Deadenylation of maternal mRNAs mediated by miR-427 in Xenopus laevis embryos.

We show that microRNA-427 (miR-427) mediates the rapid deadenylation of maternal mRNAs after the midblastula transition (MBT) of Xenopus laevis embryogenesis. By MBT, the stage when the embryonic cell cycle is remodeled and zygotic transcription of mRNAs is initiated, each embryo has accumulated approximately 10(9) molecules of miR-427 processed from multimeric pri-miR-427 transcripts synthesized after fertilization. We demonstrate that the maternal mRNAs for cyclins A1 and B2 each contain a single miR-427 target sequence, spanning less than 30 nucleotides, that is both necessary and sufficient for deadenylation, and that inactivation of miR-427 leads to stabilization of the mRNAs. Although this deadenylation normally takes place after MBT, exogenous miRNAs produced prematurely in vivo can promote deadenylation prior to MBT, indicating that turnover of the maternal mRNAs is limited by the amount of accumulated miR-427. Injected transcripts comprised solely of the cyclin mRNA 3' untranslated regions or bearing a 5' ApppG cap undergo deadenylation, showing that translation of the targeted RNA is not required. miR-427 is not unique in promoting deadenylation, as an unrelated miRNA, let-7, can substitute for miR-427 if the reporter RNA contains an appropriate let-7 target site. We propose that miR-427, like the orthologous miR-430 of zebrafish, functions to down-regulate expression of maternal mRNAs early in development.

[1]  A. Brivanlou,et al.  The miR-430/427/302 family controls mesendodermal fate specification via species-specific target selection. , 2009, Developmental cell.

[2]  Alexander F. Schier,et al.  Differential Regulation of Germline mRNAs in Soma and Germ Cells by Zebrafish miR-430 , 2006, Current Biology.

[3]  Oliver Hobert,et al.  UTR ′ Molecular architecture of a miRNA-regulated 3 Material Supplemental , 2008 .

[4]  Katherine C. Chen,et al.  Dissection of the XChk 1 Signaling Pathway in Xenopus laevis Embryos , 2000 .

[5]  Ligang Wu,et al.  MicroRNAs direct rapid deadenylation of mRNA. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[6]  D. Melton,et al.  Developmental regulation of a gastrula‐specific gene injected into fertilized Xenopus eggs. , 1985, The EMBO journal.

[7]  W. Filipowicz,et al.  Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? , 2008, Nature Reviews Genetics.

[8]  Eric H. Davidson,et al.  Gene activity in early development , 1968 .

[9]  Phillip D Zamore,et al.  Sequence-Specific Inhibition of Small RNA Function , 2004, PLoS biology.

[10]  J. Cavaille,et al.  C19MC microRNAs are processed from introns of large Pol-II, non-protein-coding transcripts , 2009, Nucleic acids research.

[11]  Marvin Wickens,et al.  A PUF family portrait: 3'UTR regulation as a way of life. , 2002, Trends in genetics : TIG.

[12]  J. Faber,et al.  Normal Table of Xenopus Laevis (Daudin) , 1958 .

[13]  Toru Suzuki,et al.  Stage‐specific expression of microRNAs during Xenopus development , 2005, FEBS letters.

[14]  V. Ambros,et al.  The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 , 1993, Cell.

[15]  A Tiny Helper Lightens the Maternal Load , 2006, Cell.

[16]  S. Cohen,et al.  Temporal Reciprocity of miRNAs and Their Targets during the Maternal-to-Zygotic Transition in Drosophila , 2008, Current Biology.

[17]  Elisa Izaurralde,et al.  Deadenylation is a widespread effect of miRNA regulation. , 2008, RNA.

[18]  M. Wickens,et al.  Mammalian GLD-2 homologs are poly(A) polymerases. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[19]  R. Aharonov,et al.  Identification of hundreds of conserved and nonconserved human microRNAs , 2005, Nature Genetics.

[20]  J. Paris,et al.  Poly(A) metabolism and polysomal recruitment of maternal mRNAs during early Xenopus development. , 1990, Developmental biology.

[21]  Thomas Tuschl,et al.  Sequence-specific inhibition of microRNA- and siRNA-induced RNA silencing. , 2004, RNA.

[22]  M. Wickens,et al.  Autoregulation of GLD-2 cytoplasmic poly(A) polymerase. , 2006, RNA.

[23]  C. Wylie,et al.  Beta-catenin signaling activity dissected in the early Xenopus embryo: a novel antisense approach. , 2000, Developmental biology.

[24]  Mihaela Zavolan,et al.  Comparative Analysis of mRNA Targets for Human PUF-Family Proteins Suggests Extensive Interaction with the miRNA Regulatory System , 2008, PloS one.

[25]  J. Belasco,et al.  Importance of Translation and Nonnucleolytic Ago Proteins for On-Target RNA Interference , 2008, Current Biology.

[26]  E. Obayashi,et al.  Crystallization of RNA-protein complexes. , 2007, Methods in molecular biology.

[27]  J. Jonák,et al.  Expression patterns of Src-family tyrosine kinases during Xenopus laevis development. , 2009, The International journal of developmental biology.

[28]  A. Shyu,et al.  Ago-TNRC6 complex triggers microRNA-mediated mRNA decay by promoting biphasic deadenylation followed by decapping , 2009, Nature Structural &Molecular Biology.

[29]  Anton J. Enright,et al.  Materials and Methods Figs. S1 to S4 Tables S1 to S5 References and Notes Micrornas Regulate Brain Morphogenesis in Zebrafish , 2022 .

[30]  B. Fritz,et al.  Zygotic control of maternal cyclin A1 translation and mRNA stability , 2002, Developmental dynamics : an official publication of the American Association of Anatomists.

[31]  J. Maller,et al.  In vivo regulation of the early embryonic cell cycle in Xenopus. , 1996, Developmental biology.

[32]  Anton J. Enright,et al.  Zebrafish MiR-430 Promotes Deadenylation and Clearance of Maternal mRNAs , 2006, Science.

[33]  T. Rana,et al.  Evolutionary Emergence of microRNAs in Human Embryonic Stem Cells , 2008, PloS one.

[34]  M. L. King,et al.  A Xenopus DAZ-like gene encodes an RNA component of germ plasm and is a functional homologue of Drosophila boule. , 1998, Development.

[35]  T. Nakayama,et al.  Post-transcriptional regulation of Xwnt-8 expression is required for normal myogenesis during vertebrate embryonic development. , 1999, Development.

[36]  P. S. Klein,et al.  β-Catenin/Tcf-regulated transcription prior to the midblastula transition , 2002, Development.

[37]  N. Sagata,et al.  Two structural variants of Nek2 kinase, termed Nek2A and Nek2B, are differentially expressed in Xenopus tissues and development. , 1999, Developmental biology.

[38]  A. Pasquinelli,et al.  Reverse 5' caps in RNAs made in vitro by phage RNA polymerases. , 1995, RNA.

[39]  J. Richter,et al.  CPEB is a specificity factor that mediates cytoplasmic polyadenylation during Xenopus oocyte maturation , 1994, Cell.

[40]  C. Oubridge,et al.  Crystallization of RNA-protein complexes. I. Methods for the large-scale preparation of RNA suitable for crystallographic studies. , 1995, Journal of molecular biology.

[41]  M. Wickens,et al.  The 3'-untranslated regions of c-mos and cyclin mRNAs stimulate translation by regulating cytoplasmic polyadenylation. , 1994, Genes & development.

[42]  T. Nakano,et al.  Embryonic stem cell. , 2001, Internal medicine.

[43]  Niklas Henriksson,et al.  Structural basis of m(7)GpppG binding to poly(A)-specific ribonuclease. , 2009, Structure.

[44]  P. Sharp,et al.  Embryonic stem cell-specific MicroRNAs. , 2003, Developmental cell.

[45]  T. Hunt,et al.  The A‐ and B‐type cyclin associated cdc2 kinases in Xenopus turn on and off at different times in the cell cycle. , 1990, The EMBO journal.

[46]  M. Wickens,et al.  PUF proteins bind Pop2p to regulate messenger RNAs , 2006, Nature Structural &Molecular Biology.

[47]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[48]  J. Minshull,et al.  Translation of cyclin mRNA is necessary for extracts of activated Xenopus eggs to enter mitosis , 1989, Cell.

[49]  R. Keller.  Early embryonic development of Xenopus laevis. , 1991, Methods in cell biology.

[50]  Chris Sander,et al.  The developmental miRNA profiles of zebrafish as determined by small RNA cloning. , 2005, Genes & development.

[51]  P. Bork,et al.  deadenylase and DCP 1 : DCP 2 decapping complexes mRNA degradation by miRNAs and GW 182 requires both CCR 4 : NOT Material , 2006 .

[52]  K. Chen,et al.  Dissection of the XChk1 signaling pathway in Xenopus laevis embryos. , 2000, Molecular biology of the cell.

[53]  R. Lehmann,et al.  The Pumilio protein binds RNA through a conserved domain that defines a new class of RNA-binding proteins. , 1997, RNA.

[54]  S. Moon,et al.  Human embryonic stem cells express a unique set of microRNAs. , 2004, Developmental biology.

[55]  E. Maxwell,et al.  Xenopus microRNA genes are predominantly located within introns and are differentially expressed in adult frog tissues via post-transcriptional regulation. , 2007, Genome research.

[56]  E. Lund,et al.  Substrate selectivity of exportin 5 and Dicer in the biogenesis of microRNAs. , 2006, Cold Spring Harbor symposia on quantitative biology.

[57]  A. Schier,et al.  Target Protectors Reveal Dampening and Balancing of Nodal Agonist and Antagonist by miR-430 , 2007, Science.

[58]  K. Ryan,et al.  Symplekin and xGLD-2 Are Required for CPEB-Mediated Cytoplasmic Polyadenylation , 2004, Cell.

[59]  F. Gourronc,et al.  ElrA and AUF 1 differentially bind cyclin B 2 mRNA , 2009 .

[60]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[61]  T. Nilsen,et al.  Mechanisms of microRNA‐mediated gene regulation , 2007, Trends in genetics : TIG.

[62]  Eric Westhof,et al.  Single Processing Center Models for Human Dicer and Bacterial RNase III , 2004, Cell.

[63]  Y. Audic,et al.  Zygotic Regulation of Maternal Cyclin A1 and B2 mRNAs , 2001, Molecular and Cellular Biology.

[64]  F. Gourronc,et al.  ElrA and AUF1 differentially bind cyclin B2 mRNA. , 2008, Biochemical and biophysical research communications.

[65]  M. L. King,et al.  DEADSouth is a germ plasm specific DEAD-box RNA helicase in Xenopus related to eIF4A , 2000, Mechanisms of Development.

[66]  M. Kirschner,et al.  A major developmental transition in early xenopus embryos: I. characterization and timing of cellular changes at the midblastula stage , 1982, Cell.

[67]  R. Guigó,et al.  A Combinatorial Code for CPE-Mediated Translational Control , 2008, Cell.

[68]  Peer Bork,et al.  Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing. , 2007, Genes & development.

[69]  F. Slack,et al.  The Caenorhabditis elegans pumilio homolog, puf-9, is required for the 3'UTR-mediated repression of the let-7 microRNA target gene, hbl-1. , 2007, Developmental biology.

[70]  F. Slack,et al.  Architecture of a validated microRNA::target interaction. , 2004, Chemistry & biology.

[71]  E. Wahle,et al.  Cap‐dependent deadenylation of mRNA , 2000, The EMBO journal.

[72]  David P. Bartel,et al.  Supporting Online Material Materials and Methods Fig. S1 Tables S1 and S2 References Database S1 Disrupting the Pairing between Let-7 and Hmga2 Enhances Oncogenic Transformation , 2022 .

[73]  R. Keller.  Chapter 5 Early Embryonic Development of Xenopus laevis , 1991 .

[74]  E. Izaurralde,et al.  The GW182 protein family in animal cells: new insights into domains required for miRNA-mediated gene silencing. , 2009, RNA.