|Genomic physics: biophysical modeling confronted to genomic data |
Auteur(s): Walter J.-C.
Ref HAL: hal-03428118_v1
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The last decade has seen a spectacular development of genomic physics both in bacteria and eukaryotes. This is due in large part to the development of experimental techniques, which allow to probe (i) the motion of nucleic acids (chromosomal DNA and RNA) in vivo by means of microscopy techniques and (ii) the interactions of these nucleic acids with other actors of the cell (like proteins and molecular motors) by means of high-throughput sequencing techniques. I will focus on three different processes : (i) the modeling of translation with a ballistic model describing the motion of ribosomes on messenger RNA, (ii) the physical mechanism of liquid-liquid phase separation, which is found to be universally spread in the cells to increase, locally and transiently, the concentration of a molecular actor (proteins, RNA etc.). We illustrate this process with the example of the bacterial DNA segregation where liquid-liquid phase separation is used to increase the local concentration in order to catalyze ATP hydrolysis. Finally (iii) I give a general framework on how polymer physics can help to infer the organization of DNA in vivo from microscopy and high-throughput sequencing experiments and apply it to the modeling of bacterial DNA in Escherichia coli and to the epigenetic regulation via polycomb domains in Drosophila.