The use of genomic imprinting to investigate the relationship between subnuclear localisation and gene expression
Evolutionary Cell and Developmental Biology (Zoology)
Final Report Abstract
The mammalian cell nucleus contains DNA in form of chromosomes but these have their typical condensed shape only while cells are dividing. At all other times, known as interphase, DNA is loosely arranged and fills the whole of the nucleus like a gel. Still, it is known that different chromosomes take up defined spaces within this gel and that there are environments within the nucleus where genes are more readily expressed and other environments where they tend to be silenced. We were interested in the potential for genes and gene regions to shuttle between such activating and silencing environments and how this can fine-tune the intensity, at which a cell expresses certain genes. As a model, we use imprinted gene regions, rare sections of the mammalian genome that are epigenetically regulated in a special way. Genes at imprinted regions are usually expressed from only one of the two copies, depending on which parent the chromosome was inherited from. Although these regions are identical in their genetic sequence, at least in inbred mice, both parental copies carry different epigenetic marks, which cause them to express a reciprocal set of imprinted genes. Using fluorescence microscopy, I analysed the expression state of the maternally expressed gene Gtl2 and the localisation of its imprinted region within the nucleus. I took 3D measurements of the distance between a DNA marker in the imprinted region and the border of the nucleus. I used embryonal stem (ES) cells that had been generated from mice, which had inherited a deletion of the DNA marker from one parent, so that only one parental chromosome was analysed at a time. This provided information about the parental origin of the analysed gene region. With this method, I found a reproducible but non-significant trend for the imprinted region to be further away from the nuclear border if the maternal copy of Gtl2 was expressed than if the gene was silenced in a cell at a given time. Using mutant ES cells, which had both copies of the imprinted region behaving as maternal and expressing Gtl2, we observed a significant shift in the same direction. This result was compatible with the idea that ES cells fine-tune Gtl2 expression from the maternally inherited chromosome by varying its location between activating and silencing environments within the nucleus, causing or following bursts of gene expression and silencing. To our surprise, the imprinted region did not appear to become silenced at the very periphery of the nucleus, which is the best characterised silencing nuclear compartment, as had been our hypothesis. Rather, it looked like activating environments at the nuclear interior, which have yet to be characterised, might play a role. This might also be the reason, why the shift in peripheral localisation between active and silent Gtl2 genes was small. We found a similarly small but significant difference between the peripheral localisation of the maternally inherited imprinted region and the paternally inherited imprinted region, which never expresses Gtl2. A shift of the paternally inherited region towards the nuclear periphery had been described before but we show for the first time that the distribution of paternally inherited Gtl2 genes, which are silenced by imprinting, and non-expressed maternal Gtl2 genes is very similar and that both differ significantly from the distribution of actively expressed Gtl2 genes. Taken together, my DFG-funded research project was able to show for first time a correlation between the intranuclear localisation and the expression state of an actively expressed endogenous gene.
Publications
- Imprinted gene repression vs. stochastic gene repression in ES cells, Conference ‚Genome Regulation in 3D‘, 28. – 30. June 2015 in Rehovot, Israel
Lisa Hülsmann
- Parental origin specific allelic bias – is this imprinting? Conference ‘Genomic Imprinting, Epigenetics and Physiological Functions’, 2. - 7. October 2016 in Erice, Italy
Lisa Hülsmann
- Parental origin specific allelic bias – is this imprinting? Fourth Annual Epigenetics Symposium, 26th June 2017 in Cambridge, UK
Lisa Hülsmann
