[ged] paper for next week journal club.

[Likit Preeyanon]

Hi, guys

I'm presenting this paper next week, Monday 2pm.
http://nar.oxfordjournals.org/content/early/2012/03/28/nar.gks280.full

Identification of allele-specific alternative mRNA processing via
transcriptome sequencing.

Abstract

Establishing the functional roles of genetic variants remains a significant
challenge in the post-genomic era. Here, we present a method,
allele-specific alternative mRNA processing (ASARP), to identify
genetically influenced mRNA processing events using transcriptome
sequencing (RNA-Seq) data. The method examines RNA-Seq data at both
single-nucleotide and whole-gene/isoform levels to identify allele-specific
expression (ASE) and existence of allele-specific regulation of mRNA
processing. We applied the methods to data obtained from the human
glioblastoma cell line U87MG and primary breast cancer tissues and found
that 26–45% of all genes with sufficient read coverage demonstrated ASE,
with significant overlap between the two cell types. Our methods predicted
potential mechanisms underlying ASE due to regulations affecting either
whole-gene-level expression or alternative mRNA processing, including
alternative splicing, alternative polyadenylation and alternative
transcriptional initiation. Allele-specific alternative splicing and
alternative polyadenylation may explain ASE in hundreds of genes in each
cell type. Reporter studies following these predictions identified the
causal single nucleotide variants (SNVs) for several allele-specific
alternative splicing events. Finally, many genes identified in our study
were also reported as disease/phenotype-associated genes in genome-wide
association studies. Future applications of our approach may provide ample
insights for a better understanding of the genetic basis of gene regulation
underlying phenotypic diversity and disease mechanisms.
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