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Research: LTRs activated by Epstein-Barr virus–induced transformation of B cells alter the transcriptome
- Amy Leung,
- Candi Trac,
- Hiroyuki Kato,
- Kevin R. Costello,
- Zhaoxia Chen,
- Rama Natarajan,
- and Dustin E. Schones
Genome Res. December 2018 28: 1791-1798; Published in Advance October 31, 2018, doi:10.1101/gr.233585.117
...populations of early human embryonic cells. Cell Stem Cell 16: 135–141. doi:10.1016/j.stem.2015.01.005 ↵Hansen KD, Sabunciyan S, Langmead B, Nagy N, Curley R, Klein G, Klein E, Salamon D, Feinberg AP. 2014. Large-scale hypomethylated blocks associated with Epstein-Barr virus–induced B-cell immortalization...
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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
...samples: tissues, primary cell lines, embryonic cell lines, and blood leukocytes (Fig. 3A; detailed tree in Supplemental Fig. S8). The blood leukocyte-derived samples, including both peripheral blood leukocytes and Epstein-Barr virus (EBV)-immortalized lymphoblastoid cell lines, clustered together...
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Letter: The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer
- Agustin F. Fernandez,
- Cecilia Rosales,
- Pilar Lopez-Nieva,
- Osvaldo Graña,
- Esteban Ballestar,
- Santiago Ropero,
- Jesus Espada,
- Sonia A. Melo,
- Amaia Lujambio,
- Mario F. Fraga,
- Irene Pino,
- Biola Javierre,
- Francisco J. Carmona,
- Francesco Acquadro,
- Renske D.M. Steenbergen,
- Peter J.F. Snijders,
- Chris J. Meijer,
- Pascal Pineau,
- Anne Dejean,
- Belen Lloveras,
- Gabriel Capella,
- Josep Quer,
- Maria Buti,
- Juan-Ignacio Esteban,
- Helena Allende,
- Francisco Rodriguez-Frias,
- Xavier Castellsague,
- Janos Minarovits,
- Jordi Ponce,
- Daniela Capello,
- Gianluca Gaidano,
- Juan Cruz Cigudosa,
- Gonzalo Gomez-Lopez,
- David G. Pisano,
- Alfonso Valencia,
- Miguel Angel Piris,
- Francesc X. Bosch,
- Ellen Cahir-McFarland,
- Elliott Kieff,
- and Manel Esteller
Genome Res. March 2009 19: 438-451; Published in Advance February 10, 2009, doi:10.1101/gr.083550.108
...the described process. Using bisulfite genomic sequencing of multiple clones, we have obtained the DNA methylation status of every CpG dinucleotide in the genome of the Human Papilloma Viruses 16 and 18 and Human Hepatitis B Virus, and in all the transcription start sites of the Epstein-Barr Virus...
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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
...differences. Using data from oxBS-seq, we were able to identify DMRs by only taking methylation changes into account between normal and matched tumor samples. Identified DMRs were grouped into small-scale DMRs and large-scale blocks according to their length (see Methods). We found that in both liver and lung...
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Research: Bacterial infection remodels the DNA methylation landscape of human dendritic cells
- Alain Pacis,
- Ludovic Tailleux,
- Alexander M. Morin,
- John Lambourne,
- Julia L. MacIsaac,
- Vania Yotova,
- Anne Dumaine,
- Anne Danckaert,
- Francesca Luca,
- Jean-Christophe Grenier,
- Kasper D. Hansen,
- Brigitte Gicquel,
- Miao Yu,
- Athma Pai,
- Chuan He,
- Jenny Tung,
- Tomi Pastinen,
- Michael S. Kobor,
- Roger Pique-Regi,
- Yoav Gilad,
- and Luis B. Barreiro
Genome Res. December 2015 25: 1801-1811; Published in Advance September 21, 2015, doi:10.1101/gr.192005.115
...-DMRs, corresponding to both hypermethylated regions (48%) and hypomethylated regions (52%) (Fig. 1B; Supplemental Table S2). To independently validate these changes, we generated methylation-sensitive pyrosequencing data on control versus MTB-infected DCs from five new individuals. We targeted 21 CpG sites that were...
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Resource: A comparison of gene expression and DNA methylation patterns across tissues and species
- Lauren E. Blake,
- Julien Roux,
- Irene Hernando-Herraez,
- Nicholas E. Banovich,
- Raquel Garcia Perez,
- Chiaowen Joyce Hsiao,
- Ittai Eres,
- Claudia Cuevas,
- Tomas Marques-Bonet,
- and Yoav Gilad
Genome Res. February 2020 30: 250-262; Published in Advance January 17, 2020, doi:10.1101/gr.254904.119
...sets, study design is unlikely to impact large-scale, highly robust trends across species. However, this study design choice is particularly important if one is interested in individual genes (as shown by an example in Fig. 1C).Putatively functional tissue-specific gene expression patternsTo analyze...
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