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| Status |
Public on Dec 21, 2023 |
| Title |
Hidden features of NAD-RNA epitranscriptome in Drosophila life cycle |
| Organisms |
Drosophila melanogaster; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
Nicotinamide adenine dinucleotide (NAD), a nucleotide-containing metabolite, can be incorporated into the RNA 5’-terminus to result in NAD-capped RNA (NAD-RNA). Since NAD has been heightened as one of the most essential metabolites in cells, its attachment to RNA might indicate a yet-to-be discovered mechanism at the epitranscriptomic level. Here, we design a highly-sensitive method, DO-seq, to capture NAD-RNAs. Using Drosophila, we identify thousands of previously unexplored NAD-RNAs and their dynamics in the fly life cycle, from embryo to adult. We show the evidence that chromosomal clustering might be the structural basis by which co-expression can couple with NAD capping on physically and functionally-linked genes. Furthermore, we note that NAD capping of cuticle genes seems to inversely correlate with gene expression. Combined, we propose NAD-RNA epitranscriptome as a hidden layer of regulation that profoundly impacts biological processes. DO-seq empowers the identification of NAD-capped RNAs, facilitating functional investigation into this modification.
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| Overall design |
DO-seq of total RNAs (2-month-old mouse livers) with spike-in RNA that had different ratios of NAD-RNA (0, 1, 5%); DO-seq with or without yDcpS treatment of mouse livers (18-month-old); NAD-RNA profiles and transcriptome profiles of Drosophila life cycle (embryo (14h-16h AEL), larva (4d AEL), pupa (7d AEL) and adult fly (3d)) were generated by deep sequencing, using Illumina Novaseq.To profile NAD-RNAs from Drosophila life cycle, total RNAs from those samples were mixed with spike-in RNA from mouse livers, and two synthetic spike-in, of which one with 5% NAD-capped forms and another with 100% m7G-capped forms. The mixtures were then subjected to DO-seq.
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| Web link |
https://doi.org/10.1016/j.isci.2023.108618
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| Contributor(s) |
Wang X, Ge S, Liu N |
| Citation(s) |
38197055 |
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| Submission date |
Mar 29, 2023 |
| Last update date |
Jan 18, 2024 |
| Contact name |
XUETING WANG |
| E-mail(s) |
wangxueting@sioc.ac.cn
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| Organization name |
IRCBC
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| Street address |
100 Hai Ke ROAD, shanghai, china
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| City |
SHANG HAI |
| State/province |
Not US or Canada |
| ZIP/Postal code |
200012 |
| Country |
China |
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| Platforms (2) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL25244 |
Illumina NovaSeq 6000 (Drosophila melanogaster) |
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| Samples (68)
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| Relations |
| BioProject |
PRJNA950069 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE228505_Counts_DO-seq_Spikein_RNA.csv.gz |
897.6 Kb |
(ftp)(http) |
CSV |
| GSE228505_Counts_DO-seq_drosophila_life_cycle.csv.gz |
799.3 Kb |
(ftp)(http) |
CSV |
| GSE228505_Counts_DO-seq_with_without_yDcpS.csv.gz |
704.6 Kb |
(ftp)(http) |
CSV |
| GSE228505_Counts_RNAseq_drosophila_life_cycle.csv.gz |
294.3 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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