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| Status |
Public on Aug 25, 2021 |
| Title |
5’ half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos [small RNA-Seq, ssDRIP-seq] |
| Organism |
Danio rerio |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
Other
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| Summary |
5’tRFls are small tRNA fragments derived from 5’ half of mature tRNAs. However, it is unknown whether 5’tRFls could feed back to regulate tRNA biogenesis. Here we show that 5’tRFlGly/GCC and 5’tRFlGlu/CTC function to promote transcription of corresponding tRNA genes and are essential for vertebrate early embryogenesis. During zebrafish embryogenesis, dynamics of 5’tRFlGly/GCC and 5’tRFlGlu/CTC levels correlates with that of tRNAGly/GCC and tRNAGlu/CTC levels. Morpholino-mediated knockdown of 5’tRFlGly/GCC or 5’tRFlGlu/CTC down-regulates tRNAGly/GCC or tRNAGlu/CTC levels respectively, and causes embryonic lethality that is efficiently rescued by co-injection of properly refolded corresponding tRNA. In zebrafish embryos, tRNA:DNA and 5’tRFl:DNA hybrids commonly exist on the template strand of tRNA genes. Mechanistically, unstable 5’tRFl:DNA hybrid may prevent the formation of transcriptionally inhibitory stable tRNA:DNA hybrids on the same tRNA loci so as to facilitate tRNA genes transcription. The uncovered mechanism may be implicated in other physiological and pathological processes.
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| Overall design |
For small RNA sequencing, total RNA were extracted respectively from wildtype zebrafish embryos (Tübingen Strain) of 6 chosen stages, and then subjected to small RNA library preparation individually.
To investigate the distribution and stability of R-loop on genome, we performed ssDRIP-seq with S9.6 antibody, which specifically recognize RNA:DNA hybrid. Two replicates from wildtype embryos of 256c, sphere and shield stage were collected to perform ssDRIPseq. RNaseH pre-treated genome DNA was used as negative control, which was also performed the standard ssDRIP-seq procedure. Genomic DNA extracted from these samples were fragmentated by restriction enzymes, and then immunoprecipitated by S9.6 antibody.The ssDNA strands in RNA:DNA hybrids were purified and subjected to library preparation.
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| Contributor(s) |
Chen L, Xu W, Liu K, Jiang Z, Han Y, Jin H, Zhang L, Shen W, Jia S, Sun Q, Meng A |
| Citation(s) |
34797706 |
| |
| Submission date |
Mar 20, 2020 |
| Last update date |
Dec 06, 2021 |
| Contact name |
Anming Meng |
| E-mail(s) |
mengam@mail.tsinghua.edu.cn
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| Organization name |
Tsinghua University
|
| Department |
School of Life Science
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| Lab |
Anming Meng Lab
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| Street address |
Tsinghuayuan Street
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platforms (2) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
| GPL24995 |
Illumina NovaSeq 6000 (Danio rerio) |
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| Samples (13)
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| This SubSeries is part of SuperSeries: |
| GSE181684 |
5’ half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos |
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| Relations |
| BioProject |
PRJNA613601 |
| SRA |
SRP253438 |
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