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#epigenomics

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	1.	Research Cytosine methylation changes in enhancer regions of core pro-fibrotic genes characterize kidney fibrosis development Yi-An Ko, Davoud Mohtat, Masako Suzuki, Ae Seo Park, Maria Concepcion Izquierdo, Sang Youb Han, Hyun Mi Kang, Han Si, Thomas Hostetter, James M Pullman, Melissa Fazzari, Amit Verma, Deyou Zheng, John M Greally, Katalin Susztak Genome Biology 2013, 14:R108 (7 October 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The enhancers of genes involved in fibrosis exhibit DNA methylation in chronically diseased kidneys, with correlated changes in gene expression
	2.	Research highlight PINTing for p53 Ramin Shiekhattar Genome Biology 2013, 14:132 (30 September 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Ramin Sheikhattar discusses new findings, published in Genome Biology, about a novel lncRNA ('PINT'), p53 and cancer
	3.	Research Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2 Oskar Marin-Bejar, Francesco P Marchese, Alejandro Athie, Yolanda Sanchez, Jovanna Gonzalez, Victor Segura, Lulu Huang, Isabel Moreno, Alfons Navarro, Mariano Monzo, Jesus Garcia-Foncillas, John L Rinn, Shuling Guo, Maite Huarte Genome Biology 2013, 14:R104 (26 September 2013) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel lincRNA, PINT, connects p53 activation with epigenetic silencing by PRC2 and is identified as a candidate tumor suppressor
	4.	Research The mutational landscape of chromatin regulatory factors across 4623 tumor samples Abel Gonzalez-Perez, Alba Jene-Sanz, Nuria Lopez-Bigas Genome Biology 2013, 14:r106 (24 September 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Identification of mutations in chromatin regulatory factors and their potential role in tumorigenesis
	5.	Research Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia Jessica Nordlund, Christofer L Bäcklin, Per Wahlberg, Stephan Busche, Eva C Berglund, Maija-Leena Eloranta, Trond Flaegstad, Erik Forestier, Britt-Marie Frost, Arja Harila-Saari, Mats Heyman, Ólafur G Jónsson, Rolf Larsson, Josefine Palle, Lars Rönnblom, Kjeld Schmiegelow, Daniel Sinnett, Stefan Söderhäll, Tomi Pastinen, Mats G Gustafsson, Gudmar Lönnerholm, Ann-Christine Syvänen Genome Biology 2013, 14:r105 (24 September 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary DNA methylation signatures associated with subtype, relapse and gene expression in pediatric acute lymphoblastic leukemia
	6.	Research Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape Kenneth Day, Lindsay L Waite, Anna Thalacker-Mercer, Andrew West, Marcas M Bamman, James D Brooks, Richard M Myers, Devin Absher Genome Biology 2013, 14:R102 (13 September 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study of DNA methylation changes in four tissues during aging finds both tissue-specific and universal age-associated methylation changes
	7.	Research PU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation Lorenzo de la Rica, Javier Rodríguez-Ubreva, Mireia García, Abul BMMK Islam, José M Urquiza, Henar Hernando, Jesper Christensen, Kristian Helin, Carmen Gómez-Vaquero, Esteban Ballestar Genome Biology 2013, 14:R99 (12 September 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Tet2 and DNMT3b act in concert with the transcription factor PU.1 to remodel the epigenome during monocyte-to-osteoclast differentiation
	8.	Research An ENU mutagenesis screen identifies novel and known genes involved in epigenetic processes in the mouse Lucia Daxinger, Sarah K Harten, Harald Oey, Trevor Epp, Luke Isbel, Edward Huang, Nadia Whitelaw, Anwyn Apedaile, Anabel Sorolla, Joan Yong, Vandhana Bharti, Joanne Sutton, Alyson Ashe, Zhenyi Pang, Nathan Wallace, Daniel J Gerhardt, Marnie E Blewitt, Jeffrey A Jeddeloh, Emma Whitelaw Genome Biology 2013, 14:R96 (11 September 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A full characterization of the Momme screen for mouse genes regulating epigenetic processes includes three novel epigenetic regulators
	9.	Method Measuring cell-type specific differential methylation in human brain tissue Carolina M Montaño, Rafael A Irizarry, Walter E Kaufmann, Konrad Talbot, Raquel E Gur, Andrew P Feinberg, Margaret A Taub Genome Biology 2013, 14:R94 (30 August 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A method for deconvolving brain tissue into neuronal and non-neuronal populations using DNA methylation signatures to allow cell-type specific analysis
	10.	Research Genome-wide analysis identifies a functional association of Tet1 and Polycomb repressive complex 2 in mouse embryonic stem cells Francesco Neri, Danny Incarnato, Anna Krepelova, Stefania Rapelli, Andrea Pagnani, Riccardo Zecchina, Caterina Parlato, Salvatore Oliviero Genome Biology 2013, 14:R91 (29 August 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genome-wide analysis of TET1 binding identifies an interaction between TET1 and PRC2 in ESCs, which recruits TET1 to regions of H3K27me3
	11.	Research highlight DNA methylation: an identity card for brain cells Ambre Bender, Michael Weber Genome Biology 2013, 14:131 (27 August 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Ambre Bender and Michael Weber highlight recent work that delineates the dynamics of DNA (hydroxy)methylation during mammalian brain development
	12.	Meeting report Conquering computational challenges of omics data and post-ENCODE paradigms Yves A Lussier, Haiquan Li, Mark Maienschein-Cline Genome Biology 2013, 14:310 (23 August 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 12th European Conference on Computational Biology (ECCB), held in Berlin, Germany, July 21-23, 2013
	13.	Research highlight DNA methylation, genotype and gene expression: who is driving and who is along for the ride? Meaghan J Jones, Anthony P Fejes, Michael S Kobor Genome Biology 2013, 14:126 (29 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Michael Kobor and colleagues discuss regulatory interactions between DNA methylation, genotype and gene expression
	14.	Review Ant genomics sheds light on the molecular regulation of social organization Romain Libbrecht, Peter R Oxley, Daniel JC Kronauer, Laurent Keller Genome Biology 2013, 14:212 (29 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Laurent Keller and colleagues review new insights into insect social organization that have arisen from ant genome sequences and epigenomics research
	15.	Correspondence The advantages of SMRT sequencing Richard J Roberts, Mauricio O Carneiro, Michael C Schatz Genome Biology 2013, 14:405 (3 July 2013) Abstract \| Full text \| PDF \| PubMed \| 2 comments \| Editor’s summary Rich Roberts, Mauricio Carneiro and Michael Schatz argue for a greater uptake of the impressive PacBio SMRT sequencing platform
	16.	Research *Thermal stress effects on grain yield in Brachypodium distachyon* occur via H2A.Z-nucleosomes** Scott A Boden, Monika Kavanová, E Finnegan, Philip A Wigge Genome Biology 2013, 14:R65 (25 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Repressing H2A.Z-nucleosome deposition phenocopies stress effects of higher temperatures on Brachypodium distachyon grain development
	17.	Research *Hyperosmotic priming of Arabidopsis* seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome** Emanuela Sani, Pawel Herzyk, Giorgio Perrella, Vincent Colot, Anna Amtmann Genome Biology 2013, 14:R59 (14 June 2013) Abstract \| Full text \| PDF \| PubMed \| f1000 \| Editor’s summary Exposure of young seedlings to salt stress causes histone modifications and transcriptional changes, enhancing stress tolerance in mature plants
	18.	Research Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids Guangming He, Beibei Chen, Xuncheng Wang, Xueyong Li, Jigang Li, Hang He, Mei Yang, Lu Lu, Yijun Qi, Xiping Wang, Xing Wang Deng Genome Biology 2013, 14:R57 (12 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the effect of genotype and tissue type on transcriptional and epigenetic changes in maize inbred lines and hybrids
	19.	Research highlight Deep C diving: mapping the low-abundance modifications of the DNA demethylation pathway John P Thomson, Jennifer M Hunter, Richard R Meehan Genome Biology 2013, 14:118 (29 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Richard Meehan and colleagues highlight recent insights into the 5th, 6th, 7th and 8th DNA bases: 5mC, 5hmC, 5fC and 5caC
	20.	Research highlight Rising from the crypt: decreasing DNA methylation during differentiation of the small intestine Sean M Cullen, Margaret A Goodell Genome Biology 2013, 14:116 (28 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight examines why differentiation in the small intestine crypt bypasses the DNA methylation changes observed in other lineage progressions
	21.	Research DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus Lucas TJ Kaaij, Marc van de Wetering, Fang Fang, Benjamin Decato, Antoine Molaro, Harmen JG van de Werken, Johan H van Es, Jurian Schuijers, Elzo de Wit, Wouter de Laat, Gregory J Hannon, Hans C Clevers, Andrew D Smith, René F Ketting Genome Biology 2013, 14:R50 (28 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Intriguingly, DNA methylation in mouse intestinal cells does not change much during differentiation
	22.	Research Genome-wide analysis of functional sirtuin chromatin targets in yeast Mingguang Li, Veena Valsakumar, Kunal Poorey, Stefan Bekiranov, Jeffrey S Smith Genome Biology 2013, 14:R48 (27 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sirtuins regulate both glycolytic gene expression and condensin/cohesin deposition, suggesting a mechanistic link between metabolism and chromatin architecture
	23.	Research 5-Hydroxymethylcytosine is an essential intermediate of active DNA demethylation processes in primary human monocytes Maja Klug, Sandra Schmidhofer, Claudia Gebhard, Reinhard Andreesen, Michael Rehli Genome Biology 2013, 14:R46 (26 May 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary TET2-mediated conversion of 5mC to 5hmC initiates active demethylation of the genome during monocyte differentiation
	24.	Research Adult monozygotic twins discordant for intra-uterine growth have indistinguishable genome-wide DNA methylation profiles Nicole YP Souren, Pavlo Lutsik, Gilles Gasparoni, Sascha Tierling, Jasmin Gries, Matthias Riemenschneider, Jean-Pierre Fryns, Catherine Derom, Maurice P Zeegers, Jörn Walter Genome Biology 2013, 14:R44 (26 May 2013) Abstract \| Full text \| PDF \| PubMed \| f1000 \| Editor’s summary Monozygotic twins discordant for birth weight have very similar DNA methylation profiles
	25.	Research Inactive or moderately active human promoters are enriched for inter-individual epialleles Carolina Gemma, Sreeram V Ramagopalan, Thomas A Down, Huriya Beyan, Mohammed I Hawa, Michelle L Holland, Paul J Hurd, Gavin Giovannoni, R David Leslie, George C Ebers, Vardhman K Rakyan Genome Biology 2013, 14:R43 (25 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Epialleles between monozygotic twins are temporally stable, associated with chromatin changes and enriched in transcriptionally inactive regions