GSE50178
GSE GEO Potentially relatedIdentification of FUS RNA targets in HeLa cells
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Summary
We identified a landscape of FUS-binding RNA targets in HeLa cells. The majority of the FUS binding sites are in introns of pre-mRNAs and less are in exons and untranslated regions. Significant FUS binding in introns flanking cassette exons, long intron (>100kb) containing transcripts and noncoding RNAs were detected in our study. We specifically determined the function of FUS in regulating the alternative splicing of cassette exons. The top FUS-associated cassette exon is exon 7 of the pre-mRNA of FUS itself. We demonstrated that FUS is a repressor of its own exon 7 splicing. FUS autoregulates its own protein levels by exon 7 alternative splicing and nonsense mediated decay. Moreover, Amyotrophic Lateral Sclerosis (ALS) linked FUS mutants are deficient in FUS autoregulation.
Overall Design
CLIP-seq of FUS in HeLa cells
Analysis (6 steps)
View Data Processing- Library strategy: CLIP-Seq
- Illumina default workflow (Casava1.4 software) was used for sequence basecalling.
- CLIP-seq reads were trimmed to remove apator sequences.
- Reads with identical sequence were collapsed into a signle read.
- Reads were aligned to the GRCh37 genome assembly using BlastN, with default parameters.
- Peaks were determined using CisGenome V2 with the following parameters: Window Size W=150 bp; Cutoff C>=12 reads; Step Size S=25 bp; Max Gap=50 bp; Min Peak Length=100 bp.
Supplementary Files (1)
GEO Samples (2)
Dataset Citations (1)
SRA Experiments (2) and Runs (2)
Total: 1527 MBSample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR956944 | 20943964 | 1591741264 | 795.3 | umzhou_HeLa_FUS_CLIP_RAW.gz, SRR956944, SRR956944.sralite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR956945 | 10409974 | 791158024 | 732.05 | umzhou_HeLa_mIgG_CLIP_RAW.gz, SRR956945, SRR956945.sralite | SRA |
Potentially Related Publications (1)
This accession was text-mined from the PMC full text of these publications. It may be referenced for comparison or reused from another study rather than generated for them.