# tRNA and tsRNA: From Heterogeneity to Multifaceted Regulators
## 4 Revisit the Regulatory Mechanisms of tRNA and tsRNA
### tsRNA Regulation: Structure Dictates Function
#### 4.2.1 Sequence Complementarity  
As they are generated from tRNAs, tsRNAs share a similar sequence with their tRNA precursors, which enables tsRNAs to compete with tRNA on the regulatory occasions where a sequence complementary mechanism is needed. For example, 5\({}^{\prime}\)tsRNAGly(GCC) can compete with tRNAGly(GCC) to base-pair with tDNA during the embryonic development of zebrafish, thus inhibiting the formation of the tRNA-dependent stable transcription-inhibiting R loop structure (a three-stranded structure composed of one RNA strand and two DNA strands) around tRNA genes, which ultimately promotes the transcription of tDNAs. On another occasion, an 18 nt 3\({}^{\prime}\)tsRNALys(AAA) could compete with mature tRNALys(AAA) to occupy the PBS in a complete base-pairing manner, leading to reverse transcription blocking and impeding the cDNA synthesis process of long terminal repeat retrotransposon, which utilizes tRNALys(AAA) as a reverse transcription primer [149]. Interestingly, a 22 nt 3'tsRNA Lys(AAA) could effectively silence ERV in a microRNA -like manner with a 2 bp mismatch when binding with the PBS of ERV. Therefore, 3'tsRNAs Lys(AAA) with different nucleotide lengths could suppress the LTR-retrotransposon activity both through impeding the cDNA synthesis of ERV and silencing ERV transcripts to protect the cells during reprogramming [149].  
The direct sequence complementary binding mechanism of tsRNA could also occur between tsRNA and mRNA in a protein-dependent or independent manner. It was reported that 3'tsRNALeu(CAG) can complementary base-pair with the structured region of ribosome proteins' transcripts, such as Ribosomal proteins 28 (RPS28) and RPS15. The base-pairing of 3'tsRNALeu(CAG) with mRNA unfolds the intramolecular structure of mRNA to allow ribosomes to pass through the structured mRNAs smoothly, thereby promoting the translation elongation process of ribosome proteins and the overall cellular translation process [150]. In addition to the sequence-complementary pairing that occurs between tsRNA and mRNA coding sequences, some tsRNAs could also bind to the intron sequences of pre-mRNAs, which leads to the silencing of nascent RNA of the target gene (nascent RNA silencing) [151].  
In consideration of the protein-dependent manner, some tsRNAs can operate a miRNA-like mechanism to bind to Argonaute (AGO) proteins to form an RNA-induced silencing complex (RISC), leading to the promotion of mRNA degradation or the inhibition of mRNA translation. This interaction typically relies on precise nucleotide pairing between tsRNA and the target mRNA. One occasion is that tsRNAs target mRNA 3'UTR with AGO proteins in a sequence-complementary manner and lead to the degradation of target mRNAs [152; 153]. Moreover, the regulatory effects of tsRNAs based on sequence complementarity sometimes only require a few nucleotide base-pairs. In fruit flies, tsRNAs target the conservative regions of mRNA through short seed sequences consisting of seven nucleotides, without affecting the mRNA stability, but inhibit the translation of target gene mRNA by AGO proteins [154]. Interestingly, these tsRNAs showed a tendency to target critical genes within the translation complex, such as ribosome proteins, which could expand the translation inhibition from several transcripts to raise an overall translation inhibition wave in cells.