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Nucleosome positioning and kinetics near transcription-start-site barriers are controlled by interplay between active remodeling and DNA sequence

DSpace at IIT Bombay

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Title Nucleosome positioning and kinetics near transcription-start-site barriers are controlled by interplay between active remodeling and DNA sequence
 
Creator PARMAR, JJ
MARKO, JF
PADINHATEERI, R
 
Subject EUKARYOTIC GENOME
YEAST GENOME
IN-VITRO
CHROMATIN
ORGANIZATION
DYNAMICS
MODEL
DISTRIBUTIONS
REPLICATION
MECHANISM
 
Description We investigate how DNA sequence, ATP-dependent chromatin remodeling and nucleosome-depleted `barriers' co-operate to determine the kinetics of nucleosome organization, in a stochastic model of nucleosome positioning and dynamics. We find that 'statistical' positioning of nucleosomes against 'barriers', hypothesized to control chromatin structure near transcription start sites, requires active remodeling and therefore cannot be described using equilibrium statistical mechanics. We show that, unlike steady-state occupancy, DNA site exposure kinetics near a barrier is dominated by DNA sequence rather than by proximity to the barrier itself. The timescale for formation of positioning patterns near barriers is proportional to the timescale for active nucleosome eviction. We also show that there are strong gene-to-gene variations in nucleosome positioning near barriers, which are eliminated by averaging over many genes. Our results suggest that measurement of nucleosome kinetics can reveal information about sequence-dependent regulation that is not apparent in steady-state nucleosome occupancy.
 
Publisher OXFORD UNIV PRESS
 
Date 2014-12-28T11:34:27Z
2014-12-28T11:34:27Z
2014
 
Type Article
 
Identifier NUCLEIC ACIDS RESEARCH, 42(1)128-136
0305-1048
1362-4962
http://dx.doi.org/10.1093/nar/gkt854
http://dspace.library.iitb.ac.in/jspui/handle/100/16371
 
Language English