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| Status |
Public on Feb 19, 2024 |
| Title |
NAP-seq Reveals Novel Classes of Structured Noncoding RNAs with Regulatory Functions |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose:Up to 80% of the human genome produces “dark matter” RNAs, most of which are noncapped RNAs (napRNAs). However, determining the functional impacts and metabolism of napRNAs requires the identification of their full-length sequences.
Method:Here, by developing a novel method, NAP-seq, to globally profile the full-length sequences of napRNAs at single-nucleotide resolution, we revealed several novel classes of exceptionally structured noncoding RNAs (ncRNAs).
Results:We discovered stably expressed linear intron RNAs (sliRNAs), a novel class of snoRNA-intron RNAs (snotrons), a new class of RNAs embedded in miRNA spacers (misRNAs) and thousands of new structured ncRNAs in humans and mice. These new napRNAs undergo dynamic changes in response to various stimuli and differentiation stages. Importantly, we showed that the novel napRNA DINAP interacts with dyskerin pseudouridine synthase 1 (DKC1) to promote cell proliferation by maintaining DKC1 protein stability.
Conclusion:Our approach establishes a paradigm for discovering novel classes of ncRNAs with regulatory potency.
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| Overall design |
Next generation sequencing was applicated in 6 human cell types, including U87, HEK293T, HepG2 (including 4 conditions: non-treated, poly(I:C)-treated, Adriamycin-treated, CoCl2-treated), and in 4 differentiation stages of mouse skeletal muscle cell C2C12, including 0 hour, 72 hours, 96 hours, 144 hours after differentiation. Third generation sequencing was applicated in non-treated HepG2. Each sample has three biological replicates (except for CoCl2-treated HepG2, which has two).
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| Contributor(s) |
Yang J, Liu S |
| Citation(s) |
38499544 |
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| Submission date |
Dec 27, 2021 |
| Last update date |
Apr 02, 2024 |
| Contact name |
Jian-Hua Yang |
| E-mail(s) |
[email protected]
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| Phone |
86-20-84112517
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| Organization name |
Sun Yat-sen University
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| Department |
School of Life Sciences
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| Street address |
No. 135, Xingang Xi Road
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| City |
Guangzhou |
| ZIP/Postal code |
510275 |
| Country |
China |
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| Platforms (3) |
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| Samples (32)
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| GSM5753584 |
HEK293T, biological replicate1 |
| GSM5753585 |
HEK293T, biological replicate2 |
| GSM5753586 |
HEK293T, biological replicate3 |
| GSM5753587 |
HepG2, non-treated, biological replicate1 |
| GSM5753588 |
HepG2, non-treated, biological replicate2 |
| GSM5753589 |
HepG2, non-treated, biological replicate3 |
| GSM5753590 |
HepG2, Adriamycin (ADR)-treated, biological replicate1 |
| GSM5753591 |
HepG2, Adriamycin (ADR)-treated, biological replicate2 |
| GSM5753592 |
HepG2, Adriamycin (ADR)-treated, biological replicate3 |
| GSM5753593 |
HepG2, CoCl2-treated, biological replicate1 |
| GSM5753594 |
HepG2, CoCl2-treated, biological replicate2 |
| GSM5753595 |
HepG2, poly(I:C)-treated, biological replicate1 |
| GSM5753596 |
HepG2, poly(I:C)-treated, biological replicate2 |
| GSM5753597 |
HepG2, poly(I:C)-treated, biological replicate3 |
| GSM5753598 |
C2C12, 0 hours after differentiation, biological replicate1 |
| GSM5753599 |
C2C12, 0 hours after differentiation, biological replicate2 |
| GSM5753600 |
C2C12, 0 hours after differentiation, biological replicate3 |
| GSM5753601 |
C2C12, 72 hours after differentiation, biological replicate1 |
| GSM5753602 |
C2C12, 72 hours after differentiation, biological replicate2 |
| GSM5753603 |
C2C12, 72 hours after differentiation, biological replicate3 |
| GSM5753604 |
C2C12, 96 hours after differentiation, biological replicate1 |
| GSM5753605 |
C2C12, 96 hours after differentiation, biological replicate2 |
| GSM5753606 |
C2C12, 96 hours after differentiation, biological replicate3 |
| GSM5753607 |
C2C12, 144 hours after differentiation, biological replicate1 |
| GSM5753608 |
C2C12, 144 hours after differentiation, biological replicate2 |
| GSM5753609 |
C2C12, 144 hours after differentiation, biological replicate3 |
| GSM5753610 |
HepG2, non-treated, nanopore sequencing, biological replicate1 |
| GSM5753611 |
HepG2, non-treated, nanopore sequencing, biological replicate2 |
| GSM5753612 |
HepG2, non-treated, nanopore sequencing, biological replicate3 |
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| Relations |
| BioProject |
PRJNA792503 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE192632_RAW.tar |
65.4 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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