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Research: Imprints and DPPA3 are bypassed during pluripotency- and differentiation-coupled methylation reprogramming in testicular germ cell tumors
- J. Keith Killian,
- Lambert C.J. Dorssers,
- Britton Trabert,
- Ad J.M. Gillis,
- Michael B. Cook,
- Yonghong Wang,
- Joshua J. Waterfall,
- Holly Stevenson,
- William I. Smith, Jr.,
- Natalia Noyes,
- Parvathy Retnakumar,
- J. Hans Stoop,
- J. Wolter Oosterhuis,
- Paul S. Meltzer,
- Katherine A. McGlynn,
- and Leendert H.J. Looijenga
Genome Res. November 2016 26: 1490-1504; Published in Advance October 20, 2016, doi:10.1101/gr.201293.115
...TGCTs may illuminate reprogramming in both normal development and testicular tumorigenesis. Herein we investigate pure-histological forms of 130 TGCTs for conserved and subtype-specific DNA methylation, including analysis of relatedness to pluripotent stem cell (ESC, iPSC), primordial germ cell (PGC...
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Research: High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice
- Hisato Kobayashi,
- Takayuki Sakurai,
- Fumihito Miura,
- Misaki Imai,
- Kentaro Mochiduki,
- Eikichi Yanagisawa,
- Akihiko Sakashita,
- Takuya Wakai,
- Yutaka Suzuki,
- Takashi Ito,
- Yasuhisa Matsui,
- and Tomohiro Kono
Genome Res. April 2013 23: 616-627; Published in Advance February 14, 2013, doi:10.1101/gr.148023.112
...-throughput bisulfite sequencing in mouse PGCs (at E13.5) showed global reduction of CpG methylation in s or genomic compartments, but demethylation-targeted DNA sequences have not been fully characterized due to low coverage (Popp et al. 2010). In other sequencing-based assays, reduced representation bisulfite...
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Research: Locus- and domain-dependent control of DNA methylation at mouse B1 retrotransposons during male germ cell development
- Kenji Ichiyanagi,
- Yungfeng Li,
- Toshiaki Watanabe,
- Tomoko Ichiyanagi,
- Kei Fukuda,
- Junko Kitayama,
- Yasuhiro Yamamoto,
- Satomi Kuramochi-Miyagawa,
- Toru Nakano,
- Yukihiro Yabuta,
- Yoshiyuki Seki,
- Mitinori Saitou,
- and Hiroyuki Sasaki
Genome Res. December 2011 21: 2058-2066; Published in Advance October 31, 2011, doi:10.1101/gr.123679.111
...C,DeanW, Feng S, Cokus SJ, Andrews S, PellegriniM, Jacobsen SE, Reik W. 2010. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature 463: 1101– 1105. Reuter M, Chuma S, Tanaka T, Franz T, Stark A, Pillai RS. 2009. Loss of the Mili-interacting Tudor domain...
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Research: 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. February 2018 28: 145-158; Published in Advance December 19, 2017, doi:10.1101/gr.225896.117
...changes in mammalian sperm methylomes at high spatial and temporal resolution. Our analyses reveal the global trend and lineage-specific features of expanding DNA hypomethylation during evolution and provide insights to how evolution of the epi may contribute to species-specific fine-tuning of conserved...
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Research: Large-scale methylation domains mark a functional subset of neuronally expressed genes
- Diane I. Schroeder,
- Paul Lott,
- Ian Korf,
- and Janine M. LaSalle
Genome Res. October 2011 21: 1583-1591; Published in Advance July 22, 2011, doi:10.1101/gr.119131.110
..., Meehan RR, Dunican DS. 2010. Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA. Biotechniques 48: 317–319. Nguyen A, Rauch TA, Pfeifer GP, HuVW. 2010. Global methylation profiling of lymphoblastoid cell lines reveals epigenetic...
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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...). Gametogenesis reprogramming results in a global erasure of DNA methylation in primordial germ cells (PGCs), affecting virtually all epigenetic-based developmental processes, with only ∼3.5% of CpG sites remaining methylated (Kobayashi et al. 2013). This includes genomic imprinting, as methylation is lost at all...
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Research: Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development
- Patricia Gerdes,
- Dorothy Chan,
- Mischa Lundberg,
- Francisco J. Sanchez-Luque,
- Gabriela O. Bodea,
- Adam D. Ewing,
- Geoffrey J. Faulkner,
- and Sandra R. Richardson
Genome Res. September 2023 33: 1465-1481; Published in Advance October 5, 2023, doi:10.1101/gr.278003.123
...; de la Rica et al. 2016; Gerdes et al. 2022). During embryonic development, the epi undergoes reprogramming including phases of global DNA demethylation (Hajkova et al. 2002; Seki et al. 2005; Abe et al. 2011; Saitou et al. 2012; Seisenberger et al. 2012; Smith et al. 2012; Cantone and Fisher 2013...
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Research: Multi-omics analyses demonstrate a critical role for EHMT1 methyltransferase in transcriptional repression during oogenesis
- Hannah Demond,
- Courtney W. Hanna,
- Juan Castillo-Fernandez,
- Fátima Santos,
- Evangelia K. Papachristou,
- Anne Segonds-Pichon,
- Kamal Kishore,
- Simon Andrews,
- Clive S. D'Santos,
- and Gavin Kelsey
Genome Res. January 2023 33: 18-31; Published in Advance January 23, 2023, doi:10.1101/gr.277046.122
...loss of EHMT1 affects DNA methylation establishment in the oocyte, we first analyzed global DNA methylation (5mC and 5hmC) by IF. We used a previously well-established method (Santos et al. 2013) and performed two replicate experiments with oocytes from different litters (average number of oocytes per...
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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
.... Our efforts to generate robust DNA methylome profiles for zygotes were not successful, possibly because zygotes are fragile compared with egg cells, and the methylation level readout from random-priming based, post-bisulfite adapter tagging (PBAT) sequencing methods are highly sensitive to library...
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Research: Decoding the function of bivalent chromatin in development and cancer
- Dhirendra Kumar,
- Senthilkumar Cinghu,
- Andrew J. Oldfield,
- Pengyi Yang,
- and Raja Jothi
Genome Res. December 2021 31: 2170-2184; Published in Advance October 19, 2021, doi:10.1101/gr.275736.121
...resemble early post-implantation epiblast (E5.5–E6.5) (Fig. 2A; Hayashi et al. 2011; Yang et al. 2019). This time period spanning pre- to post-implantation epiblast differentiation during early embryonic development is noteworthy because naive ESCs are associated with global DNA hypomethylation...
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