Biology

Dr. Mahipal Ganji
Max-Planck-Institute of Biochemie, Martinsried, Germany

Abstract:

The three-dimensional organization of genome is increasingly understood to play a decisive role in vital cellular processes. In my talk, I will present single-molecule data showing two different aspects of genome organization: structure of supercoiled DNA [1] and condensin mediated DNA-loop extrusion [2].

(1) Sequence-structure relationship of supercoiled DNA: We used our recently developed single-molecule assay [3] to visualize the plectonemes (extended intertwined DNA structures formed upon supercoiling) along supercoiled DNA. Our experiments show that the DNA sequence directly encodes the structure of supercoiled DNA by pinning plectonemes at specific sequences. We develop a physical model that predicts sequence-dependent intrinsic curvature facilitates the pinning of plectonemes. Analysis of prokaryotic genome indicates that plectonemes localize directly upstream of prokaryotic promoters, which we experimentally confirm for selected promoters. These findings therefore reveal a hidden code in the genome that helps to spatially organize the chromosomal DNA.

 (2) DNA loop-extrusion by condensin: Using the similar single-molecule assay, we provide an unambiguous evidence for DNA loop-extrusion by condensin molecules by real-time imaging. A single condensin complex is able to extrude tens of kilobases of DNA at a force-dependent speed of up to 1,500 bp/sec, using the energy of ATP hydrolysis. Condensin-induced loop extrusion is strictly asymmetric, which demonstrates that condensin anchors onto DNA and reels it from only one side. These results might provide unifying mechanism for genome organization.

References:

(1)  Kim and Ganji et al, biorxiv, 2018

(2)  Ganji et al, Science, 2018

(3)  Ganji and Kim et al, Nano Lett., 2016