Characterization of circulating transfer RNA-derived RNA fragments in cattle

Abstract

The objective was to characterize naturally occurring circulating transfer RNA-derived RNA fragments (tRFs) in cattle1. Serum from eight clinically normal adult dairy cows was collected, and small non-coding RNAs were extracted immediately after collection and sequenced by Illumina MiSeq. Sequences aligned to transfer RNA (tRNA) genes or their flanking sequences were characterized. Sequences aligned to the beginning of 5′ end of the mature tRNA were classified as tRF5; those aligned to the 3′ end of mature tRNA were classified as tRF3; and those aligned to the beginning of the 3′ end flanking sequences were classified as tRF1. There were 3,190,962 sequences that mapped to transfer RNA and small non-coding RNAs in the bovine genome. Of these, 2,323,520 were identified as tRF5s, 562 were tRF3s, and 81 were tRF1s. There were 866,799 sequences identified as other small non-coding RNAs (microRNA, rRNA, snoRNA, etc.) and were excluded from the study. The tRF5s ranged from 28 to 40 nucleotides; and 98.7% ranged from 30 to 34 nucleotides in length. The tRFs with the greatest number of sequences were derived from tRNA of histidine, glutamic acid, lysine, glycine, and valine. There was no association between number of codons for each amino acid and number of tRFs in the samples. The reason for tRF5s being the most abundant can only be explained if these sequences are associated with function within the animal.

A comprehensive overview of bull sperm-borne small non-coding RNAs and their diversity across breeds

“…Altogether, 5p-derived fragments represented 63% of all bull sperm tsRNAs, with tRF3s and 3p-tRHs being expressed at low levels (30× less expressed than 5p derived fragments). A similar pattern was also described in bull sera [59], but with a larger contrast, where 5p-derived fragments were 4000× more expressed than 3p ones. This discrepancy may be related to biological differences between tissues, as suggested by the extensive differences in tRF expression observed between human biofluids [60].…”

Genome-wide identification of functional tRNA-derived fragments in Senescence-accelerated mouse prone 8 brain

“…tiRNA-5, tiRNA-3, tRF-3, tRF-5, and i-tRF series which are generated from mature tRNAs constituted the majority in our samples, whereas the tRFs (tRF-1) generated from the primary tRNAs were in the minority. This phenomenon is consistent with previous reports (Casas et al 2015;Olvedy et al 2016;Wei et al 2012).…”

“…Then, tRFs were detected in other kinds of human cells or tissues (Zhou et al 2017;Yeung et al 2009;Wang et al 2013). tRFs were also evaluated in plants or other animals, such as barley (Hackenberg et al 2013) and cattle (Casas et al 2015). Given their widespread presence, the tRFs are expected to play key roles in many physiological and pathological processes.…”

Discovery and function of transfer RNA‐derived fragments and their role in disease

“…These tRFs were originally viewed as tRNA degradation products often found in next generation sequencing (NGS) data sets, however, the recurrence of reads matching specific domains of mature tRNAs, rather than random alignment throughout mature tRNA primary structures strongly suggested that these sncRNAs could be functional . tRFs were also uncovered in a panoply of organisms and their biogenesis was found to be dependent on cell type, physiological conditions, and developmental stages, suggesting high level conservation and specific tRNA cleavage rather than random tRNA degradation. Initial studies also showed that tRFs were a heterogeneous class of sncRNAs with different sizes that could originate from either the pre‐ or mature tRNA molecule .…”