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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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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
...-cell differentiation, suggesting that MM cells either reacquire epigenetic features of undifferentiated cells or maintain an epigenetic signature of a putative myeloma stem cell progenitor. Overall, we have identified DNA hypermethylation of developmentally regulated enhancers as a new type of epigenetic modification...
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Research: Regulation of endogenous retrovirus–derived regulatory elements by GATA2/3 and MSX2 in human trophoblast stem cells
- Cui Du,
- Jing Jiang,
- Yuzhuo Li,
- Miao Yu,
- Jian Jin,
- Shuai Chen,
- Hairui Fan,
- Todd S. Macfarlan,
- Bin Cao,
- and Ming-an Sun
Genome Res. February 2023 33: 197-207; Published in Advance February 17, 2023, doi:10.1101/gr.277150.122
..., Latos PA. 2021. MSX2 safeguards syncytiotrophoblast fate of human trophoblast stem cells. Proc Natl Acad Sci 118: e2105130118. doi:10.1073/pnas.2105130118 ↵Hubley R, Finn RD, Clements J, Eddy SR, Jones TA, Bao W, Smit AF, Wheeler TJ. 2016. The Dfam database of repetitive DNA families. Nucleic Acids Res...
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Research: 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. January 2015 25: 27-40; Published in Advance September 30, 2014, doi:10.1101/gr.169011.113
..., aging is associated with hypermethylation of DNA regions enriched in repressive histone post-translational modifications. However, the chromatin marks associated with changes in DNA methylation in adult stem cells during lifetime are still largely unknown. Here, DNA methylation profiling of mesenchymal...
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Research: DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia
- Brian Giacopelli,
- Min Wang,
- Ada Cleary,
- Yue-Zhong Wu,
- Anna Reister Schultz,
- Maximilian Schmutz,
- James S. Blachly,
- Ann-Kathrin Eisfeld,
- Bethany Mundy-Bosse,
- Sebastian Vosberg,
- Philipp A. Greif,
- Rainer Claus,
- Lars Bullinger,
- Ramiro Garzon,
- Kevin R. Coombes,
- Clara D. Bloomfield,
- Brian J. Druker,
- Jeffrey W. Tyner,
- John C. Byrd,
- and Christopher C. Oakes
Genome Res. May 2021 31: 747-761; Published in Advance March 11, 2021, doi:10.1101/gr.269233.120
...showed inferior overall survival along with up-regulated stem cell gene expression signatures. We further identified a DNA methylation signature involving STAT motifs associated with FLT3-ITD mutations. Finally, DNA methylation signatures were stable at relapse for the large majority of patients...
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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
...the importance of using paired samples from the same individual (Chatterjee et al. 2015). The striking differences in DNA methylation following HC treatment in human CD34+ cells support the importance of selecting the correct cell population for DNA methylation studies. These hematopoietic stem and progenitor...
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Research: Ribosomal DNA harbors an evolutionarily conserved clock of biological aging
- Meng Wang and
- Bernardo Lemos
Genome Res. March 2019 29: 325-333; Published in Advance February 14, 2019, doi:10.1101/gr.241745.118
...exclusively with CpG methylation within the rDNA. The ribosomal clock is sufficient to accurately estimate individual age within species, is responsive to genetic and environmental interventions that modulate life-span, and operates across species as distant as humans, mice, and dogs. Further analyses...
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Research: Transcriptional alterations in glioma result primarily from DNA methylation–independent mechanisms
- Franck Court,
- Elisa Le Boiteux,
- Anne Fogli,
- Mélanie Müller-Barthélémy,
- Catherine Vaurs-Barrière,
- Emmanuel Chautard,
- Bruno Pereira,
- Julian Biau,
- Jean-Louis Kemeny,
- Toufic Khalil,
- Lucie Karayan-Tapon,
- Pierre Verrelle,
- and Philippe Arnaud
Genome Res. October 2019 29: 1605-1621; Published in Advance September 18, 2019, doi:10.1101/gr.249219.119
...promoters in stem cells predisposes not only to hypermethylation, as widely documented, but more generally to all types of transcriptional alterations in transformed cells. In addition, the gene expression strength in healthy brain cells influences the choice between DNA methylation- and H3K27me3-associated...
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Research: Pluripotent stem cells escape from senescence-associated DNA methylation changes
- Carmen M. Koch,
- Kristina Reck,
- Kaifeng Shao,
- Qiong Lin,
- Sylvia Joussen,
- Patrick Ziegler,
- Gudrun Walenda,
- Wolf Drescher,
- Bertram Opalka,
- Tobias May,
- Tim Brümmendorf,
- Martin Zenke,
- Tomo Šarić,
- and Wolfgang Wagner
Genome Res. February 2013 23: 248-259; Published in Advance October 18, 2012, doi:10.1101/gr.141945.112
...Pluripotent stem cells escape from senescence-associated DNA methylation changes Carmen M. Koch 1 , Kristina Reck 1 , Kaifeng Shao 2 , Qiong Lin 3 , Sylvia Joussen 1 , Patrick Ziegler 4 , Gudrun Walenda 1 , Wolf...
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Research: Switching roles for DNA and histone methylation depend on evolutionary ages of human endogenous retroviruses
- Hitoshi Ohtani,
- Minmin Liu,
- Wanding Zhou,
- Gangning Liang,
- and Peter A. Jones
Genome Res. August 2018 28: 1147-1157; Published in Advance July 3, 2018, doi:10.1101/gr.234229.118
...of the LTRs is regulated by both the DNA and histone methylation, and we have demonstrated a synergy between the two for the up-regulation of the viral defense signature (Supplemental Fig. S15). Therefore, pharmacological inhibition of DNA methylation concurrent with targeting histone methyltransferases might...

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