Project description:SUPT4H1 is a transcription elongation factor comprising part of the RNA polymerase II complex. Recent studies propose a selective role for SUPT4H1 in transcription of repeat-containing transcripts; the translated products of which being a hallmark of neurodegeneration in disorders such as Huntington’s Disease and C9orf72-amyotrophic lateral sclerosis. To investigate the potential of SUPT4H1 as a therapeutic target in repeat-associated neurodegeneration, we depleted SUPT4H1 by RNA interference in order to mimic pharmacological loss of function. Using RNA sequencing we assessed SUPT4H1-knockdown induced changes is both immortalized cells (HEK293t) as well as primary human fibroblasts. Diminished SUPT4H1 leads to a global reduction in cellular RNA.
Project description:This is global mRNA gene expression data for HEK293 and cells expressing HSP70K71E ; most genes were down-regulated for HSP70K71E compared to the control Keywords: Global mRNA expression We overexpressed pCI1-EGFP (control) and Hsp70K71E-EGFP to HEK293 and collected total RNA from each condition to analyze global mRNA expression
Project description:This is global mRNA gene expression data for HEK293 and cells expressing HSP70K71E ; most genes were down-regulated for HSP70K71E compared to the control Keywords: Global mRNA expression
Project description:A green fluorescence protein (GFP)-derived dsRNA (dsRNA-GFP) has been used as an exogenous control for Apis mellifera RNAi assays by multiple research groups. Its sequence does not share any significant homology with any known honey bee genes. Although dsRNA-GFP is not expected to trigger an RNAi response in treated bees, undesirable effects on gene expression, pupal pigmentation or developmental timing have been routinely observed. To better understand the multiple molecular and phenotypic effects of dsRNA-GFP in honey bees and to evaluate its use as a control for RNAi studies, we examined the impact of dsRNA-GFP on global gene expression patterns in developing workers. We found that dsRNA-GFP causes large-scale changes in gene expression associated with multiple biological processes. Furthermore, dsRNA-GFP exposure tended to preferentially decrease, rather than increase, expression of genes compared to controls.
Project description:RNA-Seq analysis was carried out to investigate the effects of selective CDK8/19 inhibitor Senexin B on gene expression in HEK293 cells (293-WT) or the CDK8/19 double-knockout (293-dKO) derivatives.
Project description:Double-stranded RNA (dsRNA) can enter different pathways in mammalian cells, such as the sequence-specific RNA interference (RNAi) pathway, the sequence-independent interferon response, and RNA editing by adenosine deaminases. To study routing of long dsRNA into different pathways in different tissues, we generated transgenic mice carrying an inverted repeat transcribed by a strong, ubiquitously active polII promoter. Here, we provide the first report of effects caused by ubiquitous long dsRNA expression in the adult mouse. Long dsRNA is poorly processed into siRNAs in somatic cells but readily induces the RNAi effects in the oocyte, suggesting that somatic cells are missing a component of RNAi that facilitates siRNA biogenesis. Expression of dsRNA is not sufficient to activate the interferon pathway and has a minimal effect on the transcriptome in somatic cells. The interferon response in somatic cells could be induced with high doses of dsRNA expression, suggesting that somatic cells can tolerate endogenous dsRNA expression to a large extent. Our data demonstrate that the association between long dsRNA and the interferon pathway in somatic cells cannot be generalized and that cells recognize other features of dsRNA molecules, which increase or reduce the likelihood activation of a particular dsRNA-induced pathway. Brain or kidney tissue (transgenic mice), or HEK293 or HeLa cell lines (human), expressing long dsRNA within the 3'-UTR of the EGFP reporter gene.
Project description:Transcriptional profiling of BLCAP transient knockdown HEK293 cells camparing control shLuc cells with shBLCAP cells. Goal was to determine the effects of BLCAP gene depletion on global gene expression.