The Lupus Autoantigen La Prevents Mis-channeling of tRNA Fragments into the Human MicroRNA Pathway

Abstract

The Lupus autoantigen La is an RNA-binding protein that stabilizes RNA polymerase III (Pol III) transcripts and supports RNA folding and has in addition been implicated in the mammalian microRNA (miRNA) pathway. Here, we have analyzed effects of La depletion on Argonaute (Ago)-bound small RNAs in human cells. We find that in the absence of La, distinct tRNA fragments are loaded into Ago proteins. Thus, La functions as gatekeeper ensuring correct tRNA maturation and protecting the miRNA pathway from potentially functional tRNA fragments. However, one specific isoleucin pre-tRNA produces both a functional tRNA and a miRNA even when La is present. We demonstrate that the fully complementary 5' leader and 3' trailer of the pre-tRNA-Ile form a double-stranded RNA molecule that has low affinity to La. Instead, Exportin-5 (Xpo5) recognizes it as miRNA precursor and transports it into the cytoplasm for Dicer processing and Ago loading.

Characterizing Expression and Processing of Precursor and Mature Human tRNAs by Hydro-tRNAseq and PAR-CLIP

“…This stems from two observations: 1) SSB has a higher affinity for precursor over mature tRNAs, and that 2) structural data show that RRM1 is unoccupied when SSB is bound to UUU-3′-OH substrate. Our data seem to validate this observation, and could shed light into new modes of SSB-mediated processing of pre-tRNAs into either mature tRNAs or other kinds of ncRNAs (Hasler et al, 2016). …”

“…Yet, in recent years tRNAs received new attention in the context of codon-resolved translational control (Dana and Tuller, 2012; 2014; Mahlab et al, 2012; Plotkin and Kudla, 2011; Tuller et al, 2010; Weinberg et al, 2016), and due to the involvement of their metabolic byproducts in regulation and cross-talk with processing and effector functions of other classes of non-coding RNAs (ncRNAs) (Hasler et al, 2016; Ivanov et al, 2011; Lee et al, 2009). Nevertheless, the lack of reliable methods for tRNA quantification has hampered such analyses, and necessitated the use of predicted tRNA gene copy number as a surrogate index of expression (Iben and Maraia, 2014; Pechmann and Frydman, 2012; Tuller et al, 2010).…”

Molecular mechanisms of Dicer: endonuclease and enzymatic activity

“…La functions as a gatekeeper that ensures correct tRNA maturation and protects the miRNA pathway from tRF. In the absence of La (La knockdown cells), various pre-tRNAs bind to Dicer, and the tRFs derived from the 3′ ends of tRNAs are bound to AGO [60]. …”

Factors That Shape Eukaryotic tRNAomes: Processing, Modification and Anticodon–Codon Use

“…La can protect scR1 and other non-tRNA transcripts from untimely decay due to 3′ oligo(U) binding [72,73]. Nascent pre-5S rRNA is transiently bound by La and although it undergoes little if any processing, its maturation would appear to be largely independent of La (e.g., see [74,75]).…”