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Corrigendum: Corrigendum: Evolutionary expansion of DNA hypomethylation in the mammalian germline genome
- Jianghan Qu,
- Emily Hodges,
- Antoine Molaro,
- Pascal Gagneux,
- Matthew D. Dean,
- Gregory J. Hannon,
- and Andrew D. Smith
Genome Res. May 2018 28: 766.2; doi:10.1101/gr.236885.118
...Corrigendum: Evolutionary expansion of DNA hypomethylation in the mammalian germline Jianghan Qu, Emily Hodges, Antoine Molaro, Pascal Gagneux, Matthew D. Dean, Gregory J. Hannon and Andrew D. Smith Genome Research 28: 145–158 (2018)The authors would like to correct the omission of a funding source...
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Method: Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates
- Christopher Faulk
Genome Res. June 2023 33: 948-956; Published in Advance July 13, 2023, doi:10.1101/gr.277743.123
...%. Genome size directly correlates to global DNA methylation, explaining 39% of its variance. Accurate SINE and LINE transposon methylation in both the mouse and primates can be obtained with just 0.0001× coverage, or 3 Mb of reads. Sample multiplexing, field portability, and the low price...
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Research: Assessing DNA methylation detection for primary human tissue using Nanopore sequencing
- Rylee Genner,
- Stuart Akeson,
- Melissa Meredith,
- Pilar Alvarez Jerez,
- Laksh Malik,
- Breeana Baker,
- Abigail Miano-Burkhardt,
- CARD-long-read Team,
- Benedict Paten,
- Kimberley J. Billingsley,
- Cornelis Blauwendraat,
- and Miten Jain
Genome Res. April 2025 35: 632-643; Published in Advance March 7, 2025, doi:10.1101/gr.279159.124
.... 1987; Li et al. 2018), genomic imprinting (Li et al. 1993; Suzuki et al. 2007; Court et al. 2014), X-Chromosome inactivation (Sharp et al. 2011), and transcription repression (Moore et al. 2013). As a result, variations in DNA methylation have been associated with human diseases such as aging...
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Research: Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing
- Jesper Eisfeldt,
- Edward J. Higginbotham,
- Felix Lenner,
- Jennifer Howe,
- Bridget A. Fernandez,
- Anna Lindstrand,
- Stephen W. Scherer,
- and Lars Feuk
Genome Res. November 2024 34: 1763-1773; Published in Advance October 29, 2024, doi:10.1101/gr.279263.124
..., where DNA samples were previously sequenced using Illumina or Complete Genomics srGS (Yuen et al. 2017). Individuals were noted as having a diagnosis of ASD in two ways; (i) met the diagnostic criteria of the autism diagnostic interview-revised (ADI-R) or autism diagnostic observation schedule (ADOS...
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Research: Parental methylome reprogramming in human uniparental blastocysts reveals germline memory transition
- Jiawei Xu,
- Yimin Shu,
- Guidong Yao,
- Yu Zhang,
- Wenbin Niu,
- Yile Zhang,
- Xueshan Ma,
- Haixia Jin,
- Fuli Zhang,
- Senlin Shi,
- Yang Wang,
- Wenyan Song,
- Shanjun Dai,
- Luyao Cheng,
- Xiangyang Zhang,
- Wei Xie,
- Aaron J. Hsueh,
- and Yingpu Sun
Genome Res. September 2021 31: 1519-1530; Published in Advance July 30, 2021, doi:10.1101/gr.273318.120
...-of-origin-dependent, allele-specific DNA methylation (Stelzer et al. 2016). Genome-wide demethylation waves during preimplantation development differ across mammalian species (Beaujean et al. 2004; Fulka et al. 2004; Shi et al. 2004; Loi et al. 2008). The maternal is passively demethylated in a replication-dependent manner...
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Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
- Mikhail O. Maksimov,
- Cynthia Wu,
- David G. Ashbrook,
- Flavia Villani,
- Vincenza Colonna,
- Nima Mousavi,
- Nichole Ma,
- Lu Lu,
- Jonathan K. Pritchard,
- Alon Goren,
- Robert W. Williams,
- Abraham A. Palmer,
- and Melissa Gymrek
Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
...highly expressed in spermatocytes and oocytes, where germline mutations are likely to arise, Atg10 is most highly expressed in the heart and other structures less likely to be related to a mutator phenotype. We additionally identified high impact mutations in two genes not known to be involved in DNA...
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Research: Inherited DNA methylation primes the establishment of accessible chromatin during genome activation
- Guifen Liu,
- Wen Wang,
- Shengen Hu,
- Xiangxiu Wang,
- and Yong Zhang
Genome Res. July 2018 28: 998-1007; Published in Advance May 29, 2018, doi:10.1101/gr.228833.117
...hypomethylation pattern after ZGA.A recent in vitro study showed that hundreds of transcription factors prefer to bind methylated DNA (Yin et al. 2017). Consistent with this study, we observed that Pou5f3 and Nanog preferentially bind to their motifs on hypermethylated regions and contribute to the formation...
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Research: Coordination of zygotic genome activation entry and exit by H3K4me3 and H3K27me3 in porcine early embryos
- Guowei Bu,
- Wei Zhu,
- Xin Liu,
- Jingjing Zhang,
- Longtao Yu,
- Kai Zhou,
- Shangke Wang,
- Zhekun Li,
- Zhengang Fan,
- Tingting Wang,
- Taotao Hu,
- Ruifeng Hu,
- Zhiting Liu,
- Tao Wang,
- Linhui Wu,
- Xia Zhang,
- Shuhong Zhao,
- and Yi-Liang Miao
Genome Res. August 2022 32: 1487-1501; Published in Advance July 22, 2022, doi:10.1101/gr.276207.121
...in distal and promoter regions. (C) Genome browser snapshots showing the dynamics of H3K4me3 and H3K27me3 in porcine oocytes and early embryos, and DNA methylation levels (5-methylcytosines in CpG [mCG]) in porcine oocyte and spermatozoa. Genomic regions containing oocyte partially methylated domains (PMDs...
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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: Hydroxycarbamide effects on DNA methylation and gene expression in myeloproliferative neoplasms
- Stephania Contreras Castillo,
- Bertille Montibus,
- Azucena Rocha,
- Will Duke,
- Ferdinand von Meyenn,
- Donal McLornan,
- Claire Harrison,
- Ann Mullally,
- Reiner Schulz,
- and Rebecca J. Oakey
Genome Res. August 2021 31: 1381-1394; Published in Advance July 9, 2021, doi:10.1101/gr.270066.120
...Gs are indicated. (E) Locus of the promoter and regulatory region of SPI1 with DNA methylation and gene expression levels before and after 9 mo of HC treatment. Yellow shading indicates DNA methylation levels, blue shading indicates significant DMRs, and gray shading denotes gene expression levels.Genomic context...

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