Searching journal content for articles similar to Hogart et al. 22 (8): 1407.

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  1. Research: Tracing human stem cell lineage during development using DNA methylation
    • Lucas A. Salas,
    • John K. Wiencke,
    • Devin C. Koestler,
    • Ze Zhang,
    • Brock C. Christensen,
    • and Karl T. Kelsey
    Genome Res. September 2018 28: 1285-1295; Published in Advance August 2, 2018, doi:10.1101/gr.233213.117
    ...and applied a DNA methylation signature common among human fetal hematopoietic progenitor cells and have shown that this signature traces the lineage of cells and informs the study of stem cell heterogeneity in humans under homeostatic conditions.Studies of hematopoiesis have laid the foundation for advances...
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  2. Method: Allele-specific RNA N6-methyladenosine modifications reveal functional genetic variants in human tissues
    • Shuo Cao,
    • Haoran Zhu,
    • Jinru Cui,
    • Sun Liu,
    • Yuhe Li,
    • Junfang Shi,
    • Junyuan Mo,
    • Zihan Wang,
    • Hailan Wang,
    • Jiaxin Hu,
    • Lizhi Chen,
    • Yuan Li,
    • Laixin Xia,
    • and Shan Xiao
    Genome Res. August 2023 33: 1369-1380; Published in Advance September 15, 2023, doi:10.1101/gr.277704.123
    ...to the phenotypic diversity in the population, and more than 10,000 genetic variants have been revealed to be associated with diseases by -wide association study (GWAS) (Maurano et al. 2012; Wang et al. 2021). At the molecular level, genetic variants can affect a number of processes, including DNA methylation...
  3. 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...
  4. Research: Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels
    • Amanda J. Lea,
    • Julie Peng,
    • and Julien F. Ayroles
    Genome Res. October 2022 32: 1826-1839; Published in Advance October 13, 2022, doi:10.1101/gr.276430.121
    ...will be important for corroborating the patterns we see here. Finally, we did not generate environment-specific data on additional gene regulatory mechanisms such as DNA methylation, chromatin accessibility, or chromatin state. Although this work was beyond the scope of the present study, it is a key avenue...
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  5. Research: Genome-wide identification of TAL1's functional targets: Insights into its mechanisms of action in primary erythroid cells
    • Mira T. Kassouf,
    • Jim R. Hughes,
    • Stephen Taylor,
    • Simon J. McGowan,
    • Shamit Soneji,
    • Angela L. Green,
    • Paresh Vyas,
    • and Catherine Porcher
    Genome Res. August 2010 20: 1064-1083; Published in Advance June 21, 2010, doi:10.1101/gr.104935.110
    .... The TAL1/TCF3/LMO2/LDB1 complex recruits cofactors with activator or repressor functions, such as EP300, GFI1B, CBFA2T3 (ETO2), and KDM1A (Huang et al. 1999, 2000; Schuh et al. 2005; Goardon et al. 2006; Hu et al. 2009). It can also bind other DNA-bound transcription factors such as the hemopoietic...
  6. Research: Age-associated DNA methylation in pediatric populations
    • Reid S. Alisch,
    • Benjamin G. Barwick,
    • Pankaj Chopra,
    • Leila K. Myrick,
    • Glen A. Satten,
    • Karen N. Conneely,
    • and Stephen T. Warren
    Genome Res. April 2012 22: 623-632; Published in Advance February 1, 2012, doi:10.1101/gr.125187.111
    ...al. 2009; Cortellino et al. 2011; Wu et al. 2011), suggesting these age-related demethylation events are governed by an alternative active demethylation pathway or passive DNA demethylation. In contrast, analysis of age-methylated loci did not reveal a significant pattern among the surrounding...
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  7. Research: Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer
    • Andrew E. Teschendorff,
    • Usha Menon,
    • Aleksandra Gentry-Maharaj,
    • Susan J. Ramus,
    • Daniel J. Weisenberger,
    • Hui Shen,
    • Mihaela Campan,
    • Houtan Noushmehr,
    • Christopher G. Bell,
    • A. Peter Maxwell,
    • David A. Savage,
    • Elisabeth Mueller-Holzner,
    • Christian Marth,
    • Gabrijela Kocjan,
    • Simon A. Gayther,
    • Allison Jones,
    • Stephan Beck,
    • Wolfgang Wagner,
    • Peter W. Laird,
    • Ian J. Jacobs,
    • and Martin Widschwendter
    Genome Res. April 2010 20: 440-446; Published in Advance March 10, 2010, doi:10.1101/gr.103606.109
    ...cell pools. To this end, we investigated the DNA methylation profiles of cultured mesenchymal stromal/stem cells (MSC) derived from the bone marrow of eight healthy individuals spanning a wide age range (21–85 yr; Set-7) (Bork et al. 2010). Despite the small sample size, the average methylation profile...
  8. 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
    ...-specific expression (ASE) levels of 2529 genes by genotyping a genome-wide panel of single nucleotide polymorphisms in RNA and DNA from bone marrow and blood samples of 197 children with ALL. Using a reproducible, quantitative genotyping method and stringent criteria for scoring ASE, we found that 16% of the analyzed...
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  9. Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
    • Daniela M Riley,
    • Randa Elsayed,
    • Mark D Walsh,
    • Simaran Johal,
    • Ying Lin,
    • Harry Walton,
    • Till Bretschneider,
    • Sascha Ott,
    • and Andrew C Nelson
    Genome Res. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
    ...analyses reveal a highly significant association between 285 endoderm HCNEs and genes encoding DNA-binding and gene regulatory proteins, including 286 HMG domain-containing and chromatin binding factors. Notably, however, the endoderm 287 HCNEs appear to show a greater enrichment of such genes compared...
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  10. 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
    ...lacking. Here, we show that bivalent chromatin does not poise genes for rapid activation but protects promoters from de novo DNA methylation. Genome-wide studies in differentiating ESCs reveal that activation of bivalent genes is no more rapid than that of other transcriptionally silent genes, challenging...
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