Project description:In previous studies, we identified a sequence motif (GDCGG) in almost all microRNAs downregulated in the serum of patients with amyotrophic lateral sclerosis. We found that FMR1, FXR1 and FXR2 directly and specifically interact with microRNAs containing the GDCGG motif via their RGG/RG-domains. Here, we compare the specificities for microRNAs of the RGG/RG-domains of FMR1, FXR1 and FXR2 on a transcriptome-wide scale using the Affymetrix GeneChip™ miRNA 3.0 Arrays.
Project description:G-quadruplexes (rG4s) are recognized as key structures involved in RNA biology and are linked to neurodegenerative disease and cancer. However, detailed knowledge of rG4s and their binding partners is lacking. Here, a systematic, unbiased affinity proteomics approach identified 80 potential high-confidence interactors of the rG4 structure in the 5’UTR of the NRAS oncogene. Using epitope-tagged protein expression, we validated a subset of interactions including DDX3X, DDX5, DDX17, DHX9, DHX36, FXR1, FXR2, GRSF1 and NSUN5. More than half of the identified rG4 interactors were enriched in glycine-arginine (GAR) domains, and for DDX3X and DDX17, we show that the GAR domain is required for rG4 interaction. Transcriptome-wide binding analysis using DDX3X iCLIP revealed a striking association with rG4s in 5’UTRs that was lacking in the GAR-domain mutant. Overall, our work highlights a hitherto unrecognized complexity in rG4 structure-protein interactions that should be considered for the understanding of rG4 function.
Project description:G-quadruplex structures in the 5’ UTR of mRNAs are widely considered to suppress translation without affecting transcription. The current study describes the comprehensive analysis of proteins binding to four different G-quadruplex motifs located in mRNAs of the cancer-related genes Bcl-2, NRAS, MMP16, and ARPC2. Following metabolic labeling (Stable Isotope Labeling with Amino acids in Cell culture, SILAC) of proteins in the human cell line HEK293, G-quadruplex binding proteins were enriched by pull-down assays and identified by LC-orbitrap mass spectrometry. We found different patterns of interactions for the G-quadruplex motifs under investigation. While the G-quadruplexes in the mRNAs of NRAS and MMP16 specifically interacted with a small number of proteins, the Bcl-2 and ARPC2 G-quadruplexes exhibited a broad range of proteinaceous interaction partners with 99 and 82 candidate proteins identified in at least two replicates, respectively. Among the interaction partners were many proteins known to bind to RNA, including multiple heterogenous nuclear ribonucleoproteins (hnRNPs). The identified ribosomal proteins are likely to reflect stalling of the ribosome by RNA G-quadruplex structures. In addition, several proteins were identified that have not previously been described to interact with RNA. Gene ontology analysis of the set of candidate proteins revealed that many interaction partners are known to be tumor related. The majority of the identified RNA G-quadruplex interacting proteins are thought to be involved in post-transcriptional processes, particularly in splicing. These findings indicate that protein-G-quadruplex interactions may be relevant to the regulation of mRNA maturation and may play an important role in tumor biology.
Project description:Rgg-dependent transcriptional regulation in SF370 Streptococcus pyogenes strain was analyzed during post-exponential phase of growth Keywords: rgg mutant Microarray analysis was performed using RNA samples isolated from both wild-type SF370 and SF370 rgg mutant strains during post-exponential phase of growth
Project description:Rgg-dependent transcriptional regulation in Streptococcus pyogenes strains MGAS5005 and CS101 was analyzed during post-exponential phase of growth Keywords: strain comparion, post-exponential growth, rgg mutant Microarray analysis was performed using RNA samples isolated from wild-type MGAS5005 and CS101 strains as well as their rgg mutant strains during post-exponential phase of growth
Project description:Rgg-dependent transcriptional regulation in SF370 Streptococcus pyogenes strain was analyzed during post-exponential phase of growth Keywords: rgg mutant
Project description:The effect of bisquinolinium compounds PhenDC3 and 360A genome wide gene expression changes modulated via promoter based G-quadruplex (G4) motifs. The total RNA was extracted after treating HeLa S3 cells with 10 µM of no molecule (DMSO), 8979A (control molecule), PhenDC3 (G4 specific molecule) or 360A (G4 specific molecule) for 48 hrs in triplicate.
Project description:In order to study the transcriptome changes in tomato during Pto/Prf-mediated ETI, we infiltrated tomato Rio Grande (RG)-PtoR resistant plants (plants that have a functional Pto/Prf signaling pathway, Pto/Pto, Prf/Prf) and two different susceptible plants: RG-prf3 and RG-prf19 (Pto/Pto, prf/prf), with Pseudomonas syringae pv. tomato DC3000 (DC3000). The susceptible lines have a non-functional Prf gene due to a 1.1 kb deletion or a G-insertion at position 2,584 (which causes a frameshift), respectively. We collected leaf tissue at 4 and 6 h after inoculation (hai) to assess early changes in host gene expression after translocation of DC3000 effectors AvrPto and AvrPtoB, which occur at about 3 hai. The plants were then maintained in the same conditions to observe signs of disease. As expected, RG-PtoR plants did not develop speck disease whereas the RG-prf plants did. NOTE: Samples in SRA were assigned the same sample accession. This is incorrect as there are different samples, hence âÂÂSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.