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| Status |
Public on Oct 04, 2012 |
| Title |
aSyn polyA-RNAseq in PD and unaffected cortical brain samples |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
Comparison of 3'UTR ends of alpha-synuclein in PD and unaffected brain cortex
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| Contributor(s) |
Abeliovich A, Rhinn H |
| Citation(s) |
23011138 |
| Submission date |
Sep 08, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Herve RHINN |
| E-mail(s) |
hr2239@columbia.edu
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| Phone |
2123051150
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| Fax |
2123051150
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| Organization name |
Columbia University
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| Street address |
650 W. 168th. St.
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (33)
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| Relations |
| BioProject |
PRJNA174763 |
| SRA |
SRP015668 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE40710_aSyn_3UTR_Processed.txt.gz |
659 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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