Synthetic Biology

Biography

Biography: Petros Kolovos

Abstract

The last years have been a significant effort to unravel the spatial organization and the chromatin interactions of the genomes. Towards that objective, chromosome conformation capture technology and its derivatives contributed significantly. However, the need of a technique, which is affordable for most of the people and at the same time interrogates large selected regions of the genome, has become quite apparent. Furthermore, the borders of the topological associated domains (TADs) as well as the interactions within and between TADs can not been identified in an adequate manner with the usual resolution (40kb) of Hi-C. For that reason we have developed a method termed Targeted Chromatin Capture (T2C) [1]. It provides a genome wide analysis of a selected region of the genome at high resolution (single restriction fragment resolution, from 2 to 6 kbp) at low cost due to the lower sequencing effort (1/5 up to 1/13 of a Illumina based sequencing lane). TADs and their respective boundaries can be identified accurately due to the significantly improved resolution. All the interactions within and between TADs can be observed with T2C, because every restriction fragment can serve as a ‘viewpoint’ and all their interactions, both cis or trans, can be identified. Thus multiple 3C-seq, 4C-seq or 5C experiments do not have to be performed. We have used T2C for different loci and identified the same topological domains and chromatin interactions which have been observed before. Furthermore, with T2C we can answer the perpetual question of the actul structure of the genome and which model is the most prominent. Hence, T2C can be used as an affordable, cost-effective, diagnostic tool with single restriction fragment resolution to explore the local spatial organization of the genome, chromatin interactions and unravel the 3D structure without requiring laborious procedures or massive sequencing efforts.