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Corrigendum: Corrigendum: H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells
- Agustín F. Fernández,
- Gustavo F. Bayón,
- Rocío G. Urdinguio,
- Estela G. Toraño,
- María G. García,
- Antonella Carella,
- Sandra Petrus-Reurer,
- Cecilia Ferrero,
- Pablo Martinez-Camblor,
- Isabel Cubillo,
- Javier García-Castro,
- Jesús Delgado-Calle,
- Flor M. Pérez-Campo,
- José A. Riancho,
- Clara Bueno,
- Pablo Menéndez,
- Anouk Mentink,
- Katia Mareschi,
- Fabian Claire,
- Corrado Fagnani,
- Emanuela Medda,
- Virgilia Toccaceli,
- Sonia Brescianini,
- Sebastián Moran,
- Manel Esteller,
- Alexandra Stolzing,
- Jan de Boer,
- Lorenza Nisticò,
- Maria A. Stazi,
- and Mario F. Fraga
Genome Res. April 2019 29: 710.2; doi:10.1101/gr.249417.119
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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
...enrichment of regulatory regions (H3K27ac, H3K4me1, H3K4me3, and H3K27me3) and transcription factor bindings sites (SPI1, RUNX1, and GATA1) at differentially methylated CpGs overlapping CGIs or non-CGI CpGs using ChIP-seq data from healthy CD34+ cells.In CD34+ cells, HC modulates DNA methylation...
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Research: ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters
- Nina L. Haring,
- Elisabeth J. van Bree,
- Whitney S. Jordaan,
- Judith R.E. Roels,
- Gonzalo Congrains Sotomayor,
- Tiziana M. Hey,
- Fred T.G. White,
- Marc D. Galland,
- Marten P. Smidt,
- and Frank M.J. Jacobs
Genome Res. April 2021 31: 551-563; Published in Advance March 15, 2021, doi:10.1101/gr.265348.120
.... 2019; Farmiloe et al. 2020), and maintenance of DNA methylation at imprinting control regions (Li et al. 2008; Takahashi et al. 2015, 2019; Riso et al. 2016).In this study we focus on a primate-specific TE class, named after its composite domains: SINE-VNTR-Alu (SVA). There are approximately 2800 fixed...
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Research: Evolutionary expansion of DNA hypomethylation in the mammalian germline genome
- Jianghan Qu,
- Emily Hodges,
- Antoine Molaro,
- Pascal Gagneux,
- Matthew D. Dean,
- Gregory J. Hannon,
- and Andrew D. Smith
Genome Res. February 2018 28: 145-158; Published in Advance December 19, 2017, doi:10.1101/gr.225896.117
...during development and differentiation (Meissner et al. 2008; Hodges et al. 2011). These dynamics can exhibit high precision, for example, when boundaries of hypomethylated regions shift to uncover CpG island “shores” and allow additional regulatory elements to receive signals (Irizarry et al. 2009).DNA...
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Research: Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers
- Xabier Agirre,
- Giancarlo Castellano,
- Marien Pascual,
- Simon Heath,
- Marta Kulis,
- Victor Segura,
- Anke Bergmann,
- Anna Esteve,
- Angelika Merkel,
- Emanuele Raineri,
- Lidia Agueda,
- Julie Blanc,
- David Richardson,
- Laura Clarke,
- Avik Datta,
- Nuria Russiñol,
- Ana C. Queirós,
- Renée Beekman,
- Juan R. Rodríguez-Madoz,
- Edurne San José-Enériz,
- Fang Fang,
- Norma C. Gutiérrez,
- José M. García-Verdugo,
- Michael I. Robson,
- Eric C. Schirmer,
- Elisabeth Guruceaga,
- Joost H.A. Martens,
- Marta Gut,
- Maria J. Calasanz,
- Paul Flicek,
- Reiner Siebert,
- Elías Campo,
- Jesús F. San Miguel,
- Ari Melnick,
- Hendrik G. Stunnenberg,
- Ivo G. Gut,
- Felipe Prosper,
- and José I. Martín-Subero
Genome Res. April 2015 25: 478-487; Published in Advance February 2, 2015, doi:10.1101/gr.180240.114
...tracks include the chromatin state characterization in IMBCs and ChIP-seq data for H3K27ac, H3K4me1, and H3K4me3. DNAmethylation levels of NPCs andMM patient samples measured by WGBS and HumanMethylation450 BeadChip are also shown. (D–F) Correlation analysis between DNA methylation levels...
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Research: Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways
- Weishi Yu,
- Carl McIntosh,
- Ryan Lister,
- Iris Zhu,
- Yixing Han,
- Jianke Ren,
- David Landsman,
- Eunice Lee,
- Victorino Briones,
- Minoru Terashima,
- Robert Leighty,
- Joseph R. Ecker,
- and Kathrin Muegge
Genome Res. October 2014 24: 1613-1623; Published in Advance August 28, 2014, doi:10.1101/gr.172015.114
...MEFs, and ES cells We derived genomic DNA from primary murine embryonic fibroblasts (MEFs) of day 13.5 embryos of Hells#1;/ (KO) or WT littermates (Geiman et al. 2001). We used an established wild-type murine embryonic stem cell line (ES) for comparison. ES cells are derived from the inner cell mass...
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Method: Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
- Bo Zhang,
- Yan Zhou,
- Nan Lin,
- Rebecca F. Lowdon,
- Chibo Hong,
- Raman P. Nagarajan,
- Jeffrey B. Cheng,
- Daofeng Li,
- Michael Stevens,
- Hyung Joo Lee,
- Xiaoyun Xing,
- Jia Zhou,
- Vasavi Sundaram,
- GiNell Elliott,
- Junchen Gu,
- Taoping Shi,
- Philippe Gascard,
- Mahvash Sigaroudinia,
- Thea D. Tlsty,
- Theresa Kadlecek,
- Arthur Weiss,
- Henriette O’Geen,
- Peggy J. Farnham,
- Cécile L. Maire,
- Keith L. Ligon,
- Pamela A.F. Madden,
- Angela Tam,
- Richard Moore,
- Martin Hirst,
- Marco A. Marra,
- Baoxue Zhang,
- Joseph F. Costello,
- and Ting Wang
Genome Res. September 2013 23: 1522-1540; Published in Advance June 26, 2013, doi:10.1101/gr.156539.113
...unmethylated in differentiated cell types, and 41% acquired a promoter-associated histone mark (H3K4me3), while 30% acquired an enhancer-associated histone mark (H3K4me1) (Fig. 4A). These epigenetic changes underscored the importance of DNA methylation in tissue differentiation. This result was further...
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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
...modifications20 (H3K4me1, H3K4me3, H3K27me3, and H3K27ac), and DNA methylation. We used ChromHMM to21 identify 14 chromatin states, each of which represented a distinct combination of the four histone22 modifications. We found that the epigenetic landscape was highly variable across the DO founders23...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...PCR primers designed against nonregulatory regions of the gene when enrichment is not expected, and ensuring DNA shearing with fragments that are not too long in order to prevent nonspecific GOI identification. ChIP has had a revolutionary impact on our understanding of biology and has spearheaded clinical...
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Resource: Whole-genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver
- Xin Li,
- Yun Liu,
- Tal Salz,
- Kasper D. Hansen,
- and Andrew Feinberg
Genome Res. December 2016 26: 1730-1741; Published in Advance October 13, 2016, doi:10.1101/gr.211854.116
...and associates with H3K4me1 mark Our previous studies provided evidence that most t-DMRs and cDMRs surprisingly overlap with CGI shores but not CGIs, which usually disrupt methylation boundaries of CGI boundaries, and Whole- 5hmC analysis in normal and cancer Genome Research 1733 www..org that DNA methylation...

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