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#epigenomics

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	1.	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 \| 1 comment \| Editor’s summary Rich Roberts, Mauricio Carneiro and Michael Schatz argue for a greater uptake of the impressive PacBio SMRT sequencing platform
	2.	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 Biology \| Editor’s summary Exposure of young seedlings to salt stress causes histone modifications and transcriptional changes, enhancing stress tolerance in mature plants
	3.	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
	4.	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
	5.	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
	6.	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
	7.	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
	8.	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 \| Editor’s summary TET2-mediated conversion of 5mC to 5hmC initiates active demethylation of the genome during monocyte differentiation
	9.	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 Biology \| Editor’s summary Monozygotic twins discordant for birth weight have very similar DNA methylation profiles
	10.	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
	11.	Meeting report Epigenetics and transgenerational inheritance Emilie Brasset, Séverine Chambeyron Genome Biology 2013, 14:306 (24 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 'Non-coding RNA, epigenetics and transgenerational inheritance' meeting, held at Churchill College, Cambridge, UK, April 11-12, 2013.
	12.	Research Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance David Martino, Yuk Loke, Lavinia Gordon, Miina Ollikainen, Mark N Cruickshank, Richard Saffery, Jeffrey M Craig Genome Biology 2013, 14:R42 (22 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A longitudinal study of DNA methylation in twins at birth and 18 months finds that some loci drift in methylation status
	13.	Method jMOSAiCS: joint analysis of multiple ChIP-seq datasets Xin Zeng, Rajendran Sanalkumar, Emery H Bresnick, Hongda Li, Qiang Chang, Sündüz Keleş Genome Biology 2013, 14:R38 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel probabilistic method for jointly analyzing multiple ChIP-seq datasets offers an improvement over chromHMM
	14.	Research Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes James P Reddington, Sara M Perricone, Colm E Nestor, Judith Reichmann, Neil A Youngson, Masako Suzuki, Diana Reinhardt, Donncha S Dunican, James G Prendergast, Heidi Mjoseng, Bernard H Ramsahoye, Emma Whitelaw, John M Greally, Ian R Adams, Wendy A Bickmore, Richard R Meehan Genome Biology 2013, 14:R25 (25 March 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An intact DNA methylome is required for appropriate Polycomb-mediated gene repression, as revealed by H3K4me3 and PRC2 mapping in hypomethylated cells
	15.	Research DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes Dvir Aran, Sivan Sabato, Asaf Hellman Genome Biology 2013, 14:R21 (12 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new study using an innovative machine learning approach finds that distal gene regulatory sites are hypermethylated in cancers
	16.	Research The B cell transcription program mediates hypomethylation and overexpression of key genes in Epstein-Barr virus-associated proliferative conversion Henar Hernando, Claire Shannon-Lowe, Abul B Islam, Fatima Al-Shahrour, Javier Rodríguez-Ubreva, Virginia C Rodríguez-Cortez, Biola M Javierre, Cristina Mangas, Agustín F Fernández, Maribel Parra, Henri-Jacques Delecluse, Manel Esteller, Eduardo López-Granados, Mario F Fraga, Nuria López-Bigas, Esteban Ballestar Genome Biology 2013, 14:R3 (15 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DNA hypomethylation is a key feature of Epstein-Barr virus-associated B cell proliferative transformation, and occurs via a passive demethylation process
	17.	Research *Natural variation of H3K27me3 distribution between two Arabidopsis* accessions and its association with flanking transposable elements** Xue Dong, Julia Reimer, Ulrike Göbel, Julia Engelhorn, Fei He, Heiko Schoof, Franziska Turck Genome Biology 2012, 13:R117 (19 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of natural variation of H3K27me3 in 2 Arabidopsis thaliana accessions and in their F1 hybrids
	18.	Research Human genes with CpG island promoters have a distinct transcription-associated chromatin organization Tanya Vavouri, Ben Lehner Genome Biology 2012, 13:R110 (27 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study of the chromatin architecture at promoters reveals different histone modifications at those with CpG islands and those without
	19.	Research Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling Mariona Nadal-Ribelles, Núria Conde, Oscar Flores, Juan González-Vallinas, Eduardo Eyras, Modesto Orozco, Eulàlia de Nadal, Francesc Posas Genome Biology 2012, 13:R106 (18 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hog1 bypasses gene expression regulation by targeting RNA polymerase II machinery and inducing chromatin remodeling at stress-responsive loci
	20.	Opinion The birth of the Epitranscriptome: deciphering the function of RNA modifications Yogesh Saletore, Kate Meyer, Jonas Korlach, Igor D Vilfan, Samie Jaffrey, Christopher E Mason Genome Biology 2012, 13:175 (31 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary First came genomics, and then epigenomics. But is epitranscriptomics the future? A picture is emerging of RNA methylation's functional importance
	21.	Editorial What can epigenomics do for you? Alexander Meissner Genome Biology 2012, 13:420 (23 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Alexander Meissner asks not what you can do for epigenomics, but what epigenomics can do for you
	22.	Editorial The allure of the epigenome Naomi Attar Genome Biology 2012, 13:419 (23 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A guide to the articles published in our special issue on epigenomics
	23.	Research highlight Balance of DNA methylation and demethylation in cancer development Chun-Xiao Song, Chuan He Genome Biology 2012, 13:173 (23 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary How this issue's research article on 5hmC, together with other recent work, adds to our understanding of methylation processes in cancer
	24.	Review The roles of the reprogramming factors Oct4, Sox2 and Klf4 in resetting the somatic cell epigenome during induced pluripotent stem cell generation Ryan Schmidt, Kathrin Plath Genome Biology 2012, 13:251 (22 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary How a dramatic reorganization of the epigenome ultimately results in the induced pluripotent stem cell state
	25.	Review Surveying the epigenomic landscape, one base at a time Gabriel E Zentner, Steven Henikoff Genome Biology 2012, 13:250 (22 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New methods for mapping histones at higher resolution open many new doors in epigenomics research