5’ half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos [tRNA-seq]

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. tRNAs from wildtype zebrafish eggs and early embryos were detected by high throughput sequencing. Total RNAs from mature egg, 1cell, 256c sphere, shield and 24hpf stage embryos were extracted by Trizol reagent. Then, 60-120 nt length RNA was enriched by separation and elution from denature gel. RNA was treated with a combination of ALKB protein to remove some modifications before library preparation.