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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...me2 but high DNA methylation (except state 20, which is enriched in transcriptional start sites), corresponding to >80% of SUVH1 and SUVH3-binding sites; states 14 and 15 (5034 loci; 7.8% of the ), long TEs enriched in DNA methylation and H3K9me2, contributing to 25% of MBD5 and MBD6 targets, which...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...and fungal s to highlight parallel themes and contrasting modes of organization. We review the main architectural types of plant centromeres and their epigenetic states, including patterns of CENH3 nucleosome occupancy and DNA cytosine methylation. Finally, we consider the implications of centromere genetic...
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Research: Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions
- Kyuha Choi,
- Xiaohui Zhao,
- Andrew J. Tock,
- Christophe Lambing,
- Charles J. Underwood,
- Thomas J. Hardcastle,
- Heïdi Serra,
- Juhyun Kim,
- Hyun Seob Cho,
- Jaeil Kim,
- Piotr A. Ziolkowski,
- Nataliya E. Yelina,
- Ildoo Hwang,
- Robert A. Martienssen,
- and Ian R. Henderson
Genome Res. April 2018 28: 532-546; Published in Advance March 12, 2018, doi:10.1101/gr.225599.117
...methylation/H3K9me2 pathway show both increased pericentromeric SPO11-1-oligos and crossovers (Underwood et al. 2018). This indicates that although both CG and non-CG DNA methylation inhibit pericentromeric meiotic DSBs, only non-CG methylation and/or H3K9me2 inhibit crossovers (Underwood et al. 2018).Despite...
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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
...(RdDM). Best studied in Arabidopsis thaliana, during RdDM, H3K9me2 and DNA methylation recruit the plant-specific RNA polymerases (Pol) IV and V. Pol IV transcripts are processed into 24 nt siRNAs, which, loaded into members of the AGO4/6 clade, target Pol V transcripts to guide the sequence...
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Research: Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population
- Robert J. Schmitz,
- Yupeng He,
- Oswaldo Valdés-López,
- Saad M. Khan,
- Trupti Joshi,
- Mark A. Urich,
- Joseph R. Nery,
- Brian Diers,
- Dong Xu,
- Gary Stacey,
- and Joseph R. Ecker
Genome Res. October 2013 23: 1663-1674; Published in Advance June 5, 2013, doi:10.1101/gr.152538.112
...with a recently reported DNA methylome for Arabidopsis thaliana (Fig. 1A; Schmitz et al. 2011). Of the cytosines that are methylated in the LD , there are almost equal numbers of mCG andmCHG, which contrasts to the Arabidopsis thaliana methylome (Fig. 1B) and could indicate that RdDM targets a greater proportion...
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Research: Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation
- Andrew J. Tock,
- Daniel M. Holland,
- Wei Jiang,
- Kim Osman,
- Eugenio Sanchez-Moran,
- James D. Higgins,
- Keith J. Edwards,
- Cristobal Uauy,
- F. Chris H. Franklin,
- and Ian R. Henderson
Genome Res. September 2021 31: 1614-1628; Published in Advance August 23, 2021, doi:10.1101/gr.273672.120
..., and euchromatic (H3K4me3, H3K9ac, and H3K27ac) and facultative heterochromatic (H3K27me3) marks increase toward the telomeres, whereas Gypsy LTR retrotransposon density and constitutive heterochromatic marks (H3K9me2 and CG- and CHG-context DNA methylation) increase toward the centromeres (Choulet et al. 2014...
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Research: Differences in activity and stability drive transposable element variation in tropical and temperate maize
- Shujun Ou,
- Armin Scheben,
- Tyler Collins,
- Yinjie Qiu,
- Arun S. Seetharam,
- Claire C. Menard,
- Nancy Manchanda,
- Jonathan I. Gent,
- Michael C. Schatz,
- Sarah N. Anderson,
- Matthew B. Hufford,
- and Candice N. Hirsch
Genome Res. August 2024 34: 1140-1153; Published in Advance September 9, 2024, doi:10.1101/gr.278131.123
...) contributing 3.9 Mb of the size difference. Conversely, Young Ty1 LTRs that were preferentially removed in temperate s contributed 4.9 Mb or 14.1% to TE-content difference (Fig. 4F), with the ji_AC215728_13156 family contributing 2.9 Mb of this size difference. Notably, the xilon_diguus family is found in DNA...

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