Integrated spatial-temporal methods for studying the effect of lamin A protein on genome organization

  Ben Aloni  
Physics Department, Bar-Ilan

The 3D structural organization of the genome plays a key role in the nuclear functions such as gene expression and DNA replication. Inside the nucleus chromosomes are folded into distinct territories, but the rules governing positioning are incompletely understood and vary between cell types. Based on previous studies in our lab, we believe that lamin A protein plays a specific role in chromatin dynamics and therefore in chromatin organization. lamin A forms DNA cross-bonding so that the whole chromatin changes to a gel-like structure. Our study combines 4C analysis with dynamic measurements for investigating the molecular circumstances in which lamin A protein is involved in the nuclear genome organization. We study the changes in patterns with reduced level of protein expression, by comparing normal cells (Lmna+/+) with deficient cells (Lmna-/-). It is therefore well-organized and even provides rigidity to the nucleus. Topologically associating domains (TADs) represents regions across the chromatin in which physical interactions occur relatively frequently. TADs can range in size from thousands to millions of DNA bp (base pairs). We seek to characterize the typical loop size formed along the DNA, which may be the length of a single TAD, or long-range loops with a size of several TADs. By combining the two methodologies, structural genomic chromatin-capture techniques with dynamic studies in live cells, we plan to understand better the biophysical mechanisms of genome organization.