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Research: Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment
- Franck Court,
- Chiharu Tayama,
- Valeria Romanelli,
- Alex Martin-Trujillo,
- Isabel Iglesias-Platas,
- Kohji Okamura,
- Naoko Sugahara,
- Carlos Simón,
- Harry Moore,
- Julie V. Harness,
- Hans Keirstead,
- Jose Vicente Sanchez-Mut,
- Eisuke Kaneki,
- Pablo Lapunzina,
- Hidenobu Soejima,
- Norio Wake,
- Manel Esteller,
- Tsutomu Ogata,
- Kenichiro Hata,
- Kazuhiko Nakabayashi,
- and David Monk
Genome Res. April 2014 24: 554-569; Published in Advance January 8, 2014, doi:10.1101/gr.164913.113
...Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment Franck Court 1 , 15 , Chiharu Tayama 2 , 15 , Valeria Romanelli 1 , 15 , Alex...
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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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Method: Selective enrichment of damaged DNA molecules for ancient genome sequencing
- Marie-Theres Gansauge and
- Matthias Meyer
Genome Res. September 2014 24: 1543-1549; Published in Advance July 31, 2014, doi:10.1101/gr.174201.114
...in a 7,000-year-old Mesolithic European. Nature 507: 225–228. Pedersen JS, Valen E, Velazquez AM, Parker BJ, Rasmussen M, Lindgreen S, Lilje B, Tobin DJ, Kelly TK, Vang S, et al. 2014. Genome-wide nucleosome map and cytosine methylation levels of an ancient human . Genome Res 24: 454–466. Pr€ufer K...
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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
...-axis (IWGSC 2018). Gray ticks denote genomic coordinates of genetic markers used to construct the Chinese Spring × Renan genetic map. (B) Genome-wide Spearman's rank-order correlation coefficients (rs) for the indicated parameter pairs profiled in 1-Mb adjacent windows, with cells coded according to the color...
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Research: Comparative methylomics reveals gene-body H3K36me3 in Drosophila predicts DNA methylation and CpG landscapes in other invertebrates
- Lisa Nanty,
- Guillermo Carbajosa,
- Graham A. Heap,
- Francis Ratnieks,
- David A. van Heel,
- Thomas A. Down,
- and Vardhman K. Rakyan
Genome Res. November 2011 21: 1841-1850; Published in Advance September 22, 2011, doi:10.1101/gr.121640.111
...of the silkworm reveals a sparse epigenomic map. Nat Biotechnol 28: 516–520. Zemach A, Zilberman D. 2010. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Curr Biol 20: R780–R785. ZemachA,McDaniel IE, Silva P, ZilbermanD. 2010.Genome-wide evolutionary analysis of eukaryotic DNA methylation...
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PERSPECTIVE: The opossum genome: Insights and opportunities from an alternative mammal
- Paul B. Samollow
Genome Res. August 2008 18: 1199-1215; doi:10.1101/gr.065326.107
...+C content through a general GC to AT mutation bias, with methylated cytosines in CpG dinucleotides especially prone to mutation through deamination to thymine. In the absence of an opposing process, such as selection at specific sites, this mutational bias should lead to the inexorable decline of G...
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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
...-specific deposition of DNA methylation in all cytosine contexts (CG, CHG, and CHH, where H is any nucleotide but G). Once established, DNA methylation can reinforce the deposition of H3K9me2 through the action of SUPRESSOR OF VARIEGATION 3–9 HOMOLOG (SUVH) family H3K9 methyltransferases, which can read DNA...
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Research: A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response
- Alexandros Bousios,
- Concepcion M. Diez,
- Shohei Takuno,
- Vojtech Bystry,
- Nikos Darzentas,
- and Brandon S. Gaut
Genome Res. February 2016 26: 226-237; Published in Advance December 2, 2015, doi:10.1101/gr.193763.115
...the abundant Ji andOpie populations (Bousios et al. 2012a). This TE set provides a unique opportunity to study epigenetic patterns on individual elements that extend from recent to ancient insertions. Here, we map multiple siRNA libraries and bisulfite-sequencing (BS-seq) methylation data to Sireviruses, study...
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Research: Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis
- Shaofang Li,
- Lee E. Vandivier,
- Bin Tu,
- Lei Gao,
- So Youn Won,
- Shengben Li,
- Binglian Zheng,
- Brian D. Gregory,
- and Xuemei Chen
Genome Res. February 2015 25: 235-245; Published in Advance November 20, 2014, doi:10.1101/gr.182238.114
...) of P4RNAs, exons, and genes. The nucleosome positions were derived from published data (Chodavarapu et al. 2010). Genome-wide discovery of Pol IV/RDR2 products Genome Research 239 www..org distribution of P4siRNAs at these loci. P4siRNAs were present at some of the loci in dcl234, probably because DCL1...
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Research: GC skew at the 5′ and 3′ ends of human genes links R-loop formation to epigenetic regulation and transcription termination
- Paul A. Ginno,
- Yoong Wearn Lim,
- Paul L. Lott,
- Ian Korf,
- and Frédéric Chédin
Genome Res. October 2013 23: 1590-1600; Published in Advance July 18, 2013, doi:10.1101/gr.158436.113
...significant insights into the epigenetic regulation, genomic organization, and function of human genes. [Supplemental material is available for this article.] Epigenetic modifications in eukaryotes, including DNA methylation and histone marks, represent a critical layer of biological information employed...

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