entropic effects in chromatin folding - alberto colliva
TRANSCRIPT
Entropic effects in
chromatin folding
Alberto Colliva
Quantitative Laws II16/06/2016
How is DNA packing organized?
Tark-Dame et. al., PLOS Comp. Biol., 2009
What is driving the 3D organization?
Polymers
3C techniques
Dixon et. al., Nature, 2011
GC and Hi-C integration
Different cell lines and Hi-C experiments
Juicebox
Hi-C data suffer major bias
S. Rao et. al., «Juicebox», Cell, 2014 GC profile chromosome 2
Chromosome coordinates: X ,Y
YX
Enrichment in GC similar contats
HindIII NcoI
GC content (5 kb)
GC
co
nte
nt
(5 k
b)
GC
co
nte
nt
(5 k
b)
GC content (5 kb)
Data from: Lieberman-Aiden et. Al., Science. 2009
Log
(Su
rviv
al f
un
ctio
n)
Log
(Su
rviv
al f
un
ctio
n)
5 kb resolution windows
Two different restriction enzyme
GC content as a flexibility indicator
P. Cook D. Marenduzzo, J Cell Biol., 2009
A mixture of two sets of polymers show the emergence of segregation.
Molecular dynamics simulation
GC content (5 kb)
GC
co
nte
nt
(5 k
b) flex
ible
stif
f
Acknowledgement
Michele Caselle
Andrea Mazzolini
Matteo Osella
Antonio Rosanova