Searching journal content for articles similar to Zhao et al. 24 (8): 1296.

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  1. Research: H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells
    • Haifen Chen,
    • Bo Hu,
    • Cynthia Horth,
    • Eric Bareke,
    • Phillip Rosenbaum,
    • Sin Young Kwon,
    • Jacinthe Sirois,
    • Daniel N. Weinberg,
    • Faith M. Robison,
    • Benjamin A. Garcia,
    • Chao Lu,
    • William A. Pastor,
    • and Jacek Majewski
    Genome Res. May 2022 32: 825-837; Published in Advance April 8, 2022, doi:10.1101/gr.276383.121
    ...interactions. Here, we use the mouse embryonic stem cell (mESC) model to describe in detail the relationships within the H3K27-H3K36-DNA methylation subnetwork. In particular, we focus on the major epigenetic reorganization caused by deletion of the histone 3 lysine 36 methyltransferase NSD1, which in m...
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  2. Method: Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models
    • Yuelin Liu,
    • Xuan Cindy Li,
    • Farid Rashidi Mehrabadi,
    • Alejandro A. Schäffer,
    • Drew Pratt,
    • David R. Crawford,
    • Salem Malikić,
    • Erin K. Molloy,
    • Vishaka Gopalan,
    • Stephen M. Mount,
    • Eytan Ruppin,
    • Kenneth D. Aldape,
    • and S. Cenk Sahinalp
    Genome Res. July 2023 33: 1089-1100; Published in Advance June 14, 2023, doi:10.1101/gr.277608.122
    ...in the data sets, which calls for data imputation or aggregation; on the other hand, tumor lineage inference using CNAs called from single-cell sequencing data often involves ambiguities in the determination of chromosomal breakpoints that may mislead the conclusion. DNA methylation, the addition of a methyl...
  3. Research: Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors
    • Martin Cusack,
    • Hamish W. King,
    • Paolo Spingardi,
    • Benedikt M. Kessler,
    • Robert J. Klose,
    • and Skirmantas Kriaucionis
    Genome Res. October 2020 30: 1393-1406; Published in Advance September 22, 2020, doi:10.1101/gr.257576.119
    ..., and transcription factor occupancy in wild-type or DNA methylation-deficient mouse embryonic stem cells following HDAC inhibition. We observe widespread increases in chromatin accessibility at retrotransposons when HDACs are inhibited, and this is magnified when cells also lack DNA methylation. A subset...
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  4. Research: Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development
    • Vladimir B. Teif,
    • Daria A. Beshnova,
    • Yevhen Vainshtein,
    • Caroline Marth,
    • Jan-Philipp Mallm,
    • Thomas Höfer,
    • and Karsten Rippe
    Genome Res. August 2014 24: 1285-1295; Published in Advance May 8, 2014, doi:10.1101/gr.164418.113
    ...Systems Biology, Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, 69120 Heidelberg, Germany During differentiation of embryonic stem cells, chromatin reorganizes to establish cell type-specific expression programs. Here, we have dissected the linkages between DNA methylation (5mC), hydroxymethylation...
  5. Research: The human ribosomal DNA array is composed of highly homogenized tandem clusters
    • Yutaro Hori,
    • Akira Shimamoto,
    • and Takehiko Kobayashi
    Genome Res. November 2021 31: 1971-1982; Published in Advance August 18, 2021, doi:10.1101/gr.275838.121
    ...in the other samples (Supplemental Table S1, column 7), we speculate that they are genomic instability “hotspots,” where mutation is frequent in DNA repair compromised cells.Human pluripotent stem cells have a different methylation statusNext, we analyzed rDNA methylation status in human induced pluripotent...
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  6. Research: The strand-biased mitochondrial DNA methylome and its regulation by DNMT3A
    • Xiaoyang Dou,
    • Jerome D. Boyd-Kirkup,
    • Joseph McDermott,
    • Xiaoli Zhang,
    • Fang Li,
    • Bowen Rong,
    • Rui Zhang,
    • Bisi Miao,
    • Peilin Chen,
    • Hao Cheng,
    • Jianhuang Xue,
    • David Bennett,
    • Jiemin Wong,
    • Fei Lan,
    • and Jing-Dong J. Han
    Genome Res. October 2019 29: 1622-1634; Published in Advance September 19, 2019, doi:10.1101/gr.234021.117
    ...H methylation in the mitochondrial . Non-CpG methylation is rare in most tissues, but substantial in brain and embryonic stem cells (ESCs), where it is established and maintained by DNMT3A. Consistently we found that all mtDNA peak regions are non-CpGs, and KO of DNMT3A abolished a specific CpH peak in the MT...
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  7. Research: A heterozygous IDH1R132H/WT mutation induces genome-wide alterations in DNA methylation
    • Christopher G. Duncan,
    • Benjamin G. Barwick,
    • Genglin Jin,
    • Carlo Rago,
    • Priya Kapoor-Vazirani,
    • Doris R. Powell,
    • Jen-Tsan Chi,
    • Darell D. Bigner,
    • Paula M. Vertino,
    • and Hai Yan
    Genome Res. December 2012 22: 2339-2355; Published in Advance August 16, 2012, doi:10.1101/gr.132738.111
    ...A heterozygous IDH1 R132H/WT mutation induces genome-wide alterations in DNA methylation Christopher G. Duncan 1 , 6 , Benjamin G. Barwick 2 , 6 , Genglin Jin 1 , Carlo Rago 3 , Priya Kapoor-Vazirani 4 , Doris R. Powell 4...
  8. Research: Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes
    • Sakthi D. Moorthy,
    • Scott Davidson,
    • Virlana M. Shchuka,
    • Gurdeep Singh,
    • Nakisa Malek-Gilani,
    • Lida Langroudi,
    • Alexandre Martchenko,
    • Vincent So,
    • Neil N. Macpherson,
    • and Jennifer A. Mitchell
    Genome Res. February 2017 27: 246-258; Published in Advance November 28, 2016, doi:10.1101/gr.210930.116
    ...that these noncoding regions overlap DNase I hypersensitive sites (DHSs) found in accessible chromatin and that the disease-associated variants often disrupt existing or create new transcription factor bindingmotifs. Alterations in regulatory DNA by large deletion or single mutation are known to cause disease...
  9. 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
    ...in human. This is beginning to change with several recent studies reporting on the dynamic transcriptome, DNA methylome, and lineage determination of human preimplantation embryos (Vassena et al. 2011; Xue et al. 2013; Yan et al. 2013; Guo et al. 2014; Smith et al. 2014; Petropoulos et al. 2016...
  10. Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
    • Sarah M. Leichter,
    • Kami Ahmad,
    • and Steven Henikoff
    Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
    ...cells to re-enter the cell cycle partially restores a youthful H3K27me3 landscape, suggesting that DNA replication may rejuvenate chromatin structure (Yang et al. 2023). However, even mitotically active somatic stem cells display age-related increases in Polycomb repression: Aged Drosophila intestinal...
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