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Status |
Public on Jun 09, 2023 |
Title |
Extension of mRNA poly(A) tails and 3′UTRs during neuronal differentiation exhibits variable association with post-transcriptional dynamics |
Organism |
Homo sapiens |
Experiment type |
Expression profiling by high throughput sequencing Other Non-coding RNA profiling by high throughput sequencing
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Summary |
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 associated 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.
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Overall design |
Examination of changes in mRNA expression, translation, poly(A) tail length, alternative polyadenylation and miRNA expression during neuronal differentiation of SH-SY5Y cells.
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Contributor(s) |
Kiltschewskij D, Harrison P, Fitzsimmons C, Beilharz T, Cairns M |
Citation(s) |
37293985 |
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Submission date |
Jul 30, 2020 |
Last update date |
Sep 10, 2023 |
Contact name |
Dylan Kiltschewskij |
E-mail(s) |
c3146470@uon.edu.au
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Organization name |
The University of Newcastle
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Department |
School of Biomedical Sciences and Pharmacy
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Lab |
Molecular Neurobiology
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Street address |
Room MS616, Level 6, Medical Sciences Building, University Drive
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City |
Callaghan |
State/province |
NSW |
ZIP/Postal code |
2308 |
Country |
Australia |
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Platforms (2) |
GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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Samples (23)
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Relations |
BioProject |
PRJNA649751 |
SRA |
SRP274313 |
Supplementary file |
Size |
Download |
File type/resource |
GSE155432_apa.dexseq.txt.gz |
4.0 Mb |
(ftp)(http) |
TXT |
GSE155432_mirna.cpm.txt.gz |
14.8 Kb |
(ftp)(http) |
TXT |
GSE155432_mrna.cpm.txt.gz |
706.5 Kb |
(ftp)(http) |
TXT |
GSE155432_polya.length.tail.tools_revised.csv.gz |
2.0 Mb |
(ftp)(http) |
CSV |
GSE155432_ribo.cpm.txt.gz |
282.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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