Todd Blevins, PhD. Group leader at UPR 2357 – IBMP CNRS
Contact
Todd Blevins
Phone
E-Mail
Website
UPR 2357 – IBMP CNRS
Institut de Biologie Moléculaire des Plantes du CNRS
12 rue du Général Zimmer
67084 Strasbourg Cedex
France
Research topics
- Mechanisms of siRNA biogenesis and function in terrestrial plants
- RNA-directed DNA methylation via RNA polymerase IV (Pol IV)
- Pol IV function in transposable element and gene silencing
- Epigenetic versus genetic signals for Pol IV recruitment
Role in NetRNA
Eukaryotes have RNA silencing systems that regulate genes and silence transposable elements (TEs), with related pathways targeting viruses. The core mechanism relies on base-pairing of 21-29 nt small RNAs to complementary targets, guiding proteins to cleave mRNAs, inhibit translation or induce chromatin-level silencing. In plants, TE silencing is mediated by RNA polymerase IV (Pol IV), the biochemical machinery required for small RNA-directed DNA methylation. The team studies how Pol IV silences TEs and regulates genes in flowering plants. Using genomic, proteomic and structure-function approaches, they seek to understand how Pol IV reads and writes epigenetic marks, allowing it to protect genome integrity while modulating the expression of transcription factors involved in plant responses to the environment and pathogens.
Working Group
Publications
2024
Thieme, Michael; Minadakis, Nikolaos; Himber, Christophe; Keller, Bettina; Xu, Wenbo; Rutowicz, Kinga; Matteoli, Calvin; Böhrer, Marcel; Bart, Rymen; Laudencia-Chingcuanco, Debbie; Vogel, John; Sibout, Richard; Stritt, Christoph; Blevins, Todd; Roulin, Anne C.
Transposition of HOPPLA in siRNA-deficient plants suggests a limited effect of the environment on retrotransposon mobility in Brachypodium distachyon Journal Article
In: PLoS Genet, vol. 20, no. 3, pp. e1011200, 2024, ISSN: 1553-7390.
@article{nokey,
title = {Transposition of HOPPLA in siRNA-deficient plants suggests a limited effect of the environment on retrotransposon mobility in Brachypodium distachyon},
author = {Michael Thieme and Nikolaos Minadakis and Christophe Himber and Bettina Keller and Wenbo Xu and Kinga Rutowicz and Calvin Matteoli and Marcel Böhrer and Rymen Bart and Debbie Laudencia-Chingcuanco and John Vogel and Richard Sibout and Christoph Stritt and Todd Blevins and Anne C. Roulin},
doi = {10.1371/journal.pgen.1011200},
issn = {1553-7390},
year = {2024},
date = {2024-03-12},
urldate = {2024-03-12},
journal = {PLoS Genet},
volume = {20},
number = {3},
pages = {e1011200},
abstract = {Long terminal repeat retrotransposons (LTR-RTs) are powerful mutagens regarded as a major source of genetic novelty and important drivers of evolution. Yet, the uncontrolled and potentially selfish proliferation of LTR-RTs can lead to deleterious mutations and genome instability, with large fitness costs for their host. While population genomics data suggest that an ongoing LTR-RT mobility is common in many species, the understanding of their dual role in evolution is limited. Here, we harness the genetic diversity of 320 sequenced natural accessions of the Mediterranean grass Brachypodium distachyon to characterize how genetic and environmental factors influence plant LTR-RT dynamics in the wild. When combining a coverage-based approach to estimate global LTR-RT copy number variations with mobilome-sequencing of nine accessions exposed to eight different stresses, we find little evidence for a major role of environmental factors in LTR-RT accumulations in B. distachyon natural accessions. Instead, we show that loss of RNA polymerase IV (Pol IV), which mediates RNA-directed DNA methylation in plants, results in high transcriptional and transpositional activities of RLC_BdisC024 (HOPPLA) LTR-RT family elements, and that these effects are not stress-specific. This work supports findings indicating an ongoing mobility in B. distachyon and reveals that host RNA-directed DNA methylation rather than environmental factors controls their mobility in this wild grass model.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Long terminal repeat retrotransposons (LTR-RTs) are powerful mutagens regarded as a major source of genetic novelty and important drivers of evolution. Yet, the uncontrolled and potentially selfish proliferation of LTR-RTs can lead to deleterious mutations and genome instability, with large fitness costs for their host. While population genomics data suggest that an ongoing LTR-RT mobility is common in many species, the understanding of their dual role in evolution is limited. Here, we harness the genetic diversity of 320 sequenced natural accessions of the Mediterranean grass Brachypodium distachyon to characterize how genetic and environmental factors influence plant LTR-RT dynamics in the wild. When combining a coverage-based approach to estimate global LTR-RT copy number variations with mobilome-sequencing of nine accessions exposed to eight different stresses, we find little evidence for a major role of environmental factors in LTR-RT accumulations in B. distachyon natural accessions. Instead, we show that loss of RNA polymerase IV (Pol IV), which mediates RNA-directed DNA methylation in plants, results in high transcriptional and transpositional activities of RLC_BdisC024 (HOPPLA) LTR-RT family elements, and that these effects are not stress-specific. This work supports findings indicating an ongoing mobility in B. distachyon and reveals that host RNA-directed DNA methylation rather than environmental factors controls their mobility in this wild grass model.
Mohannath, Gireesh; McKinlay, Anastasia; Enganti, Ramya; Puppala, Navinchandra V.; Saradadevi, Gargi P.; Pikaard, Craig S.; Blevins, Todd
DNA hypermethylation and condensed chromatin correlate with chromosome-specific rRNA gene silencing in Arabidopsis Journal Article
In: bioRxiv, 2024, ISSN: 2692-8205.
@article{nokey,
title = {DNA hypermethylation and condensed chromatin correlate with chromosome-specific rRNA gene silencing in Arabidopsis},
author = {Gireesh Mohannath and Anastasia McKinlay and Ramya Enganti and Navinchandra V. Puppala and Gargi P. Saradadevi and Craig S. Pikaard and Todd Blevins},
doi = {10.1101/2023.02.03.526984},
issn = {2692-8205},
year = {2024},
date = {2024-03-01},
urldate = {2024-03-01},
journal = {bioRxiv},
abstract = {In eukaryotes, hundreds of ribosomal RNA (rRNA) genes are clustered at chromosomal loci called nucleolus organizer regions (NORs). Arabidopsis thaliana has two NORs, one on chromosome 2 (NOR2) and the other on chromosome 4 (NOR4). Each NOR consists of ∼ 400 rRNA gene copies. We recently showed that rRNA gene subtypes that map to NOR2 are silenced during development, whereas those that map to NOR4 are active. In several DNA methylation mutants of Arabidopsis, we show disruption of the NOR2 gene silencing to varying degrees. Significantly, the highest disruption of NOR2 gene silencing correlates with a maximum loss of cytosine methylation in the CHH context followed by the CG context, independent of RNA-directed DNA methylation (RdDM). Next, we show in Col-0 that NOR2 genes are relatively hypermethylated and NOR4 genes are hypomethylated using multiple methylation analysis of genomic DNA carried out with different types of methylation-sensitive restriction enzymes. We demonstrate similar differential methylation status between NOR2 and NOR4 genes in an introgression line named ColSf-NOR4, which carries NOR2 from Col-0 and NOR4 from ecotype Sf-2. Lastly, using Tn5 transposon-mediated transposition into native chromatin, we show that NOR2 gene chromatin is in more condensed state than NOR4 gene chromatin.
},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
In eukaryotes, hundreds of ribosomal RNA (rRNA) genes are clustered at chromosomal loci called nucleolus organizer regions (NORs). Arabidopsis thaliana has two NORs, one on chromosome 2 (NOR2) and the other on chromosome 4 (NOR4). Each NOR consists of ∼ 400 rRNA gene copies. We recently showed that rRNA gene subtypes that map to NOR2 are silenced during development, whereas those that map to NOR4 are active. In several DNA methylation mutants of Arabidopsis, we show disruption of the NOR2 gene silencing to varying degrees. Significantly, the highest disruption of NOR2 gene silencing correlates with a maximum loss of cytosine methylation in the CHH context followed by the CG context, independent of RNA-directed DNA methylation (RdDM). Next, we show in Col-0 that NOR2 genes are relatively hypermethylated and NOR4 genes are hypomethylated using multiple methylation analysis of genomic DNA carried out with different types of methylation-sensitive restriction enzymes. We demonstrate similar differential methylation status between NOR2 and NOR4 genes in an introgression line named ColSf-NOR4, which carries NOR2 from Col-0 and NOR4 from ecotype Sf-2. Lastly, using Tn5 transposon-mediated transposition into native chromatin, we show that NOR2 gene chromatin is in more condensed state than NOR4 gene chromatin.
2023
Felgines, Luisa; Rymen, Bart; Martins, Laura M.; Xu, Guanghui; Matteoli, Calvin; Himber, Christophe; Zhou, Ming; Eis, Josh; Coruh, Ceyda; Böhrer, Marcel; Kuhn, Lauriane; Chicher, Johana; Pandey, Vijaya; Hammann, Philippe; Wohlschlegel, James; Waltz, Florent; Law, Julie A.; Blevins, Todd
CLSY docking to Pol IV requires a conserved domain critical for small RNA biogenesis and transposon silencing Journal Article
In: bioRxiv, 2023, ISSN: 2692-8205.
@article{nokey,
title = {CLSY docking to Pol IV requires a conserved domain critical for small RNA biogenesis and transposon silencing},
author = {Luisa Felgines and Bart Rymen and Laura M. Martins and Guanghui Xu and Calvin Matteoli and Christophe Himber and Ming Zhou and Josh Eis and Ceyda Coruh and Marcel Böhrer and Lauriane Kuhn and Johana Chicher and Vijaya Pandey and Philippe Hammann and James Wohlschlegel and Florent Waltz and Julie A. Law and Todd Blevins},
doi = {10.1101/2023.12.26.573199},
issn = {2692-8205},
year = {2023},
date = {2023-12-26},
urldate = {2023-12-26},
journal = {bioRxiv},
abstract = {Eukaryotes must balance the need for gene transcription by RNA polymerase II (Pol II) against the danger of mutations caused by transposable element (TE) proliferation. In plants, these gene expression and TE silencing activities are divided between different RNA polymerases. Specifically, RNA polymerase IV (Pol IV), which evolved from Pol II, transcribes TEs to generate small interfering RNAs (siRNAs) that guide DNA methylation and block TE transcription by Pol II. While the Pol IV complex is recruited to TEs via SNF2-like CLASSY (CLSY) proteins, how Pol IV partners with the CLSYs remains unknown. Here we identified a conserved CYC-YPMF motif that is specific to Pol IV and is positioned on the complex exterior. Furthermore, we found that this motif is essential for the co-purification of all four CLSYs with Pol IV, but that only one CLSY is present in any given Pol IV complex. These findings support a “one CLSY per Pol IV” model where the CYC-YPMF motif acts as a CLSY-docking site. Indeed, mutations in and around this motif phenocopy pol iv null mutants. Together, these findings provide structural and functional insights into a critical protein feature that distinguishes Pol IV from other RNA polymerases, allowing it to promote genome stability by targeting TEs for silencing.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Eukaryotes must balance the need for gene transcription by RNA polymerase II (Pol II) against the danger of mutations caused by transposable element (TE) proliferation. In plants, these gene expression and TE silencing activities are divided between different RNA polymerases. Specifically, RNA polymerase IV (Pol IV), which evolved from Pol II, transcribes TEs to generate small interfering RNAs (siRNAs) that guide DNA methylation and block TE transcription by Pol II. While the Pol IV complex is recruited to TEs via SNF2-like CLASSY (CLSY) proteins, how Pol IV partners with the CLSYs remains unknown. Here we identified a conserved CYC-YPMF motif that is specific to Pol IV and is positioned on the complex exterior. Furthermore, we found that this motif is essential for the co-purification of all four CLSYs with Pol IV, but that only one CLSY is present in any given Pol IV complex. These findings support a “one CLSY per Pol IV” model where the CYC-YPMF motif acts as a CLSY-docking site. Indeed, mutations in and around this motif phenocopy pol iv null mutants. Together, these findings provide structural and functional insights into a critical protein feature that distinguishes Pol IV from other RNA polymerases, allowing it to promote genome stability by targeting TEs for silencing.
Chen, Ke; Liu, Hai; Blevins, Todd; Hao, Jie; Otten, Léon
Extensive natural Agrobacterium-induced transformation in the genus Camellia Journal Article
In: Planta, vol. 258, no. 4, pp. 81, 2023, ISSN: 1432-2048.
@article{pmid37715842,
title = {Extensive natural Agrobacterium-induced transformation in the genus Camellia},
author = {Ke Chen and Hai Liu and Todd Blevins and Jie Hao and Léon Otten},
doi = {10.1007/s00425-023-04234-9},
issn = {1432-2048},
year = {2023},
date = {2023-09-01},
urldate = {2023-09-01},
journal = {Planta},
volume = {258},
number = {4},
pages = {81},
abstract = {The genus Camellia underwent extensive natural transformation by Agrobacterium. Over a period of 15 million years, at least 12 different inserts accumulated in 72 investigated Camellia species. Like a wide variety of other wild and cultivated plants, Camellia species carry cellular T-DNA sequences (cT-DNAs) in their nuclear genomes, resulting from natural Agrobacterium-mediated transformation. Short and long DNA sequencing reads of 435 accessions belonging to 72 Camellia species (representing 12 out of 14 sections) were investigated for the occurrence of cT-DNA insertions. In all, 12 different cT-DNAs were recovered, either completely or partially, called CaTA to CaTL. Divergence analysis of internal cT-DNA repeats revealed that the insertion events span a period from 0.075 to 15 Mio years ago, and yielded an average transformation frequency of one event per 1.25 Mio years. The two oldest inserts, CaTA and CaTD, have been modified by spontaneous deletions and inversions, and by insertion of various plant sequences. In those cases where enough accessions were available (C. japonica, C. oleifera, C. chekiangoleosa, C. sasanqua and C. pitardii), the younger cT-DNA inserts showed a patchy distribution among different accessions of each species, indicating that they are not genetically fixed. It could be shown that Camellia breeding has led to intersectional transfer of cT-DNAs. Altogether, the cT-DNAs cover 374 kb, and carry 47 open reading frames (ORFs). Two Camellia cT-DNA genes, CaTH-orf358 and CaTK-orf8, represent new types of T-DNA genes. With its large number of cT-DNA sequences, the genus Camellia constitutes an interesting model for the study of natural Agrobacterium transformants.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The genus Camellia underwent extensive natural transformation by Agrobacterium. Over a period of 15 million years, at least 12 different inserts accumulated in 72 investigated Camellia species. Like a wide variety of other wild and cultivated plants, Camellia species carry cellular T-DNA sequences (cT-DNAs) in their nuclear genomes, resulting from natural Agrobacterium-mediated transformation. Short and long DNA sequencing reads of 435 accessions belonging to 72 Camellia species (representing 12 out of 14 sections) were investigated for the occurrence of cT-DNA insertions. In all, 12 different cT-DNAs were recovered, either completely or partially, called CaTA to CaTL. Divergence analysis of internal cT-DNA repeats revealed that the insertion events span a period from 0.075 to 15 Mio years ago, and yielded an average transformation frequency of one event per 1.25 Mio years. The two oldest inserts, CaTA and CaTD, have been modified by spontaneous deletions and inversions, and by insertion of various plant sequences. In those cases where enough accessions were available (C. japonica, C. oleifera, C. chekiangoleosa, C. sasanqua and C. pitardii), the younger cT-DNA inserts showed a patchy distribution among different accessions of each species, indicating that they are not genetically fixed. It could be shown that Camellia breeding has led to intersectional transfer of cT-DNAs. Altogether, the cT-DNAs cover 374 kb, and carry 47 open reading frames (ORFs). Two Camellia cT-DNA genes, CaTH-orf358 and CaTK-orf8, represent new types of T-DNA genes. With its large number of cT-DNA sequences, the genus Camellia constitutes an interesting model for the study of natural Agrobacterium transformants.
2021
Wierzbicki, Andrzej T.; Blevins, Todd; Swiezewski, Szymon
Long Noncoding RNAs in Plants Journal Article
In: Annu Rev Plant Biol, vol. 72, pp. 245-271, 2021, ISBN: 33752440, (1545-2123 (Electronic) 1543-5008 (Linking) Journal Article).
@article{nokey,
title = {Long Noncoding RNAs in Plants},
author = {Andrzej T. Wierzbicki and Todd Blevins and Szymon Swiezewski},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33752440},
doi = {10.1146/annurev-arplant-093020-035446},
isbn = {33752440},
year = {2021},
date = {2021-03-22},
urldate = {2021-01-01},
journal = {Annu Rev Plant Biol},
volume = {72},
pages = {245-271},
abstract = {Plants have an extraordinary diversity of transcription machineries, including five nuclear DNA-dependent RNA polymerases. Four of these enzymes are dedicated to the production of long noncoding RNAs (lncRNAs), which are ribonucleic acids with functions independent of their protein-coding potential. lncRNAs display a broad range of lengths and structures, but they are distinct from the small RNA guides of RNA interference (RNAi) pathways. lncRNAs frequently serve as structural, catalytic, or regulatory molecules for gene expression. They can affect all elements of genes, including promoters, untranslated regions, exons, introns, and terminators, controlling gene expression at various levels, including modifying chromatin accessibility, transcription, splicing, and translation. Certain lncRNAs protect genome integrity, while others respond to environmental cues like temperature, drought, nutrients, and pathogens. In this review, we explain the challenge of defining lncRNAs, introduce the machineries responsible for their production, and organize this knowledge by viewing the functions of lncRNAs throughout the structure of a typical plant gene. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
note = {1545-2123 (Electronic)
1543-5008 (Linking)
Journal Article},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Plants have an extraordinary diversity of transcription machineries, including five nuclear DNA-dependent RNA polymerases. Four of these enzymes are dedicated to the production of long noncoding RNAs (lncRNAs), which are ribonucleic acids with functions independent of their protein-coding potential. lncRNAs display a broad range of lengths and structures, but they are distinct from the small RNA guides of RNA interference (RNAi) pathways. lncRNAs frequently serve as structural, catalytic, or regulatory molecules for gene expression. They can affect all elements of genes, including promoters, untranslated regions, exons, introns, and terminators, controlling gene expression at various levels, including modifying chromatin accessibility, transcription, splicing, and translation. Certain lncRNAs protect genome integrity, while others respond to environmental cues like temperature, drought, nutrients, and pathogens. In this review, we explain the challenge of defining lncRNAs, introduce the machineries responsible for their production, and organize this knowledge by viewing the functions of lncRNAs throughout the structure of a typical plant gene. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.