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Tissue type-specific expression of the dsRNA-binding protein 76 and genome-wide elucidation of its target mRNAs.

Neplioueva V, Dobrikova EY, Mukherjee N, Keene JD, Gromeier M - PLoS ONE (2010)

Bottom Line: The association of RNA-binding proteins with their targets is regulated through changing subcellular distribution, post-translational modification or association with other proteins.Our data suggest that physiologic DRBP76 expression, isoform distribution and subcellular localization are profoundly altered upon malignant transformation.Thus, the functional role of DRBP76 in co- or post-transcriptional gene regulation may contribute to the neoplastic phenotype.

View Article: PubMed Central - PubMed

Affiliation: Division of Neurosurgery, Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America.

ABSTRACT

Background: RNA-binding proteins accompany all steps in the life of mRNAs and provide dynamic gene regulatory functions for rapid adjustment to changing extra- or intracellular conditions. The association of RNA-binding proteins with their targets is regulated through changing subcellular distribution, post-translational modification or association with other proteins.

Methodology: We demonstrate that the dsRNA binding protein 76 (DRBP76), synonymous with nuclear factor 90, displays inherently distinct tissue type-specific subcellular distribution in the normal human central nervous system and in malignant brain tumors of glial origin. Altered subcellular localization and isoform distribution in malignant glioma indicate that tumor-specific changes in DRBP76-related gene products and their regulatory functions may contribute to the formation and/or maintenance of these tumors. To identify endogenous mRNA targets of DRBP76, we performed RNA-immunoprecipitation and genome-wide microarray analyses in HEK293 cells, and identified specific classes of transcripts encoding critical functions in cellular metabolism.

Significance: Our data suggest that physiologic DRBP76 expression, isoform distribution and subcellular localization are profoundly altered upon malignant transformation. Thus, the functional role of DRBP76 in co- or post-transcriptional gene regulation may contribute to the neoplastic phenotype.

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Related in: MedlinePlus

Enrichment of DRBP76-associated mRNAs and their common functional grouping.A. Heatmap displaying results of clustering DRBP76 IP, mock IP and total mRNA levels for all DRBP76 targets (n = 189). B. Gene sets significantly enriched in the DRBP76 IP vs. mock IP as determined by GSEA. NES =  normalized enrichment score, FDR =  false discovery rate.
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pone-0011710-g005: Enrichment of DRBP76-associated mRNAs and their common functional grouping.A. Heatmap displaying results of clustering DRBP76 IP, mock IP and total mRNA levels for all DRBP76 targets (n = 189). B. Gene sets significantly enriched in the DRBP76 IP vs. mock IP as determined by GSEA. NES =  normalized enrichment score, FDR =  false discovery rate.

Mentions: To determine a cut-off that may define a discrete population of mRNAs associated with DRBP76, we applied a percentile rank transformation, which was used in the analysis of stem loop binding protein (SLBP) and tris-tetra-proline RIP-Chip targets [29], [30]. The DRBP76 IP average percentile rank (APR) distribution is bimodal at the high percentile ranks, whereas the mock IP APR distribution is normal (Fig. 4B). We defined DRBP76 targets as those with DRBP76 IP APRs >0.95, mock IP APRs <0.95, and a fold enrichment over mock IP >2. Altogether, we detected 189 putative DRBP76 target mRNAs (∼1.5% of the total 12,468 expressed) (Fig. S1). Importantly, for these putative targets relative mRNA abundance did not account for the association of mRNAs with DRBP76 based on the lack of correlation between DRBP76 IPs and totals (r2 = 0.04). Further, comparing DRBP76 IPs to mock IPs also exhibited little to no correlation (r2 = 0.15), indicating the RIP-Chip successfully isolated a subset of specific target mRNAs. Consequently, DRBP76 IP samples clustered together relative to mock IP samples and total mRNA samples (Fig. 5).


Tissue type-specific expression of the dsRNA-binding protein 76 and genome-wide elucidation of its target mRNAs.

Neplioueva V, Dobrikova EY, Mukherjee N, Keene JD, Gromeier M - PLoS ONE (2010)

Enrichment of DRBP76-associated mRNAs and their common functional grouping.A. Heatmap displaying results of clustering DRBP76 IP, mock IP and total mRNA levels for all DRBP76 targets (n = 189). B. Gene sets significantly enriched in the DRBP76 IP vs. mock IP as determined by GSEA. NES =  normalized enrichment score, FDR =  false discovery rate.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2909144&req=5

pone-0011710-g005: Enrichment of DRBP76-associated mRNAs and their common functional grouping.A. Heatmap displaying results of clustering DRBP76 IP, mock IP and total mRNA levels for all DRBP76 targets (n = 189). B. Gene sets significantly enriched in the DRBP76 IP vs. mock IP as determined by GSEA. NES =  normalized enrichment score, FDR =  false discovery rate.
Mentions: To determine a cut-off that may define a discrete population of mRNAs associated with DRBP76, we applied a percentile rank transformation, which was used in the analysis of stem loop binding protein (SLBP) and tris-tetra-proline RIP-Chip targets [29], [30]. The DRBP76 IP average percentile rank (APR) distribution is bimodal at the high percentile ranks, whereas the mock IP APR distribution is normal (Fig. 4B). We defined DRBP76 targets as those with DRBP76 IP APRs >0.95, mock IP APRs <0.95, and a fold enrichment over mock IP >2. Altogether, we detected 189 putative DRBP76 target mRNAs (∼1.5% of the total 12,468 expressed) (Fig. S1). Importantly, for these putative targets relative mRNA abundance did not account for the association of mRNAs with DRBP76 based on the lack of correlation between DRBP76 IPs and totals (r2 = 0.04). Further, comparing DRBP76 IPs to mock IPs also exhibited little to no correlation (r2 = 0.15), indicating the RIP-Chip successfully isolated a subset of specific target mRNAs. Consequently, DRBP76 IP samples clustered together relative to mock IP samples and total mRNA samples (Fig. 5).

Bottom Line: The association of RNA-binding proteins with their targets is regulated through changing subcellular distribution, post-translational modification or association with other proteins.Our data suggest that physiologic DRBP76 expression, isoform distribution and subcellular localization are profoundly altered upon malignant transformation.Thus, the functional role of DRBP76 in co- or post-transcriptional gene regulation may contribute to the neoplastic phenotype.

View Article: PubMed Central - PubMed

Affiliation: Division of Neurosurgery, Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America.

ABSTRACT

Background: RNA-binding proteins accompany all steps in the life of mRNAs and provide dynamic gene regulatory functions for rapid adjustment to changing extra- or intracellular conditions. The association of RNA-binding proteins with their targets is regulated through changing subcellular distribution, post-translational modification or association with other proteins.

Methodology: We demonstrate that the dsRNA binding protein 76 (DRBP76), synonymous with nuclear factor 90, displays inherently distinct tissue type-specific subcellular distribution in the normal human central nervous system and in malignant brain tumors of glial origin. Altered subcellular localization and isoform distribution in malignant glioma indicate that tumor-specific changes in DRBP76-related gene products and their regulatory functions may contribute to the formation and/or maintenance of these tumors. To identify endogenous mRNA targets of DRBP76, we performed RNA-immunoprecipitation and genome-wide microarray analyses in HEK293 cells, and identified specific classes of transcripts encoding critical functions in cellular metabolism.

Significance: Our data suggest that physiologic DRBP76 expression, isoform distribution and subcellular localization are profoundly altered upon malignant transformation. Thus, the functional role of DRBP76 in co- or post-transcriptional gene regulation may contribute to the neoplastic phenotype.

Show MeSH
Related in: MedlinePlus