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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
.../Pogo/Tc1/Mariner DNA transposons, whereas retrotransposons were coldspots. High SPO11-1-oligo transposons are enriched within gene regulatory regions and in proximity to immunity genes, suggesting a role as recombination enhancers. As transposon mobility in plant s is restricted by DNA methylation, we used...
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Research: Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants
- Kazumasa Shirai,
- Mitsuhiko P. Sato,
- Ranko Nishi,
- Masahide Seki,
- Yutaka Suzuki,
- and Kousuke Hanada
Genome Res. June 2021 31: 1060-1068; Published in Advance May 18, 2021, doi:10.1101/gr.271726.120
...affects transcriptional regulation. Consequently, DNA methylation plays important roles in development, cell differentiation, reprogramming, and stress responses in both plants and mammals (Feng et al. 2010). There are three types of DNA methylation: CG, CHG, and CHH—where H = A, T, or C. Each type of DNA...
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Research: A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements
- Stefan Oberlin,
- Alexis Sarazin,
- Clément Chevalier,
- Olivier Voinnet,
- and Arturo Marí-Ordóñez
Genome Res. September 2017 27: 1549-1562; Published in Advance August 7, 2017, doi:10.1101/gr.220723.117
..., Switzerland Retroelements, the prevalent class of plant transposons, have major impacts on host integrity and evolution. They produce multiple proteins from highly compact s and, similar to viruses, must have evolved original strategies to optimize gene expression, although this aspect has been seldom...
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LETTER: Differential methylation of genes and repeats in land plants
- Pablo D. Rabinowicz,
- Robert Citek,
- Muhammad A. Budiman,
- Andrew Nunberg,
- Joseph A. Bedell,
- Nathan Lakey,
- Andrew L. O'Shaughnessy,
- Lidia U. Nascimento,
- W. Richard McCombie,
- and Robert A. Martienssen
Genome Res. October 2005 15: 1431-1440; doi:10.1101/gr.4100405
...Differential methylation of genes and repeats in land plants Pablo D. Rabinowicz 1 , 2 , Robert Citek 3 , Muhammad A. Budiman 3 , Andrew Nunberg 3 , Joseph A. Bedell 3 , Nathan Lakey 3 , Andrew L. O'Shaughnessy 2...
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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
...-order mutants, suggests that their role in normal plant growth is complex and masked from conventional approaches to study them. This is reminiscent of work in mammals in which disruption of all MBD-encoding genes did not derepress TEs (Kaluscha et al. 2022). Indeed, methylation-sensitive DNA...
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LETTER: CpG methylation is targeted to transcription units in an invertebrate genome
- Miho M. Suzuki,
- Alastair R.W. Kerr,
- Dina De Sousa,
- and Adrian Bird
Genome Res. May 2007 17: 625-631; Published in Advance April 9, 2007, doi:10.1101/gr.6163007
...) Determinants of CpG islands: expression in early embryo and isochore structure . Genome Res. 11 : 1854 – 1860 . ↵ Rabinowicz, P.D. , Palmer, L.E. , May, B.P. , Hemann, M.T. , Lowe, S.W. , McCombie, W.R. , Martienssen, R.A. ( 2003 ) Genes and transposons are differentially methylated in plants...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...the genomic impact of transposons and their potential role in shaping phenotypic diversity.Truffles typically establish ECM relationships with plants (Tedersoo et al. 2010), are characterized by a hypogeous fruit body in which spores are sequestered, and rely on pungent aromas to attract the animals...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
..., demonstrating an unprecedented putative cis-regulatory role of Helitrons in Drosophila. Differential expression analysis between species with different preferred hosts reveals divergence in gene expression in heads and larvae. Although TEs’ presence does not affect overall gene expression, we observe 6...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...G gene body methylation of the lower-expressed allele. This suggests that epigenetically regulated ASE is likely a previously overlooked mechanism facilitating plant infection. Overall, our study reveals how dikaryotism uniquely shapes key eukaryotic features.Telomere-to-telomere (T2T) and haplotype...
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Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
- Turid Everitt,
- Tilman Rönneburg,
- Daniel Elsner,
- Anna Olsson,
- Yuanzhen Liu,
- Tuuli Larva,
- Judith Korb,
- and Matthew T. Webster
Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
...the presence of full-length PRDM9 genes in the s of both species, which suggests recombination hotspots in termites might be determined by PRDM9, as they are in mammals. We also find that recombination rates in genes are correlated with inferred levels of germline DNA methylation. The finding of low...

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