 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 16, 2021 |
| Title |
Cytoplasmic long non-coding RNAs are differentially regulated and translated during human neuronal differentiation |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| Summary |
The expression of long non-coding RNAs is highly enriched in the human nervous system. However, the function of neuronal lncRNAs in the cytoplasm and their potential translation remains poorly understood. Here we performed Poly-Ribo-Seq to understand the interaction of lncRNAs with the translation machinery and the functional consequences during neuronal differentiation of human SH-SH5Y cells. We discovered 237 cytoplasmic lncRNAs upregulated during early neuronal differentiation, 58-70% of which are associated with polysome translation complexes. Amongst these polysome associated lncRNAs, we find 45 small ORFs to be actively translated, 17 specifically upon differentiation. 15/45 of the translated lncRNA-smORFs exhibit sequence conservation within Hominidea suggesting they are under strong selective constraint in this clade. Profiling of publicly available datasets revealed that 8/45 of the translated lncRNAs are dynamically expressed during human brain development and 22/45 are associated with cancers of the central nervous system. One translated lncRNA we discovered is LINC01116, which is induced upon differentiation and contains an 87 codon smORF exhibiting increased ribosome profiling signal upon differentiation. The resulting LINC01116 peptide localises to neurites. Knockdown of LINC01116 results in a significant reduction of neurite length in differentiated cells indicating it contributes to neuronal differentiation. Our findings indicate cytoplasmic lncRNAs interact with translation complexes, are a non-canonical source of novel peptides, and contribute to neuronal function and disease. Specifically, we demonstrate a novel functional role for LINC01116 during human neuronal differentiation.
|
| |
|
| Overall design |
Poly-Ribo-Seq on human neuroblastoma cells (SH-SY5Y) in 2 conditions: undifferentiated (Control) and differentiated with RA for 3 days.
|
| |
|
| Contributor(s) |
Douka K, Birds I, Wang D, Kosteletos A, Clayton S, Byford A, Vasconcelos ER, O'Connell MJ, Deuchars J, Whitehouse A, Aspden JL |
| Citation(s) |
34193551 |
| |
| Submission date |
Feb 04, 2021 |
| Last update date |
Jul 17, 2021 |
| Contact name |
Julie Aspden |
| Organization name |
University of Leeds
|
| Department |
FBS
|
| Street address |
Woodhouse
|
| City |
Leeds |
| ZIP/Postal code |
LS2 9JT |
| Country |
United Kingdom |
| |
|
| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (18)
|
|
| Relations |
| BioProject |
PRJNA699598 |
| SRA |
SRP304780 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE166214_Control_FPP3_translated_ORFs_filtered_sorted.bed.gz |
1.5 Mb |
(ftp)(http) |
BED |
| GSE166214_Control_FPP4_translated_ORFs_filtered_sorted.bed.gz |
1.7 Mb |
(ftp)(http) |
BED |
| GSE166214_Control_FPP5_translated_ORFs_filtered_sorted.bed.gz |
1.7 Mb |
(ftp)(http) |
BED |
| GSE166214_RA_FPP3_translated_ORFs_filtered_sorted.bed.gz |
812.6 Kb |
(ftp)(http) |
BED |
| GSE166214_RA_FPP4_translated_ORFs_filtered_sorted.bed.gz |
1.5 Mb |
(ftp)(http) |
BED |
| GSE166214_RA_FPP5_translated_ORFs_filtered_sorted.bed.gz |
1.8 Mb |
(ftp)(http) |
BED |
| GSE166214_RNAseq_DESeq2.xlsx |
9.3 Mb |
(ftp)(http) |
XLSX |
| GSE166214_translated_smORF_summary.xlsx |
21.4 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...