Todd Blevins, PhD. Group leader at UPR 2357 – IBMP CNRS
![Todd Blevins](https://labex-netrna.cnrs.fr/wp-content/uploads/2021/05/Todd_Blevins.png)
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
Working Group
Publications
2021
Wierzbicki, A T; Blevins, T; Swiezewski, S
Long Noncoding RNAs in Plants Article de journal
Dans: Annu Rev Plant Biol, p. Online ahead of print, 2021, ISBN: 33752440, (1545-2123 (Electronic) 1543-5008 (Linking) Journal Article).
@article{nokey,
title = {Long Noncoding RNAs in Plants},
author = {A T Wierzbicki and T Blevins and S 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 = {2021-01-01},
journal = {Annu Rev Plant Biol},
pages = {Online ahead of print},
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}
}
2020
Bohrer, M; Rymen, B; Himber, C; Gerbaud, A; Pflieger, D; Laudencia-Chingcuanco, D; Cartwright, A; Vogel, J; Sibout, R; Blevins, T
Integrated Genome-Scale Analysis and Northern Blot Detection of Retrotransposon siRNAs Across Plant Species Article de journal
Dans: Methods Mol Biol, vol. 2166, p. 387-411, 2020, ISBN: 32710422, (1940-6029 (Electronic) 1064-3745 (Linking) Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.).
@article{nokey,
title = {Integrated Genome-Scale Analysis and Northern Blot Detection of Retrotransposon siRNAs Across Plant Species},
author = {M Bohrer and B Rymen and C Himber and A Gerbaud and D Pflieger and D Laudencia-Chingcuanco and A Cartwright and J Vogel and R Sibout and T Blevins},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=32710422},
doi = {10.1007/978-1-0716-0712-1_23},
isbn = {32710422},
year = {2020},
date = {2020-01-01},
journal = {Methods Mol Biol},
volume = {2166},
pages = {387-411},
abstract = {Cells have sophisticated RNA-directed mechanisms to regulate genes, destroy viruses, or silence transposable elements (TEs). In terrestrial plants, a specialized non-coding RNA machinery involving RNA polymerase IV (Pol IV) and small interfering RNAs (siRNAs) targets DNA methylation and silencing to TEs. Here, we present a bioinformatics protocol for annotating and quantifying siRNAs that derive from long terminal repeat (LTR) retrotransposons. The approach was validated using small RNA northern blot analyses, comparing the species Arabidopsis thaliana and Brachypodium distachyon. To assist hybridization probe design, we configured a genome browser to show small RNA-seq mappings in distinct colors and shades according to their nucleotide lengths and abundances, respectively. Samples from wild-type and pol IV mutant plants, cross-species negative controls, and a conserved microRNA control validated the detected siRNA signals, confirming their origin from specific TEs and their Pol IV-dependent biogenesis. Moreover, an optimized labeling method yielded probes that could detect low-abundance siRNAs from B. distachyon TEs. The integration of de novo TE annotation, small RNA-seq profiling, and northern blotting, as outlined here, will facilitate the comparative genomic analysis of RNA silencing in crop plants and non-model species.},
note = {1940-6029 (Electronic)
1064-3745 (Linking)
Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Rymen, B; Ferrafiat, L; Blevins, T
Non-coding RNA polymerases that silence transposable elements and reprogram gene expression in plants Article de journal
Dans: Transcription, vol. 11, no. 3-4, p. 172-191, 2020, ISBN: 33180661, (2154-1272 (Electronic) 2154-1272 (Linking) Journal Article Research Support, Non-U.S. Gov't).
@article{nokey,
title = {Non-coding RNA polymerases that silence transposable elements and reprogram gene expression in plants},
author = {B Rymen and L Ferrafiat and T Blevins},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33180661},
doi = {10.1080/21541264.2020.1825906},
isbn = {33180661},
year = {2020},
date = {2020-01-01},
journal = {Transcription},
volume = {11},
number = {3-4},
pages = {172-191},
abstract = {Multisubunit RNA polymerase (Pol) complexes are the core machinery for gene expression in eukaryotes. The enzymes Pol I, Pol II and Pol III transcribe distinct subsets of nuclear genes. This family of nuclear RNA polymerases expanded in terrestrial plants by the duplication of Pol II subunit genes. Two Pol II-related enzymes, Pol IV and Pol V, are highly specialized in the production of regulatory, non-coding RNAs. Pol IV and Pol V are the central players of RNA-directed DNA methylation (RdDM), an RNA interference pathway that represses transposable elements (TEs) and selected genes. Genetic and biochemical analyses of Pol IV/V subunits are now revealing how these enzymes evolved from ancestral Pol II to sustain non-coding RNA biogenesis in silent chromatin. Intriguingly, Pol IV-RdDM regulates genes that influence flowering time, reproductive development, stress responses and plant-pathogen interactions. Pol IV target genes vary among closely related taxa, indicating that these regulatory circuits are often species-specific. Data from crops like maize, rice, tomato and Brassica rapa suggest that dynamic repositioning of TEs, accompanied by Pol IV targeting to TE-proximal genes, leads to the reprogramming of plant gene expression over short evolutionary timescales.},
note = {2154-1272 (Electronic)
2154-1272 (Linking)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2019
Blevins, T; Podicheti, R; Pikaard, C S
Analysis of siRNA Precursors Generated by RNA Polymerase IV and RNA-Dependent RNA Polymerase 2 in Arabidopsis Article de journal
Dans: Methods Mol Biol, vol. 1933, p. 33-48, 2019, ISBN: 30945177, (1940-6029 (Electronic) 1064-3745 (Linking) Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't).
@article{nokey,
title = {Analysis of siRNA Precursors Generated by RNA Polymerase IV and RNA-Dependent RNA Polymerase 2 in Arabidopsis},
author = {T Blevins and R Podicheti and C S Pikaard},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=30945177},
doi = {10.1007/978-1-4939-9045-0_2},
isbn = {30945177},
year = {2019},
date = {2019-01-01},
journal = {Methods Mol Biol},
volume = {1933},
pages = {33-48},
abstract = {Noncoding RNAs perform diverse regulatory functions in living cells. In plants, two RNA polymerase II-related enzymes, RNA polymerases IV and V (Pol IV and V), specialize in the synthesis of noncoding RNAs that silence a subset of transposable elements and genes via RNA-directed DNA methylation (RdDM). In this process, Pol IV partners with RNA-dependent RNA polymerase 2 (RDR2) to produce double-stranded RNAs that are then cut by an RNase III enzyme, Dicer-like 3 (DCL3), into 24 nt small interfering RNAs (siRNAs). The siRNAs are loaded into an Argonaute family protein, primarily AGO4, and guide the complex to complementary DNA target sequences where RdDM and repressive chromatin modifications ensue. The dependence of 24 nt siRNA biogenesis on Pol IV and RDR2 has been known for more than a decade, but the elusive pre-siRNA transcripts synthesized by Pol IV and RDR2 have only recently been identified. This chapter describes the approaches that enabled our identification of Pol IV/RDR2-dependent RNAs (P4R2 RNAs) in Arabidopsis thaliana. These included the use of a triple Dicer mutant (dcl2 dcl3 dcl4) to cause P4R2 RNAs to accumulate, genome-wide identification and mapping of P4R2 RNAs using a modified Illumina small RNA-Seq protocol, and multiple bioinformatic pipelines for data analysis and displaying results.},
note = {1940-6029 (Electronic)
1064-3745 (Linking)
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ferrafiat, L; Pflieger, D; Singh, J; Thieme, M; Bohrer, M; Himber, C; Gerbaud, A; Bucher, E; Pikaard, C S; Blevins, T
The NRPD1 N-terminus contains a Pol IV-specific motif that is critical for genome surveillance in Arabidopsis Article de journal
Dans: Nucleic Acids Res, vol. 47, no. 17, p. 9037-9052, 2019, ISBN: 31372633, (1362-4962 (Electronic) 0305-1048 (Linking) Journal Article Research Support, Non-U.S. Gov't).
@article{nokey,
title = {The NRPD1 N-terminus contains a Pol IV-specific motif that is critical for genome surveillance in Arabidopsis},
author = {L Ferrafiat and D Pflieger and J Singh and M Thieme and M Bohrer and C Himber and A Gerbaud and E Bucher and C S Pikaard and T Blevins},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=31372633},
doi = {10.1093/nar/gkz618},
isbn = {31372633},
year = {2019},
date = {2019-01-01},
journal = {Nucleic Acids Res},
volume = {47},
number = {17},
pages = {9037-9052},
abstract = {RNA-guided surveillance systems constrain the activity of transposable elements (TEs) in host genomes. In plants, RNA polymerase IV (Pol IV) transcribes TEs into primary transcripts from which RDR2 synthesizes double-stranded RNA precursors for small interfering RNAs (siRNAs) that guide TE methylation and silencing. How the core subunits of Pol IV, homologs of RNA polymerase II subunits, diverged to support siRNA biogenesis in a TE-rich, repressive chromatin context is not well understood. Here we studied the N-terminus of Pol IV's largest subunit, NRPD1. Arabidopsis lines harboring missense mutations in this N-terminus produce wild-type (WT) levels of NRPD1, which co-purifies with other Pol IV subunits and RDR2. Our in vitro transcription and genomic analyses reveal that the NRPD1 N-terminus is critical for robust Pol IV-dependent transcription, siRNA production and DNA methylation. However, residual RNA-directed DNA methylation observed in one mutant genotype indicates that Pol IV can operate uncoupled from the high siRNA levels typically observed in WT plants. This mutation disrupts a motif uniquely conserved in Pol IV, crippling the enzyme's ability to inhibit retrotransposon mobilization. We propose that the NRPD1 N-terminus motif evolved to regulate Pol IV function in genome surveillance.},
note = {1362-4962 (Electronic)
0305-1048 (Linking)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {},
pubstate = {published},
tppubtype = {article}
}