Understanding how our genes are regulated is a central question in biology. Studies have highlighted multiple levels of regulation for genomic expression, ranging from transcription factors binding to nuclear organization of the genome. Recent technical optimization of chromosome conformation capture (3C) analysis has revealed new levels of chromosome compartmentalization. Interphase chromosomes are arranged into specific kilo- to mega-base sized domains, known as Topologically Associated Domains (TADs). Functionally, most enhancer-promoter interactions occur within the same TAD. Moreover, during differentiation, genes clustered within the same TAD display a similar expression pattern, and alteration of these domains result in aberrant expression of the genes, suggesting their involvement in transcriptional regulation. TADs appear remarkably stable between cell types, but can differ in the level of compaction inside individual TADs. TADs encompassing inactive genes are more compact than TADs comprising active ones. This raises the question whether TAD compaction directly regulates or somehow limits gene expression. This project aims at answering this question using a model system, dosage compensation (DC) in the nematode, Caenorhabditis elegans. It has been previously shown that on the X chromosome, more compact TADs correlate with the down-regulation of X-linked genes in hermaphrodites compared to males. This provides an ideal system to understand the mechanism of transcriptional regulation by TAD formation. I have setup a chromatin conformation capture technique coupled with long molecule sequencing (Oxford Nanopore Technology) to capture gene structures at high resolution, in DC and non-DC environment. In contrast to standard HiC that captures pair-wise contacts, this approach can directly identify multi-way chromosomal contacts from within single cells. My aim is to understand how chromatin structure is modified at the gene level by TAD formation and whether and how this regulates gene expression, thereby deciphering the importance of genome folding in transcriptional regulation.

Affiliations:
- Faculty of Electrical Engineering, Mathematics and Computer Science, University of Delft, Netherlands
- Centre for Molecular Medicine, Utrecht University, Netherlands
- Institute of Cell Biology, University of Bern, Bern, CH