The biogenesis of mature microRNAs (miRNAs) involves the cleavage of primary miRNAs by Drosha and the cleavage of the resulting precursor (pre)-miRNAs by Dicer. Previous work from Narry Kim's laboratory has shown that the pluripotency factor LIN28 can induce the terminal uridylation of pre-let-7 miRNA in embryonic stem (ES) cells to block Dicer cleavage and let-7 maturation. This has important consequences as mature let-7 promotes the differentiation of ES cells and development. Because LIN28 does not posses uridylyl transferase activity, how it is involved in inducing pre-let-7 uridylation was unknown. Three studies now reveal that the mammalian terminal uridylyl transferase (TUTase) zinc finger CCHC domain-containing protein 11 (ZCCHC11; also known as TUT4), and its Caenorhabditis elegans orthologue poly(U) polymerase 2 (PUP-2), is the TUTase that regulates LIN28-mediated pre-let-7 uridylation.
“ZCCHC11 ... is the TUTase that regulates LIN28-mediated pre-let-7 uridylation.”
Studies by Heo et al. and Hagan et al. identify ZCCHC11 as the only one of seven mammalian TUTases that can uridylate pre-let-7 in mouse ES cells. Heo et al. show that small interfering RNA-mediated knockdown of ZCCHC11 or LIN28 reduces the level of pluripotency markers in mouse ES cells, which is consistent with the role of mature let-7 in promoting ES cell differentiation. They also present data suggesting that LIN28 recruits ZCCHC11 to pre-let-7 by recognizing a GGAG motif in the terminal loop of this pre-miRNA. Several additional miRNAs that contain the GGAG motif, including other let-7 family members and miR-107, miR-143 and miR-200c, also undergo uridylation in a LIN28-dependent manner. This suggests that the ability of LIN28 and ZCCHC11 to repress pre-miRNA processing by inducing uridylation may not be specific to let-7. Hagan et al. show that knockdown of ZCCHC11 or LIN28, using small interfering RNA, stops the inhibition of let-7 processing, leads to the accumulation of mature let-7 miRNA and results in the repression of reporter genes that are inhibited by mature let-7.
Finally, Lehrbach et al. examined the post-transcriptional regulation of let-7 in C. elegans. They found that LIN-28 also binds to pre-let-7 and prevents its processing by Dicer,and that thisis dependent on the ZCCHC11 orthologue, PUP-2. Furthermore, LIN-28 stimulates the uridylation of pre-let-7 by PUP-2 in vitro.
Together, these studies show that the newly defined let-7–LIN28–TUTase pathway is evolutionarily conserved to control the processing of let-7. However, as the terminal loop of pre-let-7 is not conserved in C. elegans, the exact mechanistic details might differ between organisms. Future studies are likely to confirm whether this pathway regulates the processing of other miRNAs in C. elegans and mouse ES cells.
ORIGINAL RESEARCH PAPERS
Heo, I. et al. TUT4 in concert with Lin28 suppresses microRNA biogenesis through pre-microRNA uridylation. Cell 138, 696–708 (2009)
Hagan, J. P. et al. Lin28 recruits the TUTase Zcchc11 to inhibit let-7 maturation in mouse embryonic stem cells. Nature Struct. Mol. Biol. 27 Aug 2009 (doi: 10.1038/nsmb.1676)
Lehrbach, N. J. et al. LIN-28 and the poly(U) polymerase PUP-2 regulate let-7 microRNA processing in Caenorhabditis elegans. Nature Struct. Mol. Biol. 27 Aug 2009 (doi: 10.1038/nsmb.1675)
Vamsi, K. & Lin, H. MicroRNAs: key regulators of stem cells. Nature Rev. Mol. Cell Biol. 10, 116–125 (2009)
Kim, V. N. et al. Biogenesis of small RNAs in animals. Nature Rev. Mol. Cell Biol. 10, 126–139 (2009)
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Wrighton, K. Keeping let-7 young. Nat Rev Mol Cell Biol 10, 652 (2009). https://doi.org/10.1038/nrm2776