Transfer RNA‐derived fragments: origins, processing, and functions

@article{Sobala2011TransferRF,
  title={Transfer RNA‐derived fragments: origins, processing, and functions},
  author={Andrew Sobala and Gyorgy Hutvagner},
  journal={Wiley Interdisciplinary Reviews: RNA},
  year={2011},
  volume={2}
}
Deep sequencing approaches have revealed multiple types of small RNAs with known and unknown functions. In this review we focus on a recently identified group of small RNAs that are derived from transfer RNAs (tRNAs), tRNA fragments (tRFs). We review the mechanism of their processing and their functions in mammalian cells, and highlight points of possible cross‐talk between tRFs and the canonical small RNA pathway characterized by small interfering RNAs (siRNAs), microRNAs (miRNAs), and Piwi… 
tRNA-Derived Fragments (tRFs): Emerging New Roles for an Ancient RNA in the Regulation of Gene Expression
TLDR
This review will describe the features of the known subtypes of these RNAs; including sequence characteristics, protein interactors, expression characteristics, biogenesis, and similarity to canonical miRNA pathways, and speculate as to the origin and rationale for the conservation of this novel class of noncoding RNAs amongst both prokaryotes and eukaryotes.
Hints of tRNA-Derived Small RNAs Role in RNA Silencing Mechanisms
TLDR
This review aims to make a compilation of the most relevant research literature in this field with the purpose of shedding light on the relation of these primitive tRNA-derived molecules with the gene silencing machinery.
Small Non-coding Transfer RNA-Derived RNA Fragments (tRFs): Their Biogenesis, Function and Implication in Human Diseases
TLDR
In this review, a growing number of reports have shown that tRFs are not random degradation products but are functional ncRNAs made of specific tRNA cleavage.
Computational Approaches to tRNA-Derived Small RNAs
TLDR
The tools and databases for tDR identification and collection are summarized, with the aim of helping researchers choose the best tools for their analysis and inspiring the invention or improvement of tools in the field.
Description of plant tRNA-derived RNA fragments (tRFs) associated with argonaute and identification of their putative targets
TLDR
Using public deep sequencing libraries of immunoprecipitated Argonaute proteins (AGO-IP) and bioinformatics approaches, the Arabidopsis thaliana AGO-IP tRFs are identified and represent a useful starting point for future studies on t RFs in plants.
Transfer RNA as a source of small functional RNA.
TLDR
This review summarizes recent studies of tRNA fragments that have provided new insights into tRNA biology by examining the molecular functions of tRNAs and proteins with which they interact.
tRNA-Derived Short Non-coding RNA as Interacting Partners of Argonaute Proteins
TLDR
This review focuses on the tRNA-derived ncRNAs associated with Argonaute proteins and summarize recent studies on their conceivable biogenesis factors and on their emerging roles in gene expression regulation as regulatory RNAs.
Beyond microRNA--novel RNAs derived from small non-coding RNA and their implication in cancer.
TLDR
This review summarizes new findings describing the detection and alterations in expression of snoRNA-derived (sdRNA) and tRNA- derived (tRF) RNAs and presents current hypotheses on the function of these RNAs.
Biochemical properties and progress in cancers of tRNA‐derived fragments
TLDR
Current progress of tRFs and some tsRNAs such as tRF‐Leu‐CAG, which have been studied or will be further investigated in tumorgenesis and diagnostic biomarkers in the clinic are focused on.
Age-driven modulation of tRNA-derived fragments in Drosophila and their potential targets
TLDR
Drosophila tRF reads mapped to both nuclear and mitochondrial tRNA genes for all 20 amino acids, while previous studies have usually reported fragments from only a few tRNAs, suggesting that involvement of tRFs in the RNA interfering pathway may play a role in brain activity or brain changes with age.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 73 REFERENCES
A novel class of small RNAs: tRNA-derived RNA fragments (tRFs).
TLDR
The data suggest that tRFs are not random by-products of tRNA degradation or biogenesis, but an abundant and novel class of short RNAs with precise sequence structure that have specific expression patterns and specific biological roles.
Small silencing RNAs: an expanding universe
Since the discovery in 1993 of the first small silencing RNA, a dizzying number of small RNA classes have been identified, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and
Argonaute proteins: key players in RNA silencing
TLDR
This work has shown that Argonaute proteins, a highly conserved protein family, can bind small non-coding RNAs and control protein synthesis, affect messenger RNA stability and even participate in the production of a new class of small RNAs, Piwi-interacting RNAs.
Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs.
TLDR
It is shown that the processing of small RNAs derived from tRNA(Gln) is dependent on Dicer in vivo and that Dicer cleaves the tRNA in vitro.
Hidden layers of human small RNAs
TLDR
The data shows that well-characterized non-coding RNA, such as tRNA, snoRNA, and snRNA are cleaved at sites specific to the class of ncRNA, indicating that the small RNAs are a product of dsRNA formation and their subsequent cleavage.
Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs
TLDR
It is shown that processing of mature mRNAs through an as yet unknown mechanism may generate complex populations of both long and short RNAs whose apparently capped 5′ ends coincide.
A human snoRNA with microRNA-like functions.
TLDR
A class of small RNAs in human cells that originate from snoRNAs and can function like miRNAs is identified, suggesting a role for ACA45-processing products in posttranscriptional gene silencing.
Small RNAs derived from snoRNAs.
TLDR
It is shown that small RNAs with evolutionary conservation of size and position are derived from the vast majority of snoRNA loci in animals (human, mouse, chicken, fruit fly), Arabidopsis, and fission yeast.
A novel class of small RNAs bind to MILI protein in mouse testes
TLDR
A new class of small RNAs that bind to MILI in mouse male germ cells, where they accumulate at the onset of meiosis are described, and are referred to as ‘Piwi-interacting RNAs’ or piRNAs.
Human tRNA-derived small RNAs in the global regulation of RNA silencing.
TLDR
Findings support that tsRNAs are involved in the global control of small RNA silencing through differential Argonaute association, suggesting that small RNA-mediated gene regulation may be even more finely regulated than previously realized.
...
1
2
3
4
5
...