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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
...methylation (gbM) (Zhang et al. 2006; Cokus et al. 2008; Lister et al. 2008). In contrast with heterochromatic mC, gbM is associated with ubiquitously and moderately expressed genes in plants (Zhang et al. 2006; Coleman-Derr and Zilberman 2012; Takuno and Gaut 2012). Despite being present in almost all land...
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Method: Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA
- Romualdas Vaisvila,
- V.K. Chaithanya Ponnaluri,
- Zhiyi Sun,
- Bradley W. Langhorst,
- Lana Saleh,
- Shengxi Guan,
- Nan Dai,
- Matthew A. Campbell,
- Brittany S. Sexton,
- Katherine Marks,
- Mala Samaranayake,
- James C. Samuelson,
- Heidi E. Church,
- Esta Tamanaha,
- Ivan R. Corrêa, Jr.,
- Sriharsa Pradhan,
- Eileen T. Dimalanta,
- Thomas C. Evans, Jr.,
- Louise Williams,
- and Theodore B. Davis
Genome Res. July 2021 31: 1280-1289; Published in Advance June 17, 2021, doi:10.1101/gr.266551.120
..., enabling cytosines and the corresponding cytosine modifications to be differentiated.Currently, there is no exclusive enzymatic method to detect 5mC and 5hmC to single-base resolution. Here enzymatic methyl-seq (EM-seq) is described, the first purely enzymatic conversion method for mapping 5mC and 5hmC. EM...
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Resource: Integrated annotations and analyses of small RNA–producing loci from 47 diverse plants
- Alice Lunardon,
- Nathan R. Johnson,
- Emily Hagerott,
- Tamia Phifer,
- Seth Polydore,
- Ceyda Coruh,
- and Michael J. Axtell
Genome Res. March 2020 30: 497-513; Published in Advance March 16, 2020, doi:10.1101/gr.256750.119
...transposable elements (TEs) and other repeats to induce DNA methylation and reinforce transcriptional silencing. In contrast, 21–22 nt siRNAs are derived from Pol II transcripts and are copied by RDR6 into dsRNAs and processed by DCL2/DCL4. They act in the noncanonical RdDM pathway to establish the silencing...
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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
...of differentially methylated regions (DMRs) revealed that DMRs mostly cosegregated with the genotype from which they were derived, but examples of the uncoupling of genotype and epigenotype were identified. Linkage mapping of methylation states assessed from whole-genome bisulfite sequencing of 83 RILs uncovered...
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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
...to maintain heterochromatin and integrity.5S rDNA also display low levels of DNA methylation and H3K9me1/2 in SpirodelaBesides TE silencing, DNA methylation, H3K9me2, and RdDM are also involved in the epigenetic regulation of other repeats in plants. To investigate if the unique patterns seen on TEs also...
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LETTER: Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium
- Jennifer S. Hawkins,
- HyeRan Kim,
- John D. Nason,
- Rod A. Wing,
- and Jonathan F. Wendel
Genome Res. October 2006 16: 1252-1261; Published in Advance September 5, 2006, doi:10.1101/gr.5282906
...that the C-value enigma can be largely explained by the differential amplification and proliferation among organisms of the repetitive fraction of the ( Bennetzen 2000b , 2002 ; Kidwell 2002 ). In plants, amplification and insertion of newly activated long terminal repeat (LTR) retrotransposable elements...
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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
...repeats (satellites), and/or specific families of transposons. The functional region of the centromere is defined by loading of a specific histone 3 variant (CENH3), which nucleates the kinetochore and shows dynamic regulation. In many plants, the centromeres are composed of satellite repeat arrays...
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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
..., in early land plants like P. patens, the pathway is completely redundant with other sRNA-independent DNA methyltransferases introducing de novo DNA methylation (Yaari et al. 2019) as opposed to the widespread defects observed in rice (Fig. 1; Supplemental Figs. S1–S3; Xu et al. 2020; Zheng et al. 2021...
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Research: Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis
- Alexandra Dallaire,
- Bethan F. Manley,
- Maya Wilkens,
- Iliana Bista,
- Clement Quan,
- Edouard Evangelisti,
- Charles R. Bradshaw,
- Navin B. Ramakrishna,
- Sebastian Schornack,
- Falk Butter,
- Uta Paszkowski,
- and Eric A. Miska
Genome Res. December 2021 31: 2290-2302; Published in Advance November 12, 2021, doi:10.1101/gr.275752.121
....ac.ukAbstractArbuscular mycorrhizal (AM) fungi form mutualistic relationships with most land plant species. AM fungi have long been considered as ancient asexuals. Long-term clonal evolution would be remarkable for a eukaryotic lineage and suggests the importance of alternative mechanisms to promote genetic variability facilitating...
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Research: Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations
- Caifu Jiang,
- Aziz Mithani,
- Eric J. Belfield,
- Richard Mott,
- Laurence D. Hurst,
- and Nicholas P. Harberd
Genome Res. November 2014 24: 1821-1829; Published in Advance October 14, 2014, doi:10.1101/gr.177659.114
...accumulate ∼45% more differentially methylated cytosine positions (DMPs) at CG sites (CG-DMPs) than controls, and also show that while many (∼75%) of these CG-DMPs are inherited, some can be lost in subsequent generations. Finally, we show that stress-associated CG-DMPs arise more frequently in genic than...
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