Alternative titles; symbols
HGNC Approved Gene Symbol: TUT4
Cytogenetic location: 1p32.3 Genomic coordinates (GRCh38): 1:52,423,275-52,553,463 (from NCBI)
ZCCHC11 is an RNA uridyltransferase (EC 2.7.7.52) that uses UTP to add uridines to the 3-prime end of substrate RNA molecules (Jones et al., 2009).
By sequencing clones obtained from a size-fractionated KG-1 immature myeloid leukemia cell line cDNA library, Nagase et al. (1996) obtained a partial ZCCHC11 clone, which they designated KIAA0191. Northern blot analysis detected highest expression in skeletal muscle and testis, with low to moderate expression in all other tissues and cell lines examined.
By searching for proteins that interacted with TIFA (609028) in activated murine macrophages, followed by database analysis and RT-PCR of HEK293T cells, Minoda et al. (2006) obtained full-length ZCCHC11 and a variant encoding a short ZCCHC11 isoform, which they called ZCCHC11L and ZCCHC11S, respectively. The deduced 1,644-amino acid ZCCHC11L protein contains an N-terminal C2H2 zinc finger, followed by a poly(A) polymerase (PAP; see 605553)/2-prime,5-prime oligoadenylate synthetase (25A; see 164350) (PAP/25A)-associated domain, a CCHC-type zinc finger, a nucleotidyltransferase domain, a second PAP/25A-associated domain, and 2 C-terminal CCHC-type zinc fingers. Full-length mouse and human ZCCHC11L share 84% amino acid identity. Compared with ZCCHC11L, the 435-amino acid ZCCHC11S isoform contains N- and C-terminal truncations, but it retains the N-terminal C2H2 zinc finger and first PAP/25A domain. Western blot analysis detected ZCCHC11L at an apparent molecular mass of 200 kD and ZCCHC11S at an apparent molecular mass of 60 kD. Immunofluorescence analysis detected ZCCHC11 in the nucleus of HEK293T cells.
Jones et al. (2009) cloned mouse Zcchc11. The deduced 1,644-amino acid protein has the same domain structure as human ZCCHC11, and the polymerase beta (POLB; 174760) nucleotidyltransferase domain is highly conserved in eukaryotes. Mouse Zcchc11 mRNA expression was ubiquitous, whereas Zcchc11 protein expression was tissue specific, with highest levels in thymus, spleen, testis, and lung.
Minoda et al. (2006) showed that a substantial proportion of ZCCHC11 translocated from the nucleus to the cytoplasm following lipopolysaccharide (LPS) stimulation of HEK293T cells. ZCCHC11L coimmunoprecipitated with TIFA only following LPS treatment, and it specifically suppressed LPS-induced NF-kappa-B (see 164011) activation. Mutation analysis showed that the N-terminal half of ZCCHC11 was responsible for NF-kappa-B inhibitory activity, and ZCCHC11S was as potent as full-length ZCCHC11L at inhibiting NF-kappa-B. The basal protein level of ZCCHC11S was low, but it increased dramatically after treatment with LPS or other Toll-like receptor (TLR; see 603030) activators. Treatment with a proteasome inhibitor also led to ZCCHC11S protein accumulation, suggesting that ZCCHC11S was ubiquitinated and degraded by the proteasome at basal levels and accumulated in response to LPS stimulation. ZCCHC11S appeared to inhibit NF-kappa-B by suppressing phosphorylation of I-kappa-B (NFKBIA; 164008).
Jones et al. (2009) found that recombinant mouse Zcchc11 and endogenous human ZCCHC11 showed nucleotidyltransferase activity, with greatest activity with UTP, followed by CTP, ATP, and GTP. ZCCHC11 did not show RNA substrate specificity and used all RNA substrates examined. Knockdown of ZCCHC11 via small interfering RNA in activated A549 human lung epithelial cells or HEK293T cells reduced the levels of several cytokines, including IL6 (147620), but increased IL8 (146930) concentration. Jones et al. (2009) showed that ZCCHC11 did not directly regulate IL6 expression, but instead uridylated and inactivated members of the MIR26 microRNA family, MIR26A (see 612151) and MIR26B (612152), which targeted the 3-prime UTR of IL6 mRNA to downregulate IL6 expression.
LIN28 (see LIN28A, 611043) represses LET7 family microRNAs (miRNAs) (see MIRLET7A1, 605386) by binding to the terminal loop of the stem-loop structure of precursor (pre-) and primary (pri-) LET7 miRNAs and inhibiting further maturation. Thornton et al. (2012) found that mouse Lin28 downregulated Let7 by interacting with mouse Zcchc11 and/or human ZCCHC6 (613467) and enhancing their oligouridylation of the 3-prime end of pre-Let7 in vitro. Mutation analysis revealed that the N-terminal C2H2-type zinc finger of Zcchc11 interacted with Lin28. The TRF4 domain and the CCHC zinc finger just C-terminal to the active site of Zcchc11 were required for Lin28-enhanced uridylation. Lin28 enhanced uridylation by both enzymes in a dose-dependent manner. Depletion of Zcchc11 and/or Zcchc6 in embryonic mouse cells via small interfering RNA revealed that the enzymes redundantly downregulated Let7 mRNAs. Knockdown of both enzymes upregulated mature Let7 more dramatically than knockdown of either enzyme alone.
Lim et al. (2014) found that purified human TUT7 (ZCCHC6) and TUT4 (ZCCHC11) selectively recognized and uridylated RNAs with short A-tails (less than 25 nucleotides) in vitro and in HeLa cells, suggesting that uridylation may occur following deadenylation. In HeLa cells depleted of TUT4 and TUT7, but not TUT2 (PAPD4; 614121), the vast majority of mRNAs lost oligo(U) tails and their half-lives were extended. Suppression of mRNA decay factors in multiple decay pathways led to the accumulation of oligo(U) mRNAs. Poly(A) recognition was independent of the 3-prime UTR sequence. The recombinant PAP enzyme PABPC1 (604679) antagonized uridylation of poly(A) mRNAs, possibly contributing to the specificity of TUT4 and TUT7 for short A-tails. A mimic of the miRNA MIR1 (see 609326) induced uridylation of its mRNA targets, and TUT4 and TUT7 were required for enhanced decay of MIR1 targets. Lim et al. (2014) concluded that TUT4 and TUT7 may act redundantly in uridylation of deadenylated mRNAs and that 3-prime uridylation of mRNA functions as a molecular mark for global mRNA decay.
Morgan et al. (2017) showed that 3-prime terminal uridylation of mRNA mediated by TUT4 and TUT7 sculpts the mouse maternal transcriptome by eliminating transcripts during oocyte growth. Uridylation mediated by TUT4 and TUT7 is essential for both oocyte maturation and fertility. In comparison to somatic cells, the oocyte transcriptome has a shorter poly(A) tail and a higher relative proportion of terminal oligo-uridylation. Deletion of TUT4 and TUT7 leads to the accumulation of a cohort of transcripts with a high frequency of very short poly(A) tails, and a loss of 3-prime oligo-uridylation. By contrast, deficiency of TUT4 and TUT7 does not alter gene expression in a variety of somatic cells. In summary, Morgan et al. (2017) showed that poly(A) tail length and 3-prime terminal uridylation have essential and specific functions in shaping a functional maternal transcriptome.
By radiation hybrid analysis, Nagase et al. (1996) mapped the ZCCHC11 gene to chromosome 1. Minoda et al. (2006) stated that the ZCCHC11 gene maps to chromosome 1q23.3.
Jones, M. R., Quinton, L. J., Blahna, M. T., Neilson, J. R., Fu, S., Ivanov, A. R., Wolf, D. A., Mizgerd, J. P. Zcchc11-dependent uridylation of microRNA directs cytokine expression. Nature Cell Biol. 11: 1157-1163, 2009. [PubMed: 19701194] [Full Text: https://doi.org/10.1038/ncb1931]
Lim, J., Ha, M., Chang, H., Kwon, S. C., Simanshu, D. K., Patel, D. J., Kim, V. N. Uridylation by TUT4 and TUT7 marks mRNA for degradation. Cell 159: 1365-1376, 2014. [PubMed: 25480299] [Full Text: https://doi.org/10.1016/j.cell.2014.10.055]
Minoda, Y., Saeki, K., Aki, D., Takaki, H., Sanada, T., Koga, K., Kobayashi, T., Takaesu, G., Yoshimura, A. A novel zinc finger protein, ZCCHC11, interacts with TIFA and modulates TLR signaling. Biochem. Biophys. Res. Commun. 344: 1023-1030, 2006. Note: Erratum: Biochem. Biophys. Res. Commun. 353: 1121 only, 2007. [PubMed: 16643855] [Full Text: https://doi.org/10.1016/j.bbrc.2006.04.006]
Morgan, M., Much, C., DiGiacomo, M., Azzi, C., Ivanova, I., Vitsios, D. M., Pistolic, J., Collier, P., Moreira, P. N., Benes, V., Enright, A. J., O'Carroll, D. mRNA 3-prime uridylation and poly(A) tail length sculpt the mammalian maternal transcriptome. Nature 548: 347-351, 2017. [PubMed: 28792939] [Full Text: https://doi.org/10.1038/nature23318]
Nagase, T., Seki, N., Ishikawa, K., Tanaka, A., Nomura, N. Prediction of the coding sequences of unidentified human genes. V. The coding sequences of 40 new genes (KIAA0161-KIAA0200) deduced by analysis of cDNA clones from human cell line KG-1. DNA Res. 3: 17-24, 1996. [PubMed: 8724849] [Full Text: https://doi.org/10.1093/dnares/3.1.17]
Thornton, J. E., Chang, H.-M., Piskounova, E., Gregory, R. I. Lin28-mediated control of let-7 microRNA expression by alternative TUTases Zcchc11 (TUT4) and Zcchc6 (TUT7). RNA 18: 1875-1885, 2012. [PubMed: 22898984] [Full Text: https://doi.org/10.1261/rna.034538.112]