Searching journal content for articles similar to Galm et al. 12 (1): 153.

Displaying results 1-10 of 38
For checked items
  1. Mini-Review: Evolution of genome-wide methylation profiling technologies
    • Carolina Montano and
    • Winston Timp
    Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
    ...of the fifth carbon atom of cytosine, typically in mammals in a CG dinucleotide context. This dinucleotide is depleted largely across the and found predominantly in clusters known as “CpG islands” (Bird 1986). Cytosine methylation is catalyzed by methyltransferases (e.g., DNMT1, DNMT3A) that transfer a methyl...
    OPEN ACCESS ARTICLE
  2. Method: Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
    • Rachel M. Petersen,
    • Christopher M. Vockley,
    • and Amanda J. Lea
    Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
    ...at the single-cell level, at which most CpG sites are either completely methylated or unmethylated. This framework is particularly powerful because nearly all MD genetic effect sites identified in our assay exhibit variable methylation in vivo, either across individuals within a single cell type or between...
    OPEN ACCESS ARTICLE
  3. Method: Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA
    • Romualdas Vaisvila,
    • V.K. Chaithanya Ponnaluri,
    • Zhiyi Sun,
    • Bradley W. Langhorst,
    • Lana Saleh,
    • Shengxi Guan,
    • Nan Dai,
    • Matthew A. Campbell,
    • Brittany S. Sexton,
    • Katherine Marks,
    • Mala Samaranayake,
    • James C. Samuelson,
    • Heidi E. Church,
    • Esta Tamanaha,
    • Ivan R. Corrêa, Jr.,
    • Sriharsa Pradhan,
    • Eileen T. Dimalanta,
    • Thomas C. Evans, Jr.,
    • Louise Williams,
    • and Theodore B. Davis
    Genome Res. July 2021 31: 1280-1289; Published in Advance June 17, 2021, doi:10.1101/gr.266551.120
    ...in a . In contrast, enzymatically converted DNA does not have the same fragmentation bias. This results in EM-seq libraries that have even GC-bias profiles and dinucleotide distributions. This even coverage is especially relevant to the assessment of CpG methylation state. Also of interest was how efficiently...
    OPEN ACCESS ARTICLE
  4. 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
    ....16%) and the overall (82.87%). These values correlate with transposon age and CpG density, where Alus are younger and more CpG dense than LINE-1s, and both are under selection for increased DNA methylation to suppress mobilization.View larger version: In this window In a new window Figure 6. Transposon DNA methylation...
  5. Research: Combinatorial DNA methylation codes at repetitive elements
    • Christophe Papin,
    • Abdulkhaleg Ibrahim,
    • Stéphanie Le Gras,
    • Amandine Velt,
    • Isabelle Stoll,
    • Bernard Jost,
    • Hervé Menoni,
    • Christian Bronner,
    • Stefan Dimitrov,
    • and Ali Hamiche
    Genome Res. June 2017 27: 934-946; Published in Advance March 27, 2017, doi:10.1101/gr.213983.116
    ...cytosine modification densities and CA densities at CA repeats. CA repeats were sorted in quartiles based on their number of CpA dinucleotides. (F ) In vitro glycosylase assays revealing that the recombinant protein TDG excises formylcytosine exclusively in a CpG or CpA context. (G) Average distance to TSS...
  6. ARTICLE: Allele-specific gene expression patterns in primary leukemic cells reveal regulation of gene expression by CpG site methylation
    • Lili Milani,
    • Anders Lundmark,
    • Jessica Nordlund,
    • Anna Kiialainen,
    • Trond Flaegstad,
    • Gudmundur Jonmundsson,
    • Jukka Kanerva,
    • Kjeld Schmiegelow,
    • Kevin L. Gunderson,
    • Gudmar Lönnerholm,
    • and Ann-Christine Syvänen
    Genome Res. January 2009 19: 1-11; Published in Advance November 7, 2008, doi:10.1101/gr.083931.108
    ...methylation of CpG sites in the promoter regions of genes has been identified in leukemic cell lines or primary ALL cells, and correlated with the expression of individual genes, but such studies have been hampered by a limited representation of the studied genomic regions and/or by a small number of cell...
    OPEN ACCESS ARTICLE
  7. Methods: Multiplex padlock targeted sequencing reveals human hypermutable CpG variations
    • Jin Billy Li,
    • Yuan Gao,
    • John Aach,
    • Kun Zhang,
    • Gregory V. Kryukov,
    • Bin Xie,
    • Annika Ahlford,
    • Jung-Ki Yoon,
    • Abraham M. Rosenbaum,
    • Alexander Wait Zaranek,
    • Emily LeProust,
    • Shamil R. Sunyaev,
    • and George M. Church
    Genome Res. September 2009 19: 1606-1615; Published in Advance June 12, 2009, doi:10.1101/gr.092213.109
    ...in multiple samples. Several technologies have been recently developed but await substantial improvements. We report the 10,000-fold improvement of a previously developed padlock-based approach, and apply the assay to identifying genetic variations in hypermutable CpG regions across human chromosome 21. From...
  8. 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
    ...in cancer. Thus, our data demonstrate that the global epigenetic landscape is dynamically altered at key regulatory regions outside of promoters. (NDR) Nucleosome-depleted region; (small white circle) unmethylated CpG site; (small black circle) methylated CpG site; (large circle) nucleosome; (4me1 [green...
    OPEN ACCESS ARTICLE
  9. 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
    ..., were analyzed as compared with four wild-type IDH1 parental cell line replicates. Comparison of the relative methylation (b) distribution of all assayed CpG sites in KI-1, KI-2, and parental cells revealed a significant shift in the relative DNA methylation (b) density distribution upon IDH1R132H...
  10. Method: Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma
    • Nancy H. Nabilsi,
    • Loic P. Deleyrolle,
    • Russell P. Darst,
    • Alberto Riva,
    • Brent A. Reynolds,
    • and Michael P. Kladde
    Genome Res. February 2014 24: 329-339; Published in Advance October 8, 2013, doi:10.1101/gr.161737.113
    ...not been rigorously proven to be heritable (Schreiber and Bernstein 2002; Fuks 2005; Esteller 2007). Aberrant DNAmethylation of CpG (hereafter, CG) dinucleotides is a well-documented phenomenon in cancer (Baylin and Jones 2011). It is widely accepted that DNA methylation near transcriptional start sites...
For checked items

Search Results

Next 10 » New Search

Modify Results

Citation format:
Results / page:
Results order:

This search

  • Alert me when new articles matching this search are published
  • Download all citations on this page to my citation manager

Preprint Server



Current Issue

  1. March 2026, 36 (3)
  1. Current Issue
  1. Alert me to new issues of Genome Research