lin-28 is a conserved regulator of cell fate succession in animals. In Caenorhabditis elegans, it is a component of the heterochronic gene pathway that governs larval developmental timing, while its vertebrate homologs promote pluripotency and control differentiation in diverse tissues. The RNA binding protein encoded by lin-28 can directly inhibit let-7 microRNA processing by a novel mechanism that is conserved from worms to humans. We found that C. elegans LIN-28 protein can interact with four distinct let-7 family pre-microRNAs, but in vivo inhibits the premature accumulation of only let-7. Surprisingly, however, lin-28 does not require let-7 or its relatives for its characteristic promotion of second larval stage cell fates. In other words, we find that the premature accumulation of mature let-7 does not account for lin-28's precocious phenotype. To explain let-7's role in lin-28 activity, we provide evidence that lin-28 acts in two steps: first, the let-7–independent positive regulation of hbl-1 through its 3′UTR to control L2 stage-specific cell fates; and second, a let-7–dependent step that controls subsequent fates via repression of lin-41. Our evidence also indicates that let-7 functions one stage earlier in C. elegans development than previously thought. Importantly, lin-28's two-step mechanism resembles that of the heterochronic gene lin-14, and the overlap of their activities suggests a clockwork mechanism for developmental timing. Furthermore, this model explains the previous observation that mammalian Lin28 has two genetically separable activities. Thus, lin-28's two-step mechanism may be an essential feature of its evolutionarily conserved role in cell fate succession.
References
[1]
Ambros V, Horvitz HR (1984) Heterochronic mutants of the nematode Caenorhabditis elegans. Science 226: 409–416.
[2]
Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, et al. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901–906.
[3]
Resnick TD, McCulloch KA, Rougvie AE (2010) miRNAs give worms the time of their lives: small RNAs and temporal control in Caenorhabditis elegans. Dev Dyn 239: 1477–1489.
[4]
Moss EG (2007) Heterochronic genes and the nature of developmental time. Curr Biol 17: R425–434.
[5]
Ambros V (2011) MicroRNAs and developmental timing. Curr Opin Genet Dev.
[6]
Abbott AL, Alvarez-Saavedra E, Miska EA, Lau NC, Bartel DP, et al. (2005) The let-7 MicroRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans. Dev Cell 9: 403–414.
[7]
Seggerson K, Tang L, Moss EG (2002) Two genetic circuits repress the Caenorhabditis elegans heterochronic gene lin-28 after translation initiation. Dev Biol 243: 215–225.
[8]
Jeon M, Gardner HF, Miller EA, Deshler J, Rougvie AE (1999) Similarity of the C. elegans developmental timing protein LIN-42 to circadian rhythm proteins. Science 286: 1141–1146.
[9]
Hammell CM, Karp X, Ambros V (2009) A feedback circuit involving let-7-family miRNAs and DAF-12 integrates environmental signals and developmental timing in Caenorhabditis elegans. Proc Natl Acad Sci U S A 106: 18668–18673.
[10]
Pepper AS, McCane JE, Kemper K, Yeung DA, Lee RC, et al. (2004) The C. elegans heterochronic gene lin-46 affects developmental timing at two larval stages and encodes a relative of the scaffolding protein gephyrin. Development 131: 2049–2059.
[11]
Maller Schulman BR, Liang X, Stahlhut C, DelConte C, Stefani G, et al. (2008) The let-7 microRNA target gene, Mlin41/Trim71 is required for mouse embryonic survival and neural tube closure. Cell Cycle 7: 3935–3942.
[12]
Kloosterman WP, Wienholds E, Ketting RF, Plasterk RH (2004) Substrate requirements for let-7 function in the developing zebrafish embryo. Nucleic Acids Res 32: 6284–6291.
[13]
Wulczyn FG, Smirnova L, Rybak A, Brandt C, Kwidzinski E, et al. (2007) Post-transcriptional regulation of the let-7 microRNA during neural cell specification. Faseb J 21: 415–426.
[14]
Lin YC, Hsieh LC, Kuo MW, Yu J, Kuo HH, et al. (2007) Human TRIM71 and its nematode homologue are targets of let-7 microRNA and its zebrafish orthologue is essential for development. Mol Biol Evol 24: 2525–2534.
[15]
Sokol NS, Xu P, Jan YN, Ambros V (2008) Drosophila let-7 microRNA is required for remodeling of the neuromusculature during metamorphosis. Genes Dev 22: 1591–1596.
[16]
Caygill EE, Johnston LA (2008) Temporal regulation of metamorphic processes in Drosophila by the let-7 and miR-125 heterochronic microRNAs. Curr Biol 18: 943–950.
[17]
West JA, Viswanathan SR, Yabuuchi A, Cunniff K, Takeuchi A, et al. (2009) A role for Lin28 in primordial germ-cell development and germ-cell malignancy. Nature 460: 909–913.
[18]
Balzer E, Heine C, Jiang Q, Lee VM, Moss EG (2010) LIN28 alters cell fate succession and acts independently of the let-7 microRNA during neurogliogenesis in vitro. Development 137: 891–900.
[19]
Yang DH, Moss EG (2003) Temporally regulated expression of Lin-28 in diverse tissues of the developing mouse. Gene Expr Patterns 3: 719–726.
[20]
Moss EG, Tang L (2003) Conservation of the heterochronic regulator Lin-28, its developmental expression and microRNA complementary sites. Dev Biol 258: 432–442.
[21]
Polesskaya A, Cuvellier S, Naguibneva I, Duquet A, Moss EG, et al. (2007) Lin-28 binds IGF-2 mRNA and participates in skeletal myogenesis by increasing translation efficiency. Genes Dev 21: 1125–1138.
[22]
Yokoyama S, Hashimoto M, Shimizu H, Ueno-Kudoh H, Uchibe K, et al. (2008) Dynamic gene expression of Lin-28 during embryonic development in mouse and chicken. Gene Expr Patterns 8: 155–160.
[23]
Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, et al. (2007) Induced pluripotent stem cell lines derived from human somatic cells. Science 318: 1917–1920.
[24]
Zhu H, Shah S, Shyh-Chang N, Shinoda G, Einhorn WS, et al. (2010) Lin28a transgenic mice manifest size and puberty phenotypes identified in human genetic association studies. Nat Genet 42: 626–630.
[25]
Viswanathan SR, Powers JT, Einhorn W, Hoshida Y, Ng TL, et al. (2009) Lin28 promotes transformation and is associated with advanced human malignancies. Nat Genet 41: 843–848.
[26]
Viswanathan SR, Daley GQ, Gregory RI (2008) Selective blockade of microRNA processing by Lin28. Science 320: 97–100.
[27]
Heo I, Joo C, Cho J, Ha M, Han J, et al. (2008) Lin28 mediates the terminal uridylation of let-7 precursor MicroRNA. Mol Cell 32: 276–284.
[28]
Heo I, Joo C, Kim YK, Ha M, Yoon MJ, et al. (2009) TUT4 in concert with Lin28 suppresses microRNA biogenesis through pre-microRNA uridylation. Cell 138: 696–708.
[29]
Lehrbach NJ, Armisen J, Lightfoot HL, Murfitt KJ, Bugaut A, et al. (2009) LIN-28 and the poly(U) polymerase PUP-2 regulate let-7 microRNA processing in Caenorhabditis elegans. Nat Struct Mol Biol 16: 1016–1020.
[30]
Hagan JP, Piskounova E, Gregory RI (2009) Lin28 recruits the TUTase Zcchc11 to inhibit let-7 maturation in mouse embryonic stem cells. Nat Struct Mol Biol 16: 1021–1025.
[31]
Van Wynsberghe PM, Kai ZS, Massirer KB, Burton VH, Yeo GW, et al. (2011) LIN-28 co-transcriptionally binds primary let-7 to regulate miRNA maturation in Caenorhabditis elegans. Nat Struct Mol Biol 18: 302–308.
[32]
Newman MA, Thomson JM, Hammond SM (2008) Lin-28 interaction with the Let-7 precursor loop mediates regulated microRNA processing. Rna 14: 1539–1549.
[33]
Piskounova E, Viswanathan SR, Janas M, LaPierre RJ, Daley GQ, et al. (2008) Determinants of microRNA processing inhibition by the developmentally regulated RNA-binding protein Lin28. J Biol Chem 283: 21310–21314.
[34]
Balzer E, Moss EG (2007) Localization of the developmental timing regulator Lin28 to mRNP complexes, P-bodies and stress granules. RNA Biol 4: 16–25.
[35]
Xu B, Zhang K, Huang Y (2009) Lin28 modulates cell growth and associates with a subset of cell cycle regulator mRNAs in mouse embryonic stem cells. Rna 15: 357–361.
[36]
Xu B, Huang Y (2009) Histone H2a mRNA interacts with Lin28 and contains a Lin28-dependent posttranscriptional regulatory element. Nucleic Acids Res 37: 4256–4263.
[37]
Qiu C, Ma Y, Wang J, Peng S, Huang Y (2010) Lin28-mediated post-transcriptional regulation of Oct4 expression in human embryonic stem cells. Nucleic Acids Res 38: 1240–1248.
[38]
Peng S, Chen LL, Lei XX, Yang L, Lin H, et al. (2011) Genome-wide studies reveal that lin28 enhances the translation of genes important for growth and survival of human embryonic stem cells. Stem Cells 29: 496–504.
[39]
Slack FJ, Basson M, Liu Z, Ambros V, Horvitz HR, et al. (2000) The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Mol Cell 5: 659–669.
[40]
Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294: 853–858.
[41]
Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858–862.
[42]
Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294: 862–864.
[43]
Ruby JG, Jan C, Player C, Axtell MJ, Lee W, et al. (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127: 1193–1207.
[44]
Bussing I, Slack FJ, Grosshans H (2008) let-7 microRNAs in development, stem cells and cancer. Trends Mol Med 14: 400–409.
[45]
Ambros V, Horvitz HR (1987) The lin-14 locus of Caenorhabditis elegans controls the time of expression of specific postembryonic developmental events. Genes Dev 1: 398–414.
[46]
Roush S, Slack FJ (2008) The let-7 family of microRNAs. Trends Cell Biol 18: 505–516.
[47]
Hook B, Bernstein D, Zhang B, Wickens M (2005) RNA-protein interactions in the yeast three-hybrid system: affinity, sensitivity, and enhanced library screening. Rna 11: 227–233.
[48]
Esquela-Kerscher A, Johnson SM, Bai L, Saito K, Partridge J, et al. (2005) Post-embryonic expression of C. elegans microRNAs belonging to the lin-4 and let-7 families in the hypodermis and the reproductive system. Dev Dyn 234: 868–877.
[49]
Li M, Jones-Rhoades MW, Lau NC, Bartel DP, Rougvie AE (2005) Regulatory mutations of mir-48, a C. elegans let-7 family MicroRNA, cause developmental timing defects. Dev Cell 9: 415–422.
[50]
Ding L, Spencer A, Morita K, Han M (2005) The developmental timing regulator AIN-1 interacts with miRISCs and may target the argonaute protein ALG-1 to cytoplasmic P bodies in C. elegans. Mol Cell 19: 437–447.
[51]
Zhang L, Ding L, Cheung TH, Dong MQ, Chen J, et al. (2007) Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2. Mol Cell 28: 598–613.
[52]
Abrahante JE, Daul AL, Li M, Volk ML, Tennessen JM, et al. (2003) The Caenorhabditis elegans hunchback-like gene lin-57/hbl-1 controls developmental time and is regulated by microRNAs. Dev Cell 4: 625–637.
[53]
Lin SY, Johnson SM, Abraham M, Vella MC, Pasquinelli A, et al. (2003) The C elegans hunchback homolog, hbl-1, controls temporal patterning and is a probable microRNA target. Dev Cell 4: 639–650.
[54]
Fay DS, Stanley HM, Han M, Wood WB (1999) A Caenorhabditis elegans homologue of hunchback is required for late stages of development but not early embryonic patterning. Dev Biol 205: 240–253.
[55]
Ambros V (1989) A hierarchy of regulatory genes controls a larva-to-adult developmental switch in C. elegans. Cell 57: 49–57.
[56]
Sulston JE, Horvitz HR (1977) Post-embryonic cell lineages of the nematode, Caenorhabditis elegans. Dev Biol 56: 110–156.
[57]
Del Rio-Albrechtsen T, Kiontke K, Chiou SY, Fitch DH (2006) Novel gain-of-function alleles demonstrate a role for the heterochronic gene lin-41 in C. elegans male tail tip morphogenesis. Dev Biol 297: 74–86.
[58]
Rougvie AE (2001) Control of developmental timing in animals. Nat Rev Genet 2: 690–701.
[59]
Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843–854.
[60]
Wightman B, Ha I, Ruvkun G (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75: 855–862.
[61]
Hong Y, Lee RC, Ambros V (2000) Structure and function analysis of LIN-14, a temporal regulator of postembryonic developmental events in Caenorhabditis elegans. Mol Cell Biol 20: 2285–2295.
[62]
Moss EG, Lee RC, Ambros V (1997) The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA. Cell 88: 637–646.
[63]
Causier B, Schwarz-Sommer Z, Davies B (2010) Floral organ identity: 20 years of ABCs. Semin Cell Dev Biol 21: 73–79.
[64]
Wood WB (1988) The Nematode Caenorhabditis elegans. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory.
[65]
Koh K, Rothman JH (2001) ELT-5 and ELT-6 are required continuously to regulate epidermal seam cell differentiation and cell fusion in C. elegans. Development 128: 2867–2880.
[66]
Timmons L, Court DL, Fire A (2001) Ingestion of bacterially expressed dsRNAs can produce specific and potent genetic interference in Caenorhabditis elegans. Gene 263: 103–112.
[67]
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(?Delta Delta C(T)) Method. Methods 25: 402–408.
[68]
Nguyen CQ, Hall DH, Yang Y, Fitch DH (1999) Morphogenesis of the Caenorhabditis elegans male tail tip. Dev Biol 207: 86–106.