Searching journal content for articles similar to Cohen et al. 19 (12): 2193.

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  1. 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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  2. Research: The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation
    • Lei Zhao,
    • Ming-an Sun,
    • Zejuan Li,
    • Xue Bai,
    • Miao Yu,
    • Min Wang,
    • Liji Liang,
    • Xiaojian Shao,
    • Stephen Arnovitz,
    • Qianfei Wang,
    • Chuan He,
    • Xuemei Lu,
    • Jianjun Chen,
    • and Hehuang Xie
    Genome Res. August 2014 24: 1296-1307; Published in Advance May 16, 2014, doi:10.1101/gr.163147.113
    ...-hmCs are enriched in gene bodies. This may explain the difference in methylation observed for TET1-binding sites and 5-hmC enriched regions. Asymmetric non-CpG DNA methylation decreases during early differentiation Non-CpG methylation has been shown to be abundantly present in embryonic stem cells...
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  3. Research: Dynamic reversal of random X-Chromosome inactivation during iPSC reprogramming
    • Adrian Janiszewski,
    • Irene Talon,
    • Joel Chappell,
    • Samuel Collombet,
    • Juan Song,
    • Natalie De Geest,
    • San Kit To,
    • Greet Bervoets,
    • Oskar Marin-Bejar,
    • Caterina Provenzano,
    • Lotte Vanheer,
    • Jean-Christophe Marine,
    • Florian Rambow,
    • and Vincent Pasque
    Genome Res. October 2019 29: 1659-1672; Published in Advance September 12, 2019, doi:10.1101/gr.249706.119
    ...(Supplemental Fig. S4D). Thus, although H3K27me3 may restrict the activation of silenced genes on the Xi, it is not sufficient to explain the delay in reactivation of late genes. Additionally, on the Xi, H3K36me3 and H3K4me3 were depleted on all classes of genes. DNA methylation (Milagre et al. 2017) was also...
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  4. Research: Switching roles for DNA and histone methylation depend on evolutionary ages of human endogenous retroviruses
    • Hitoshi Ohtani,
    • Minmin Liu,
    • Wanding Zhou,
    • Gangning Liang,
    • and Peter A. Jones
    Genome Res. August 2018 28: 1147-1157; Published in Advance July 3, 2018, doi:10.1101/gr.234229.118
    ...al. 2017). Recent studies on mouse embryonic cells have reported that LTR silencing mechanisms depend on DNA methylation, heterochromatin conformation, and the PRC2 complex (Leung and Lorincz 2012; Walter et al. 2016), but less is known about the epigenetic silencing mechanisms of LTRs in human...
  5. 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...
  6. Research: Regulation of endogenous retrovirus–derived regulatory elements by GATA2/3 and MSX2 in human trophoblast stem cells
    • Cui Du,
    • Jing Jiang,
    • Yuzhuo Li,
    • Miao Yu,
    • Jian Jin,
    • Shuai Chen,
    • Hairui Fan,
    • Todd S. Macfarlan,
    • Bin Cao,
    • and Ming-an Sun
    Genome Res. February 2023 33: 197-207; Published in Advance February 17, 2023, doi:10.1101/gr.277150.122
    ..., placenta is abundant with partially methylated domains (Schroeder et al. 2013; Decato et al. 2017) which are also featured in many tumors (Hansen et al. 2011). Mechanistically, one previous study speculated that placenta and tumor share converged DNA methylation pathways that mediate the establishment...
  7. Research: Germline and somatic imprinting in the nonhuman primate highlights species differences in oocyte methylation
    • Clara Y. Cheong,
    • Keefe Chng,
    • Shilen Ng,
    • Siew Boom Chew,
    • Louiza Chan,
    • and Anne C. Ferguson-Smith
    Genome Res. May 2015 25: 611-623; Published in Advance April 10, 2015, doi:10.1101/gr.183301.114
    ...- and tissue-specific domains of imprinted expression exist. Using the cynomolgus macaque ( Macaca fascicularis ) to assess primate-specific imprinting, we present a comprehensive view of tissue-specific imprinted expression and DNA methylation at established imprinted gene clusters. For example, like mouse...
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  8. Research: Transcriptome analyses of rhesus monkey preimplantation embryos reveal a reduced capacity for DNA double-strand break repair in primate oocytes and early embryos
    • Xinyi Wang,
    • Denghui Liu,
    • Dajian He,
    • Shengbao Suo,
    • Xian Xia,
    • Xiechao He,
    • Jing-Dong J. Han,
    • and Ping Zheng
    Genome Res. April 2017 27: 567-579; Published in Advance February 21, 2017, doi:10.1101/gr.198044.115
    ...with the time frames of reprogramming, ZGA, and cell-fate commitment, respectively. Importantly, comparison of the ZGA-related network modules among the three species revealed less robust surveillance of genomic instability in primate oocytes and embryos than in rodents, particularly in the pathways of DNA...
  9. Research: The role of DNA methylation in directing the functional organization of the cancer epigenome
    • Fides D. Lay,
    • Yaping Liu,
    • Theresa K. Kelly,
    • Heather Witt,
    • Peggy J. Farnham,
    • Peter A. Jones,
    • and Benjamin P. Berman
    Genome Res. April 2015 25: 467-477; Published in Advance March 6, 2015, doi:10.1101/gr.183368.114
    ...The role of DNA methylation in directing the functional organization of the cancer epigenome Fides D. Lay 1 , 2 , 6 , Yaping Liu 2 , 3 , 6 , 7 , Theresa K. Kelly 1 , 8 , Heather Witt 1 , Peggy J. Farnham 1 , Peter A. Jones 1...
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  10. Research: Pervasive polymorphic imprinted methylation in the human placenta
    • Courtney W. Hanna,
    • Maria S. Peñaherrera,
    • Heba Saadeh,
    • Simon Andrews,
    • Deborah E. McFadden,
    • Gavin Kelsey,
    • and Wendy P. Robinson
    Genome Res. June 2016 26: 756-767; Published in Advance January 14, 2016, doi:10.1101/gr.196139.115
    ...triploid samples that overlap previously reported imprinted DMRs (Court et al. 2014). DNA methylation for human germ cells, early embryonic stages (zygote, two-cell, four-cell, eight-cell, and morula stage embryos), inner cell mass, and trophectoderm is an average of CpG sites across each DMR measured...
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