Project description:In the associated paper FXR1 is shown to package exceptionally long mRNAs in the cytoplasm and organizes them into an mRNP network. We performed iCLIP of FXR-WT and its mutant FXR1-V361P in HeLa cells where we knocked down endogenous FXR1 and replaced it with either GFP-tagged WT or V361P-mutant FXR1. The GFP-tagged proteins were immunoprecipitated using an anti-GFP antibody.
Project description:iCLIP of HeLa cells with anti-TFIP11 antibody to investigate RNA binding locations of TFIP11 as part of a larger study on the function of TFIP11.
Project description:We sequenced total RNA from HeLa WT cells to quantify the expression of protein-coding mRNAs and lincRNAs. RPKM values were used to normalize iCLIP binding to RNA abundance.
Project description:HeLa cells were cultured in DMEM, supplemented with 10% (v/v) FCS and penicillin/streptomycin under 5% CO2 at 37°C. For iCLIP, HeLa cells expressing eIF4A3-GFP or PTB-GFP were induced with doxycycline to adjust the level of recombinant protein to the level of the endogenous counterpart and irradiated with 150 mJ/cm2 UV light (254 nm). The iCLIP cDNA libraries for eIF4A3 and PTB were sequenced with 50 bp on an Illumina HiSeq instrument.
Project description:To understand the effect of U1 AMO treatment on wdr33 binding profile , we carried out CstF64 iCLIP-seq experiments in HeLa cells treated with either control or U1 AMO.
Project description:To understand the effect of U1 AMO treatment on CstF64 binding profile , we carried out CstF64 iCLIP-seq experiments in HeLa cells treated with either control or U1 AMO.
Project description:To better understand the mechanism of U1A functions in human cells, we performed U1A iCLIP-seq analysis in HeLa cells. iCLIP-seq is a previously well-established protocol that is believed to detect protein-RNA interaction at individual-nucleotide resolution. Indeed, successful completion of U1A iCLIP-seq has helped us to illuminate more detailed mechanism through which U1 snRNP prevents mRNA PCPA (premature cleavage and polyadenylation)