboratory, 318 West 12th Avenue, Columbus, Ohio 43210, USA
| | - Kaushik Panda
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, 500 Aronoff Laboratory, 318 West 12th Avenue, Columbus, Ohio 43210, USA
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, SE-750 07 Uppsala, Sweden
| | - R Keith Slotkin
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, 500 Aronoff Laboratory, 318 West 12th Avenue, Columbus, Ohio 43210, USA
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Sigman MJ, Slotkin RK. The First Rule of Plant Transposable Element Silencing: Location, Location, Location. Plant Cell 2016; 28:304-13. [PMID: 26869697 PMCID: PMC4790875 DOI: 10.1105/tpc.15.00869] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 12/18/2015] [Accepted: 02/10/2016] [Indexed: 05/18/2023]
Abstract
Transposable elements (TEs) are mobile units of DNA that comprise large portions of plant genomes. Besides creating mutations via transposition and contributing to genome size, TEs play key roles in chromosome architecture and gene regulation. TE activity is repressed by overlapping mechanisms of chromatin condensation, epigenetic transcriptional silencing, and targeting by small interfering RNAs. The specific regulation of different TEs, as well as their different roles in chromosome architecture and gene regulation, is specified by where on the chromosome the TE is located: near a gene, within a gene, in a pericentromere/TE island, or at the centromere core. In this Review, we investigate the silencing mechanisms responsible for inhibiting TE activity for each of these chromosomal contexts, emphasizing that chromosomal location is the first rule dictating the specific regulation of each TE.
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Affiliation(s)
- Meredith J Sigman
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
| | - R Keith Slotkin
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
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Fultz D, Choudury SG, Slotkin RK. Silencing of active transposable elements in plants. Curr Opin Plant Biol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Ferracin M, Gautheret D, Hubé F, Mani SA, Mattick JS, Ørom UA, Santulli G, Slotkin RK, Szweykowska-Kulinska Z, Taube JH, Vazquez F, Yang JH. The Non-Coding RNA Journal Club: Highlights on Recent Papers. Noncoding RNA 2015. [PMCID: PMC5932541 DOI: 10.3390/ncrna1010087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Manuela Ferracin
- Department of Morphology, Pathology Oncology and Experimental Biology Section, University of Ferrara, Ferrara 44121, Italy; E-Mail:
- Laboratory for Technologies of Advanced Therapies, University of Ferrara, 44121 Ferrara, Italy
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91198 Gif sur Yvette, France; E-Mail:
| | - Florent Hubé
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Bâtiment Lamarck B, Case Courrier 7042, 35 rue Hélène Brion, 75013 Paris, France; E-Mail:
| | - Sendurai A. Mani
- Department of Molecular Pathology, The University of Texas MD Anderson Cancer Center, 77054 Houston, TX, USA; E-Mails: (S.A.M.); (J.T.)
| | - John S. Mattick
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia, and St Vincent’s Clinical School, University of New South Wales, Sydney, 2010 New South Wales, Australia; E-Mail:
| | - Ulf Andersson Ørom
- Noncoding RNA Research Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; E-Mail:
| | - Gaetano Santulli
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, College of Physicians and Surgeons, Columbia University Medical Center, New York, 10032 NY, USA; E-Mail:
| | - R. Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, 43210 OH, USA; E-Mail:
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland; E-Mail:
| | - Joseph H. Taube
- Department of Molecular Pathology, The University of Texas MD Anderson Cancer Center, 77054 Houston, TX, USA; E-Mails: (S.A.M.); (J.T.)
| | - Franck Vazquez
- MDPI AG, Non-Coding RNA Editorial Office; Klybeckstrasse 64, 4057 Basel, Switzerland
- Author to whom correspondence should be addressed; E-Mail:
| | - Jian-Hua Yang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, 510275 Guangzhou, China; E-Mail:
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Singh PK, Bourque G, Craig NL, Dubnau JT, Feschotte C, Flasch DA, Gunderson KL, Malik HS, Moran JV, Peters JE, Slotkin RK, Levin HL. Mobile genetic elements and genome evolution 2014. Mob DNA 2014; 5:26. [PMID: 30117500 PMCID: PMC4363357 DOI: 10.1186/1759-8753-5-26] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 10/02/2014] [Indexed: 11/10/2022] Open
Abstract
The Mobile Genetic Elements and Genome Evolution conference was hosted by Keystone Symposia in Santa Fe, NM USA, 9 March through 14 March 2014. The goal of this conference was to bring together scientists from around the world who study transposable elements in diverse organisms and researchers who study the impact these elements have on genome evolution. The meeting included over 200 scientists who participated through poster presentations, short talks selected from abstracts, and invited speakers. The talks were organized into eight sessions and two workshops. The topics varied from diverse mechanisms of mobilization to the evolution of genomes and their defense strategies against transposable elements.
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Affiliation(s)
- Parmit Kumar Singh
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| | - Guillaume Bourque
- McGill University and Genome Quebec Innovation Center, Montreal, Canada
| | - Nancy L Craig
- School of Medicine, The Johns Hopkins University, Baltimore, MD USA.,Howard Hughes Medical Institute, Chevy Chase, MD USA
| | - Josh T Dubnau
- Cold Spring Harbor Laboratory, Cold Spring Harbor, Cold Spring, NY USA
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Diane A Flasch
- Department of Human Genetics, University of Michigan, Ann Arbor, MI USA
| | | | - Harmit Singh Malik
- Howard Hughes Medical Institute, Chevy Chase, MD USA.,Division of Basic Science, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - John V Moran
- Howard Hughes Medical Institute, Chevy Chase, MD USA.,Department of Human Genetics, University of Michigan, Ann Arbor, MI USA
| | - Joseph E Peters
- Department of Microbiology, Cornell University, Ithaca, NY USA
| | - R Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, OH USA
| | - Henry L Levin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
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McCue AD, Panda K, Nuthikattu S, Choudury SG, Thomas EN, Slotkin RK. ARGONAUTE 6 bridges transposable element mRNA-derived siRNAs to the establishment of DNA methylation. EMBO J 2014; 34:20-35. [PMID: 25388951 DOI: 10.15252/embj.201489499] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Transposable elements (TEs) generate mutations and chromosomal instability when active. To repress TE activity, eukaryotic cells evolved mechanisms to both degrade TE mRNAs into small interfering RNAs (siRNAs) and modify TE chromatin to epigenetically inhibit transcription. Since the populations of small RNAs that participate in TE post-transcriptional regulation differ from those that establish RNA-directed DNA methylation (RdDM), the mechanism through which transcriptionally active TEs transition from post-transcriptional RNAi regulation to chromatin level control has remained unclear. We have identified the molecular mechanism of a plant pathway that functions to direct DNA methylation to transcriptionally active TEs. We demonstrated that 21-22 nucleotide (nt) siRNA degradation products from the RNAi of TE mRNAs are directly incorporated into the ARGONAUTE 6 (AGO6) protein and direct AGO6 to TE chromatin to guide its function in RdDM. We find that this pathway functions in reproductive precursor cells to primarily target long centromeric high-copy transcriptionally active TEs for RdDM prior to gametogenesis. This study provides a direct mechanism that bridges the gap between the post-transcriptional regulation of TEs and the establishment of TE epigenetic silencing.
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Affiliation(s)
- Andrea D McCue
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Kaushik Panda
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | | | - Sarah G Choudury
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Erica N Thomas
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - R Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
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Panda K, Slotkin RK. Proposed mechanism for the initiation of transposable element silencing by the RDR6-directed DNA methylation pathway. Plant Signal Behav 2013; 8:25206. [PMID: 23759554 PMCID: PMC3999056 DOI: 10.4161/psb.25206] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 05/29/2013] [Indexed: 05/18/2023]
Abstract
The activity of transposable elements is epigenetically suppressed by both transcriptional and post-transcriptional mechanisms. We recently identified a direct connection between the small RNA-mediated post-transcriptional mRNA degradation of actively transcribing transposable elements and the de novo methylation of transposable element DNA, providing a mechanistic link between these two established pathways of transposable element silencing. Here we provide a model for the initiation, establishment and epigenetic maintenance of transposable element silencing that incorporates recent data in this rapidly emerging field.
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Abstract
Transposable elements (TEs) are known to influence the regulation of neighboring genes through a variety of mechanisms. Additionally, it was recently discovered that TEs can regulate non-neighboring genes through the trans-acting nature of small interfering RNAs (siRNAs). When the epigenetic repression of TEs is lost, TEs become transcriptionally active, and the host cell acts to repress mutagenic transposition by degrading TE mRNAs into siRNAs. In this study, we have performed a genome-wide analysis in the model plant Arabidopsis thaliana and found that TE siRNA-based regulation of genic mRNAs is more pervasive than the two formerly characterized proof-of-principle examples. We identified 27 candidate genic mRNAs that do not contain a TE fragment but are regulated through partial complementarity by the accumulation of TE siRNAs and are therefore influenced by TE epigenetic activation. We have experimentally confirmed several gene targets and demonstrated that they respond to the accumulation of specific 21 nucleotide TE siRNAs that are incorporated into the Arabidopsis Argonaute1 protein. Additionally, we found that one TE siRNA specifically targets and inhibits the formation of a host protein that acts to repress TE activity, suggesting that TEs harbor and potentially evolutionarily select short sequences to act as suppressors of host TE repression.
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Affiliation(s)
- Andrea D McCue
- Department of Molecular Genetics & Center for RNA Biology; The Ohio State University; Columbus, OH, USA
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Abstract
In plants, RNA silencing is a fundamental regulator of gene expression, heterochromatin formation, suppression of transposable elements, and defense against viruses. The sequence specificity of these processes relies on small noncoding RNA (sRNA) molecules. Although the spreading of RNA silencing across the plant has been recognized for nearly two decades, only recently have sRNAs been formally demonstrated as the mobile silencing signals. Here, we discuss the various types of mobile sRNA molecules, their short- and long-range movement, and their function in recipient cells.
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Nuthikattu S, McCue AD, Panda K, Fultz D, DeFraia C, Thomas EN, Slotkin RK. The initiation of epigenetic silencing of active transposable elements is triggered by RDR6 and 21-22 nucleotide small interfering RNAs. Plant Physiol 2013; 162:116-31. [PMID: 23542151 PMCID: PMC3641197 DOI: 10.1104/pp.113.216481] [Citation(s) in RCA: 211] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 03/28/2013] [Indexed: 05/18/2023]
Abstract
Transposable elements (TEs) are mobile fragments of DNA that are repressed in both plant and animal genomes through the epigenetic inheritance of repressed chromatin and expression states. The epigenetic silencing of TEs in plants is mediated by a process of RNA-directed DNA methylation (RdDM). Two pathways of RdDM have been identified: RNA Polymerase IV (Pol IV)-RdDM, which has been shown to be responsible for the de novo initiation, corrective reestablishment, and epigenetic maintenance of TE and/or transgene silencing; and RNA-dependent RNA Polymerase6 (RDR6)-RdDM, which was recently identified as necessary for maintaining repression for a few TEs. We have further characterized RDR6-RdDM using a genome-wide search to identify TEs that generate RDR6-dependent small interfering RNAs. We have determined that TEs only produce RDR6-dependent small interfering RNAs when transcriptionally active, and we have experimentally identified two TE subfamilies as direct targets of RDR6-RdDM. We used these TEs to test the function of RDR6-RdDM in assays for the de novo initiation, corrective reestablishment, and maintenance of TE silencing. We found that RDR6-RdDM plays no role in maintaining TE silencing. Rather, we found that RDR6 and Pol IV are two independent entry points into RdDM and epigenetic silencing that perform distinct functions in the silencing of TEs: Pol IV-RdDM functions to maintain TE silencing and to initiate silencing in an RNA Polymerase II expression-independent manner, while RDR6-RdDM functions to recognize active Polymerase II-derived TE mRNA transcripts to both trigger and correctively reestablish TE methylation and epigenetic silencing.
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Martínez G, Slotkin RK. Developmental relaxation of transposable element silencing in plants: functional or byproduct? Curr Opin Plant Biol 2012; 15:496-502. [PMID: 23022393 DOI: 10.1016/j.pbi.2012.09.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 07/12/2012] [Accepted: 09/05/2012] [Indexed: 05/14/2023]
Abstract
In plants, the developmental relaxation of transposable element silencing (DRTS) occurs at distinct spatial and temporal points in the normal development of a wild-type individual. Several examples of DRTS have now been described, including in maize shoot apical meristems, and in Arabidopsis meiocytes, endosperm and nurse cells of gametophytes. In this opinion article, we review the known DRTS events and speculate on the function, if any, of DRTS in plants.
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Affiliation(s)
- Germán Martínez
- The Department of Molecular Genetics and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
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47
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Borges F, Gardner R, Lopes T, Calarco JP, Boavida LC, Slotkin RK, Martienssen RA, Becker JD. FACS-based purification of Arabidopsis microspores, sperm cells and vegetative nuclei. Plant Methods 2012; 8:44. [PMID: 23075219 PMCID: PMC3502443 DOI: 10.1186/1746-4811-8-44] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 10/08/2012] [Indexed: 05/19/2023]
Abstract
BACKGROUND The male germline in flowering plants differentiates by asymmetric division of haploid uninucleated microspores, giving rise to a vegetative cell enclosing a smaller generative cell, which eventually undergoes a second mitosis to originate two sperm cells. The vegetative cell and the sperm cells activate distinct genetic and epigenetic mechanisms to control pollen tube growth and germ cell specification, respectively. Therefore, a comprehensive characterization of these processes relies on efficient methods to isolate each of the different cell types throughout male gametogenesis. RESULTS We developed stable transgenic Arabidopsis lines and reliable purification tools based on Fluorescence-Activated Cell Sorting (FACS) in order to isolate highly pure and viable fractions of each cell/nuclei type before and after pollen mitosis. In the case of mature pollen, this was accomplished by expressing GFP and RFP in the sperm and vegetative nuclei, respectively, resulting in 99% pure sorted populations. Microspores were also purified by FACS taking advantage of their characteristic small size and autofluorescent properties, and were confirmed to be 98% pure. CONCLUSIONS We provide simple and efficient FACS-based purification protocols for Arabidopsis microspores, vegetative nuclei and sperm cells. This paves the way for subsequent molecular analysis such as transcriptomics, DNA methylation analysis and chromatin immunoprecipitation, in the developmental context of microgametogenesis in Arabidopsis.
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Affiliation(s)
- Filipe Borges
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Rui Gardner
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Telma Lopes
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Joseph P Calarco
- Cold Spring Harbor Laboratory, 1 Bungtown Road, 11724, Cold Spring Harbor, NY, USA
| | - Leonor C Boavida
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - R Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, 43210, Columbus, OH, USA
| | - Robert A Martienssen
- Cold Spring Harbor Laboratory, 1 Bungtown Road, 11724, Cold Spring Harbor, NY, USA
| | - Jörg D Becker
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
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McCue AD, Slotkin RK. Transposable element small RNAs as regulators of gene expression. Trends Genet 2012; 28:616-23. [PMID: 23040327 DOI: 10.1016/j.tig.2012.09.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 08/31/2012] [Accepted: 09/05/2012] [Indexed: 11/30/2022]
Abstract
Transposable elements (TEs) are a source of endogenous small RNAs in animals and plants. These TE-derived small RNAs have been traditionally treated as functionally distinct from gene-regulating small RNAs, such as miRNAs. Two recent reports in Drosophila and Arabidopsis have blurred the lines of this distinction. In both examples, epigenetically and developmentally regulated bursts in TE expression produce gene-regulating small RNAs. In the Drosophila early embryo, maternally deposited TE-derived PIWI-interacting small RNAs (piRNAs) play a role in regulating the nanos mRNA through small RNA binding sites in the nanos 3' untranslated region (UTR). In Arabidopsis, when Athila retrotransposons are epigenetically activated, their transcripts are processed into small RNAs, which directly target the 3'UTR of the genic oligouridylate binding protein 1B (UBP1b) mRNA. Based on these two examples, we suggest that other TE-derived small RNAs regulate additional genes and propose that, through small RNAs, the epigenetic status of TEs could widely influence the genic transcriptome.
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Affiliation(s)
- Andrea D McCue
- Department of Molecular Genetics & Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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McCue AD, Nuthikattu S, Reeder SH, Slotkin RK. Gene expression and stress response mediated by the epigenetic regulation of a transposable element small RNA. PLoS Genet 2012; 8:e1002474. [PMID: 22346759 PMCID: PMC3276544 DOI: 10.1371/journal.pgen.1002474] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 11/28/2011] [Indexed: 12/29/2022] Open
Abstract
The epigenetic activity of transposable elements (TEs) can influence the regulation of genes; though, this regulation is confined to the genes, promoters, and enhancers that neighbor the TE. This local cis regulation of genes therefore limits the influence of the TE's epigenetic regulation on the genome. TE activity is suppressed by small RNAs, which also inhibit viruses and regulate the expression of genes. The production of TE heterochromatin-associated endogenous small interfering RNAs (siRNAs) in the reference plant Arabidopsis thaliana is mechanistically distinct from gene-regulating small RNAs, such as microRNAs or trans-acting siRNAs (tasiRNAs). Previous research identified a TE small RNA that potentially regulates the UBP1b mRNA, which encodes an RNA–binding protein involved in stress granule formation. We demonstrate that this siRNA, siRNA854, is under the same trans-generational epigenetic control as the Athila family LTR retrotransposons from which it is produced. The epigenetic activation of Athila elements results in a shift in small RNA processing pathways, and new 21–22 nucleotide versions of Athila siRNAs are produced by protein components normally not responsible for processing TE siRNAs. This processing results in siRNA854's incorporation into ARGONAUTE1 protein complexes in a similar fashion to gene-regulating tasiRNAs. We have used reporter transgenes to demonstrate that the UPB1b 3′ untranslated region directly responds to the epigenetic status of Athila TEs and the accumulation of siRNA854. The regulation of the UPB1b 3′ untranslated region occurs both on the post-transcriptional and translational levels when Athila TEs are epigenetically activated, and this regulation results in the phenocopy of the ubp1b mutant stress-sensitive phenotype. This demonstrates that a TE's epigenetic activity can modulate the host organism's stress response. In addition, the ability of this TE siRNA to regulate a gene's expression in trans blurs the lines between TE and gene-regulating small RNAs. The portion of the genome that does not encode for genes is often overlooked as a source of cellular regulatory information. Here, we demonstrate that regulatory information controlling expression and protein production from a gene called UBP1b is coming from a distant non-gene transposable element (TE). TEs are fragments of DNA that, unlike genes, are capable of duplicating themselves from one location in the genome to another, and occupy nearly half of the human genome. TEs are often referred to as “junk DNA,” as the study of cellular regulation and function is focused on genes. The regulation of TEs is distinct from genes, as a process termed epigenetic silencing heritably represses TE expression and activity. We have demonstrated that the epigenetic status (active versus silenced) of the Athila TE family regulates the UBP1b gene through the activity of a TE small RNA. The function of the UPB1b gene is to respond to and regulate cellular stress, and the epigenetic regulatory status of the Athila TE therefore modulates this stress response. This demonstrates that the epigenetic regulation of TEs can be a source of gene regulatory information, influencing a basic cellular function such as the stress response.
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Affiliation(s)
- Andrea D. McCue
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Saivageethi Nuthikattu
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Sarah H. Reeder
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - R. Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- The Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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50
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Borges F, Pereira PA, Slotkin RK, Martienssen RA, Becker JD. MicroRNA activity in the Arabidopsis male germline. J Exp Bot 2011; 62:1611-20. [PMID: 21357774 PMCID: PMC5536363 DOI: 10.1093/jxb/erq452] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 12/13/2010] [Accepted: 12/15/2010] [Indexed: 05/19/2023]
Abstract
Most of the core proteins involved in the microRNA (miRNA) pathway in plants have been identified, and almost simultaneously hundreds of miRNA sequences processed in the Arabidopsis sporophyte have been discovered by exploiting next-generation sequencing technologies. However, there is very limited understanding about potentially distinct mechanisms of post-transcriptional regulation between different cell lineages. In this review the focus is on the Arabidopsis male gametophyte (pollen), where the germline differentiates after meiosis giving rise to the male gametes. Based on comparative analysis of miRNAs identified in sperm cells by in-depth sequencing, their possible functions during germ cell specification and beyond fertilization are discussed. In addition, 25 potentially novel miRNAs processed in sperm cells and pollen were identified, as well as enriched variations in the sequence length of known miRNAs, which might indicate subfunctionalization by association with a putative germline-specific Argonaute complex. ARGONAUTE 5 (AGO5), by close homology to AGO1 and localizing preferentially to the sperm cell cytoplasm in mature pollen, may be part of such a complex.
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