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BITS2007 Meeting
BITS2007 Meeting



26-28 April 2007 Napoli, Italy

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Prediction of human targets for viral encoded microRNAs by thermodynamics and empirical constraints
 
Motivation
MicroRNAs (miRNAs) are small RNA molecules that modulate
gene expression through
degradation of specific mRNAs and/or repression of their
translation. miRNAs are
involved in both physiological and pathological processes,
such as apoptosis and
cancer. Their presence has been demonstrated in several
organisms as well as in
viruses. Virus encoded miRNAs can act as regulators of viral
gene expression, but
they may also interfere with  host gene expression. In
particular, viral miRNAs may
control cell proliferation by targeting cell-cycle and
apoptosis regulators in host
cells: accordingly, they could be involved in the
pathogenesis of cancer.
Computational prediction of miRNA/target pairs is a
fundamental step in these
studies. 


Methods
Here we describe the use of miRiam, a novel program based on
both thermodynamics
features and empirical constraints, to specifically predict
viral miRNAs/human
targets interactions. More precisely, miRiam exploits target
mRNA secondary structure
accessibility and  interaction rules, inferred from
validated miRNA/mRNA pairs. A set
of genes involved in apoptosis and cell-cycle regulation was
identified as target for
our studies, a choice supported by the knowledge that DNA
tumor viruses interfere with
these processes in humans. miRNAs were selected from two
cancer related viruses,
Epstein-Barr Virus (EBV) and Kaposi-Sarcoma Associated
Herpes Virus (KSHV). 


Results
The results of our prediction show that several of the mRNAs
we analyzed (such as
BID, BAX, CASP3, CASP10, TP53)  possess good binding scores
to these miRNAs. This
suggests that besides the protein based host regulation
mechanism, a post
transcriptional level interference may exist. Future work
will be aimed at providing
the experimental validation of these computational predictions.
 
Id: 109
Place: Napoli, Italy
Centro Congressi "Federico II"
Via Partenope 36
Napoli
Starting date:
26-Apr-2007   15:00
Duration: 20'
Contribution type: Oral
Primary Authors: FERRO, Alfredo (Dipartimento di Matematica e Informatica, Universita` di Catania; Dipartimento di Scienze Biomediche, Universita` di Catania)
Co-Authors: FORTE, Stefano (Dipartimento di Matematica e Informatica, Universita` di Catania; Dipartimento di Scienze Biomediche, Universita` di Catania)
GIUGNO, Rosalba (Dipartimento di Matematica e Informatica, Universita` di Catania)
LAGANA`, Alessandro (Dipartimento di Matematica e Informatica, Universita` di Catania; Dipartimento di Scienze Biomediche, Universita` di Catania)
PULVIRENTI, Alfredo (Dipartimento di Matematica e Informatica, Universita` di Catania)
BARBAGALLO, Davide (Dipartimento di Scienze Biomediche, Universita` di Catania)
DI PIETRO, Cinzia (Dipartimento di Scienze Biomediche, Universita` di Catania)
MAJORANA, Alessandra (Dipartimento di Scienze Biomediche, Universita` di Catania)
PURRELLO, Michele (Dipartimento di Scienze Biomediche, Universita` di Catania)
RAGUSA, Marco (Dipartimento di Scienze Biomediche, Universita` di Catania)
BONCI, Desiree (Istituto Superiore di Sanita`, Roma)
DE MARIA, Ruggero (Istituto Superiore di Sanita`, Roma; Fondazione Istituto Oncologico del Mediterraneo, Catania)
PAGLIUCA, Alfredo (Istituto Superiore di Sanita`, Roma)
Presenters: FERRO, Alfredo
Material: slide Slides
 
Included in session: Session 1: Structural and functional analysis of genomes
Included in track: Structural and functional analysis of genomes
 




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




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