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E-GEOD-40710 - aSyn polyA-RNAseq in PD and unaffected cortical brain samples

Status
Released on 4 October 2012, last updated on 17 July 2013
Organism
Homo sapiens
Samples (33)
Protocols (4)
Description
We sought to more precisely characterize the different alpha-synuclein (aSyn) 3’UTR mRNA species in normal and PD human brain. High-throughput, whole-transcriptome sequencing of the 3’UTR ends of polyadenylated mRNA transcripts (termed pA-RNAseq; see Methods) was performed on a cohort of 17 unaffected and 17 PD cerebral cortical tissue samples. This revealed 5 aSyn 3’UTR isoforms, with lengths of 290, 480, 560, 1070 and 2520 nt. Of these, the 560 nt and 2520 nt forms were predominant. The existence and relative preponderance of these species was further confirmed by Northern Blot. We next hypothesized, that aSyn 3’UTR selection might be altered in PD. Comparison of pA-RNAseq profiles from PD and unaffected cerebral cortex samples revealed an increase in the preponderance of the long 3’UTR species (>560 nt) relative to shorter species (<560 nt). Such a relative increase in aSynL was confirmed by Quantitative real-time RT-PCR (rt-qPCR) and appeared specific for PD, as the increase was also observed by comparison to RNA from amyotrophic lateral sclerosis patient samples. We note that the modified aSyn 3’UTR selection associated with PD patient tissue was detected in cerebral cortex tissue, which typically harbors pathological evidence of the disease process without frank cell loss; thus, this phenotype is unlikely to be a secondary consequence of neurodegeneration. Comparison of 3'UTR ends of alpha-synuclein in PD and unaffected brain cortex
Experiment type
RNA-seq of non coding RNA 
Contacts
Herve RHINN <hr2239@columbia.edu>, Asa Abeliovich, Herve Rhinn
Citation
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-40710.idf.txt
Sample and data relationshipE-GEOD-40710.sdrf.txt
Additional data (1)E-GEOD-40710.additional.1.zip
Links