Mechanism of Dis3l2 substrate recognition in the Lin28–let-7 pathway

Abstract

Summary paragraph The pluripotency factor Lin28 inhibits the biogenesis of the let-7 family of mammalian microRNAs1–4. Lin28 is highly expressed in embryonic stem cells and has a fundamental role in regulation of development5, glucose metabolism6 and tissue regeneration7. Alternatively, Lin28 overexpression is correlated with the onset of numerous cancers8, while let-7, a tumor suppressor, silences several human oncogenes5. Lin28 binds to precursor let-7 (pre-let-7) hairpins9, triggering the 3' oligo-uridylation activity of TUT4/710–12. The oligoU tail added to pre-let-7 serves as a decay signal, as it is rapidly degraded by Dis3L213,14, a homolog of the catalytic subunit of the RNA exosome. The molecular basis of Lin28 mediated recruitment of TUT4/7 to pre-let-7 and its subsequent degradation by Dis3L2 is largely unknown. To examine the mechanism of Dis3L2 substrate recognition we determined the structure of mouse Dis3L2 in complex with an oligoU RNA to mimic the uridylated tail of pre-let-7. Three RNA binding domains form an open funnel on one face of the catalytic domain that allows RNA to navigate a path to the active site different from its exosome counterpart. The resulting path reveals an extensive network of uracil-specific interactions spanning the first twelve nucleotides of an oligoU-tailed RNA. We identify three U-specificity zones that explain how Dis3L2 recognizes, binds and processes uridylated pre-let-7 in the final step of the Lin28/let-7 pathway.

Lin28a uses distinct mechanisms of binding to RNA and affects miRNA levels positively and negatively

“…However, only pre-miRNA-9 pulled down Dis3l2 in a uridylation-independent manner. This is surprising as Dis3l2 was shown to bind 3 ′ ends of RNAs with preference toward multiple U residues (Faehnle et al 2014). Furthermore, pre-let-7a_ (U)15, pre-miRNA-9_(U)15, and premiRNA-9 mt, but not pre-let-7a-1 mt, pulled down Dis3l2 with similar efficiency (Fig.…”

The epigenetic landscape of renal cancer

“…Mutations in DIS3L2 cause Perlman syndrome, a rare congenital overgrowth syndrome characterized by the development of Wilms tumours 40 . Loss of DIS3L2 results in an increase in polyuridylated LET-7 and the upregulation of many mRNAs [223][224][225] ; however, the precise influence of DIS3L2 loss on the levels or activity of mature LET-7 mi RNAs is yet to be clarified 223,226 . Mutations (exonic deletions) of DIS3L2 have been identified in 30% of sporadic Wilms tumour 40 .…”

“…Moreover, LIN28 overexpression induces Wilms tumours in mice 222 . LIN-28 targets LET-7 pre-mi RNAs for degradation by polyuridylating them at their 3ʹ end, which targets them for degradation by the DIS3-like exonuclease 2 (DIS3L2) 223,224 (FIG. 5).…”

A retrovirus packages nascent host noncoding RNAs from a novel surveillance pathway

“…Although this could reflect their localization to other cell structures, such as the nuclear pore or cytoplasmic organelles, a role for the nuclear exosome is supported by our finding that some U6 RNAs that accumulate when EXOSC3 and DIS3L2 are codepleted contain nontemplated poly(A) tracts, as expected if they were targets of a TRAMP polymerase. Since all of the characterized U6 tails terminate in oligo(U), a modification that enhances DIS3L2 activity (Faehnle et al 2014), newly synthesized ncRNAs that escape degradation by the nuclear exosome may be exported to the cytoplasm, where they undergo oligo(U) addition and degradation by DIS3L2. Although these exosome and DIS3L2 pathways are another example of redundancy in RNA decay pathways (Houseley and Tollervey 2009), the finding that truncated U6 RNAs accumulate upon EXOSC3 or DIS3 depletion (Fig.…”