Transcription factor dynamics in living mouse embryos and stem cells revealed by Monte Carlo simulations and fluorescence correlation spectroscopy

J. ANGIOLINI; K. KAUR; E. MOCSKOS; L. BRUNO; N. PLACHTA; V. LEVI

Córdoba

Congreso; Reunión Anual de la sociedad argentina de biofísica; 2013

Sociedad Argentina de Biofísica

Transcription factors (TFs) control cell differentiation during embryonic development, yet their diffusion dynamics in vivo remain poorly understood.TF diffusion has recently been measured in living mouse embryos using fluorescence correlation spectroscopy (FCS) (Kaur et al., Nat Comm 4, 1637, 2013). Here, we developed a model considering that TF diffuses in the nucleus and binds to DNA with different affinities. Moreover, we run Monte Carlo and FCS simulations to confirm the model predictions. Our findings reveal two populations of DNA binding sites with different TF affinities.By using the model proposed and a global fitting routine, we analyzed the FCS data of the TF Oct4 in embryonic stem cells and recovered the fractions of this TF bound to different sites. Additionally, we determined the diffusion coefficient, kon* and koff values for each binding population. Finally, we analyzed FCS data obtained in the presence of drugs that modify chromatin condensation and using an Oct4 mutant unable to bind DNA. Our model provides a biophysical explanation of TF dynamics a complex mammalian in vivo system.