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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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Significant enrichment of DRBP76-associated mRNAs from HEK 293 cells and histone mRNAs in brain tumor derived HTB-14 cells.Transcripts rank-ordered by average percentile rank representing differential enrichment in DRBP76 IP from HTB-14 cells. A. Black lines indicate the rank of each individual DRBP76-associated mRNA identified from HEK293 cells (p<0.001). B. Black lines indicate the rank of each individual histone mRNA detected (p<0.001).
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pone-0011710-g007: Significant enrichment of DRBP76-associated mRNAs from HEK 293 cells and histone mRNAs in brain tumor derived HTB-14 cells.Transcripts rank-ordered by average percentile rank representing differential enrichment in DRBP76 IP from HTB-14 cells. A. Black lines indicate the rank of each individual DRBP76-associated mRNA identified from HEK293 cells (p<0.001). B. Black lines indicate the rank of each individual histone mRNA detected (p<0.001).

Mentions: HTB-14 glioma cells share DRBP76 isoform distribution with HEK293 cells, but the protein is far less abundant in cytoplasm in the former (Fig. 1F), recapitulating the situation in patient GBM tissues (Fig. 1E). To establish whether relative cytoplasmic exclusion of DRBP76 in HTB-14 cells produces distinct association with mRNAs, we conducted RIP-Chip analyses from HTB-14 cell lysates. These revealed that DRBP76-associated mRNAs identified from HEK293 cell were indeed significantly enriched (p<0.001) in DRBP76 RIPs from HTB-14 cells (Fig. 7A). Furthermore, the significant enrichment of mRNAs encoding histone proteins by DRBP76 discovered in HEK293 cells was recapitulated in HTB-14 cells (Fig. 7B). Altogether these data suggest a large degree of similarity between DRBP76 mRNA targets in HEK293 and HTB-14 cells, in line with similar DRBP76 isoform expression in these transformed cell lines.


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)

Significant enrichment of DRBP76-associated mRNAs from HEK 293 cells and histone mRNAs in brain tumor derived HTB-14 cells.Transcripts rank-ordered by average percentile rank representing differential enrichment in DRBP76 IP from HTB-14 cells. A. Black lines indicate the rank of each individual DRBP76-associated mRNA identified from HEK293 cells (p<0.001). B. Black lines indicate the rank of each individual histone mRNA detected (p<0.001).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0011710-g007: Significant enrichment of DRBP76-associated mRNAs from HEK 293 cells and histone mRNAs in brain tumor derived HTB-14 cells.Transcripts rank-ordered by average percentile rank representing differential enrichment in DRBP76 IP from HTB-14 cells. A. Black lines indicate the rank of each individual DRBP76-associated mRNA identified from HEK293 cells (p<0.001). B. Black lines indicate the rank of each individual histone mRNA detected (p<0.001).
Mentions: HTB-14 glioma cells share DRBP76 isoform distribution with HEK293 cells, but the protein is far less abundant in cytoplasm in the former (Fig. 1F), recapitulating the situation in patient GBM tissues (Fig. 1E). To establish whether relative cytoplasmic exclusion of DRBP76 in HTB-14 cells produces distinct association with mRNAs, we conducted RIP-Chip analyses from HTB-14 cell lysates. These revealed that DRBP76-associated mRNAs identified from HEK293 cell were indeed significantly enriched (p<0.001) in DRBP76 RIPs from HTB-14 cells (Fig. 7A). Furthermore, the significant enrichment of mRNAs encoding histone proteins by DRBP76 discovered in HEK293 cells was recapitulated in HTB-14 cells (Fig. 7B). Altogether these data suggest a large degree of similarity between DRBP76 mRNA targets in HEK293 and HTB-14 cells, in line with similar DRBP76 isoform expression in these transformed cell lines.

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