Post-transcriptional gene regulation: RNA-protein
interactions, RNA processing, mRNA stability and localization
Co-chairs:
Contact:
Quaid Morris (quaid.morris@utoronto.ca)
Background
Post-transcriptional regulation (PTR)
of gene expression is a rapidly emerging area attracting considerable interest
from both experimental and computational biologists. In higher eukaryotes, there is widespread PTR
of mRNA composition, stability and localization, all of which are responsible
for creating complex patterns of gene expression. From an evolutionary perspective, PTR may
play as important a role as transcriptional regulation in explaining human
diversity (Kwan, Benovoy et al. 2007) and distinguishing humans
from other primates (Calarco, Xing et al. 2007). Malfunctioning PTR mechanisms, like microRNA mis-regulation or aberrent splicing, are strongly associated with human
disease, mostly notably cancer (Lu, Getz
et al. 2005).
Messenger RNAs
are regulated post-transcriptionally by a series of
inter-dependent mechanisms. They are
frequently regulated by alternative splicing, which can affect not only the exon composition of an mRNA but also can introduce
pre-mature stop codons (Lewis,
Green et al. 2003) to affect
mRNA stability; by being targeted for decay by microRNAs
or RNA-binding proteins (RBPs) like Pumillo; and by a complex variety of mRNA localization
mechanisms (Lecuyer, Yoshida et al. 2007) that are likely mediated by RBPs. Cis-regulatory signal encoded in mRNAs, like internal
ribosomal entry sites (IRES) and microRNA target sites, can further regulate gene expression by controlling
the translation of the mRNA.
Scope
Studying post-transcriptional, pre-translational regulation
presents a number of new computational challenges. The goal of this session is to introduce some
recent work in the area of post-transcriptional regulation to a wider
computational community, discuss some of the unique computational problems
faced in this area, and to present some preliminary solutions to these
problems.
Our session will explore new
developments in computational methods, and new computational problems, in all
of areas of the study of post-transcriptional regulation applied to mRNAs and
affected by cis-regulatory signals encoded in mRNAs.
Here are some suggested topics broken
down by subject area:
Alternative
splicing
- Quantifying alternative isoform levels using exon body
and exon junction tiling arrays or next-generation
sequencing
- Detecting new splice variants through
the analysis of EST databases and exon tiling array
data
- Associating SNP genotypes with
changes in splicing
RNA-protein
interactions
- Motif models for RNA-binding proteins
(RBP)
- Algorithms for fitting motif models
to in vitro RBP binding data, or to
groups of mRNAs with similar PTR.
Evolutionary
models
- Models of the evolution of PTR
mechanisms
- Detecting conservation and change of RNA-binding
protein sites
- Evolutionary models of miRNA target site or RBP target site accessibility.
Regulatory
Networks
- Methods for inferring networks of
post-transcriptional regulation, or networks that combine both transcriptional
and post-transcriptional regulatory networks.
MicroRNAs
- Methods for predicting microRNA targets based on sequence, expression, secondary
structure
Call for Abstracts
We are soliciting abstracts describing recent experimental
and/or computational research in post-transcriptional regulation. Accepted abstracts will be presented during
the conference but will not appear in the proceedings volume, so will not be
official publications. Abstracts will be evaluated by the co-chairs.
Submission instructions
Please submit your one page abstracts in PDF format to ptr.session.psb09@gmail.com. Abstract
should be in a form suitable for redistribution and should contain a title; an
author list that indicates the presenting and corresponding authors as well as
each author’s affiliation, email and mailing address; abstract text; and
optionally figures or references.
Important Dates
• Abstract submission deadline:
• Notification of abstract acceptance:
• Meeting: