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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: 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.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: 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.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