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RNA-binding protein RPS27 and gene expression regulation in Kaposi’s sarcoma

ABSTRACT: RNA-binding protein RPS27 and gene expression regulation in Kaposi’s sarcoma

PROVIDER: PRJNA878524 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21491960_1.fastq.gz	Fastqsanger.gz
	SRR21491960_2.fastq.gz	Fastqsanger.gz
	SRR21491961_1.fastq.gz	Fastqsanger.gz
	SRR21491961_2.fastq.gz	Fastqsanger.gz
	SRR21491962_1.fastq.gz	Fastqsanger.gz

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RNA-binding protein RPS27 and gene expression regulation in Kaposi’s sarcoma [RNA-seq]

Project description:RNA-binding protein RPS27 and gene expression regulation in Kaposi’s sarcoma [RNA-seq]

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RNA-binding protein RPS27 and gene expression regulation in Kaposi’s sarcoma [RIP-seq]

Project description:RNA-binding protein RPS27 and gene expression regulation in Kaposi’s sarcoma [RIP-seq]

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RNA-binding protein RPS27 and gene expression regulation in Kaposi’s sarcoma [RIP-seq]

Project description:In order to clarify the post-transcriptional regulatory network of RPS27 in KS. We constructed a transcriptomic binding network using iRIP-seq. The KS lesions of the other two patients were used for separately.

2023-10-20 | GSE212960 | GEO

RNA-binding protein RPS27 and gene expression regulation in human umbilical vein endothelial cells (HUVECs)

Project description:RPS27, a significantly down-regulated and validated RBP in kaposi's sarcoma (KS), and known to be associated with viral infection. As KS is an endothelial cell cancer, we used HUVECs as the cell model to explore the functions of RPS27. RNA-seq technology was used to investigate the differentially expressed genes in HUVECs. By using small interference RNAs (siRNAs) to silence the expression of RPS27 (siRPS27), we detected significant decrease of RPS27 expression in RNA levels comparing with the negative control (siNC) samples.

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RNA-binding protein RPS27 and gene expression regulation in Kaposi’s sarcoma [RNA-seq]

Project description:RNA-seq technology was used to investigate the differentially expressed genes and regulated alternative splicing events in Kaposi's sarcoma lesions and adjacent non-tumor tissues. We then performed gene expression profiling analysis using data obtained from RNA-seq.

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RNA-binding protein RPS27 and gene expression regulation in Kaposi’s sarcoma

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-10-20 | GSE212962 | GEO

Apoptosis regulation by Kaposi’s sarcoma microRNAs

Project description:Herpesviruses are known to encode micro (mi)RNAs and to use them to regulate the expression of both viral and cellular genes. The genome of Kaposi’s sarcoma herpesvirus (KSHV) encodes a cluster of twelve miRNAs, which are abundantly expressed during both latency and lytic infection. Relatively few cellular targets of KSHV miRNAs are known. Here, we used a microarray expression profiling approach to analyze the transcriptome of both B lymphocytes and endothelial cells stably expressing KSHV miRNAs and monitor the changes induced by the presence of these miRNAs. We generated a list of potential cellular targets by looking for miRNA seed-match-containing transcripts that were significantly down regulated upon KSHV miRNAs expression. Interestingly, the overlap of putative targets identified in B lymphocytes and endothelial cells was minimal, suggesting a tissue-specific target-regulation by viral miRNAs. Among the putative targets, we identified caspase 3, a critical factor for the control of apoptosis, which we validated using luciferase reporter assays and western blotting. In functional assays we obtained further evidence that KSHV miRNAs indeed protect cells from apoptosis. Single-channel hybridization to Affymetrix oligonucleotides microarrays. DG75 and EA.hy926 cells were transducted in triplicates with the K10/12 and K12/12 lentiviral constructs expressing the KSHV miRNAs, or with a GFP-expressing construct as control. The K10/12 construct expressed only the ten intronic miRNAs miR-K12-1 to 9 and miR-K12-11 while the K12/12 construct also expressed miR-K12-10 and miR-K12-12 in addition.

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Apoptosis regulation by Kaposi’s sarcoma microRNAs

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Kaposi’s Sarcoma-associated Herpesvirus Viral Protein Kinase Augments Cell Survival

Project description:Kaposi’s Sarcoma-associated Herpesvirus Viral Protein Kinase Augments Cell Survival

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Subfunctionalized expression drives evolutionary retention of ribosomal protein paralogs Rps27 and Rps27l in vertebrates

Project description:The formation of paralogs through gene duplication is a core evolutionary process. For paralogs that encode components of protein complexes such as the ribosome, a central question is whether they encode functionally distinct proteins, or whether they exist to maintain appropriate total expression of equivalent proteins. Here, we systematically tested evolutionary models of paralog function using the ribosomal protein paralogs Rps27 (eS27) and Rps27l (eS27L) as a case study. Evolutionary analysis suggests that Rps27 and Rps27l likely arose during whole-genome duplication(s) in a common vertebrate ancestor. We show that Rps27 and Rps27l have inversely correlated mRNA abundance across mouse cell types, with the highest Rps27 in lymphocytes and the highest Rps27l in mammary alveolar cells and hepatocytes. By endogenously tagging the Rps27 and Rps27l proteins, we demonstrate that Rps27- and Rps27l-ribosomes associate preferentially with different transcripts. Furthermore, murine Rps27 and Rps27l loss-of-function alleles are homozygous lethal at different developmental stages. However, strikingly, expressing Rps27 protein from the endogenous Rps27l locus or vice versa completely rescues loss-of-function lethality and yields mice with no detectable deficits. Together, these findings suggest that Rps27 and Rps27l are evolutionarily retained because their subfunctionalized expression patterns render both genes necessary to achieve the requisite total expression of two equivalent proteins across cell types. Our work represents the most in-depth characterization of a mammalian ribosomal protein paralog to date and highlights the importance of considering both protein function and expression when investigating paralogs.

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