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BITS2007 Meeting
BITS2007 Meeting



26-28 April 2007 Napoli, Italy

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Integrated experimental and systems biology approach to the identification of transcriptional regulatory network of p63 transcription factor
 
Motivation
In spite of the large amount of data deriving from high-throughput genomic
technologies, understanding how genes and proteins are connected and operate within
networks is still a biological challenge. 
We developed an integrated experimental and systems biology approach to identify the
biological pathways and the direct targets of p63 transcription factor, using primary
keratinocytes as a cell culture model. p63, a member of the p53 family, is essential
for the development of various ectodermal structures including skin, but its
mechanism of action remains largely unknown.


Methods
A retrovirus expressing an inducible p63 gene was generated by fusing the coding
portion of p63 with a tamoxifen-responsive estrogen receptor. Identification of
immediate-early genes upon p63 activation was achieved by a time-series microarray
analysis. Significant gene expression profiles were obtained for 800 genes. To infer
the network surrounding p63 gene, we developed an algorithm called TSNI (Time Series
Network Identification). TSNI modeled the network as a system of ordinary
differential equations based on relating changes in gene transcript concentrations to
each other and to the external stimuli. TSNI ranked the genes according to the
probability of being the direct targets of p63. 


Results
We selected top 100 genes as to be significant targets of DNP63a gene. These genes
were found to belong to cell cycle control, cell adhesion and keratinocytes
differentiation pathways, in agreement with what should be the targets of p63
according to literature. To verify the putative p63 target genes, we measured global
changes in gene expression in p63 knockdown keratinocytes versus wild-type and we
performed a ChIp on chip analysis on custom Agilent array targets to validate the
TSNI predicted genes as functional targets. Our novel approach identified a number of
genes that are significantly regulated by p63 at early time points and are involved in
cell cycle control, cell adhesion and keratinocytes differentiation. We are currently
deciphering the molecular function of these essential genes in stratified epithelia.
 
Id: 112
Place: Napoli, Italy
Centro Congressi "Federico II"
Via Partenope 36
Napoli
Starting date:
28-Apr-2007   09:20
Duration: 20'
Contribution type: Oral
Primary Authors: DELLA GATTA, Giusy (Telethon Institute of Genetics and Medicine, Via Pietro Castellino 111, Naples, Italy; Seconda Universita degli studi di Napoli, Italy)
BANSAL, Mukesh (Telethon Institute of Genetics and Medicine, Via Pietro Castellino 111, Naples, Italy; European school of Molecular Medicine, Naples Italy)
Co-Authors: AMBESI, Alberto (University of Columbia, New York, US)
MISSERO, Caterina (CEINGE, Naples, Italy)
DIEGO, Di Bernardo (Telethon Institute of Genetics and Medicine, Via Pietro Castellino 111, Naples, Italy; European school of Molecular Medicine, Naples Italy)
Presenters: DELLA GATTA, Giusy
Material: slide Slides
 
Included in session: Session 6: Gene expression and system biology
Included in track: Gene expression and system biology
 




bits2007_support@ceinge.unina.it | Last modified 08 July 2009 10:35 |




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