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

Li G, Bahn JH, Lee JH, Peng G, Chen Z, Nelson SF, Xiao X - Nucleic Acids Res. (2012)

Bottom Line: Establishing the functional roles of genetic variants remains a significant challenge in the post-genomic era.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Integrative Biology and Physiology, David Geffen School of Medicine and Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA.

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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Number of genes with ASE patterns in the breast cancer data classified into different categories. Similar as Figure 4; a total of 830 genes were included that could be classified using our approach (see ‘Materials and Methods’ section).
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gks280-F6: Number of genes with ASE patterns in the breast cancer data classified into different categories. Similar as Figure 4; a total of 830 genes were included that could be classified using our approach (see ‘Materials and Methods’ section).

Mentions: Among the 14 570 heterozygous SNVs (in 4433 genes) that satisfy the power requirement (N reads ≥ 20), 4052 (in 2001 genes) were identified with ASE patterns. Thus, the proportions of SNVs and genes demonstrating ASE are 27.8 and 45.1%, respectively. We next classified the genes according to the predicted cis-regulatory mechanisms, using the same approach as for U87MG cells. As shown in Figure 6, 225 genes demonstrated ASE due to whole-gene-level regulation and 605 genes showed ASARP. ASAS events again constitute the largest category (80%) among all three types of alternative mRNA processing events, followed by the ASAP events. This distribution of ASE patterns in different mechanistic categories is largely similar as that in the U87MG cells.Figure 6.


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

Li G, Bahn JH, Lee JH, Peng G, Chen Z, Nelson SF, Xiao X - Nucleic Acids Res. (2012)

Number of genes with ASE patterns in the breast cancer data classified into different categories. Similar as Figure 4; a total of 830 genes were included that could be classified using our approach (see ‘Materials and Methods’ section).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3401465&req=5

gks280-F6: Number of genes with ASE patterns in the breast cancer data classified into different categories. Similar as Figure 4; a total of 830 genes were included that could be classified using our approach (see ‘Materials and Methods’ section).
Mentions: Among the 14 570 heterozygous SNVs (in 4433 genes) that satisfy the power requirement (N reads ≥ 20), 4052 (in 2001 genes) were identified with ASE patterns. Thus, the proportions of SNVs and genes demonstrating ASE are 27.8 and 45.1%, respectively. We next classified the genes according to the predicted cis-regulatory mechanisms, using the same approach as for U87MG cells. As shown in Figure 6, 225 genes demonstrated ASE due to whole-gene-level regulation and 605 genes showed ASARP. ASAS events again constitute the largest category (80%) among all three types of alternative mRNA processing events, followed by the ASAP events. This distribution of ASE patterns in different mechanistic categories is largely similar as that in the U87MG cells.Figure 6.

Bottom Line: Establishing the functional roles of genetic variants remains a significant challenge in the post-genomic era.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Integrative Biology and Physiology, David Geffen School of Medicine and Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA.

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.

Show MeSH
Related in: MedlinePlus