COMPLEXITY OF tRNA REGULATION: SELECTIVE tRNA GENE EXPRESSION IN HUMAN MAINTAINS tRNA ANTICODON POOL ON DIFFERENTIATION OF CELL

 

In general, under protein synthesis, ribosomes match mRNA codons to their respective amino acid via complimentary anticodons of tRNAs (transfer RNAs). tRNAs are adaptor molecules of approximately 76 nucleotide adaptor molecules abundant than ribosomes in cells. The prominent function of these adaptor molecules is decoding mRNA. However, their similarity makes ribosomes distinguish them even if differed by a single nucleotide is a challenge. Another challenge is tRNAs binding to their specific amino acid which modulates the rate and fidelity of tRNA translation. And any changes in this function of tRNA can be linked to cancer and neurological diseases.

How come these are regulated? How can tRNA recognise the proper amino acids and charge them while matching with the proper codon on the mRNA sequence? The tRNA repertories of human cells and their mechanism for controlling it are still unknown to mankind. Due to the multicopy nature and simplified promoter structure, it is challenging to predict the regulation of tRNA genes. Similarly, quantification of tRNA transcripts is difficult due to their stable structure and numerous chemical modifications resulting in poor characterization of tRNA expression. In the human nuclear genome, 619 tRNA genes code for 432 unique tRNA transcripts from 57 tRNA anticodon families. 

RNA polymerase III (Pol III) plays a crucial role in transcribing nuclear-encoded tRNA genes. The initiation of tRNA transcription involves the assembly of transcription factor IIIC (TFIIIC) on short intragenic promoter elements known as the A box and B box. TFIIIC, in turn, recruits transcription factor IIIB (TFIIIB) to the variable regions upstream of tRNA loci. This intricate process positions Pol III for initiation, and TFIIIB can retain it for multiple rounds of transcription. The A box and B box sequences are essential for the specificity of this transcriptional machinery, ensuring the accurate transcription of tRNA genes.

Post-transcriptional modification based on various response

The regulatory model governing tRNA transcription is often considered simplistic, with the tRNA gene copy number (also known as copy number variants (CNVs), which is the number of copies of a particular gene in a person's genotype) commonly used as a proxy for tRNA expression levels. During rapid growth in yeast, nearly all tRNA loci are transcribed, highlighting a close correlation between gene copy number and expression levels. However, this straightforward relationship becomes more complex in mammalian tissues. Despite the transcription of almost all tRNA loci during rapid growth, Pol III enrichment at tRNA genes varies among different mammalian tissues. This suggests a more nuanced regulatory mechanism in mammalian cells, challenging the simplistic assumptions made based on gene copy numbers. Simply, tRNA gene regulation, the amount of tRNA that should be produced in different types of cells and the amount of tRNA gene expression for the production is unknown.

The molecular basis and quantitative impact of this selective transcription on tRNA levels remain largely unknown. Understanding the factors influencing Pol III enrichment at tRNA genes in different tissues is crucial for unravelling the intricacies of tRNA expression regulation in mammals.

Recently a paper “Selective gene expression maintains human tRNA anticodon pools during differentiation” from Nature Cell Biology used quantitative tRNA profiling and chromatin immunoprecipitation with sequencing to measure tRNA expression, solving the mystery of how tRNA gene expression is regulated to control tRNA repertoires.

It was identified that tRNA repertories are remodelled when human induced pluripotent stem cells (hiPSC) differentiate into neuronal and cardiac cell types. On applying orthogonal methods on hiPSC (human induced pluripotent stem cells)- based models, it is identified that even though remodelling of tRNA repertories is present, the level of mature tRNAs with specific anticodons are stable across diverse human cell types mediated by constitutively high transcription of one-third of the predicted human tRNA genes, that they have defined as housekeeping genes. Housekeeping tRNA genes are mostly unaffected by MAF1-mediated Pol III repression, identified as the mechanism for silencing low-occupancy tRNA loci during differentiation. 

The paper suggests that preserving stable tRNA anticodon pools and uniform codon usage across cell types guarantees consistent decoding rates during development, regardless of cell identity.  Also, it is suggested that unique A and B boxes along with specific motifs in the 5′ flanking sequence of housekeeping tRNA genes might support the recruitment or recycling of Pol III at these sites, allowing them to evade MAF1-mediated repression during differentiation. It is discovered that these genes exhibit consistent expression and represent the predominant tRNA isodecoders (a pair of transfer RNA molecules that share the same anticodon but have different body sequences) within each anticodon family. This mechanism is responsible for the overall stability of tRNA anticodon pools and decoding rates across diverse cell types, even amid tRNA-repertoire changes during differentiation.

REFERENCE

Gao L, Behrens A, Rodschinka G, Forcelloni S, Wani S, Strasser K, et al. Selective gene expression maintains human tRNA anticodon pools during differentiation. Nature Cell Biology. 2024; doi:10.1038/s41556-023-01317-3 

IMAGE CREDITS

Genetic Engineering & Biotechnology news,https://images.app.goo.gl/6CaFCDyDovJeZ5f5A

Nature, https://images.app.goo.gl/YeVipKzQVoxgbExw9

ReseachGate, https://images.app.goo.gl/vFvA6PyPGEgxz2aZ8