GSE199650
GSE GEOThe 2',3' cyclic phosphatase Angel1 facilitates mRNA degradation during human ribosome-associated quality control
Relations
Summary
The Ribosome-associated Quality Control (RQC) pathway serves to resolve ribosomes stalled during the translation process and degrade the associated mRNA and nascent polypeptide. Here we identify the 2',3' cyclic phosphatase Angel1 as a rate-limiting factor in this process in human cells. Angel1 associates with proteins of the RQC pathway and with mRNA coding regions, consistent with a factor that monitors the translation process. Depletion of Angel1 causes stabilization of reporter mRNAs that are targeted for RQC by the absence of stop codons, but not an mRNA targeted for nonsense-mediated decay. Angel1 catalytic activity is critical for its function in RQC, as a catalytic inactivating mutation causes loss of RQC function. We also identify N4BP2 as the human RQC endonuclease. Given the biochemical activity of Angel1 as a 2',3' cyclic phosphatase, our observations suggest that a rate-limiting step in RQC-mediated mRNA decay is the resolution of a cyclic phosphate, possibly one generated upon N4BP2 cleavage.
Overall Design
Identification of RNA sequences bound by Angel1 using enhanced cross-linking and immunoprecipitation (eCLIP) in HEK293 expressing FLAG-Angel1.
Analysis (11 steps)
View Data Processing- Raw reads were processed using the eCLIP pipeline.
- Reads were then trimmed with cutadapt
- Reads were then trimmed again with cutadapt to remove double-ligation events.
- Trimmed and filtered reads were then mapped with STAR against a repeat element database
- Unmapped reads filtered of repeat elements were then mapped with STAR against a human genome (GRCh37)
- Aligned reads were sorted with samtools
- Sorted reads were collapsed with umi_tools.
- BAM files were used to identify peak clusters with Clipper.Â
Supplementary Files (1)
GEO Samples (6)
SRA Experiments (6) and Runs (6)
Total: 5308 MBSample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR18516357 | 5918376 | 591837600 | 241.19 | Flag_IP.fastq.gz, SRR18516357, SRR18516357.lite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR18516356 | 17012957 | 1701295700 | 657.49 | Flag_input.fastq.gz, SRR18516356, SRR18516356.lite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR18516355 | 37724736 | 3772473600 | 1470.81 | IP1_IP.fastq.gz, SRR18516355, SRR18516355.lite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR18516354 | 27020401 | 2702040100 | 1050.37 | IP1_input.fastq.gz, SRR18516354, SRR18516354.lite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR18516353 | 27098792 | 2709879200 | 1047.21 | IP2_IP.fastq.gz, SRR18516353, SRR18516353.lite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR18516352 | 21691369 | 2169136900 | 840.9 | IP2_input.fastq.gz, SRR18516352, SRR18516352.lite | SRA |
Linked Publications (1)
Data Files (6)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | Flag_input.fastq.gz | RIP-Seq | 657.5 MB | link | |||
| — | Flag_IP.fastq.gz | RIP-Seq | 241.2 MB | link | |||
| — | IP1_input.fastq.gz | RIP-Seq | 1.0 GB | link | |||
| — | IP1_IP.fastq.gz | RIP-Seq | 1.4 GB | link | |||
| — | IP2_input.fastq.gz | RIP-Seq | 840.9 MB | link | |||
| — | IP2_IP.fastq.gz | RIP-Seq | 1.0 GB | link |