PhD Advisor: Professor Christian Froekjaer Jensen

Abstract:
Genomes require physical boundaries to separate active and repressed chromatin, a function traditionally attributed to insulator proteins. Here, we demonstrate that genomic insulation is also a physical property encoded into the DNA polymer. In C. elegans, transcription-coupled mutational bias remodels Helitron transposon minisatellites to match the DNA helical repeat. This intrinsic curvature pins supercoiled DNA into nucleosome-depleted plectonemes, creating mechanical barriers that partition chromosomes into gene-sized regulatory domains. Constrained by DNA mechanics, this structural strategy evolves convergently across Metazoa into a shared mechanical code at Drosophila insulators and human CTCF sites. Strikingly, active human LINE-1 retrotransposons encode a similar plectoneme structure. Thus, sequence-encoded mechanics represent a universal solution to transcription-silencing conflicts—a topological barrier harnessed by host genomes to organize chromatin, and seized by selfish elements to survive.

Bio:
Faisal Alkhaldi is a PhD student in Prof. Christian Froekjaer Jensen's laboratory.