D. Michieletto, M. Lusic, D. Marenduzzo, E. Orlandini, Physical Principles of HIV Integration, bioRxiv, 2018
D. Michieletto, M. Chiang, D. Colì, A. Papantonis, E. Orlandini, P. R. Cook, D. Marenduzzo, Shaping Epigenetic Memory via Genomic Bookmarking, Nucleic Acids Res., 46(1), 2018
D. Michieletto, N. Nahali, A. Rosa, Glassiness and Heterogeneous Dynamics in Dense Solutions of Ring Polymers, Phys. Rev. Lett., 119(197801), 2017
C.A. Brackley, J. Johnson, D. Michieletto, A.N. Morozov, M. Nicodemi, P.R. Cook, D. Marenduzzo, Nonequilibrium Chromosome Looping via Molecular Slip Links , Phys. Rev. Lett. 119(138101), 2017
Y. A. Fosado, D. Michieletto, D. Marenduzzo, Dynamical Scaling and Phase Coexistence in Topologically-Constrained DNA Melting, Phys. Rev. Lett., 119(118002), 2017
D. Michieletto and M. S. Turner, A Topologically Driven Glass in Ring Polymers , Proc. Natl. Acad. Sci. USA, 113(19), 2016
D. Michieletto, E. Orlandini and D. Marenduzzo, Polymer Model with Epigenetic Recolouring Reveals a Pathway for the De Novo Establishment and 3D Organization of Chromatin Domains, Phys. Rev. X, 6(041047), 2016
D. Michieletto, On the Tree-Like Structure of Rings in Dense Solutions, Soft Matter, 12, 2016
D. Michieletto, D. Marenduzzo, E. Orlandini, Is the Kinetoplast DNA a Percolating Network of Linked Rings at its Critical Point? , Phys. Biol., 12(036001), 2015
D. Michieletto, D. Marenduzzo, E. Orlandini, G. P. Alexander, M. S. Turner, Threading Dynamics of Ring Polymers in a Gel, ACS Macro Lett., 3, 2014
M1 Integration dynamics of a viral "loop" (green) within DNA (grey and orange). The orange DNA region sticks to the histone-like particle (blue) thus forming a nucleosome-like structure. Successful reconnection moves satisfying detailed balance preferentially occur within the highly bent region wrapped around the histone, in agreement with long-standing experiments. While counter-intuitive, this finding can be understood within our physical framework, as the recombination moves must overcome an energy barrier that is lower within distorted DNA segments.
M2 Diblock co-polymer model for DNA/chromatin with different stiffness. Here HIV loops (green) are observed to integrate within flexible (blue) regions while the stiffer (red) segements are depleted of HIV integration sites.
M3 HIV integration is biased by the 3D chromosomal folding. Here, unfolded chromatin (left) is compared against folded chromatin, where blue beads possess a self-attractive interaction mimicking the action of bridge (HP1) proteins for heterochromatin. The resulting folded structure resembles a "daisy", with a large heterochromatin core screened by euchromatin (red) loops. We find that because of this 3D arrangement HIV preferentially integrate within the euchromatin loops thus rationalising long-standing experimental observations.
See publication [pdf] and SM [pdf] for more details.
Epigenetic Transitions and Knotted Solitons in Stretched Chromatin Sci Rep 2017
M1 Compact-epigenetically ordered phase
M2 Stretched-epigentically disordered phase
M3 Multi-domain phase from multiple nucleation points
M4 Knotted soliton 1
M5 Knotted soliton 2
See publication [ link ] for more details.