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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

Identification of DRBP76-associated mRNAs using RIP-Chip.A. Distribution of DRBP76 IP vs. mock IP t-scores. Deviation of data from the diagonal quantile:quantile plot indicates the non-Gaussian nature of the DRBP76 IP vs. mock IP distribution, corresponding with transcripts specifically enriched in the DRBP76 IP. B. Distribution of the average percentile ranks (APR) of 5 biological replicates for DRBP76 IPs and mock IPs. Transcripts considered DRBP76 RNP-associated are indicated by black boxes.
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pone-0011710-g004: Identification of DRBP76-associated mRNAs using RIP-Chip.A. Distribution of DRBP76 IP vs. mock IP t-scores. Deviation of data from the diagonal quantile:quantile plot indicates the non-Gaussian nature of the DRBP76 IP vs. mock IP distribution, corresponding with transcripts specifically enriched in the DRBP76 IP. B. Distribution of the average percentile ranks (APR) of 5 biological replicates for DRBP76 IPs and mock IPs. Transcripts considered DRBP76 RNP-associated are indicated by black boxes.

Mentions: We used RIP-Chip to identify mRNAs associated with RNP complexes containing DRBP76 from cytoplasmic HEK293 extracts. Five biological replicates each of DRBP76, mock (isotype-matched mouse IgG) immunoprecipitates, and total cellular RNA samples were analyzed using spotted cDNA microarrays that interrogated 3.5×104 genes. To qualify for subsequent analysis and be defined as ‘enriched’, a probe had to be >2-fold above local background in any of the IPs or the totals. T-scores, p-values and log-fold changes were calculated comparing DRBP76 IP versus mock IP for all probes expressed (n = 12,468). Visual inspection of the t-score distribution and the quantile:quantile plot indicated the right tail of the DRBP76 vs. mock IP distribution deviated from a normal distribution (Fig. 4A). Since probes with very high t-scores correspond to the right tail, substantially more mRNAs were enriched in the DRBP76 IP than the mock IP.


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)

Identification of DRBP76-associated mRNAs using RIP-Chip.A. Distribution of DRBP76 IP vs. mock IP t-scores. Deviation of data from the diagonal quantile:quantile plot indicates the non-Gaussian nature of the DRBP76 IP vs. mock IP distribution, corresponding with transcripts specifically enriched in the DRBP76 IP. B. Distribution of the average percentile ranks (APR) of 5 biological replicates for DRBP76 IPs and mock IPs. Transcripts considered DRBP76 RNP-associated are indicated by black boxes.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0011710-g004: Identification of DRBP76-associated mRNAs using RIP-Chip.A. Distribution of DRBP76 IP vs. mock IP t-scores. Deviation of data from the diagonal quantile:quantile plot indicates the non-Gaussian nature of the DRBP76 IP vs. mock IP distribution, corresponding with transcripts specifically enriched in the DRBP76 IP. B. Distribution of the average percentile ranks (APR) of 5 biological replicates for DRBP76 IPs and mock IPs. Transcripts considered DRBP76 RNP-associated are indicated by black boxes.
Mentions: We used RIP-Chip to identify mRNAs associated with RNP complexes containing DRBP76 from cytoplasmic HEK293 extracts. Five biological replicates each of DRBP76, mock (isotype-matched mouse IgG) immunoprecipitates, and total cellular RNA samples were analyzed using spotted cDNA microarrays that interrogated 3.5×104 genes. To qualify for subsequent analysis and be defined as ‘enriched’, a probe had to be >2-fold above local background in any of the IPs or the totals. T-scores, p-values and log-fold changes were calculated comparing DRBP76 IP versus mock IP for all probes expressed (n = 12,468). Visual inspection of the t-score distribution and the quantile:quantile plot indicated the right tail of the DRBP76 vs. mock IP distribution deviated from a normal distribution (Fig. 4A). Since probes with very high t-scores correspond to the right tail, substantially more mRNAs were enriched in the DRBP76 IP than the mock IP.

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