Transfer RNA-derived small RNAs in the cancer transcriptome

Abstract

The cellular lifetime includes stages such as differentiation, proliferation, division, senescence and apoptosis. These stages are driven by a strictly ordered process of transcription dynamics. Molecular disruption to RNA polymerase assembly, chromatin remodelling and transcription factor binding through to RNA editing, splicing, post-transcriptional regulation and ribosome scanning can result in significant costs arising from genome instability. Cancer development is one example of when such disruption takes place. RNA silencing is a term used to describe the effects of post-transcriptional gene silencing mediated by a diverse set of small RNA molecules. Small RNAs are crucial for regulating gene expression and microguarding genome integrity. RNA silencing studies predominantly focus on small RNAs such as microRNAs, short-interfering RNAs and piwi-interacting RNAs. We describe an emerging renewal of interest in a 'larger' small RNA, the transfer RNA (tRNA). Precisely generated tRNA-derived small RNAs, named tRNA halves (tiRNAs) and tRNA fragments (tRFs), have been reported to be abundant with dysregulation associated with cancer. Transfection of tiRNAs inhibits protein translation by displacing eukaryotic initiation factors from messenger RNA (mRNA) and inaugurating stress granule formation. Knockdown of an overexpressed tRF inhibits cancer cell proliferation. Recovery of lacking tRFs prevents cancer metastasis. The dual oncogenic and tumour-suppressive role is typical of functional small RNAs. We review recent reports on tiRNA and tRF discovery and biogenesis, identification and analysis from next-generation sequencing data and a mechanistic animal study to demonstrate their physiological role in cancer biology. We propose tRNA-derived small RNA-mediated RNA silencing is an innate defence mechanism to prevent oncogenic translation. We expect that cancer cells are percipient to their ablated control of transcription and attempt to prevent loss of genome control through RNA silencing.

Keywords: Cancer; Non-coding RNA; RNA silencing; Small RNA; tRNA.

Fig. 1

Biogenesis and mode of action of miRNAs in RNA silencing. A miRNA gene is expressed from the genome where it undergoes processing in the nucleus before exportation to the cytoplasm. It undergoes further processing to create a mature ~22 nt miRNA (in red). The miRNA binds to a multi-domain protein assembly forming a ribonucleoprotein complex known as the RNA-induced silencing complex (RISC). RISC uses the miRNA sequence to bind to complementary sequences in target mRNAs and physically obstruct translation. RISC also contains an Argonaute protein which is capable of cleaving the mRNA if there is perfect base pairing with the miRNA seed sequence. This type of post-transcriptional gene silencing takes place for up to two-thirds of genes in humans

Fig. 2

The basic premise of microguarding. External signals such as carcinogens or products of sexual reproduction (in green) may enter the cell through receptors and cause genome instability by triggering a fluctuation of abhorrent gene expression. In response, small RNAs (in red) are rapidly switched on to form a silencing ribonucleoprotein complex (RNP) to counteract this deleterious, exogenously induced transcription

Fig. 3

Schematic of tRNA-derived small RNA biogenesis from a mature tRNA^Gly molecule. The stress-activated ribonuclease Angiogenin cleaves the mature tRNA in the anticodon loop to produce two tRNA halves or tiRNAs. The production of tRF-3s is derived from a cleavage in the 3′ T arm loop (as the arrow indicates). The production of tRF-5s is derived from a cleavage in the 5′ D arm loop (as the arrow indicates). Conflicting reports show these cleavages to be Dicer-dependent and Dicer-independent. It is theorised that an RNase generates the majority of tRF-3s and tRF-5s instead of Dicer. In the nucleus, RNase Z produces tRF-1s from the trailer sequence of a precursor tRNA (not shown)

Fig. 4

Oncogenic genes are expressed by the cancer cell which promote its survival and metastasis. YBX1 is an RNA-binding protein which stabilises the oncogenic transcripts for translation, resulting in more metastasis (left-hand side). The cancer cell increases production of tRNA-derived small RNAs, which compete for YBX1 binding. Oncogenic transcripts are destabilised (in red), and translation is diminished, resulting in less metastasis (right-hand side). This innate system is open to manipulation through the use of RNA mimics and inhibitors