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AKAP12 UV RNA immunoprecipitation followed by high throughput sequencing

ABSTRACT: AKAP12 UV RNA immunoprecipitation followed by high throughput sequencing

PROVIDER: PRJNA1040162 | ENA |

REPOSITORIES: ENA

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AKAP12 UV RNA immunoprecipitation followed by high throughput sequencing

Project description:Regulation of subcellular mRNA localisation is a fundamental biological mechanism, which adds a spatial dimension to the diverse layers of post-transcriptional control of gene expression. Insights into this phenomenon have been described in a multitude of cell types and across taxonomic kingdoms, highlighting its biological significance. The cellular compartment in which mRNAs are located may define distinct aspects of the encoded proteins, ranging from production rate and complex formation to localised activity. Ultimately, mRNA localisation supports compartmentalised mechanistic outputs that can respond to local stimuli, orient migration, or even shape cells. We used an unbiased method to profile the RNA-bound proteome in migrating endothelial cells and found that the plasma membrane (PM)-associated A-kinase anchor protein 12 (AKAP12) interacts with various mRNAs, including mRNAs encoding kinases with Actin remodelling activity. To identify transcripts bound by AKAP12, we carried out UV crosslinking experiments followed by RNA immunoprecipitation and high throughput sequencing. Our data offer novel insights in complex mechanisms of spatial control of gene expression.

2024-03-28 | GSE247682 | GEO

Conditional Hfq association with small non-coding RNAs in Pseudomonas aeruginosa revealed through comparative UV crosslinking immunoprecipitation followed by high-throughput sequencing

Project description:Conditional Hfq association with small non-coding RNAs in Pseudomonas aeruginosa revealed through comparative UV crosslinking immunoprecipitation followed by high-throughput sequencing

| PRJNA561327 | ENA

Conditional Hfq association with small non-coding RNAs in Pseudomonas aeruginosa revealed through comparative UV crosslinking immunoprecipitation followed by high-throughput sequencing [RNA-Seq]

Project description:Bacterial small non-coding RNAs (sRNAs) play post-transcriptional regulatory roles in cellular responses to changing environmental cues and in adaptation to harsh conditions. Generally, the RNA-binding protein Hfq helps sRNAs associate with target mRNAs to modulate their translation and to modify global RNA pools depending on physiological state. Here, a combination of in vivo UV crosslinking immunoprecipitation followed by high-throughput sequencing (CLIP-seq) and total RNA-seq showed that Hfq interacts with different regions of the P. aeruginosa transcriptome under planktonic versus biofilm conditions. In the present approach, P. aeruginosa Hfq preferentially interacted with repeats of the AAN triplet motif at mRNA 5’ UTRs and sRNAs, and U-rich sequences at rho-independent terminators. Further transcriptome analysis suggested that sRNAs association with Hfq is primarily a function of their expression levels, strongly supporting that the pool of Hfq-associated RNAs is equilibrated by RNA concentration-driven cycling on and off Hfq. Overall, our combinatorial CLIP-seq and total RNA-seq approach highlights conditional sRNA associations with Hfq as a novel aspect of post-transcriptional regulation in P. aeruginosa.

2019-11-15 | GSE136111 | GEO

Conditional Hfq association with small non-coding RNAs in Pseudomonas aeruginosa revealed through comparative UV crosslinking immunoprecipitation followed by high-throughput sequencing [RIP-Seq]

2019-11-15 | GSE136110 | GEO

Conditional Hfq association with small non-coding RNAs in Pseudomonas aeruginosa revealed through comparative UV crosslinking immunoprecipitation followed by high-throughput sequencing [RIP-Seq]

| PRJNA561330 | ENA

Conditional Hfq association with small non-coding RNAs in Pseudomonas aeruginosa revealed through comparative UV crosslinking immunoprecipitation followed by high-throughput sequencing [RNA-Seq]

| PRJNA561332 | ENA

Identification of Wig-1-associated RNAs by RNA-immunoprecipitation followed by high-throughput sequencing in HCT116 and Saos2 cancer cell lines

Project description:Identification of Wig-1-associated RNAs by RNA-immunoprecipitation followed by high-throughput sequencing in HCT116 and Saos2 cancer cell lines

2015-12-31 | E-MTAB-2840 | biostudies-arrayexpress

Total RNA sequencing of AKAP12 knockdown cells

Project description:We compared gene expression in AKAP12 knockdown and control cells in the SW480 background.

2020-09-16 | GSE147739 | GEO

AHT-ChIP-seq, a completely automated robotic protocol to perform chromatin immunoprecipitation in high-throughput

Project description:Transcription factor binding locations by ChIP followed by high throughput sequencing. To build and validate an automated Chromatin Immunoprecipitation and high throughput Illumina sequencing pipeline

2013-06-01 | E-MTAB-1579 | biostudies-arrayexpress

Identification of Wig-1-associated RNAs by RNA-immunoprecipitation followed by high-throughput sequencing in HCT116 and Saos2 cancer cell lines

Project description:Identification of Wig-1-associated RNAs by RNA-immunoprecipitation followed by high-throughput sequencing in HCT116 and Saos2 cancer cell lines

| PRJEB7004 | ENA

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