Computational protocol: Antisense transcripts of the expanded C9ORF72 hexanucleotide repeat form nuclear RNA foci and undergo repeat-associated non-ATG translation in c9FTD/ALS

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Protocol publication

[…] Folding of the RNA sequence comprising CCCCGG repeats of 10 (60 bases), 50 (300 bases), and 200 (1,200 bases) was carried out as previously described to determine secondary structure motifs []. The secondary structure prediction and modeling was built by examining the output from several RNA prediction packages: MFOLD, Sfold, Vienna RNA Package (RNAfold) [, , , , , , , ]. MFOLD utilizes a minimum free energy RNA structure prediction algorithm, Sfold utilizes statistical sampling of all possible structures, while Vienna Package has several options, including an minimum free energy calculation. Equivalent structures were given from each package for the ten repeat cases. MFOLD was used as the primary secondary structure prediction package for consistency across all models. Free energies were calculated for each secondary structure prediction at the level of decomposition (base pairing) and global energy []. MFOLD verifies each secondary structure prediction generated for valid structure []. MFOLD parameters include the following: (1) linear RNA sequence; (2) zero constraints, forces, or prohibitions on all bases allowing maximal sampling; (3) folding temperature of 37 °C; (4) physiological ionic conditions; (5) structure draw mode: untangle with loop fix; and (6) the remainder of MFOLD settings were set to default. […]

Pipeline specifications

Software tools Mfold, Sfold, RNAfold
Application RNA structure analysis
Diseases Amyotrophic Lateral Sclerosis, Neurodegenerative Diseases, Neurotoxicity Syndromes, Genetic Diseases, Inborn, Frontotemporal Dementia, Drug-Related Side Effects and Adverse Reactions