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Research: Hydroxycarbamide effects on DNA methylation and gene expression in myeloproliferative neoplasms
- Stephania Contreras Castillo,
- Bertille Montibus,
- Azucena Rocha,
- Will Duke,
- Ferdinand von Meyenn,
- Donal McLornan,
- Claire Harrison,
- Ann Mullally,
- Reiner Schulz,
- and Rebecca J. Oakey
Genome Res. August 2021 31: 1381-1394; Published in Advance July 9, 2021, doi:10.1101/gr.270066.120
...than 30 years in the MPN clinical area, effects on DNA methylation have not been comprehensively studied -wide in relevant cell types, and currently there is a limited understanding about the global mechanistic effects of this agent. To gain insight into the effects of HC, gene expression analysis...
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Resource: A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements
- Salam Idriss,
- Mohammad Hallal,
- Abdullah El-Kurdi,
- Hasan Zalzali,
- Inaam El-Rassi,
- Erik A. Ehli,
- Christel M. Davis,
- Philip E.D. Chung,
- Deena M.A. Gendoo,
- Eldad Zacksenhaus,
- Raya Saab,
- and Pierre Khoueiry
Genome Res. February 2023 33: 269-282; Published in Advance January 17, 2023, doi:10.1101/gr.277037.122
...tumors, thus paving the way for better targeted therapies for PB.Cis-regulatory elements (CREs) including promoters, enhancers, and repressors are noncoding DNA sequences harboring binding sites for transcription factors (TFs) required to activate or repress target gene expression (Ong and Corces 2011...
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Research: Variation in histone configurations correlates with gene expression across nine inbred strains of mice
- Anna L Tyler,
- Catrina Spruce,
- Romy Kursawe,
- Annat Haber,
- Robyn L Ball,
- Wendy A Pitman,
- Alexander D Fine,
- Narayanan Raghupathy,
- Michael Walker,
- Vivek M Philip,
- Christopher L Baker,
- J. Matthew Mahoney,
- Gary A. Churchill,
- Jennifer J Trowbridge,
- Michael L Stitzel,
- Kenneth Paigen,
- Petko M Petkov,
- and Gregory W Carter
Genome Res. May 22, 2023 gr.277467.122; Published in Advance May 22, 2023, doi:10.1101/gr.277467.122
...expression regulation. We illustrate how DO gene expression can be27 aligned with inbred epigenetic states to identify putative cis-regulatory regions. Finally, we provide28 a data resource that documents strain-specific variation in chromatin state and DNA methylation29 in hepatocytes across nine widely...
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Research: Cytosine modifications modulate the chromatin architecture of transcriptional enhancers
- Elise A. Mahé,
- Thierry Madigou,
- Aurélien A. Sérandour,
- Maud Bizot,
- Stéphane Avner,
- Frédéric Chalmel,
- Gaëlle Palierne,
- Raphaël Métivier,
- and Gilles Salbert
Genome Res. June 2017 27: 947-958; Published in Advance April 10, 2017, doi:10.1101/gr.211466.116
...relationship between cytosine modifications and the chromatin architecture of enhancers remains elusive. To gain insights into their function, 5mC and 5hmC levels were perturbed by inhibiting DNA methyltransferases and TETs during differentiation of mouse embryonal carcinoma cells into neural progenitors...
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Research: Critical threshold levels of DNA methyltransferase 1 are required to maintain DNA methylation across the genome in human cancer cells
- Yi Cai,
- Hsing-Chen Tsai,
- Ray-Whay Chiu Yen,
- Yang W. Zhang,
- Xiangqian Kong,
- Wei Wang,
- Limin Xia,
- and Stephen B. Baylin
Genome Res. April 2017 27: 533-544; Published in Advance February 23, 2017, doi:10.1101/gr.208108.116
...Diagenode. A detailed protocol is described in the Supplemental Methods. Genome-wide methylation and gene expression analyses Genome-wide DNA methylation is measured by Infinium HumanMethylation450 (HM450) BeadChip array (Illumina) according to the manufacturer’s instructions. Global gene expression profiles were...
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Research: Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice
- Yuan Fang,
- Lifen Chen,
- Kande Lin,
- Yilong Feng,
- Pengyue Zhang,
- Xiucai Pan,
- Jennifer Sanders,
- Yufeng Wu,
- Xiu-e Wang,
- Zhen Su,
- Caiyan Chen,
- Hairong Wei,
- and Wenli Zhang
Genome Res. August 2019 29: 1287-1297; Published in Advance July 1, 2019, doi:10.1101/gr.246009.118
...inhibitor used for the induction of global DNA demethylation in both mammals and plants (Zhou et al. 2002). Zebularine treatment reduced overall DNA methylation levels by ∼30%, and this led to a global reduction in R-loop intensities of ∼22% (Fig. 3D; Supplemental Fig. S6C).To investigate which types of TEs...
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Research: Recurrent epimutations activate gene body promoters in primary glioblastoma
- Raman P. Nagarajan,
- Bo Zhang,
- Robert J.A. Bell,
- Brett E. Johnson,
- Adam B. Olshen,
- Vasavi Sundaram,
- Daofeng Li,
- Ashley E. Graham,
- Aaron Diaz,
- Shaun D. Fouse,
- Ivan Smirnov,
- Jun Song,
- Pamela L. Paris,
- Ting Wang,
- and Joseph F. Costello
Genome Res. May 2014 24: 761-774; Published in Advance April 7, 2014, doi:10.1101/gr.164707.113
...for this article.] A hallmark of many cancers is the decrease in 5-methylcytosine in genomic DNA relative to non-neoplastic cells or tissue, termed global hypomethylation (Feinberg and Vogelstein 1983; GamaSosa et al. 1983; Wild and Flanagan 2010). Although the degree of global hypomethylation can be severe...
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Research: The role of DNA methylation in directing the functional organization of the cancer epigenome
- Fides D. Lay,
- Yaping Liu,
- Theresa K. Kelly,
- Heather Witt,
- Peggy J. Farnham,
- Peter A. Jones,
- and Benjamin P. Berman
Genome Res. April 2015 25: 467-477; Published in Advance March 6, 2015, doi:10.1101/gr.183368.114
...; Widschwendter et al. 2007) and is postulated to be part of a global “epigenetic switch” from Polycomb repression to DNA methylation (Gal-Yam et al. 2008; Jin et al. 2009). Indeed, the histone marks and expression levels of NP genes in DKO1 cells strongly resembled those of normal colonic mucosa (Supplemental...
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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
...) and noncancer samples (GM12878 and H1-HESC). The chromatin ChIP-seq tracks demonstrate that the hypomethylated region is marked by cancer-specific repressive H3K27me3 and EZH2 binding (cancer = K562, HeLa, HepG2; noncancer = HMEC, GM12878, NH-A). Dynamic DNA methylation across human tissues Genome Research 559...
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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
...-translational histone modifications, and nucleosome occupancy (Coolen et al. 2010; Taberlay and Jones 2011; Bert et al. 2013), can lead to global changes of the cancer epi coupled with associated deregulation of cancer gene expression signatures. DNA methylation currently remains the most characterized epigenetic...
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