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The dynamics of the mammalian epigenome during transcription factor-induced cell fate conversion

Periodic Reporting for period 1 - 3Dconvert (The dynamics of the mammalian epigenome during transcription factor-induced cell fate conversion)

Reporting period: 2015-05-01 to 2017-04-30

The genetic code stored in our DNA is continuously read by the cells in our body in order for them - and our body as a whole - to function properly. The basic unit of genetic information is the gene, and the human genome contains ten of thousands of such genes. The combination of genes used ('read') by a cell determines its identity and function, granting the cell a unique 'gene expression' signature. Gene expression needs to be tightly controlled for cells to continue doing their job and to adapt to sudden changes in circumstances, for example when cells have to respond to an infection. Perhaps not surprisingly, the improper regulation of gene expression can have disastrous consequences: cells can no longer function or will start to behave differently. In the latter this can lead to developmental defects or give rise to cancer. It is therefore of utmost importance to understand the mechanisms that control our genes and what goes wrong in diseases to improve predicting and treating human illnesses. In this research project, we have studied in great detail how the three-dimensional organisation of our DNA and genes influences the control of gene expression.Our objectives are to map the map the dynamics of 3D DNA folding at high resolution as cells change their identity and to relate this the regulation of gene expression.
High-resolution maps of genome topology, gene expression, chromatin state and transcription factor binding were generated for 7 timepoints during the conversion of primary B cells to induced pluripotent stem (iPS) cells. In total, the project has yielded 114 high-quality genomic datasets that have been integrated using state-of-art computational tools to obtain a dynamic picture of the relationship between 3D genome folding and gene regulation in cells that are undergoing a drastic change in identity and function. This has led to several important conclusions regarding how genome topology impacts on gene regulation, how transcription factors shape the 3D genome landscape and why certain genes are activated early while other are activated late during cell reprogramming. We have communicated and will continue to communicate our results to the general public and scientific community through various ways. Until now, we have presented our findings at an international symposium organised by the CRG revolving around 3D genome dynamics and featuring world-class speakers, we have published them as a preprint and utilised social media to alert the general public and the scientific community. We will continue to do so, as we have secured an invited talk at the world's largest stem cell conference (the ISSCR Annual Meeting 2017, Boston), have submitted abstracts to other major conferences (e.g. EMBO series) and are actively pursuing peer-reviewed publication of our work. Direct exploitation of the results generated by this action are the continuation of a new research line in the host laboratory. Knowledge on technologies implemented has been transferred through direct hands-on training of personnel in the host laboratory, and both wet lab and computational expertise acquired during this action will directly benefit the host institute and its ERC Synergy 4DGenome program. Together with colleagues working with Hi-C technology we have recently organized (March 2017) an international course to train other scientists in the proper use of chromosome conformation capture techniques.
We have advanced the state-of-the-art by revealing for the first time the dynamics of DNA folding at various levels of organisation when cells change their identity. The host laboratory's highly efficient cell conversion systems have granted us a unique opportunity to follow genome topology as it reorganizes during cell reprogramming and to integrate these changes with gene expression, transcription factor binding and chromatin state dynamics. Our results provide a substantial increase in our understanding of gene regulation, and we predict that future studies will find fertile ground in building upon these findings to understand how gene regulation is disturbed in situations of cancer or developmental defects.
The multiple layers of genome organization.