Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA153059 | ENA |
REPOSITORIES: ENA
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Project description:To identify which mRNAs bind to RBM4/HIF-2a Two PAR-CLIPs were performed: One of an RBM4 immunoprecipitation, and the other of a HIF-2a immunoprecipitation and excising the associated RBM4 band.
2012-05-06 | E-GEOD-36247 | biostudies-arrayexpress
Project description:We hypothesized that RBM4 regulates HERVs by directly binding to their transcripts. To test this possibility, we performed photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP). We performed four independent PAR-CLIP replicates of our own using HAP1 cells stably expressing a FLAG-tagged RBM4 (FLAG-RBM4) transgene under control of a doxycycline-inducible promoter. Following metabolic labeling with 4-thiouridine (4SU) and crosslinking with ultraviolet light (UV) of 312 nm wavelength, we isolated RNA covalently linked to FLAG-RBM4. The RNA recovered from four biological replicates was converted into cDNA libraries and deep sequenced.
2020-09-03 | GSE147895 | GEO
Project description:To identify which mRNAs bind to RBM4/HIF-2a
2012-05-06 | GSE36247 | GEO
Project description:This is a part of the study that shows that a host microRNA, miR-138, represses herpes simplex virus 1 (HSV-1) gene expression through both viral and host targets. These PAR-CLIP analyses identified viral and host targets of miR-138 in Neuro-2a (mouse neuroblastoma) and 293T (human embryonic kidney) cells. We constructed two cell lines derived from Neuro-2a cells, one overexpressing miR-138 (N2A138) and one antagonizing miR-138 (N2Aanti138). We also constructed two cell lines derived from 293T cells, one overexpressing miR-138 (293T138) and one control cells (293Tcontrol). Uninfected N2A138 and N2Aanti138 were compared by PAR-CLIP for host targets in Neuro-2A cells. 293T138 and 293Tcontrol cells infected for 4 and 8 hours were compared by PAR-CLIP for HSV-1 targets in 293T cells. 293T138 and 293Tcontrol cells infected for 4 hours were also compared for host targets in 293T cells.
2020-04-27 | GSE127503 | GEO
Project description:Integrative AUF1 PAR-CLIP analysis uncovers AUF1 roles in translation and genome integrity (PAR-CLIP)
| PRJNA230574 | ENA
Project description:The identification of RNAs that are recognized by RNA-binding proteins (RNA-BPs) using techniques such as Crosslinking and Immunoprecipitation (CLIP) has revolutionized the genome-wide discovery of RNA-BP RNA targets. Among the different versions of CLIP that have been developed, the use of photoactivable nucleoside analogs has resulted in high efficiency photoactivable ribonucleoside-enhanced CLIP (PAR-CLIP) in vivo. Nonetheless, PAR-CLIP has not yet been applied in prokaryotes. To determine if PAR-CLIP can be used in prokaryotes, we determined suitable conditions for the incorporation of 4-thiouridine (4SU), a photoactivable nucleoside, into E. coli RNA and for the isolation of RNA crosslinked to RNA-BPs of interest. Applying this technique to Hfq, a well-characterized regulator of small RNA (sRNA)-messenger RNA (mRNA) interactions, we showed that PAR-CLIP identified most of the known sRNA targets of Hfq, as well as functionally relevant sites of Hfq-mRNA interactions at nucleotide resolution. Based on our findings, PAR-CLIP represents an improved method to identify both the RNAs and the specific regulatory sites that are recognized by RNA-BPs in prokaryotes.
2022-10-18 | MSV000090547 | MassIVE
Project description:General activation of hypoxia-inducible factor (HIF) pathways is classically associated with adverse prognosis in cancer and has been proposed to contribute to oncogenic drive. In clear cell renal carcinoma (CCRC) HIF pathways are upregulated by inactivation of the von-Hippel-Lindau tumour suppressor. However HIF-1a and HIF-2a have contrasting effects on experimental tumour progression. To better understand this paradox we examined pan-genomic patterns of HIF DNA binding and associated gene expression in response to manipulation of HIF-1a and HIF-2a and related the findings to CCRC prognosis. Our findings reveal distinct pan-genomic organization of HIF isoform-specific DNA binding at thousands of sites. Overall associations were observed between HIF-1a-specific binding, and genes associated with favourable prognosis and between HIF-2a-specific binding and adverse prognosis. However within each isoform-specific set, individual gene associations were heterogeneous in sign and magnitude, suggesting that activation of each HIF-a isoform contributes a highly complex mix of pro- and anti-tumorigenic effects ChIP and RNASeq of HIF-1a and HIF-2a transfection in 786-O cell lines
2015-07-10 | E-GEOD-67237 | biostudies-arrayexpress