Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
Dev Biol
2012 Feb 01;3621:104-13. doi: 10.1016/j.ydbio.2011.11.015.
Show Gene links
Show Anatomy links
Select microRNAs are essential for early development in the sea urchin.
Song JL
,
Stoeckius M
,
Maaskola J
,
Friedländer M
,
Stepicheva N
,
Juliano C
,
Lebedeva S
,
Thompson W
,
Rajewsky N
,
Wessel GM
.
???displayArticle.abstract???
microRNAs (miRNAs) are small noncoding RNAs that mediate post-transcriptional gene regulation and have emerged as essential regulators of many developmental events. The transcriptional network during early embryogenesis of the purple sea urchin, Strongylocentrotus purpuratus, is well described and can serve as an excellent model to test functional contributions of miRNAs in embryogenesis. We examined the loss of function phenotypes of major components of the miRNA biogenesis pathway. Inhibition of de novo synthesis of Drosha and Dicer in the embryo led to consistent developmental defects, a failure to gastrulate, and embryonic lethality, including changes in the steady state levels of transcription factors and signaling molecules involved in germ layer specification. We annotated and profiled small RNA expression from the ovary and several early embryonic stages by deep sequencing followed by computational analysis. miRNAs as well as a large population of putative piRNAs (piwi-interacting RNAs) had dynamic accumulation profiles through early development. Defects in morphogenesis caused by loss of Drosha could be rescued with four miRNAs. Taken together our results indicate that post-transcriptional gene regulation directed by miRNAs is functionally important for early embryogenesis and is an integral part of the early embryonic gene regulatory network in S. purpuratus.
Aravin,
A novel class of small RNAs bind to MILI protein in mouse testes.
2006, Pubmed
Aravin,
A novel class of small RNAs bind to MILI protein in mouse testes.
2006,
Pubmed
Baek,
The impact of microRNAs on protein output.
2008,
Pubmed
Bartel,
MicroRNAs: target recognition and regulatory functions.
2009,
Pubmed
Ben-Tabou de-Leon,
Experimentally based sea urchin gene regulatory network and the causal explanation of developmental phenomenology.
2009,
Pubmed
,
Echinobase
Benson,
GenBank: update.
2004,
Pubmed
Berninger,
Computational analysis of small RNA cloning data.
2008,
Pubmed
Brennecke,
Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila.
2007,
Pubmed
Brodersen,
Revisiting the principles of microRNA target recognition and mode of action.
2009,
Pubmed
Bushati,
Temporal reciprocity of miRNAs and their targets during the maternal-to-zygotic transition in Drosophila.
2008,
Pubmed
Byrum,
Blocking Dishevelled signaling in the noncanonical Wnt pathway in sea urchins disrupts endoderm formation and spiculogenesis, but not secondary mesoderm formation.
2009,
Pubmed
,
Echinobase
Campo-Paysaa,
microRNA complements in deuterostomes: origin and evolution of microRNAs.
2011,
Pubmed
,
Echinobase
Cheers,
Rapid microinjection of fertilized eggs.
2004,
Pubmed
,
Echinobase
Christodoulou,
Ancient animal microRNAs and the evolution of tissue identity.
2010,
Pubmed
,
Echinobase
Davidson,
A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo.
2002,
Pubmed
,
Echinobase
Duboc,
Nodal and BMP2/4 signaling organizes the oral-aboral axis of the sea urchin embryo.
2004,
Pubmed
,
Echinobase
Fabian,
Regulation of mRNA translation and stability by microRNAs.
2010,
Pubmed
Flowers,
Nodal/activin signaling establishes oral-aboral polarity in the early sea urchin embryo.
2004,
Pubmed
,
Echinobase
Friedländer,
Discovering microRNAs from deep sequencing data using miRDeep.
2008,
Pubmed
Friedländer,
miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades.
2012,
Pubmed
Friedman,
Most mammalian mRNAs are conserved targets of microRNAs.
2009,
Pubmed
Fukagawa,
Dicer is essential for formation of the heterochromatin structure in vertebrate cells.
2004,
Pubmed
Ghildiyal,
Small silencing RNAs: an expanding universe.
2009,
Pubmed
Giraldez,
MicroRNAs regulate brain morphogenesis in zebrafish.
2005,
Pubmed
Girard,
A germline-specific class of small RNAs binds mammalian Piwi proteins.
2006,
Pubmed
Grivna,
A novel class of small RNAs in mouse spermatogenic cells.
2006,
Pubmed
Gunawardane,
A slicer-mediated mechanism for repeat-associated siRNA 5' end formation in Drosophila.
2007,
Pubmed
Guo,
Mammalian microRNAs predominantly act to decrease target mRNA levels.
2010,
Pubmed
Han,
Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex.
2006,
Pubmed
Heimberg,
MicroRNAs and the advent of vertebrate morphological complexity.
2008,
Pubmed
Hendrickson,
Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA.
2009,
Pubmed
Houwing,
A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish.
2007,
Pubmed
Juliano,
Germ line determinants are not localized early in sea urchin development, but do accumulate in the small micromere lineage.
2006,
Pubmed
,
Echinobase
Juliano,
Nanos functions to maintain the fate of the small micromere lineage in the sea urchin embryo.
2010,
Pubmed
,
Echinobase
Kanellopoulou,
Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing.
2005,
Pubmed
Krek,
Combinatorial microRNA target predictions.
2005,
Pubmed
Lagos-Quintana,
Identification of novel genes coding for small expressed RNAs.
2001,
Pubmed
Langmead,
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
2009,
Pubmed
Lee,
The nuclear RNase III Drosha initiates microRNA processing.
2003,
Pubmed
Lee,
Evolutionary conservation of microRNA regulatory circuits: an examination of microRNA gene complexity and conserved microRNA-target interactions through metazoan phylogeny.
2007,
Pubmed
Leguia,
Synaptotagmin I is involved in the regulation of cortical granule exocytosis in the sea urchin.
2006,
Pubmed
,
Echinobase
Lewis,
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets.
2005,
Pubmed
Logan,
Nuclear beta-catenin is required to specify vegetal cell fates in the sea urchin embryo.
1999,
Pubmed
,
Echinobase
Lund,
Deadenylation of maternal mRNAs mediated by miR-427 in Xenopus laevis embryos.
2009,
Pubmed
Mayr,
Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells.
2009,
Pubmed
Nakagawa,
Caspase-dependent conversion of Dicer ribonuclease into a death-promoting deoxyribonuclease.
2010,
Pubmed
Niwa,
The evolution of animal microRNA function.
2007,
Pubmed
Okamitsu,
Dicer is required for the normal development of sea urchin, Hemicentrotus pulcherrimus.
2010,
Pubmed
,
Echinobase
Oliveri,
Gene regulatory network controlling embryonic specification in the sea urchin.
2004,
Pubmed
,
Echinobase
Oliveri,
A regulatory gene network that directs micromere specification in the sea urchin embryo.
2002,
Pubmed
,
Echinobase
Oliveri,
Activation of pmar1 controls specification of micromeres in the sea urchin embryo.
2003,
Pubmed
,
Echinobase
Pauli,
Non-coding RNAs as regulators of embryogenesis.
2011,
Pubmed
Persson,
The non-coding RNA of the multidrug resistance-linked vault particle encodes multiple regulatory small RNAs.
2009,
Pubmed
Peter,
A gene regulatory network controlling the embryonic specification of endoderm.
2011,
Pubmed
,
Echinobase
Peterson,
MicroRNAs and metazoan macroevolution: insights into canalization, complexity, and the Cambrian explosion.
2009,
Pubmed
Ransick,
cis-regulatory processing of Notch signaling input to the sea urchin glial cells missing gene during mesoderm specification.
2006,
Pubmed
,
Echinobase
Revilla-i-Domingo,
A missing link in the sea urchin embryo gene regulatory network: hesC and the double-negative specification of micromeres.
2007,
Pubmed
,
Echinobase
Rodriguez,
Seawi--a sea urchin piwi/argonaute family member is a component of MT-RNP complexes.
2005,
Pubmed
,
Echinobase
Rouget,
Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo.
2010,
Pubmed
Rozen,
Primer3 on the WWW for general users and for biologist programmers.
2000,
Pubmed
Saito,
Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome.
2006,
Pubmed
Samanta,
The transcriptome of the sea urchin embryo.
2006,
Pubmed
,
Echinobase
Selbach,
Widespread changes in protein synthesis induced by microRNAs.
2008,
Pubmed
Sempere,
The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint.
2006,
Pubmed
Sherwood,
LvNotch signaling mediates secondary mesenchyme specification in the sea urchin embryo.
1999,
Pubmed
,
Echinobase
Stark,
Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution.
2005,
Pubmed
Stark,
A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands.
2008,
Pubmed
Stoeckius,
Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression.
2009,
Pubmed
Sweet,
The role of micromere signaling in Notch activation and mesoderm specification during sea urchin embryogenesis.
1999,
Pubmed
,
Echinobase
Sweet,
LvDelta is a mesoderm-inducing signal in the sea urchin embryo and can endow blastomeres with organizer-like properties.
2002,
Pubmed
,
Echinobase
Tyler,
Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci.
2008,
Pubmed
Vagin,
A distinct small RNA pathway silences selfish genetic elements in the germline.
2006,
Pubmed
Watanabe,
Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes.
2006,
Pubmed
Wessel,
Sequential expression of germ-layer specific molecules in the sea urchin embryo.
1985,
Pubmed
,
Echinobase
Wheeler,
The deep evolution of metazoan microRNAs.
2009,
Pubmed
Wienholds,
MicroRNA expression in zebrafish embryonic development.
2005,
Pubmed
Wienholds,
MicroRNA function in animal development.
2005,
Pubmed
Wikramanayake,
Nuclear beta-catenin-dependent Wnt8 signaling in vegetal cells of the early sea urchin embryo regulates gastrulation and differentiation of endoderm and mesodermal cell lineages.
2004,
Pubmed
,
Echinobase
Xie,
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals.
2005,
Pubmed
Zhang,
Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP.
2002,
Pubmed
