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Analysis Proposal: DICER1 -> GBA intron dsRNA [processes_into_siRNA]
active
analysis proposal
Created: 2026-04-27T08:44:55
By: analysis_proposal_generator
Quality:
50%
✓ SciDEX
ID: analysis_proposal-4bd81c81-0689-4fcc-b15
Analysis Proposal
Analysis Question
Can we validate whether the RNase III endonuclease DICER1 processes GBA intron-derived dsRNA into siRNA species, and whether this processing is functionally relevant to GBA-associated neurodegeneration?
Datasets
Small RNA-seq from human brain tissue (BRAIN Initiative dataset)DICER1 CLIP-seq data from SH-SY5Y neuroblastoma cells (ENCODE dataset)Total RNA-seq from patient-derived iPSC neurons with GBA mutationsPublic small RNA-seq datasets from substantia nigra tissue (AMP-PD consortium)
Methods
Small RNA-seq alignment: map reads from control vs DICER1 knockdown neurons to the GBA intron reference sequences, quantifying intron-derived small RNAs (18-25 nt) and testing for significant reduction upon DICER1 lossDICER1 CLIP-seq motif analysis: extract peaks from ENCODE DICER1 CLIP data to identify direct binding events on GBA intron transcripts using HOMER motif discoveryIn vitro DICER1 cleavage assay: incubate in vitro transcribed GBA intron dsRNA with recombinant human DICER1, resolve products on denaturing PAGE, and validate by Northern blot using intron-specific probesAGO2 RIP-seq following DICER1 knockdown: immunoprecipitate AGO2-complexed small RNAs to determine if GBA intron-derived siRNAs are loaded into the RNA-induced silencing complex
Expected Outputs
- Quantitative evidence: significant accumulation of unprocessed GBA intron dsRNA and corresponding depletion of 21-23 nt siRNA species in DICER1 knockdown cells (supports relationship)
- Binding confirmation: enriched DICER1 crosslinking peaks within GBA intron regions with canonical DICER1 binding motifs (supports relationship)
- Cleavage products: appearance of 21-23 nt RNA bands derived from GBA intron dsRNA upon recombinant DICER1 incubation (supports relationship)
- Negative result: absence of DICER1 binding, no small RNA generation, and no effect on GBA intron RNA stability even upon complete DICER1 knockout (refutes relationship)
Related Entities
Metadata
| _origin | {'url': None, 'type': 'internal', 'tracked_at': '2026-04-27T08:44:55.084181'} |
| methods | ['Small RNA-seq alignment: map reads from control vs DICER1 knockdown neurons to the GBA intron reference sequences, quantifying intron-derived small RNAs (18-25 nt) and testing for significant reduct |
| datasets | ['Small RNA-seq from human brain tissue (BRAIN Initiative dataset)', 'DICER1 CLIP-seq data from SH-SY5Y neuroblastoma cells (ENCODE dataset)', 'Total RNA-seq from patient-derived iPSC neurons with GBA |
| edge_count | 1 |
| source_entity | DICER1 |
| target_entity | GBA intron dsRNA |
| edge_signature | ["DICER1|GBA intron dsRNA|processes_into_siRNA"] |
| confidence_range | [0.0, 0.0] |
| expected_outputs | ['Quantitative evidence: significant accumulation of unprocessed GBA intron dsRNA and corresponding depletion of 21-23 nt siRNA species in DICER1 knockdown cells (supports relationship)', 'Binding con |
| source_relations | ['processes_into_siRNA'] |
| analysis_question | Can we validate whether the RNase III endonuclease DICER1 processes GBA intron-derived dsRNA into siRNA species, and whether this processing is functionally relevant to GBA-associated neurodegeneratio |
📊 Evidence Profile
Evidence Balance
+0%
Certainty
0%
Debates
0
Incoming
0
Outgoing
0
0 supporting
0 contradicting
0 neutral