The 2014 IMB Meeting on Nuclear RNA, Gene Regulation, and Chromatin Structure took place from the 9th till the 12th of October at the Institute for Molecular Biology (IMB) in Mainz, Germany. The IMB itself, as newly established, private Institution, located at the heart oft the Johannes Gutenberg University campus, is committed to provide an excellent place for basic and applied research in developmental biology, epigenetics, DNA repair and related biomedical areas. For me as a student of biochemistry as well as medicine with a rather metabolic oriented research background but a strong interest in epigenetics, the meeting constituted a great chance to learn and network.
Due to the manageable size of the meeting and relatively small number of attendees, an open and almost familiar atmosphere was created that enabled one to easily get in touch with any researcher of interest. Coming from a completely different field of research, I felt somehow doubtful about completely understanding the presented work but all my questions were kindly answered during the numerous poster sessions.
The meeting was divided into four main sessions that focused on:
- small RNA pathways and chromatin,
- splicing and chromatin,
- non-coding RNA in dosage compensation and
- telomere biology and lncRNAs, respectively.
Each session comprised well-known researchers from all over the world mixed with numerous up and coming young scientists. Steven E. Jacobsen (UCLA) and Ruth Lehmann (Skirball Institute, NYU School of Medicine) gave the two keynote lectures.
All in all, the meeting was strongly focused on basic research with rather slight links to translational research or clinics.
RNA Directed DNA Methylation
Steven E. Jacobsen, PhD
Steven E. Jacobsen is an Investigator at the Howard Hughes Medical Institute and Professor of Molecular Cell and Developmental Biology at the University of California, Los Angeles, USA. His research is focused on mechanisms of epigenetic inheritance in plants, including the genetics and genomics of DNA methylation, histone methylation as well as small RNA driven silencing pathways. With over 130 epigenetic related publications he made fundamental contributions to this emerging field of research.
Jacobsen lectured on the RNA dependent DNA Methylation (RdDM) pathway that Arabidopsis thaliana utilizes to maintain and probably establish cytosine DNA methylation in order to silence genes and transposons. While the well-studied DNA methyltransferases MET1, CMT3 and DRM2 are responsible for maintaining pre-established methylation patterns via classical mechanisms, apparently DRM2 – a homolog of mammalian Dnmt3 – is the only one to mediate RdDM. DRM2 recruitment to the respective DNA site is thereby mediated by a complex interplay of Polymerase IV (PolIV), Polymerase V (PolV), the RNA species produced by them and numerous other factors.
Since PolIV and PolV DNA binding does not show any significant sequence specificity, epigenetic marks are most likely to depict their recognition sites. PolIV was shown to interact with SHH1, which binds to H3K9me, a silencing mark to be frequently found at RdDM sites, while PolV´s indirect interaction with SUVH2 targets it to methylated DNA. By the fusion of SUVH2 with a zinc finger domain targeted to an unmethylated epiallele of the homeodomain transcription factor FWA, Jacobsen´s lab demonstrated that SUVH2 is sufficient to recruit PolV, establish DNA methylation and ultimately cause gene silencing.
Mechanistically, PolV and PolV associated with RdDM sites produce 24 nucleotide siRNAs and lncRNAs, respectively. These RNAs interact with a number of further factors like AGO4 to establish a very complex network that ultimately results in the recruitment of DRM2 to preserve existing methylation patterns. Interestingly, there is a close interdependence between such methylation marks and other epigenetic modifications like for example histone methylation, which generates robust reinforcement loops. Nevertheless, it remains unclear how the initial establishment of RdDM takes place.
The Investigation of 3D Genome Architecture Using the Prediction of Trans-Splicing Events
Markus Schüler, PhD
Markus Schüler is a member of the Epigenetic Regulation and Chromatin Architecture group lead by Ana Pombo at the Max-Delbrück Centre for Molecular Medicine, Berlin, Germany. He received his PhD in Bioinformatics from the Max Planck Institute for Molecular Genetics in Berlin and works in a very interdisciplinary manner to apply bioinformatical approaches in order to unravel the complex structure of genomes and its impact on transcriptional regulation.
In his talk Schüler gave insights to the potential of tracking down trans-splicing events to gain further information about the three-dimensional arrangement of the genome. The recently discovered phenomenon of trans-splicing describes splicing events between two nascent RNA molecules that lead to the generation of fusion RNAs. The absolutely requirement hereby is a close proximity between both RNAs which can be due to a close proximity of the transcriptional machineries and genes themselves. Hence trans-splicing events may be a hint to close vicinity of the involved genes within the three-dimensional genome.
In a time-series of differentiation from mouse embryonic stem cells to terminally differentiated neurons, genome-wide datasets were generated using mRNA deep sequencing as well as RNA ChIP with an antibody selective for actively transcribing RNA Polymerase II. By using state-of-the-art bioinformatics and algorithms like TopHat and STAR combined with intense false-positive filtering, Schüler was able to identify several hundreds of high-confidence trans-splicing events. The respective pairs of source genes were then tested concerning proximity by analyzing genome-wide chromosome conformation capture (Hi-C) measurements in matched cell populations.
All in all, the results pointed to a correlation of trans-splicing events and local proximity of the respective source genes. This suggests that trans-splicing may occur co-transcriptionally and hold the potential to be the basis for the development of powerful tools to study functional genome structure.
**Big thanks to David Merle at the Medical University of Graz in Austria for contributing nice coverage of these talks.