differentiation. Dr de Laat utilized 4C, a method that com- bines chromosome conformation capture with next-generation sequencing, to investigate all contact points on a particular sequence in the genome. The resolution of the method permit- ted mapping of regulatory sequences within a few kilobases and identified contact points as close as 10 kb.26,27 Work from Dr de Laat and others showed that inactive chromatin regions show little contacts in ESCs, while the genome of differentiated cells is spatially more defined. Inactive regions in neural precursor cells showed more specific contacts than in ESCs. Reprogramming of neural precursor cells into iPS cells made the genome spatially less defined. These findings are consistent with those of Dixon et al.28 and provide further evidence for the presence of spatially unorga- nized inactive chromatin in ESC. Dr de Laat also observed this phenomenon in more slowly dividing human iPS. What causes this change in chromatin architecture? Hi-C showed preferred contacts among Nanog binding sites in ESC but not in neural precursor cells, suggesting a role for pluripotency factors in shap- ing higher order chromatin structure. Long Non-Coding RNAs and Transcript Regulation Ramin Shiekhattar, from the Wistar Institute (USA), introduced the audience to a novel role of long non-coding RNAs (lncRNAs) in the regulation of gene expression. The human genome con- tains over 6,000 lncRNAs that range from 100 to 9,500 nt and average around 1,000 nt. The expression patterns of lncRNAs appear to be highly tissue-specific; in addition, the histone modi- fications H3K4me, H3K4me3 and H3K36me3 are often found at lncRNA genes. Long non-coding RNAs are not exported to the cytoplasm, and several lncRNAs were shown to activate their neighboring genes is cis.29 These lncRNAs are mostly found to be associated with chromatin. Dr Shiekhattar found that lncRNAs could function in an enhancer-like fashion. This function is RNA dependent. For lncRNA-a7, he showed that Mediator confers this enhancer function. Mediator and lncRNA-a7 regu- late DNA looping from the lncRNA promoter to the target gene promoter, thus activating the target gene in cis. Outlook In its 10th anniversary, the EMBL Transcription and Chromatin meeting celebrated a long-standing tradition of bringing together the leaders in the field and providing an interactive platform for discussion and socializing. Once again, this meeting impressed with an excellent line-up of speakers, a well-organized execution and a very pleasant environment. As a result, this only leaves us anxiously looking forward to the next meeting in 2014. On a final note, I would like to end this report by acknowledging the excellent job of Henk Stunnenberg, who, after organizing the last ten meetings, will leave the organizing committee; I anticipate that the remaining organizers, Eileen Furlong, Ali Shilatifard and Marc Timmers, will not disappoint in continuing with the tradition of making the EMBL Conference on Transcription and Chromatin meeting one of the best meetings in the field. Disclosure of Potential Conflicts of Interest No potential conflicts of interest were disclosed. Acknowledgments I would like to thank Carolina Garcia Sabaté and Krasimira Todorova (EMBL Heidelberg) for administrative help, Epigenie (http://epigenie.com) for covering the conference registra- tion fee, the UCSD Graduate School of Biological Sciences for travel support and Prof James T. Kadonaga for guidance, rec- ommendations and continuous support. I am also grateful to all cited authors, Dr Barbara Rattner, Dr Alexandra Lusser, Dr Tamar Juven-Gershon and Dr Rebecca Wright for suggestions and editing of this manuscript. S.D. is supported by NIH grant GM041249 to James T. Kadonaga. 1. 2. 3. 4. 5. References Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, et al. Conversion of 5-methylcyto- sine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009; 324:930-5; PMID:19372391; http://dx.doi.org/10.1126/sci- ence.1170116. He Y-F, Li B-Z, Li Z, Liu P, Wang Y, Tang Q, et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 2011; 333:1303-7; PMID:21817016; http://dx.doi. org/10.1126/science.1210944. Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA, et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 2011; 333:1300-3; PMID:21778364; http://dx.doi. org/10.1126/science.1210597. Yu M, Hon GC, Szulwach KE, Song CX, Zhang L, Kim A, et al. Base-resolution analysis of 5-hydroxy- methylcytosine in the mammalian genome. Cell 2012; 149:1368-80; PMID:22608086; http://dx.doi. org/10.1016/j.cell.2012.04.027. Jia G, Fu Y, Zhao X, Dai Q, Zheng G, Yang Y, et al. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol 2011; 7:885-7; PMID:22002720; http://dx.doi. org/10.1038/nchembio.687. 6. Eberl HC, Mann M, Vermeulen M. Quantitative pro- teomics for epigenetics. Chembiochem 2011; 12:224- 34; PMID:21243711; http://dx.doi.org/10.1002/ cbic.201000429. 7. Ying QL, Wray J, Nichols J, Batlle-Morera L, Doble B, Woodgett J, et al. The ground state of embry- onic stem cell self-renewal. Nature 2008; 453:519- 23; PMID:18497825; http://dx.doi.org/10.1038/ nature06968. 8. Marks H, Kalkan T, Menafra R, Denissov S, Jones K, Hofemeister H, et al. The transcriptional and epig- enomic foundations of ground state pluripotency. Cell 2012; 149:590-604; PMID:22541430; http://dx.doi. org/10.1016/j.cell.2012.03.026. 9. Chia NY, Chan YS, Feng B, Lu XY, Orlov YL, Moreau D, et al. A genome-wide RNAi screen reveals determi- nants of human embryonic stem cell identity. Nature 2010; 468:316-20; PMID:20953172; http://dx.doi. org/10.1038/nature09531. 10. Zaret KS, Carroll JS. Pioneer transcription factors: establishing competence for gene expression. Genes Dev 2011; 25:2227-41; PMID:22056668; http:// dx.doi.org/10.1101/gad.176826.111. 11. Cuthbert GL, Daujat S, Snowden AW, Erdjument- Bromage H, Hagiwara T, Yamada M, et al. Histone deimination antagonizes arginine methylation. Cell 2004; 118:545-53; PMID:15339660; http://dx.doi. org/10.1016/j.cell.2004.08.020. 12. Mayer A, Heidemann M, Lidschreiber M, Schreieck A, Sun M, Hintermair C, et al. CTD tyrosine phos- phorylation impairs termination factor recruitment to RNA polymerase II. Science 2012; 336:1723- 5; PMID:22745433; http://dx.doi.org/10.1126/sci- ence.1219651. 13. Smolle M, Venkatesh S, Gogol MM, Li H, Zhang Y, Florens L, et al. Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange. Nat Struct Mol Biol 2012; 19:884-92; PMID:22922743; http://dx.doi. org/10.1038/nsmb.2312. 14. Venkatesh S, Smolle M, Li H, Gogol MM, Saint M, Kumar S, et al. Set2 methylation of histone H3 lysine?36 suppresses histone exchange on transcribed genes. Nature 2012; 489:452-5; PMID:22914091; http://dx.doi.org/10.1038/nature11326. 15. Kim T, Buratowski S. Dimethylation of H3K4 by Set1 recruits the Set3 histone deacetylase complex to 5' transcribed regions. Cell 2009; 137:259-72; PMID:19379692; http://dx.doi.org/10.1016/j. cell.2009.02.045. 16. Gilchrist DA, Dos Santos G, Fargo DC, Xie B, Gao YA, Li LP, et al. Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation. Cell 2010; 143:540- 51; PMID:21074046; http://dx.doi.org/10.1016/j. cell.2010.10.004. www.landesbioscience.com Epigenetics 1215