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  1. Research: Resetting of the 24-nt siRNA landscape in rice zygotes
    • Chenxin Li,
    • Jonathan I. Gent,
    • Hengping Xu,
    • Hong Fu,
    • Scott D. Russell,
    • and Venkatesan Sundaresan
    Genome Res. February 2022 32: 309-323; Published in Advance December 23, 2021, doi:10.1101/gr.275981.121
    ...challenges, the epigenetic changes that accompany the transition from differentiated gametes to totipotent zygote are poorly understood. Because siRNAs serve as both regulators and outputs of the epi, we characterized small RNA transcriptomes of zygotes from rice. Zygote small RNAs exhibit extensive maternal...
  2. 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
    ...: arturo.mari-ordonez@gmi.oeaw.ac.atAbstractA handful of model plants have provided insight into silencing of transposable elements (TEs) through RNA-directed DNA methylation (RdDM). Guided by 24 nt long small-interfering RNAs (siRNAs), this epigenetic regulation installs DNA methylation and histone...
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  3. Research: Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains
    • Vivek Hari Sundar G,
    • Chenna Swetha,
    • Debjani Basu,
    • Kannan Pachamuthu,
    • Steffi Raju,
    • Tania Chakraborty,
    • Rebecca A. Mosher,
    • and P.V. Shivaprasad
    Genome Res. May 2023 33: 715-728; Published in Advance June 5, 2023, doi:10.1101/gr.277353.122
    ...and morphological phenotypes upon perturbation, especially in monocots with higher proportion of transposons. It has been conclusively documented that reproductive structures in rice, including gametes, undergo massive reprogramming in terms of sRNA production and DNA methylation in a locus-specific manner (Chenxin...
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  4. 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
    ...also bind states 10 and 17; and finally, state 16 (1802 loci; 1% of the ), which is defined by all mC readers and most histone marks, with repeats and, notably, ribosomal RNA, and corresponding to the shared cluster from Figure 2E (Supplemental Fig. S5C). Genome-wide correlation of ChIP-seq signal...
  5. Research: Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation
    • Charles J. Underwood,
    • Kyuha Choi,
    • Christophe Lambing,
    • Xiaohui Zhao,
    • Heïdi Serra,
    • Filipe Borges,
    • Joe Simorowski,
    • Evan Ernst,
    • Yannick Jacob,
    • Ian R. Henderson,
    • and Robert A. Martienssen
    Genome Res. April 2018 28: 519-531; Published in Advance March 12, 2018, doi:10.1101/gr.227116.117
    ...to wild type (Fig. 2C; Supplemental Table S6). Together, these data indicate that mutations in the H3K9me2/non-CG pathway primarily activate crossover frequency in proximity to the centromeres.View larger version: In this window In a new window Figure 2. Genome-wide mapping of crossover frequency in cmt3...
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