Rice chromosome architecture at nucleosome-level resolution
Authors: Amina Kurbidaeva; Michael Purugganan
Affiliation: New York University
Keywords: Comparative genomics & genome evolution
The three-dimensional structure of genome plays an integral role in gene expression regulation. Chromosomes are partitioned into compartments, characterized by active or repressive chromatin states. Topologically associated domains (TADs) are defined as regions of high chromatin interconnectivity and restrict enhancer-promoter crosstalk maintaining proper gene expression and co-regulation with the domain. In addition, chromatin loops bring into proximity distant regulatory parts of the genome, such as enhancers, promoters, and tethering elements. These three levels of genome organization can be best characterized by Micro-C, a Hi-C-based method in which micrococcal nuclease is used instead of restriction enzymes to fragment chromatin, enabling nucleosome resolution chromosome folding maps. For the first time to our knowledge, we applied Micro-C to study the 3D genome organization of a plant genome, using Oryza sativa. This allowed us to look into the genome structure of rice with an unprecedented resolution, providing a basis for future comparative genomics studies. An understanding of 3D genome organization will allow us to explain regulatory evolution processes shaping speciation and domestication within the Oryza genus.