Abcam and co-organizers once again pulled off a delightful meeting – this time bridging two exciting approaches to epigenetic research: single cell analyses and epigenomics. No less than 147 scientists were gathered at one of the leading centers of biomedical research it Europe – the Institute of Genetics and Molecular and Cellular Biology (IGBMC) in Strasbourg – to share their latest findings.
If there could only be one thing everyone could agree on, it was that there is a great deal of heterogeneity among even closely related cells with respect to DNA methylation, 3D organization of chromatin and transcription – topics that were all touched upon.
One excellent talk after another, the audience was treated to the latest single-cell based technologies deployed in making sense of this heterogeneity. As if that wasn’t good enough, two superb keynote lectures were delivered by John Gurdon and Tony Kouzarides.
Probing Yeast Chromatin Structure by Micro-C
Oliver Rando – University of Massachusetts Medical School, USA
Chromsome Conformation Capture (3C) – based technologies such as Hi-C have contributed tremendously to our understanding of genomes are organized or folded in eukaryotic nuclei. While we now know a lot more about the tertiary structure of chromatin at the megabase scale, Oliver Rando’s lab recognized that there is a ‘blind spot’ when it comes to 2-12 nucleosome length scale of chromatin structure at level of the intensely debated “30 nm fiber”.
So they came up with a modification to the Hi-C technique that they name Micro-C, where they applied Micrococcal nuclease to fragment chromatin instead of restriction enzymes, which enabled them to have nucleosome level resolution to study chromatin structure. They applied Micro-C to yeast chromatin and they discovered, to their surprise, that the general folding principles are conserved with mammals.
Given that the yeast genome is much smaller, with much smaller genes relative to mammals, they find that it is the number of genes within folded domains that is conserved and not the size of these domains. Perhaps more controversially, the find no evidence to support the existence of the 30 nm fiber structure in vivo.
Nuclear Position and Gene Expression: The Chicken vs. The Egg
Wouter de Laat – Hubrecht Institute-KNAW& University Medical Center Utrecht, The Netherlands
Transcription state of genes is linked to their position in the nucleus. Chromo centers (CCs) are one such nuclear structure that maintain a silenced state and characterized by repressive histone modifications. Since CCs dynamically reposition during cellular differentiation, the De Laat lab wondered if genes move to CCs to get silenced or do they get silenced and move to CCs?
They addressed this chicken vs egg problem using an elegant system where they targeted a transgene to CCs using a histone modification reader domain. They saw that recruitment to CCs leads to acquisition of repressive histone marks and silencing of a reporter gene.
Mapping Genome-Nuclear Lamina Interactions in Single Cells
Bas van Steensel – Netherlands Cancer Institute, Amsterdam, Netherlands
The nuclear lamina (NL) interacts with thousands of genomic regions called Lamina Associated Domains (LADs) that cover about 30-40% of our genomes. The Van Steensel lab further developed their DamID technique to map NL-LAD interaction and applied it to single cells. Using human KBM7 haploid cell line to make interpretation easier, they compared the LADs of about 118 cells.
Their analyses revealed the variability of LADs between individual cells. While some LADs were consistently present in all cells, they also discovered some LADs existed only in a subset of the cells analyzed. Some chromosomes also had more LADs than other chromosomes confirming earlier studies using other methods.
Bradley E. Bernstein– Broad Institute, Cambridge, MA, USA
In the last talk of this excellent meeting, Bradely Bernstein brought our attention to cancer biology and how single-cell-, epigenomics-based approaches can give insights into understanding tumor heterogeneity and identification of therapeutic targets. Focusing on glioblastomas (GBMs), his lab identified a set of 4 transcription factors whose expression was sufficient to reprogram differentiated GBM cells into a stem cell-like state with high tumor-propagating properties.
In a follow-up work, they performed single-cell RNA-seq to evaluate tumor heterogeneity in GBMs. Perhaps depressingly, they found that there is an extensive variation even between the tumor-propagating stem-like cells which makes therapeutic intervention that much more difficult.
It was however very encouraging to see that single-cell approaches can be invaluable in understanding cancer biology.
*EpiGenie would like to thank Adam Kebede for his outstanding coverage of this great meeting.