Project description:To investigate the changes in circRNAs expression after SVA infection in PK-15 cells, we established a model of SVA-infected PK-15 cells.
Project description:Retroelement activation is emerging as a significant factor in the pathogenesis of neurodegenerative diseases. SINE-VNTR-Alu (SVAs) are hominid-specific retroelements that create genetic variation through insertion polymorphisms and variable short tandem repeat (STR) lengths. We investigate how the SVA (CCCTCT)n STR contributes to the striatal neurodegenerative disorder X-linked Dystonia Parkinsonism (XDP), where the repeat expansion length within the pathogenic SVA is inversely correlated with disease onset age. Phenotypic and transcriptomic analysis of XDP and isogenic SVA-deleted striatal organoids revealed that the SVA insertion drives hallmarks of neurodegeneration, including transcriptional dysregulation, decreased neuronal activity, and apoptosis, which are ameliorated by SVA deletion. We identify a (AGAGGG)n hexamer-containing RNA in the SVA that increases expression during organoid maturation and drives R-loop formation in organoids and XDP brain tissue. Knockdown of the (AGAGGG)n hexamer-containing RNA by antisense oligonucleotides rescues apoptosis in the XDP organoids. We demonstrate that a retrotransposon-derived tandem repeat RNA could cause neurodegeneration.
Project description:X-linked dystonia parkinsonism (XDP) is an inherited neurodegenerative disease characterized by the antisense insertion of an SVA retrotransposon into the TAF1 gene, encoding for the largest subunit of the basal transcription factor TFIID, which is essential for RNA polymerase II activity. This SVA insertion has been associated with altered TAF1 expression levels, but the cause of this outcome and its link to the development of XDP remain unknown. Unique to the XDP SVA compared to other SVA retrotransposons in the human genome is the amplification of the (GGGAGA)n repeat domain, creating a unique G4-prone region, whose length correlates with age at onset and disease severity. By ChIP-seq and ChIP-qPCR with the anti-G4 antibody BG4, we assessed that G4s are present in the folded state in the XDP SVA of these cells. Using available G4 ligands, we demonstrated that stabilization of the XDP SVA G4s reduces TAF1 transcripts in the exons around and downstream of the SVA, while increasing the transcription of the upstream exons, possibly through a positive feedback loop.
Project description:SVA retrotransposons remain active in humans and contribute to individual genetic variation. Polymorphic SVA alleles harbor gene-regulatory potential and can cause genetic disease. However, how SVA insertions are controlled and functionally impact human disease is unknown. Here, we dissect the epigenetic regulation and influence of SVAs in cellular models of X-linked dystonia-parkinsonism (XDP), a neurodegenerative disorder caused by an SVA insertion at the TAF1 locus. We demonstrate that the KRAB zinc finger protein ZNF91 establishes H3K9me3 and DNA methylation over SVAs, including polymorphic alleles, in human neural progenitor cells. The resulting mini-heterochromatin domains attenuate the cis-regulatory impact of SVAs. This is critical for XDP pathology; removal of local heterochromatin severely aggravates the XDP molecular phenotype, resulting in increased TAF1 intron retention and reduced expression. Our results provide unique mechanistic insights into how human polymorphic transposon insertions are recognized, and their regulatory impact constrained by an innate epigenetic defense system.
Project description:We have performed microarray hybridization studies on forty clinical isolates from twelve common serovars within Salmonella enterica subspecies I (sspI) to identify the conserved gene pool present.