Mechanisms of phosphorylation spreading by kinases Mec1 and Tel1 after a DNA double strand break in budding yeast

One of the hallmarks of DNA damage is the rapid phosphorylation of H2A histones near the site of a DNA double-strand break, extending out to ~50 kb from the break site. The phosphorylated H2A, known as γ-H2AX, plays a role in the recruitment and retention of DNA repair factors. In budding yeast, the kinases Mec1 and Tel1 are responsible for phosphorylating H2A histones, but it is not known how the kinases spread from the break site to the distant H2A’s.

We monitored γ-H2AX formation using ChIP-qPCR after creating a site-specific break on Chromosome III. Experimentally measured γ-H2AX profiles by the two kinases are significantly different from each other suggesting that different mechanisms are used to reach H2A histones around the break. We consider four modes of phosphorylation propagation: (a) 3D diffusion of a kinase initially bound to the break, (b) looping of chromatin to bring a kinase tethered to the break to distant sites along the chromatin, (c) directed sliding of a kinase along the chromatin, and (d) 1D diffusion of a kinase along the chromatin. Using Bayesian model selection, we determined that the activity of Mec1 is best described by looping while Tel1 is best described by directed sliding.