MEEting REpOR t Epigenetics 7:10, 1211–1216; October 2012; © 2012 Landes Bioscience MEEting REpOR t Report on the 10th EMBL Conference on Transcription and Chromatin August 25–28, 2012 EMBL Advanced Training Centre, Heidelberg, Germany Sascha Duttke Section of Molecular Biology; University of California, San Diego; La Jolla, CA USA Keywords: EMBL, Heidelberg, chromatin, transcription, histone modifications, histone mimics, stem cells, pluripotency, reprogramming, RNA epigenetics, DNA hydroxymethylation, chromatin dynamics Over 400 scientists from 38 countries gathered in the marvelous city of Heidelberg, g ermany to attend the 10th EMBL Conference on t ranscription and Chromatin. Surrounded by dark-green forest and overlooking a historic city, the charming environment of the EMBL as well as an all- star lineup of presenters attracted scientists from all over the world to discuss the latest findings and the future directions in the field. Superbly organized by Henk Stunnenberg, Eileen Furlong, Ali Shilatifard and Marc t immers, the main topics of the conference included Dn A, Rn A and histone modifications, pluripotency and cellular reprogramming, transcriptional regulation, as well as chromatin dynamics and the effect of chromatin on gene regulation. in a pleasant summer climate that facilitated a stimulating and collaborative atmosphere, over 50 outstanding talks and more than 200 posters were presented. i apologize in advance to those speakers whose excellent work i have been unable to include in this report due to space constraints. Nucleic Acid Modifications, RNA Epigenetics and a Putative Sixth Base Anjana Rao, from the La Jolla Institute of Allergy and Immunology (San Diego, CA), kicked off this very exciting session by intro- ducing the potential mechanism of cytosine demethylation by the TET family enzymes and its role in cellular differentiation. TET proteins convert 5-methyl-cytosine (5-mC) to 5-hydroxy- methyl-cytosine (5-hmC) and higher oxidized forms, 5-formyl- cytosine (5-fC) and 5-carboxyl-cytosine (5-caC), which can be reconverted to cytosine.1-3 Genome-wide quantification of cyto- sine modifications in embryonic stem cells (ESCs) estimated 5% of all cytosines to be methylated and approximately 0.5% of them to be hydroxymethylated; the higher oxidized forms, 5-fC and 5-caC, are only present in a few thousand to a few hundred cop- ies per ESC.3 Dr Rao presented new insights into the mamma- lian TET protein family, which consists of three members. TET1 Correspondence to: Sascha Duttke; Email: sduttke@ucsd.edu Submitted: 09/06/12; Accepted: 09/06/12 http://dx.doi.org/10.4161/epi.22095 and TET2 are preferentially expressed in ESCs, while TET3 is mostly found in differentiated cells. TET2 lacks the functionally important CXXC domain, which got separated during evolu- tion and now functions as an independent gene encoding IDAX (CXXC4). CXXC domains are intertwined double zinc fingers that bind unmethylated CG sequences in DNA. Dr Rao showed data suggesting that CXXC domains had an auto-inhibitory role in TET1 and TET3, and that IDAX had a dual regulatory role involving TET2 recruitment to DNA as well as TET2 degrada- tion. IDAX was previously reported to be an inhibitor of Wnt signaling, therefore connecting Wnt signaling to DNA modifi- cation during embryonic development. Together, Dr Rao’s work suggests the exciting model that TET protein function is regu- lated during differentiation and embryonic development, thereby changing cytosine modification patterns and the chromatin environment. Dr Chuan He, from the University of Chicago, presented a technique to investigate the presence of 5-hmC on genome-wide scale. Protection of both 5-mC and 5-hmC from C to U conver- sion upon bisulfite treatment makes it impossible to distinguish between these two DNA modifications upon traditional bisulfite sequencing. This limitation can be overcome by TET-assisted bisulfite sequencing (TAB-Seq).4 In short, in this method, the bacteriophage T4 β-glucosyltransferase selectively glycosylates the hydroxyl group of 5-hmC. Utilization of glucose with an azide group (N3) allowed further modification such as addition of a biotin molecule, which facilitates enrichment. Glycosylated, and thus masked, 5-hmC is, unlike 5-mC, protected from TET- mediated oxidation. Hence, 5-hmC is read as C after bisulfite treatment while C and 5-mC are read as T. Using TAB-Seq, Dr He generated single base resolution maps of 5-hmC sites in the mammalian genome. 5-hmC displayed an asymmetric genome wide distribution, where 99% of all sites were at CG nucleo- tides. 5-hmC was further enriched in distal regulatory elements, including p300 and CTCF binding sites as well as DNaseI hyper- sensitive sites. Dr He also provided evidence for 5-hmC to be an active demethylation intermediate. It will thus be exciting to look forward to the functional roles of 5-hmC. TAB-Seq is commer- cially available from Wisegene. www.landesbioscience.com Epigenetics 1211