Searching journal content for articles similar to Takeshima et al. 19 (11): 1974.

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  1. Research: GC skew defines distinct RNA polymerase pause sites in CpG island promoters
    • Wendy A. Kellner,
    • Joshua S.K. Bell,
    • and Paula M. Vertino
    Genome Res. November 2015 25: 1600-1609; Published in Advance August 14, 2015, doi:10.1101/gr.189068.114
    ...GC skew defines distinct RNA polymerase pause sites in CpG island promoters Wendy A. Kellner 1 , 3 , 4 , Joshua S.K. Bell 1 , 3 and Paula M. Vertino 1 , 2 1Department of Radiation Oncology, Emory University School of Medicine, Atlanta...
  2. Method: Predicting transfer RNA gene activity from sequence and genome context
    • Bryan P. Thornlow,
    • Joel Armstrong,
    • Andrew D. Holmes,
    • Jonathan M. Howard,
    • Russell B. Corbett-Detig,
    • and Todd M. Lowe
    Genome Res. January 2020 30: 85-94; Published in Advance December 19, 2019, doi:10.1101/gr.256164.119
    ...islands scores as the observed frequency of CpG dinucleotides compared to their expected frequency given the G + C content of a region. We found that these scores, when calculated for the 350 bases upstream of each gene, are significantly correlated with active tRNA genes (Spearman's rank correlation, P...
  3. Research: Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome
    • Wilfried M. Guiblet,
    • Michael DeGiorgio,
    • Xiaoheng Cheng,
    • Francesca Chiaromonte,
    • Kristin A. Eckert,
    • Yi-Fei Huang,
    • and Kateryna D. Makova
    Genome Res. July 2021 31: 1136-1149; Published in Advance June 29, 2021, doi:10.1101/gr.269589.120
    ...), in regulation of non-L1 TE life cycle (Lexa et al. 2014), in distal interactions between promoters and enhancers (Hou et al. 2019; Williams et al. 2020), and in protecting CpG islands from methylation (Halder et al. 2010; Mao et al. 2018; Jara-Espejo and Peres Line 2020)—remain hypothetical. If G4s...
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  4. Mini-Review: The paradox of R-loops: guardians of the genome or drivers of disease?
    • Shachinthaka D. Dissanayaka Mudiyanselage,
    • Phillip Wulfridge,
    • and Kavitha Sarma
    Genome Res. September 2025 35: 1919-1928; Published in Advance August 6, 2025, doi:10.1101/gr.278992.124
    ...RNA-polymerase-II-transcribed genes. Cell 151: 835–846. doi:10.1016/j.cell.2012.09.041 ↵Arab K, Karaulanov E, Musheev M, Trnka P, Schäfer A, Grummt I, Niehrs C. 2019. GADD45A binds R-loops and recruits TET1 to CpG island promoters. Nat Genet 51: 217–223. doi:10.1038/s41588-018-0306-6 ↵Ariel F, Lucero...
  5. Resource: Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis
    • Rui Yokomori,
    • Kotaro Shimai,
    • Koki Nishitsuji,
    • Yutaka Suzuki,
    • Takehiro G. Kusakabe,
    • and Kenta Nakai
    Genome Res. January 2016 26: 140-150; Published in Advance December 14, 2015, doi:10.1101/gr.184648.114
    ...frequently used as TSSs. Despite the absence of CpG islands, Ciona TATA-less promoters showed low expression specificity like CpG-associated human TATA-less promoters. By using TSS-seq, we also predicted trans -spliced gene TSSs and found that their downstream regions had higher G+T content than those...
  6. Method: Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA
    • Aaron L. Statham,
    • Mark D. Robinson,
    • Jenny Z. Song,
    • Marcel W. Coolen,
    • Clare Stirzaker,
    • and Susan J. Clark
    Genome Res. June 2012 22: 1120-1127; Published in Advance March 30, 2012, doi:10.1101/gr.132076.111
    ..., Yamashita S, Shimazu T, Niwa T, Ushijima T. 2009. The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islands. Genome Res 19: 1974–1982. Widschwendter M, Fiegl H, Egle D, Mueller-Holzner E, Spizzo G, Marth C, Weisenberger DJ, Campan M, Young J, Jacobs I, et al...
  7. 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
    ...targets (Fig. 4C), suggesting that CpG density alone can be an excellent predictor of H3K4me3 levels. A corollary to this conclusion would be that CpG density, together with H3K27me3 levels, can predict bivalent chromatin (Fig. 4B,D). Indeed, a machine learning approach based on multinomial logistic...
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  8. Research: DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon–intron structure
    • Sahar Gelfman,
    • Noa Cohen,
    • Ahuvi Yearim,
    • and Gil Ast
    Genome Res. May 2013 23: 789-799; Published in Advance March 15, 2013, doi:10.1101/gr.143503.112
    ...results, DNA methylation is a strong marker of an exon when these;140,000 human exons are considered (Supplemental Fig. S9A). The methylated CpGs were constructed for alternative and constitutive exons that are expressed sequence tag (EST)-based since the RNA-seq data provided reliable inclusion level...
  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
    ...from wild-type HCT116 cells (Birney et al. 2007) showed that CpG sites that became hypermethylated in the HCT116 IDH1R132H/WT cells are depleted of RNA polymerase II (Pol II) binding and histone H3 lysine 4 trimethylation (H3K4me3) relative to sites that become hypomethylated or remain unchanged...
  10. Research: The chromatin environment shapes DNA replication origin organization and defines origin classes
    • Christelle Cayrou,
    • Benoit Ballester,
    • Isabelle Peiffer,
    • Romain Fenouil,
    • Philippe Coulombe,
    • Jean-Christophe Andrau,
    • Jacques van Helden,
    • and Marcel Méchali
    Genome Res. December 2015 25: 1873-1885; Published in Advance November 11, 2015, doi:10.1101/gr.192799.115
    ...1992). Conversely, recent analyses revealed the presence of GC-rich elements in eukaryotic origins, such as CpG islands (CGI) (Delgado et al. 1998; Prioleau 2009; Cayrou et al. 2011; Costas et al. 2011) and an Origin G-rich Repeated Element (OGRE) that can form G4 (Cayrou et al. 2011, 2012a). G4were...
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