PAR-CLIP-seq of HA-METTL14 in HepG2 cells
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ABSTRACT:
PROVIDER: PRJNA499119 | ENA |
REPOSITORIES: ENA
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Project description:The METTL3-METTL14 heterodimer is the core component of the N6-methyltransferase complex (MTC) that catalyzes methylation of adenosine residues at the N(6) position of RNA. As the non-catalytic subunit of MTC, METTL14 functions as the RNA-binding scaffold that recognizes the RNA substrate. To identify METTL14 binding sites in the transcriptome, we overexpressed HA-tagged METTL14 in HepG2 cells and performed PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) using HA antibody. Subsequent deep sequencing identified 5,961 METTL14 binding sites, in which the GGAC motif was enriched.
2019-02-21 | GSE121948 | GEO
Project description:The METTL3-METTL14 heterodimer is the core component of the N6-methyltransferase complex (MTC) that catalyzes methylation of adenosine residues at the N(6) position of RNA. As the non-catalytic subunit of the MTC, METTL14 functions as the RNA-binding scaffold that recognizes the RNA substrate. We found METTL14 could interacte with chromatin through recognition of H3K36me3. ChIP-seq with HA-tagged METTL14 using an HA antibody identified 300 peaks in HepG2 cells, among which 53% peaks were located in the gene body and only 3% peaks were located in the promoter. The binding sites of METTL14 on chromatin correlate with that of H3K36me3.To investigat whether this interaction is Pol II dependent, we treated cells with a Pol II inhibitor 5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside (DRB) for a short time. Interestingly, we found the interaction of METTL14 with chromatin in gene body region was not affected by DRB treatment .
2019-02-21 | GSE121943 | GEO
Project description:ChIP-seq of HA-METTL14 in HepG2 cells
| PRJNA499113 | 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:AGO-PAR-CLIP was employed to identify microRNA binding sites in BCBL-1, a Kaposi's sarcoma-associated herpesvirus (KSHV) infected B-cell line and DG75, a KSHV negative B-cell line as a control. By using our novel computational method (PARma) and differential analysis of PAR-CLIP data, highly accurate target sites of KSHV microRNAs can be defined. Examination of microRNA target sites in two different cell lines using replicate PAR-CLIP experiments
2013-06-27 | E-GEOD-43909 | biostudies-arrayexpress
Project description:AGO-PAR-CLIP was employed to identify microRNA binding sites in BCBL-1, a Kaposi's sarcoma-associated herpesvirus (KSHV) infected B-cell line and DG75, a KSHV negative B-cell line as a control. By using our novel computational method (PARma) and differential analysis of PAR-CLIP data, highly accurate target sites of KSHV microRNAs can be defined.
2013-06-27 | GSE43909 | GEO
Project description:We performed PAR-CLIP in three variants using ELAVL1 (HuR) as example.
2019-02-02 | GSE113628 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE21574: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: QKI data GSE21575: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: IGF2BP data GSE21577: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: miRNA inhibition data GSE21918: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: sequencing data Refer to individual Series
2010-04-29 | E-GEOD-21578 | biostudies-arrayexpress
Project description:We developed a method for measuring non-specific background in PAR-CLIP data demonstrating that covalently crosslinked background binding is common, reproducible and apparently universal. Furthermore, we show that quantitative determination of background is essential for identifying targets of weakly binding RNA-binding proteins and can substantially improve motif analysis. To define background binding events in PAR-CLIP data we performed the standard PAR-CLIP protocol (Hafner et al., Cell 2010.) on lysates expressing a commonly used non-RBP control, FLAG-GFP. After FLAG-tag immunopurification of UV 365nm irradiated lysates prepared from cells supplemented with 4-thiouridine (4SU), RNA was partially digested with RNase T1, radiolabeled and separated by SDS-PAGE. Reads were sequenced by Illumina HiSeq. PAR-CLIP was also performed for HuR. Included as well is a total from lysates treated like PAR-CLIP, but without immunoprecipitation (see sample description for more detail).
2013-11-07 | E-GEOD-50989 | biostudies-arrayexpress
Project description:In this study, we performed PAR-CLIP experiment in HEK293T to explore RNAs directly bound by YB-1.
2024-01-18 | GSE249896 | GEO