This year’s EMBO Conference on Chromatin and Epigenetics (May 8-12, 2013) took place in Heidelberg, famous for hosting the oldest university in Germany, in the newly constructed EMBL advanced training Centre, at the European Molecular Biology Laboratory (EMBL). The conference was organized by an international team (Asifa Akhtar, Geneviève Almoouzni, Peter Fraser, Jason Lieb and Jane Mellor), which compiled a broad scientific program covering a wide range of fields in epigenetics.
The conference started off with a introductory session covering all the topics of the conference such as: interplay between chromatin and transcription, DNA methylation, epigenetic memory, pericentric heterochromatin and nuclear structure and, last but not least, small non coding RNAs and model organisms in epigenetics.
The conference presented an interesting view on some new approaches in the field, like for example: HiC applications and single cell Dam-ID to dissect nuclear organization, STARR-seq to identify enhancers, Nascent Chromatin capture (NCC) proteomics to profile chromatin replication and in vivo-FRAP to dissect nuclear dynamics in the embryo. Newly identified histones modifications were as well discussed like: H3K122ac, H3K64ac/me3 and H2AQ104me were presented. The meeting ended on a Sunday with a half a day session on epigenetic and cell plasticity.
The conference was a good opportunity to meet many people at the frontiers of the field, establish contacts, reinforce pre-existing ones and check out for novelties. The schedule was tough, but ensured enough time to metabolize the talks and to debate them in coffee breaks or during the lunches and dinners up in the “EMBL hill”. There were moments of fun as well, like the party on Saturday night and a free evening to visit the town too, while of course, talking about epigenetics!
The Epigenome of Groundstate Mouse Embryonic Stem Cells
Hendrik Stunnenberg, NCMLs, Radbound University Nijmegen, The Netherlands
Stunnenberg talked about his recent work in characterizing the naïve ground state of mouse embryonic stem cells (ESC). He started highlighting the fact that ESC grown in serum are heterogeneous in contrast to cells grown in 2i, which appear more homogenous and are thought to represent the naive ground state. They did transcription profile of cells grown in serum or 2i with the result that in serum is observed an upregulation of differentiation genes while in 2i an upregulation of metabolic genes. He noticed that, globally, ESCs grown in serum do not recapitulate the global DNA hypomethylation observed at the inner cell mass (ICM) state.
The ESCs established and maintained in 2i are hypomethylated resembling more, the ground state of pluripotency, thought to be in the ICM. 5-hmdC is globally enriched in ESC grown in serum, as assessed by MS. Then they used the medium switch, from serum to 2i, as a system to model DNA demethylation. They tried to assess the levels of the major player in DNA methylation and their activity during medium switch, observing no apparent difference in DNMT1, UHRF1. Some differences in DNA demethylation kinetics were observed by floxing SETDB1 during the medium switch, which induced faster demethylation. They noticed that by adding vitamin C to 2i medum, which was shown to upregulate Tet enzymes, they would get fast demethylation in the medium switch, presuming an involvement of 5-hmdC in this process.
Epigenetic Pathways in Transcription and Cancer
Tony Kouzarides, Cambridge University UK
Kouzarides started with a broad introduction highlighting the epigenetic players (MLL, p300, TET, DNMTs) mutated in cancer and the progress made with drugs targeting these pathways. He then went presenting a new histone modification such as: H2AQ104me or 105 in yeast. The methylation was identified after a manual annotation of a mass spectrometry dataset. After a very long and laborious screening in yeast, the enzyme responsible for it was identified to be Nop1. Nop1, or fibrillarin in mammals, was known to be involved in ribosomal biogenesis and to interact genetically with the RNA PolI transcription factor RRN3.In MCF10A shows nucleolar localization. ChIP-seq identified the protein to be bound to one single locus, the ribosomal genes DNA locus. It appears to have a role in PolI dependent transcription, through histone remodeling via an interaction with the FACT complex. He concluded off by saying that inhibitors are in clinical trial.
Probing Position Effects in High Throughput
Bas van Steensel, The Netherlands
Bas van Steensel introduced this new high throughput technique called TRIP, which allows the random integration of a gene reporter in the DNA, through cotransfection of its plasmid with one encoding a transposase. The presence of a bar-coding system will allow to track the integration site. He could observe a broad range of expression levels, not representing noise, because reproducible. Neighboring insertions tend to show the same expression levels. Insertions in lamina associated domains (LADs) show attenuated transcription. Chromatin compaction plays as well a big role in repression. H3K9me3 regions and LADs show less transcription factor binding. They find that insertions close to a gene or to an enhancer, show high expression. TRIP is thus an useful technique to probe the position effect for an element of choice (enhancer, promoter, insulator…) in a high throughput fashion. For sure it will answer important questions in molecular biology in the next future!
Small-RNA Guided Epigenetic Regulation of Transposon Expression in the Drosophila Germline
Katalin Fejes Toth, California Institute of Technology, USA
Fejes Toth started off her talk by introducing piwi proteins and piwi-interacting RNAs (piRNA). They are expressed in the gonads of Metazoans to protect them from the random mobilization of transposons. If absent there are gonad defects and sterility. Some piRNA are in the cytoplasm where they guide piwi complexes to destroy complimentary transposon transcripts by endonucleolytic cleavage. In Drosophila, some others are nuclear, and they are recruited to chromatin where they colocalize with RNAPolII. When Piwi is knocked down in the germline, there is an increased expression of transposable elements, with increased PolII at their TSS and a decrease in H3K9me3. A mutated Piwi, not able to bind to pi-RNA, is not effective in a rescue experiment. This shows that Piwi is required to target pi-RNA and to induce a silent chromatin state at target transposons loci . They are trying to use this system to induce heterochromatin formation.
Cancer genetics and epigenetics: two sides of the same coin?
Peter Jones, USC Norris Comprehensive Cancer Center , USA
The plenary lecture was given by Peter Jones. He started with the microscopy image from which Flemming in 1879 noted that there was something that stained differently which he called chromatin. Nowadays chromatin is still used by pathologists for cancer diagnosis. He followed on, highlighting the fact that often mutations are at CpG sites, as for example in the p53 gene. In general cancer are hypomethylated, but promoters are hypermethylated. Furthermore, a lot of mutations are in epigenetic players. In general, DNA methylation does not silence genes, but locks them in an OFF state. But DNA methylation cannot be separated from nucleosome occupancy; thus, to be able to map this, he presented NOME-seq that allows the parallel detection of both. This technique helps explaining why cancer acquires promoter hypermethylation at nucleosome depleted regions. Then he went on summarizing the successful story of the DNMTs inhibitor azacytidine. He concluded his talk defining epigenetics as a “sweet spot” for therapy development and with the idea of moving forward azacytidine usage to solid tumors and in combination with immunotherapy.
Only two years from now and we will have the possibility to broaden our mind by listening again at wonderful and inspiring talks at the next Chromatin and Epigenetics Conference.
** EpiGenie would love to thank Melania Zauri for her comprehensive coverage of this great meeting.