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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 10, 2019 |
| Title |
Choice of alternative polyadenylation sites, mediated by the RNA-binding protein Elavl3, plays a role in differentiation of inhibitory neuronal progenitors |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Alternative polyadenylation is a widespread mechanism involving about half of the expressed genes, resulting in varying lengths of the 3' UTR and changes of the post-transcriptional processing, localization, miRNA targeting and stability of mRNAs. During neuronal differentiation a variety of mRNAs change the length of their 3' UTR, promoting the longer version of the transcripts. Little is known about polyA+ site usage during differentiation of mammalian neural progenitors. Here we exploit a model of adherent neural stem (ANS) cells, which homogeneously and efficiently differentiate into GABAergic neurons. RNAseq data shows a global trend towards lengthening of the 3’ UTRs during differentiation. Enriched expression of the long 3’ UTR variants of Pes1 and Gng2 was detected in areas of cortical and subcortical neuronal differentiation, respectively, in the mouse brain by two-probes FISH analyses. In Drosophila the choice of polyA+ site has been shown to be regulated by the RNA-binding protein Elav, which inhibits polyadenylation at proximal sites while interacting with paused Pol-II promoters. Among the coding genes upregulated during differentiation of ANS cells we found Elavl3, a neural-specific RNA-binding protein homologous to Drosophila Elav. The silencing of Elavl3 in ANS cells resulted in impaired elongation of the 3’UTR length and delayed neuronal differentiation. These results indicate that choice of the polyA+ site and lengthening of 3’ UTRs is a possible additional mechanism of posttranscriptional RNA modification involved in neuronal differentiation.
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| Overall design |
We studied the transcriptome in four time points during in vitro neuronal differentiation of murine neural stem cells. We had different numbers of biological replicates for each time point, specifically: T0-3 replicates, T1-3 replicates, T2-4 replicates, T3 2 replicates.
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| Contributor(s) |
Grassi E, Santoro R, Umbach A, Grosso A, Oliviero S, Neri F, Conti L, Provero P, Di Cunto F, Merlo GR |
| Citation(s) |
30687010 |
| Submission date |
Aug 27, 2018 |
| Last update date |
Jun 03, 2021 |
| Contact name |
Elena Grassi |
| E-mail(s) |
grassi.e@gmail.com
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| Organization name |
Molecular Biotechnology Center
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| Department |
Dept. of Molecular Biotechnology and Health Sciences
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| Street address |
Via Nizza 52
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| City |
Torino |
| ZIP/Postal code |
10126 |
| Country |
Italy |
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| Platforms (1) |
| GPL16173 |
Illumina HiScanSQ (Mus musculus) |
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| Samples (12)
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| GSM3357452 |
ANS cells in complete growth medium, full proliferation, sample 1 |
| GSM3357453 |
ANS cells 2 days after change in medium D1, much reduced proliferation, sample 1 |
| GSM3357454 |
ANS cells 2 days after change in medium B, absent proliferation begin differentiation, sample 1 |
| GSM3357455 |
ANS cells 10 days after change in medium B, overt differentiation, GAD+, sample 1 |
| GSM3357456 |
ANS cells in complete growth medium, full proliferation, sample 2 |
| GSM3357457 |
ANS cells 2 days after change in medium D1, much reduced proliferation, sample 2 |
| GSM3357458 |
ANS cells 2 days after change in medium B, absent proliferation begin differentiation, sample 2 |
| GSM3357459 |
ANS cells in complete growth medium, full proliferation, sample 3 |
| GSM3357460 |
ANS cells 2 days after change in medium D1, much reduced proliferation, sample 3 |
| GSM3357461 |
ANS cells 2 days after change in medium B, absent proliferation begin differentiation, sample 3 |
| GSM3357462 |
ANS cells 10 days after change in medium B, overt differentiation, GAD+, sample 4 |
| GSM3357463 |
ANS cells 2 days after change in medium B, absent proliferation begin differentiation, sample 4 |
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| Relations |
| BioProject |
PRJNA488055 |
| SRA |
SRP158907 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE119073_RAW.tar |
1.1 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE119073_gene_expression_ok_wt_samples.tab.gz |
1.3 Mb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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