Searching journal content for articles similar to Statham et al. 22 (6): 1120.

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  1. Method: methyl-ATAC-seq measures DNA methylation at accessible chromatin
    • Roman Spektor,
    • Nathaniel D. Tippens,
    • Claudia A. Mimoso,
    • and Paul D. Soloway
    Genome Res. June 2019 29: 969-977; Published in Advance June 3, 2019, doi:10.1101/gr.245399.118
    ...of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA. Genome Res 22: 1120–1127. doi:10.1101/gr.132076.111 ↵Suzuki M, Liao W, Wos F, Johnston AD, DeGrazia J, Ishii J, Bloom T, Zody MC, Germer S, Greally JM. 2018. Whole- bisulfite sequencing with improved...
  2. Research: Transcriptional alterations in glioma result primarily from DNA methylation–independent mechanisms
    • Franck Court,
    • Elisa Le Boiteux,
    • Anne Fogli,
    • Mélanie Müller-Barthélémy,
    • Catherine Vaurs-Barrière,
    • Emmanuel Chautard,
    • Bruno Pereira,
    • Julian Biau,
    • Jean-Louis Kemeny,
    • Toufic Khalil,
    • Lucie Karayan-Tapon,
    • Pierre Verrelle,
    • and Philippe Arnaud
    Genome Res. October 2019 29: 1605-1621; Published in Advance September 18, 2019, doi:10.1101/gr.249219.119
    ...that most transcriptional alterations in tumor samples were DNA methylation–independent. Instead, altered histone H3 trimethylation at lysine 27 (H3K27me3) was the predominant molecular defect at deregulated genes. Our results also suggest that the presence of a bivalent chromatin signature at CpG island...
  3. Resource: Dynamic DNA methylation across diverse human cell lines and tissues
    • Katherine E. Varley,
    • Jason Gertz,
    • Kevin M. Bowling,
    • Stephanie L. Parker,
    • Timothy E. Reddy,
    • Florencia Pauli-Behn,
    • Marie K. Cross,
    • Brian A. Williams,
    • John A. Stamatoyannopoulos,
    • Gregory E. Crawford,
    • Devin M. Absher,
    • Barbara J. Wold,
    • and Richard M. Myers
    Genome Res. March 2013 23: 555-567; Published in Advance January 16, 2013, doi:10.1101/gr.147942.112
    ...to the gene-body methylation of expressed genes. The single nucleotide resolution of bisulfite sequencing allows us to detect both methylation and DNA sequence variants in the same molecules, and we used this information to identify loci with allele-specific or allele-biased methylation (Gertz et al. 2011...
  4. Research: Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
    • Phillippa C. Taberlay,
    • Aaron L. Statham,
    • Theresa K. Kelly,
    • Susan J. Clark,
    • and Peter A. Jones
    Genome Res. September 2014 24: 1421-1432; Published in Advance June 10, 2014, doi:10.1101/gr.163485.113
    ...usingnucleosome occupancy and methylome sequencing (NOMe-seq) (Kelly et al. 2012). NOMe-seq exploits the ability of M.CviPI (Xu et al. 1998) to methylate GpC sites within regions of DNA that are not occupied by nucleosomes or other tight-binding proteins (Fig. 1; Jessen et al. 2004, 2006; Hoose and Kladde 2006...
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  5. Method: A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs
    • Christian Pflueger,
    • Dennis Tan,
    • Tessa Swain,
    • Trung Nguyen,
    • Jahnvi Pflueger,
    • Christian Nefzger,
    • Jose M. Polo,
    • Ethan Ford,
    • and Ryan Lister
    Genome Res. August 2018 28: 1193-1206; Published in Advance June 15, 2018, doi:10.1101/gr.233049.117
    ...bisulfite sequencing (targeted bsPCR-seq), chromatin immunoprecipitation (ChIP), or ChIP bisulfite sequencing (ChIP-bs-seq) (Fig. 1B; Brinkman et al. 2012). Initially we measured induced on-target DNA methylation at the UNC5C promoter and a proxy for potential off-target DNA methylation at the promoters...
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