Computational protocol: Transcriptional and Post-Transcriptional Regulation of SPAST, the Gene Most Frequently Mutated in Hereditary Spastic Paraplegia

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Protocol publication

[…] To identify potential TF binding motifs 5′ of SPAST exon 1, we used human SPAST genomic sequence and screened for evolutionary conservation among sequenced mammalian genomes . BLAST analyses for sequence similarity (http://blast.ncbi.nlm.nih.gov/Blast.cgi) utilized standard parameters for searches of the non-redundant (NR), high throughput genome sequence (HTGS), and whole genome shotgun (WGS) databases. All extended 5′ sequences spanning the SPAST promoter from 21 mammalian genomes are provided in . For analysis of the Alu insertion in the SPAST 3′-UTR, we also used BLAST analysis of primate genomes in the Trace Archives WGS database. When necessary, due to low overall sequence similarity, mammalian and non-mammalian genome sequences for the SPAST promoter and 3′-UTR were obtained from the Ensembl genome browser (http://www.ensembl.org/index.html). To identify potential miRNA binding sites in the 3′-UTR of the SPAST mRNA, miRNA predictions used TargetScan 5.2 (http://www.targetscan.org/), which is one of two programs shown to most accurately predict in vivo miRNA targeting sequences , while miRNA sequences are from miRBase (http://www.mirbase.org/). For promoter and 3′-UTR multi-sequence alignments, we used ClustalW 2.1 (http://www.ebi.ac.uk/Tools/clustalw2/index.html). To generate a consensus primate phylogenetic tree for the 10 species of interest, we used version 3 of the 10kTrees website (http://10ktrees.fas.harvard.edu/) . […]

Pipeline specifications

Software tools TargetScan, Clustal W
Databases miRBase
Applications Phylogenetics, WGS analysis, Genome data visualization
Diseases Spastic Paraplegia, Hereditary, Neurodegenerative Diseases