Evolution Driven Criticality: how genomics paves the way for epigenetics
This event is part of the Biophysics/Condensed Matter Seminar Series.
We use a physical model of nucleosome formation based on sequence dependent DNA bending properties to investigate the role of nucleosome positioning in genome function and evolution. We show the existence in most eukaryotic organisms of nucleosome-inhibiting energy barriers (NIEBs) that condition the statistical positioning of neighboring nucleosomes. In human, 1.6 millions of NIEBs flanked by compacted nucleosomes are observed both in vitro and in vivo. Likely encoded in the local GC content, these 1 kb-size regions of intrinsic nucleosome occupancy, covering about 35% of the genome, are equally found in GC-rich and GC-poor isochores, in early and late replicating regions, in intergenic and genic regions but not at gene promoters and replication initiation loci. The comparison of interspecies and intraspecies rates of divergence confirms the existence of some selection pressure to maintain both an optimal GC content depletion in NIEBs relative to the local bulk GC content. We further show that these 1 kb-sized chromatin patterns are widely distributed along vertebrate chromosomes still covering more than a third of the genome. We report numerical results of mesoscopic 3D modeling of the nucleosomal array in vertebrates that strongly suggest that a highly susceptible 11nm chromatin fiber has been selected during evolution near a critical point to facilitate the epigenetic regulation of nuclear functions in a cell-type specific fashion. We conclude by putting into light chromatinmediated regulation of nuclear functions (transcription and replication) in higher eukaryotes as the paradigm of Evolution Driven Criticality (EDC).
Drillon, G., Audit, B., Argoul, F., Arneodo, A., 2016. Evidence of selection for an accessible nucleosomal array in human. BMC Genomics 17, 526 .
Brunet, F.G., Audit, B., Drillon, G., Argoul, F., Volf, J.N., Arneodo, A., 2018. Evidence for DNA sequence encoding of an accessible nucleosomal array across vertebrates. Biophys. J. 114, 2308-2316.
Walther, J., Dans Puiggros, P.D., Orozco, M., Arbona, J.M., Argoul, F., Audit, B., Arneodo, A., 2018. Evidence of selection for a “critical” nucleosomal array highly susceptible to epigenetic regulation across vertebrates. In preparation.