“An All-star lineup of presenters and a pleasant atmosphere made the 11th EMBL Transcription and Chromatin meeting certainly one to remember.” That was how EpiGenie friend and reporter Sascha Duttke (UCSD) described this latest EMBL meeting. Read on to check out his full report.
11th EMBL Transcription and Chromatin Conference Overview
About 460cientists from 32 countries met in Heidelberg to share the latest insights in transcription and chromatin. DNA methylation, topologically associating domains (TADs), enhancers, bidirectional transcription, basal transcription, and the effect of chromatin and its modifications on gene expression were among the central topics. The overall high quality of the presentations and sheer volume of novel material made it a true challenge to choose what to summarize, as it would be impossible to cover everything that deserves attention.
DNA Methylation and Reprogramming
Henk Stunnenberg, Univerisity of Nijmegen
Dr. Stunnenberg kicked off this year’s meeting with the latest insights in DNA methylation and its role in stem cell reprogramming. Mouse ESCs grown with inhibitors of MEK and GSK3 (2i media) are in ground state and globally hypomethylated compared to those grown in serum (primed state) (Stunnenberg, Cell, April 2012 ). Stunnenberg’s laboratory utilized this system to investigate the mechanism and kinetics of DNA methylation occurring when moving ESCs from serum to 2i media. Under both growth conditions, TET1, TET2 and DNMT1 expression are similar, but DNMT3a/b and DNMT3L are down regulated by 4-32 times in 2i cells.
Demethylation occurs over several days but could be accelerated by supplementing with vitamin C. An increase in global 5hmC levels argued for a TET-mediated demethtylation mechanism. Kinetic analyses suggested demethylation to switch from a fast, TET dependent demethylation to a passive mechanism. Notably, the kinetics varied between different genomic regions. In the absence of TET1/2, vitamin C did not increase DNA de-methylation. Surprisingly, TET1/2 were dispensable for ESC de-differentiation from primed to ground state. It could thus be speculated that DNA methylation may not play an essential role in ESC reprogramming from serum (primed) to 2i (ground state) cells.
Genome Wide Enhancer Actions in Development
Eileen Furlong, Genome Biology Unit, EMBL
One of the most dynamic alterations in gene regulation is observed during early development. Dr. Furlong’s group thus compared chromatin interactions as mapped by 4C at two different stages of Drosophila development to assess changes in enhancer interactions (Ghavi-Helm, Nature, August 2014). The enhancers contacted, on average, ten targets of which about half did not map to annotated regions, reinforcing the idea that an enhancer may regulate multiple genes.
Although the vast majority of Drosophila enhancers known previously were within 10kb, Furlongs’ genome wide analyses found that 73% of enhancer contact regions greater than 50 kb away. Long-range interactions are also common in more compact genomes such as Drosophila. Notably, the vast majority of enhancer interactions remain unchanged during the two developmental stages examined; just 6% were more dynamic.
Moreover, these apparently stable DNA loops in developmental time occur hours prior to the genes’ expression and contain paused Pol II at their promoters. Together, this highlights a potential important role for global DNA topology in development and the regulation of gene expression.
DNA Localization and Transcription
Wendy Bickmore, Medical Research Council, Human Genetics Unit
The nuclear periphery is occupied by inactive or poorly transcribed genes and enriched for inactive chromatin marks. This organization can change during differentiation raising the question whether the loss of transcription targets the chromatin to the nuclear periphery or vice versa. Dr. Bickmore and colleagues utilized fluorescent probes in combination with synthetic transcription activators targeting genes at the nuclear periphery in mouse embryonic stem cells to reveal that chromatin remodeling events direct positioning of transcriptionally active DNA away from the nuclear periphery. Together this suggests that chromatin modification may guide nuclear organization of the genome.
Transcription Without Active Chromatin Marks
Silvia Perez, Center for Genomic Regulation
Dr. Perez utilized the available modENCODE data to investigate the histone marks of regulated genes during Drosophila development. Intriguingly, regulated genes lack histone marks associated to active transcription such as H3K4me3, H3K9ac or H3K27ac which were present at promoters of stably expressed genes. The same results could be observed when looking at tissue-specific genes in less heterogenous tissues as imaginal discs in 3rd. instar larvae.
Nascent RNA experiments demonstrated that genes lacking active histone marks were indeed actively transcribed. Regulated and tissue-specific genes were mainly classified as BLACK chromatin, described by Filion et al., (Cell, October 2010) as repressed chromatin void of many histone marks, although in this case the genes re-expressed even at high levels. The current model proposes active transcription to facilitate the establishment of the chromatin marks which in turn facilitate downstream events. Nevertheless, the genes do not display the active marks despite being actively transcribed.
Diverse Roles for Histone Modifications
Tony Kouzarides, Gurdon Institute and University of Cambridge
Histone modifications are known transcriptional regulators. Dr. Kouzarides expanded this view by presenting several novel modifications with distinct functions. Citrullination of a histone H1 arginine residue close to its DNA binding site by PADI4, resulted in its displacement and subsequent chromatin decondenstaion (Christophorou el al Nature, March 2014). In this way, PADI4, which is found in neutrophils and pluripotent stem cells, regulates the opening up of higher order chromatin.
Another novel modification presented was the methylation of glutamine in histone H2A – Q105 in yeast or Q104 in human, which is mediated by Nop1 or fibrillarin respectively (Tessarz et al, Nature, January 2014). Notably, this modification is constrained to the 35S ribosomal DNA transcriptional unit and thus the first modification identified to be dedicated to a specific RNA polymerase, namely pol I.
Kouzarides further demonstrated a role for histone methylation in the regulation of DNA replication. Trimethylation of H3K36 in yeast is mediated by Set2 and commonly associated with actively transcribed promoters. H3K36me1, however, is enriched at DNA replication sites. Kourzarides group found that H3K36me1 positively regulates the binding of the DNA replication licensing factor MCM2 in S-phase, while the adjacent H3K37me1 antagonized the process. Mutation of H3K37àA, which phenocopies K37me1, caused a delay in the G1 to S transition and decreased the binding affinity of the whole MCM complex. H3K36me1 but not the trimethyl variant was found to be mediated by Set4. No modifying enzyme for H3K37 is yet known. These data also suggest a role of histone modifications in regulating the cellular switch form transcription to DNA replication, which do not occur at the same time.
The 11th EMBL Transcription and Chromatin meeting once again impressed with an excellent line-up, well-organized execution and an outstanding environment. Not surprisingly, this ever-growing meeting attracted over 550 scientists most of which are already looking forward to the next one in late August of 2016.
**EpiGenie would like to thank Sascha Duttke, who is a PhD student in the Kadonaga lab at UC San Diego for providing this conference coverage.**