Non-coding RNAs as regulators of embryogenesis

Lee, R. C., Feinbaum, R. L. & Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843–854 (1993).

Wightman, B., Ha, I. & Ruvkun, G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75, 855–862 (1993).

Brown, C. J. et al. The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 71, 527–542 (1992).

Brockdorff, N. et al. The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell 71, 515–526 (1992).

Borsani, G. et al. Characterization of a murine gene expressed from the inactive X chromosome. Nature 351, 325–329 (1991).

Jacob, F. & Monod, J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318–356 (1961).

Britten, R. J. & Davidson, E. H. Gene regulation for higher cells: a theory. Science 165, 349–357 (1969).

Mattick, J. S., Taft, R. J. & Faulkner, G. J. A global view of genomic information-moving beyond the gene and the master regulator. Trends Genet. 26, 21–28 (2009).

Jacquier, A. The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nature Rev. Genet. 10, 833–844 (2009).

Carninci, P. Molecular biology: the long and short of RNAs. Nature 457, 974–975 (2009).

Mercer, T., Dinger, M. & Mattick, J. Long non-coding RNAs: insights into functions. Nature Rev. Genet. 10, 155–159 (2009).

Bartel, D. P. MicroRNAs: target recognition and regulatory functions. Cell 136, 215–233 (2009).

Bushati, N. & Cohen, S. M. microRNA functions. Annu. Rev. Cell Dev. Biol. 23, 175–205 (2007).

Koziol, M. J. & Rinn, J. L. RNA traffic control of chromatin complexes. Curr. Opin. Genet. Dev. 20, 142–148 (2010).

Henderson, I. R. & Jacobsen, S. E. Epigenetic inheritance in plants. Nature 447, 418–424 (2007).

Wollmann, H. & Weigel, D. Small RNAs in flower development. Eur. J. Cell Biol. 89, 250–257 (2010).

Chitwood, D. H. & Timmermans, M. C. Small RNAs are on the move. Nature 467, 415–419 (2010).

Swiezewski, S., Liu, F., Magusin, A. & Dean, C. Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462, 799–802 (2009).

Okamura, K. & Lai, E. C. Endogenous small interfering RNAs in animals. Nature Rev. Mol. Cell Biol. 9, 673–678 (2008).

Ghildiyal, M. & Zamore, P. D. Small silencing RNAs: an expanding universe. Nature Rev. Genet. 10, 94–108 (2009).

Giraldez, A. J. et al. MicroRNAs regulate brain morphogenesis in zebrafish. Science 308, 833–838 (2005).

Giraldez, A. J. et al. Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312, 75–79 (2006). This study demonstrates that a single miRNA family promotes the concerted elimination of hundreds of maternal RNAs in zebrafish and thereby sharpens the transition between maternal and zygotic gene expression programmes. The authors furthermore show that miR-430 destabilizes target mRNAs by causing their deadenylation.

Choi, W.-Y., Giraldez, A. J. & Schier, A. F. Target protectors reveal dampening and balancing of Nodal agonist and antagonist by miR-430. Science 318, 271–274 (2007). This study provides evidence for the physiological role of specific miRNA–mRNA interactions. Interference with miR-430 targeting of the Nodal agonist and antagonist by 'target protectors' identifies essential roles for miR-430 in regulating this key embryonic signalling pathway.

Wang, Y., Medvid, R., Melton, C., Jaenisch, R. & Blelloch, R. DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self-renewal. Nature Genet. 39, 380–385 (2007).

Suh, N. et al. MicroRNA function is globally suppressed in mouse oocytes and early embryos. Curr. Biol. 20, 271–277 (2010).

Tang, F. et al. Maternal microRNAs are essential for mouse zygotic development. Genes Dev. 21, 644–648 (2007).

Murchison, E. P. et al. Critical roles for Dicer in the female germline. Genes Dev. 21, 682–693 (2007).

Alvarez-Saavedra, E. & Horvitz, H. R. Many families of C. elegans microRNAs are not essential for development or viability. Curr. Biol. 20, 367–373 (2010). To date, this study provides the most comprehensive analyses of miRNA function in vivo . Loss-of-function mutants for individual as well as all members of redundantly acting miRNA families often revealed no or only subtle phenotypes. These results highlight the importance and challenge of miRNA loss-of-function analyses.

Brenner, J. L., Jasiewicz, K. L., Fahley, A. F., Kemp, B. J. & Abbott, A. L. Loss of individual microRNAs causes mutant phenotypes in sensitized genetic backgrounds in C. elegans. Curr. Biol. 20, 1321–1325 (2010).

Tadros, W. & Lipshitz, H. D. The maternal-to-zygotic transition: a play in two acts. Development 136, 3033–3042 (2009).

Schier, A. F. The maternal-zygotic transition: death and birth of RNAs. Science 316, 406–407 (2007).

Lund, E., Liu, M., Hartley, R. S., Sheets, M. D. & Dahlberg, J. E. Deadenylation of maternal mRNAs mediated by miR-427 in Xenopus laevis embryos. RNA 15, 2351–2363 (2009).

Bushati, N., Stark, A., Brennecke, J. & Cohen, S. M. Temporal reciprocity of miRNAs and their targets during the maternal-to-zygotic transition in Drosophila. Curr. Biol. 18, 501–506 (2008).

Wu, E. et al. Pervasive and cooperative deadenylation of 3′UTRs by embryonic MicroRNA families. Mol. Cell 40, 558–570 (2010).

Rouget, C. et al. Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo. Nature 467, 1128–1132 (2010).

Mishima, Y. et al. Differential regulation of germline mRNAs in soma and germ cells by zebrafish miR-430. Curr. Biol. 16, 2135–2142 (2006).

Kedde, M. et al. RNA-binding protein Dnd1 inhibits microRNA access to target mRNA. Cell 131, 1273–1286 (2007). This study describes one of the first examples for mechanisms that modulate miRNA activity. The conserved RNA-binding protein DND1 counteracts miRNA-mediated repression in human cells and zebrafish primordial germ cells.

Takeda, Y., Mishima, Y., Fujiwara, T., Sakamoto, H. & Inoue, K. DAZL relieves miRNA-mediated repression of germline mRNAs by controlling poly(A) tail length in zebrafish. PLoS ONE 4, e7513 (2009).

Kee, K., Angeles, V. T., Flores, M., Nguyen, H. N. & Reijo Pera, R. A. Human DAZL, DAZ and BOULE genes modulate primordial germ-cell and haploid gamete formation. Nature 462, 222–225 (2009).

Landgraf, P. et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129, 1401–1414 (2007).

Bernstein, E. et al. Dicer is essential for mouse development. Nature Genet. 35, 215–217 (2003).

Murchison, E. P., Partridge, J. F., Tam, O. H., Cheloufi, S. & Hannon, G. J. Characterization of Dicer-deficient murine embryonic stem cells. Proc.Natl Acad. Sci. USA 102, 12135–12140 (2005).

Kanellopoulou, C. et al. Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev. 19, 489–501 (2005).

Wang, Y. et al. Embryonic stem cell-specific microRNAs regulate the G1-S transition and promote rapid proliferation. Nature Genet. 40, 1478–1483 (2008). This paper provides compelling evidence that miRNAs are essential for ES cell self-renewal. Expression of a single miRNA family member of the ESCC miRNAs can rescue the proliferation defect of ES cells that lack mature miRNAs.

Judson, R. L., Babiarz, J. E., Venere, M. & Blelloch, R. Embryonic stem cell-specific microRNAs promote induced pluripotency. Nature Biotech. 27, 459–461 (2009).

Melton, C., Judson, R. L. & Blelloch, R. Opposing microRNA families regulate self-renewal in mouse embryonic stem cells. Nature 463, 621–626 (2010). This study presents evidence that two opposing families of miRNAs control ES cell maintenance and differentiation. Self-renewal-promoting ESCC miRNAs (see also reference 44) are antagonized by let-7, which functions as a regulator of ES cell differentiation.

Johnson, C. D. et al. The let-7 microRNA represses cell proliferation pathways in human cells. Cancer Res. 67, 7713–7722 (2007).

Rybak, A. et al. The let-7 target gene mouse lin-41 is a stem cell specific E3 ubiquitin ligase for the miRNA pathway protein Ago2. Nature Cell Biol. 11, 1411–1420 (2009).

Wang, Y., Keys, D. N., Au-Young, J. K. & Chen, C. MicroRNAs in embryonic stem cells. J. Cell. Physiol. 218, 251–255 (2009).

Marson, A. et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134, 521–533 (2008).

Xu, N., Papagiannakopoulos, T., Pan, G., Thomson, J. & Kosik, K. MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells. Cell 137, 647–658 (2009).

Newman, M. A., Thomson, J. M. & Hammond, S. M. Lin-28 interaction with the Let-7 precursor loop mediates regulated microRNA processing. RNA 14, 1539–1549 (2008).

Viswanathan, S., Daley, G. & Gregory, R. Selective blockade of microRNA processing by Lin28. Science 320, 97–100 (2008). References 52 and 53 identify the stem cell factor and RNA-binding protein LIN28 as an inhibitor of let-7 maturation.

Heo, I. et al. Lin28 mediates the terminal uridylation of let-7 precursor MicroRNA. Mol. Cell 32, 276–284 (2008).

Rybak, A. et al. A feedback loop comprising lin-28 and let-7 controls pre-let-7 maturation during neural stem-cell commitment. Nature Cell Biol. 10, 987–993 (2008).

Krol, J., Loedige, I. & Filipowicz, W. The widespread regulation of microRNA biogenesis, function and decay. Nature Rev. Genet. 11, 597–610 (2010).

Nakagawa, M. et al. Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts. Nature Biotech. 26, 101–106 (2008).

West, J. A. et al. A role for Lin28 in primordial germ-cell development and germ-cell malignancy. Nature 460, 909–913 (2009).

Guttman, M. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223–227 (2009). In this first comprehensive study of lncRNAs, the authors use the chromatin signature of RNA polymerase II-transcribed regions (H3K4me3 and H3K36me3) to identify lincRNAs in four mouse cell types. Many of these lincRNAs are predicted to function in a wide range of biological processes.

Guttman, M. et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nature Biotech. 28, 503–510 (2010).

Sheik Mohamed, J., Gaughwin, P. M., Lim, B., Robson, P. & Lipovich, L. Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells. RNA 16, 324–337 (2009).

Dinger, M. E. et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res. 18, 1433–1445 (2008).

Loewer, S. et al. Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nature Genet. 42, 1113–1117 (2010).

Schier, A. F. Nodal morphogens. Cold Spring Harb. Perspect. Biol. 1, a003459 (2009).

Martello, G. et al. MicroRNA control of Nodal signalling. Nature 449, 183–188 (2007).

Rosa, A., Spagnoli, F. M. & Brivanlou, A. H. The miR-430/427/302 family controls mesendodermal fate specification via species-specific target selection. Dev. Cell 16, 517–527 (2009).

Flynt, A. S., Li, N., Thatcher, E. J., Solnica-Krezel, L. & Patton, J. G. Zebrafish miR-214 modulates Hedgehog signaling to specify muscle cell fate. Nature Genet. 39, 259–263 (2007).

Leucht, C. et al. MicroRNA-9 directs late organizer activity of the midbrain-hindbrain boundary. Nature Neurosci. 11, 641–648 (2008).

Li, Y., Wang, F., Lee, J.-A. & Gao, F.-B. MicroRNA-9a ensures the precise specification of sensory organ precursors in Drosophila. Genes Dev. 20, 2793–2805 (2006).

Lai, E. C., Tam, B. & Rubin, G. M. Pervasive regulation of Drosophila Notch target genes by GY-box-, Brd-box-, and K-box-class microRNAs. Genes Dev. 19, 1067–1080 (2005).

Lee, J. T. Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome. Genes Dev. 23, 1831–1842 (2009).

Koerner, M. V., Pauler, F. M., Huang, R. & Barlow, D. P. The function of non-coding RNAs in genomic imprinting. Development 136, 1771–1783 (2009).

Schmidt, J. V., Levorse, J. M. & Tilghman, S. M. Enhancer competition between H19 and Igf2 does not mediate their imprinting. Proc. Natl Acad. Sci. USA 96, 9733–9738 (1999).

Mancini-Dinardo, D., Steele, S. J., Levorse, J. M., Ingram, R. S. & Tilghman, S. M. Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes. Genes Dev. 20, 1268–1282 (2006).

Sleutels, F., Zwart, R. & Barlow, D. P. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415, 810–813 (2002).

Umlauf, D. et al. Imprinting along the Kcnq1 domain on mouse chromosome 7 involves repressive histone methylation and recruitment of Polycomb group complexes. Nature Genet. 36, 1296–1300 (2004).

Nagano, T. et al. The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 322, 1717–1720 (2008).

Pandey, R. R. et al. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol. Cell 32, 232–246 (2008). References 77 and 78 demonstrate essential roles for imprinted lncRNAs in recruiting chromatin modifiers to neighbouring genes, resulting in monoallelic silencing of entire gene clusters in cis.

Terranova, R. et al. Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos. Dev. Cell 15, 668–679 (2008).

Mohammad, F., Mondal, T., Guseva, N., Pandey, G. K. & Kanduri, C. Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1. Development 137, 2493–2499 (2010).

Haig, D. Genomic imprinting and kinship: how good is the evidence? Annu. Rev. Genet. 38, 553–585 (2004).

Penny, G. D., Kay, G. F., Sheardown, S. A., Rastan, S. & Brockdorff, N. Requirement for Xist in X chromosome inactivation. Nature 379, 131–137 (1996).

Ogawa, Y., Sun, B. K. & Lee, J. T. Intersection of the RNA interference and X-inactivation pathways. Science 320, 1336–1341 (2008).

Kanellopoulou, C. et al. X chromosome inactivation in the absence of Dicer. Proc. Natl Acad. Sci. USA 106, 1122–1127 (2009).

Sun, B. K., Deaton, A. M. & Lee, J. T. A transient heterochromatic state in Xist preempts X inactivation choice without RNA stabilization. Mol. Cell 21, 617–628 (2006).

Tian, D., Sun, S. & Lee, J. T. The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell 143, 390–403 (2010).

Wutz, A., Rasmussen, T. P. & Jaenisch, R. Chromosomal silencing and localization are mediated by different domains of Xist RNA. Nature Genet. 30, 167–174 (2002).

Navarro, P., Page, D. R., Avner, P. & Rougeulle, C. Tsix-mediated epigenetic switch of a CTCF-flanked region of the Xist promoter determines the Xist transcription program. Genes Dev. 20, 2787–2792 (2006).

Zhao, J., Sun, B. K., Erwin, J. A., Song, J.-J. & Lee, J. T. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 322, 750–756 (2008). Analogous to the function of imprinted ncRNAs (see references 77 and 78), this study provides evidence that a conserved ncRNA originating from the Xic recruits repressive chromatin-modifying complexes of the Polycomb group family (PRC2) in cis . Recruitment of PRC2 is essential for the nucleation of silencing of one entire X chromosome in mammalian females.

Gelbart, M. E. & Kuroda, M. I. Drosophila dosage compensation: a complex voyage to the X chromosome. Development 136, 1399–1410 (2009).

Akhtar, A. & Becker, P. B. Activation of transcription through histone H4 acetylation by MOF, an acetyltransferase essential for dosage compensation in Drosophila. Mol. Cell 5, 367–375 (2000).

Meller, V. H. & Rattner, B. P. The roX genes encode redundant male-specific lethal transcripts required for targeting of the MSL complex. EMBO J. 21, 1084–1091 (2002).

Deng, X., Rattner, B. P., Souter, S. & Meller, V. H. The severity of roX1 mutations is predicted by MSL localization on the X chromosome. Mech. Dev. 122, 1094–1105 (2005).

Stuckenholz, C., Meller, V. H. & Kuroda, M. I. Functional redundancy within roX1, a noncoding RNA involved in dosage compensation in Drosophila melanogaster. Genetics 164, 1003–1014 (2003).

Gilfillan, G. D. et al. Chromosome-wide gene-specific targeting of the Drosophila dosage compensation complex. Genes Dev. 20, 858–870 (2006).

Alekseyenko, A. A. et al. A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell 134, 599–609 (2008).

Kind, J. & Akhtar, A. Cotranscriptional recruitment of the dosage compensation complex to X-linked target genes. Genes Dev. 21, 2030–2040 (2007).

Lewis, E. B. A gene complex controlling segmentation in Drosophila. Nature 276, 565–570 (1978).

Lipshitz, H. D., Peattie, D. A. & Hogness, D. S. Novel transcripts from the Ultrabithorax domain of the bithorax complex. Genes Dev. 1, 307–322 (1987).

Bender, W. & Fitzgerald, D. Transcription activates repressed domains in the Drosophila bithorax complex. Development 129, 4923–4930 (2002).

Hogga, I. & Karch, F. Transcription through the iab-7 cis-regulatory domain of the bithorax complex interferes with maintenance of Polycomb-mediated silencing. Development 129, 4915–4922 (2002).

Petruk, S. et al. Transcription of bxd noncoding RNAs promoted by trithorax represses Ubx in cis by transcriptional interference. Cell 127, 1209–1221 (2006).

Sanchez-Elsner, T., Gou, D., Kremmer, E. & Sauer, F. Noncoding RNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax. Science 311, 1118–1123 (2006).

Orom, U. A. et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 143, 46–58 (2010).

Martianov, I., Ramadass, A., Serra Barros, A., Chow, N. & Akoulitchev, A. Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 445, 666–670 (2007).

Kanhere, A. et al. Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2. Mol. Cell 38, 675–688 (2010).

Rinn, J. L. et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129, 1311–1323 (2007).

Tsai, M.-C. et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science 329, 689–693 (2010). References 107 and 108 identify the lncRNA HOTAIR as trans -acting repressor of gene expression of the HOXD cluster (reference 107) and of several other loci throughout the genome (reference 108). HOTAIR 's silencing activity arises from its interaction with at least two repressive chromatin-modifying complexes, PRC2 (references 107,108) and LSD1–CoREST–REST (reference 108).

Gupta, R. A. et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464, 1071–1076 (2010).

Zappulla, D. C. & Cech, T. R. RNA as a flexible scaffold for proteins: yeast telomerase and beyond. Cold Spring Harb. Symp. Quant. Biol. 71, 217–224 (2006).

Khalil, A. M. et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl Acad. Sci. USA 106, 11667–11672 (2009).

Huarte, M. et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142, 409–419 (2010).

Bond, A. M. et al. Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry. Nature Neurosci. 12, 1020–1027 (2009). One of the few in vivo studies on lncRNA function available to date; phenotypic analysis of Evf2 lncRNA knockout mice provides evidence that this lncRNA has essential roles for the development and function of GABAergic neurons.

Yekta, S., Shih, I.-H. & Bartel, D. P. MicroRNA-directed cleavage of HOXB8 mRNA. Science 304, 594–596 (2004).

Mansfield, J. H. et al. MicroRNA-responsive 'sensor' transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nature Genet. 36, 1079–1083 (2004).

Stark, A. et al. A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev. 22, 8–13 (2008).

Ronshaugen, M., Biemar, F., Piel, J., Levine, M. & Lai, E. C. The Drosophila microRNA iab-4 causes a dominant homeotic transformation of halteres to wings. Genes Dev. 19, 2947–2952 (2005).

Tyler, D. M. et al. Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci. Genes Dev. 22, 26–36 (2008).

Bender, W. MicroRNAs in the Drosophila bithorax complex. Genes Dev. 22, 14–19 (2008).

Thomsen, S., Azzam, G., Kaschula, R., Williams, L. S. & Alonso, C. R. Developmental RNA processing of 3′UTRs in Hox mRNAs as a context-dependent mechanism modulating visibility to microRNAs. Development 137, 2951–2960 (2010).

Amaral, P. P. & Mattick, J. S. Noncoding RNA in development. Mamm. Genome 19, 454–492 (2008).

Gao, F. B. Context-dependent functions of specific microRNAs in neuronal development. Neural Dev. 5, 25 (2010).

Conaco, C., Otto, S., Han, J.-J. & Mandel, G. Reciprocal actions of REST and a microRNA promote neuronal identity. Proc. Natl Acad. Sci. USA 103, 2422–2427 (2006).

Visvanathan, J., Lee, S., Lee, B., Lee, J. W. & Lee, S.-K. The microRNA miR-124 antagonizes the anti-neural REST/SCP1 pathway during embryonic CNS development. Genes Dev. 21, 744–749 (2007).

Yoo, A. S., Staahl, B. T., Chen, L. & Crabtree, G. R. MicroRNA-mediated switching of chromatin-remodelling complexes in neural development. Nature 460, 642–646 (2009).

Makeyev, E. V., Zhang, J., Carrasco, M. A. & Maniatis, T. The MicroRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing. Mol. Cell 27, 435–448 (2007).

Boutz, P. L., Chawla, G., Stoilov, P. & Black, D. L. MicroRNAs regulate the expression of the alternative splicing factor nPTB during muscle development. Genes Dev. 21, 71–84 (2007).

Chen, J. F. et al. The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nature Genet. 38, 228–233 (2006).

Zhao, Y., Samal, E. & Srivastava, D. Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 436, 214–220 (2005).

Zhao, Y. et al. Dysregulation of cardiogenesis, cardiac conduction, and cell cycle in mice lacking miRNA-1-2. Cell 129, 303–317 (2007).

Zhao, C., Sun, G., Li, S. & Shi, Y. A feedback regulatory loop involving microRNA-9 and nuclear receptor TLX in neural stem cell fate determination. Nature Struct. Mol. Biol. 16, 365–371 (2009).

Clark, A. et al. The microRNA miR-124 controls gene expression in the sensory nervous system of Caenorhabditis elegans. Nucleic Acids Res. 38, 3780–3793 (2010).

Johnston, R. J. & Hobert, O. A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426, 845–849 (2003). One of the first studies that implicated miRNAs in regulating cell fate decisions.

Johnston, R. J. & Hobert, O. A novel C. elegans zinc finger transcription factor, lsy-2, required for the cell type-specific expression of the lsy-6 microRNA. Development 132, 5451–5460 (2005).

Didiano, D., Cochella, L., Tursun, B. & Hobert, O. Neuron-type specific regulation of a 3′UTR through redundant and combinatorially acting cis-regulatory elements. RNA 16, 349–363 (2010).

Ponjavic, J., Oliver, P. L., Lunter, G. & Ponting, C. P. Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain. PLoS Genet. 5, e1000617 (2009).

Mercer, T. R., Dinger, M. E., Sunkin, S. M., Mehler, M. F. & Mattick, J. S. Specific expression of long noncoding RNAs in the mouse brain. Proc. Natl Acad. Sci. USA 105, 716–721 (2008).

Young, T. L., Matsuda, T. & Cepko, C. L. The noncoding RNA taurine upregulated gene 1 is required for differentiation of the murine retina. Curr. Biol. 15, 501–512 (2005).

Feng, J. et al. The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev. 20, 1470–1484 (2006).

Schratt, G. M. et al. A brain-specific microRNA regulates dendritic spine development. Nature 439, 283–289 (2006).

Korpal, M., Lee, E. S., Hu, G. & Kang, Y. The miR-200 family inhibits epithelial-mesenchymal transition and cancer cell migration by direct targeting of E-cadherin transcriptional repressors ZEB1 and ZEB2. J. Biol. Chem. 283, 14910–14914 (2008).

Park, S.-M., Gaur, A. B., Lengyel, E. & Peter, M. E. The miR-200 family determines the epithelial phenotype of cancer cells by targeting the E-cadherin repressors ZEB1 and ZEB2. Genes Dev. 22, 894–907 (2008).

Gregory, P. A. et al. The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1. Nature Cell Biol. 10, 593–601 (2008). References 141–143 identify the miR-200 family as essential regulators of the gene regulatory network that guards the EMT. These studies also indicate that misregulation of pathways that are normally active during development can cause disease during later stages of development.

Rajasethupathy, P. et al. Characterization of small RNAs in Aplysia reveals a role for miR-124 in constraining synaptic plasticity through CREB. Neuron 63, 803–817 (2009).

Thiery, J. P., Acloque, H., Huang, R. Y. J. & Nieto, M. A. Epithelial-mesenchymal transitions in development and disease. Cell 139, 871–890 (2009).

Cano, A. & Nieto, M. A. Non-coding RNAs take centre stage in epithelial-to-mesenchymal transition. Trends Cell Biol. 18, 357–359 (2008).

Burk, U. et al. A reciprocal repression between ZEB1 and members of the miR-200 family promotes EMT and invasion in cancer cells. EMBO Rep. 9, 582–589 (2008).

Wellner, U. et al. The EMT-activator ZEB1 promotes tumorigenicity by repressing stemness-inhibiting microRNAs. Nature Cell Biol. 11, 1487–1495 (2009).

Beltran, M. et al. A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev. 22, 756–769 (2008).

Frankel, L. B. et al. Programmed cell death 4 (PDCD4) is an important functional target of the microRNA miR-21 in breast cancer cells. J. Biol. Chem. 283, 1026–1033 (2008).

Asangani, I. A. et al. MicroRNA-21 (miR-21) post-transcriptionally downregulates tumor suppressor Pdcd4 and stimulates invasion, intravasation and metastasis in colorectal cancer. Oncogene 27, 2128–2136 (2008).

Davis, B. N., Hilyard, A. C., Lagna, G. & Hata, A. SMAD proteins control DROSHA-mediated microRNA maturation. Nature 454, 56–61 (2008).

Davis, B. N., Hilyard, A. C., Nguyen, P. H., Lagna, G. & Hata, A. Smad proteins bind a conserved RNA sequence to promote microRNA maturation by Drosha. Mol. Cell 39, 373–384 (2010).

Miska, E. A. et al. Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genet. 3, e215 (2007).

Abbott, A. L. et al. 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 (2005).

Grimson, A. et al. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 455, 1193–1197 (2008).

Christodoulou, F. et al. Ancient animal microRNAs and the evolution of tissue identity. Nature 463, 1084–1088 (2010).

Clop, A. et al. A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nature Genet. 38, 813–818 (2006).

Hanyu-Nakamura, K., Sonobe-Nojima, H., Tanigawa, A., Lasko, P. & Nakamura, A. Drosophila Pgc protein inhibits P-TEFb recruitment to chromatin in primordial germ cells. Nature 451, 730–733 (2008).

Kondo, T. et al. Small peptides switch the transcriptional activity of shavenbaby during Drosophila embryogenesis. Science 329, 336–339 (2010).

Kondo, T. et al. Small peptide regulators of actin-based cell morphogenesis encoded by a polycistronic mRNA. Nature Cell Biol. 9, 660–665 (2007).

Candeias, M. M. et al. P53 mRNA controls p53 activity by managing Mdm2 functions. Nature Cell Biol. 10, 1098–1105 (2008).

Jenny, A. et al. A translation-independent role of oskar RNA in early Drosophila oogenesis. Development 133, 2827–2833 (2006).

Waters, L. S. & Storz, G. Regulatory RNAs in bacteria. Cell 136, 615–628 (2009).

Iliopoulos, D. et al. Loss of miR-200 inhibition of Suz12 leads to polycomb-mediated repression required for the formation and maintenance of cancer stem cells. Mol. Cell 39, 761–772 (2010).

Shimono, Y. et al. Downregulation of miRNA-200c links breast cancer stem cells with normal stem cells. Cell 138, 592–603 (2009).

Lee, J. T. The X as model for RNA's niche in epigenomic regulation. Cold Spring Harb. Perspect. Biol. 2, a003749 (2010).

Cheng, L.-C., Pastrana, E., Tavazoie, M. & Doetsch, F. miR-124 regulates adult neurogenesis in the subventricular zone stem cell niche. Nature Neurosci. 12, 399–408 (2009).