Kiltschewskij et al. 2023 (PRJNA649751)
General Details
| Title | Extension of mRNA poly(A) tails and 3′UTRs during neuronal differentiation exhibits variable association with post-transcriptional dynamics |
|---|---|
| Organism | |
| Number of Samples | 5 |
| Release Date | 2020/07/30 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
|---|---|
Repository Details
| SRA | SRP274313 |
|---|---|
| ENA | SRP274313 |
| GEO | GSE155432 |
| BioProject | PRJNA649751 |
Publication
| Title | |
|---|---|
| Authors | Kiltschewskij DJ, Harrison PF, Fitzsimmons C, Beilharz TH, Cairns MJ |
| Journal | Nucleic acids research |
| Publication Date | 2023 Aug 25 |
| Abstract | Differentiation of neural progenitor cells into mature neuronal phenotypes relies on extensive temporospatial coordination of mRNA expression to support the development of functional brain circuitry. Cleavage and polyadenylation of mRNA has tremendous regulatory capacity through the alteration of mRNA stability and modulation of microRNA (miRNA) function, however the extent of utilization in neuronal development is currently unclear. Here, we employed poly(A) tail sequencing, mRNA sequencing, ribosome profiling and small RNA sequencing to explore the functional relationship between mRNA abundance, translation, poly(A) tail length, alternative polyadenylation (APA) and miRNA expression in an in vitro model of neuronal differentiation. Differential analysis revealed a strong bias towards poly(A) tail and 3'UTR lengthening during differentiation, both of which were positively correlated with changes in mRNA abundance, but not translation. Globally, changes in miRNA expression were predominantly associated with mRNA abundance and translation, however several miRNA-mRNA pairings with potential to regulate poly(A) tail length were identified. Furthermore, 3'UTR lengthening was observed to significantly increase the inclusion of non-conserved miRNA binding sites, potentially enhancing the regulatory capacity of these molecules in mature neuronal cells. Together, our findings suggest poly(A) tail length and APA function as part of a rich post-transcriptional regulatory matrix during neuronal differentiation. © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. |
| PMC | PMC10450200 |
| PMID | 37293985 |
| DOI |
| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SRR17096848 | PRJNA649751 | Homo sapiens | NA_Neuronally differentiated SH-SY5Y | Ribo-Seq | 0.0 |  |
 |
 |
 |
|
|
||
| SRR17096849 | PRJNA649751 | Homo sapiens | NA_Neuronally differentiated SH-SY5Y | Ribo-Seq | 0.0 | |
|
|
|
|
|
||
| SRR17096850 | PRJNA649751 | Homo sapiens | NA_Neuronally differentiated SH-SY5Y | Ribo-Seq | 0.0 | |
|
|
|
|
|
||
| SRR17096851 | PRJNA649751 | Homo sapiens | NA_Neuronally differentiated SH-SY5Y | Ribo-Seq | 0.0 | |
|
|
|
|
|
||
| SRR17096852 | PRJNA649751 | Homo sapiens | NA_Neuronally differentiated SH-SY5Y | Ribo-Seq | 0.0 | |
|
|
|
|
|
||
| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) |
ⓘ For more Information on the columns shown here see: About