bbc 2015

BeNeLux Bioinformatics Conference – Antwerp, December 7-8 2015
Abstract ID: P
Poster
10th Benelux Bioinformatics Conference bbc 2015
P70. THE IMPACT OF HMGA PROTEINS ON REPLICATION ORIGINS
DISTRIBUTION
A. Zouaoui 1 , M. Kahli 2 , E. Besnard 3 , R. Desprat 1 , N. Kirsten 4 , P. Ben-sadoun 1 & J.M. Lemaitre 1 .
Institute for Regenerative Medicine and Biotherapy, France 1 ; Institut de Biologie de l’École Normale Supérieure (ENS),
France 2 ; The Gladstone Institutes, University of California San Francisco (UCSF), United States 3 ; Helmholtz Zentrum
München, Research Unit Gene Vectors, Munich, Germany 4 .
Proliferative cells can have an irreversible stop in the cell
cycle that is called cellular senescence which can induct
the development of cancer and ageing. Senescence is
characterized by the development of Dense
Heterochromatic Foci (SAHF) and the decline of the DNA
replication. High-Mobility Group A proteins promote
SAHF formation, a proliferative stop and stabilize
senescence when overexpressed.
In a cell, DNA replication is regulated on several
genomics sites called replication origin (« Oris »). Prereplication
proteic complex is required for DNA
replication to occur. In the pre-replication complex, the
ORC1 protein is involved in recognition of the origin of
replication. DNA autoradiography of eukaryote cells
allowed to find that human replication origins are
bidirectional and spaced at 20-400kb intervals (Huberman
and Riggs, 1968). At each origin, replication forks are
formed and new short nascent strand are synthetized. A
popular method to map replication origins is the
purification of Short Nascent Strand (SNS). Several
laboratories have identified up to 50 000 origins using
microarray and sequencing techniques. Our laboratory has
developed an origin mapping method divided in four cell
type: IMR90, H9, iPSC and HeLa (Besnard et al., 2012).
The Short Nascent Strand was isolated, sequenced and
analyzed. 250 000 origin peaks have been identified with a
peak detection tool named SoleSearch (Blahnik KR, Dou
L, O’Geen H, et al. 2010).
The objective is to find the most sensitive method to
analyze the origin distribution in proliferative and
senescent cells to observe if senescence has an impact on
the origin distribution. The implication of HMGA proteins
on the DNA replication is investigated. Two new methods
are in development to analyze the replication origin with
two more sensitive tools. In the first method, we search
origin peaks with Macs2 tool (Zhang et al., 2008) which
uses a new statistic and algorithm model. In a second time,
origin enrichment is observed with Homer tool (Heinz S et
al., 2010).
Two methods are currently in development to identify the
replication origin site by Illumina GaII sequencing of short
nascent strand. Human SNS-seq reads of 36bp were
mapped to human genome build GRCH38 with BWA tool
(ref). Origin peaks were called by MACS2 and origin
enrichment by Homer. To compare the two methods,
active origins in HeLa cells were detected with each
method. Correlation between ORC1 peaks and origins
identified is calculated to choose the most sensitive
method. The impact of pre-senecence is observed in
comparing origins distribution observed in proliferative
and senescent cells. Origins distribution is compared
before and after induction of HMGA proteins to
investigate the implication of these proteins on the DNA
replication during senescence.
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