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Identification of RNA targets of EB1 using RIP-seq in Drosophila ovaries

ABSTRACT: Identification of RNA targets of EB1 using RIP-seq in Drosophila ovaries

PROVIDER: PRJEB38201 | ENA |

REPOSITORIES: ENA

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Identification of RNA targets of EB1 using RIP-seq in Drosophila ovaries

Project description:Identification of RNAs that bind to EB1-GFP using RNA-immunoprecipitation followed by sequencing. Ovaries from flies expressing EB1-GFP (and GFP alone as a control) were used to immunoprecipitate crosslinked RNA-EB1GFP complexes using GFP Trap beads. The experiment was performed with three biological replicates for each.

2021-07-24 | E-MTAB-9078 | biostudies-arrayexpress

Cut&Run in Drosophila melanogaster control, mutant and knockdown ovaries

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Project description:A key function for RNA-binding proteins in orchestrating plant development and environmental responses is well established. However, the lack of a genome-wide view on their in vivo binding targets and binding landscapes represents a gap in understanding the mode of action of plant RNA-binding proteins. Here, we conducted RNA Immunoprecipitation (RIP-seq) for genome-wide determining the binding repertoire of the circadian clock-regulated Arabidopsis thaliana glycine-rich RNA-binding protein AtGRP7.

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Identification of miR-205 targets using an RIP-Chip assay with AGO2 antibody

Project description:In this study, the prognostic properties of miR-205 expression levels are investigated in a well-documented prostate cancer cohort. We show that miR-205 is correlated to shortened overall survival, significantly dividing the PCa patients into high and low risk groups. Furthermore, miR-205 is shown to inversely correlate to occurrence of metastases. In situ hybridization is also performed, demonstrating high miR-205 expression in the basal cells of benign prostate tissue glands. A RIP-Chip assay using an AGO2 antibody was implemented and the miR-205 targets identified were found to be enriched in MAPK/ERK, Toll-like receptor and IL-6 signaling pathways. We also found individual targets involved in cancer and androgen receptor signaling. Ectopic levels of miR-205 are shown to decrease the level of androgen receptor both at the mRNA and protein levels in prostate cancer cell lines. This is further corroborated in the prostate cancer cohort were miR-205 expression levels in the prostatic tissues are found to inversely correlate to assessment of androgen receptor (AR) immunostaining and to serum levels of PSA, a protein regulated by AR signaling. The level of miR-205 is also found to be significantly lower in castration resistant prostate cancer patients than in hormone naïve patients. Our data indicates that miR-205 is regulated by androgens and act by different mechanisms in androgen depleted settings, e.g. giving opposite effects on adhesion. Taken together these findings imply that miR-205 might have therapeutic potential especially for the castration resistant and currently untreatable form of prostate cancer. Experiment done with biological triplicates. Three with miR-205 ectopic expression and three with negative control mimic ectopic expression. Followed by a RIP-Chip, ending with mRNA extraction and gene expression array.

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Project description:H3K4me3 profiling in Drosophila melanogaster ovaries

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