Professor Daniel Panne E: email@example.com
Dr Thomas Schalch E: firstname.lastname@example.org
It has been proposed that DNA folding by a process called ‘loop extrusion’ is a central organising principle of genome conformation. The hypothesis is that loop extrusion reels in genomic DNA into loops, a process which ‘individualises’ chromatin fibres and brings distant loci into proximity. The resulting higher-order packing of chromosomal DNA is thought to have important structural and regulatory consequences for a number of DNA-based processes.
We discovered recently that a subunit of the cohesin complex interacts directly with the chromatin insulator CTCF and that this interaction is required for the formation of loops at TAD boundaries. Similar CTCF-like motifs are present in a number of additional genome regulators that each control different key chromosomal process. Our hypothesis is that these interactions specify where in the genome cohesin productively catalyses DNA looping.
The exciting possibility arises that loop extrusion by cohesin thus contributes to a number of fundamental genome transactions including DNA replication, repair and transcription. We here propose an interdisciplinary approach involving biochemical and structural biology approaches to study how cohesin and CTCF interact with chromatin. We will specifically seek a bottom-up understanding of how these interactions control 3D genome organisation and contribute to fundamental aspects of genome biology.
The project involves detailed biochemical studies, recombinant overexpression of individual components and subcomplexes together with structural studies by cryoEM. This will form part of a larger interdisciplinary project with integrative imaging across scales, including super-resolution STORM and higher-resolution CLEM imaging to study large-scale chromosomal features. We will also use genomics approaches such as Hi-C to assess the consequences for genome folding, and will study how these interactions direct cohesin’s localization and residence time on chromatin.
Nature 578, 472–476 (2020); NSMB 27, 233–239 (2020); Nature 562, 538–544 (2018).