Zebrafish; Developmental Biology; RNA, Untranslated; MicroRNAs
Small RNAs in Development
Stem Cell Center, Yale: Stem Cell Genetics
In our laboratory we use zebrafish as a model system to investigate the
role of microRNAs during vertebrate development. We combine genetics,
embryology, genomics, chemical and computational biology to address a
central question in biology: how does a fertilized egg develop into a
complex multicellular embryo. This process requires a precise spatial
and temporal regulation of gene expression. MicroRNAs are ~22nt RNA
molecules that repress gene expression post-transcriptionaly. More than
4% of the vertebrate genes encode microRNAs that are predicted to
regulate more than 25% of the protein coding genes. Thus, microRNAs
provide novel regulatory layer of unknown function with potential
widespread implications in development and disease. We have generated
zebrafish embryos mutant in the microRNA processing machinery (Dicer).
Dicer mutants lack all microRNAs and fail to undergo normal
gastrulation, brain and muscle morphogenesis.
Extensive Research Description
Two main projects are currently ongoing: 1) We have identified a novel microRNA miR-430 that accelerates the deadenylation of maternal products during embryogenesis to facilitate gastrulation. Interestingly, misexpression of the human homologues (miR-372, miR-17-93) have oncogenic potential. Thus, identification of the in vivo miR-430 targets might provide a fundamental link between development and cancer. 2) MicroRNAs are expressed at the onset of differentiation and continue to be expressed through adulthood. We have observed that miRNAs accelerate target mRNA degradation. Thus, microRNAs targets can be identified by looking at mRNAs upregulated in the absence of the microRNA. We are using microarray analysis in dicer mutant embryos to identify tissue specific microRNA targets in neurons and muscle cells. Computational projects in the lab will analyze the regulatory motifs in microRNAs and 3’UTR elements of their targets to identify the gene networks controlled by microRNAs. Combining in vivo target identification with phenotypic characterization of dicer mutants will help us to understand the function of tissue specific microRNAs during cell fate specification and tissue homeostasis.
- Lee MT#, Ashley R#. Bonneau AR, Takacs CM, Bazzini AA, DiVito KR, Fleming ES, Giraldez AJ‡. Nanog, SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal-to-zygotic transition. Nature, 2013 Sep 22. doi: 10.1038/nature12632
- Stahlhut C, Suarez Y, Lu J, Mishima Y‡, and Giraldez AJ‡. miR-1/206 regulate angiogenesis by modulating Vegf-A expression. Development, 2012 Dec 1;139(23):4356-64. doi: 10.1242/dev.083774
- Bazzini AA, Lee MT, Giraldez AJ‡. Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish. Science. 13 April 2012: 233-23
- Staton AA, Knaut H and Giraldez AJ. miRNA regulation of Sdf1 chemokine signaling provides genetic robustness to germ cell migration. Nature Genetics. 2011 Mar;43(3):204-11. Epub 2011 Jan 23.
- Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, Ma E, Mane S, Hannon GJ, Lawson ND, Wolfe SA, Giraldez AJ. A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity. Science. 2010 Jun 25;328(5986):1694-8