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Amy Pasquinelli

Amy Pasquinelli

Professor and Vice Chair
Section of Molecular Biology, UCSD

e-mail: apasquin@biomail.ucsd.edu
Lab Homepage: Pasquinelli Lab

   The recent discovery of microRNAs (miRNAs) has revolutionized our understanding of gene control. Genetic studies in the nematode Caenorhabditis elegans (Figure 1) revealed the first members of what we now recognize as an extensive family of regulatory RNAs that exist in most multicellular organisms.  Already there is evidence that specific miRNAs play key roles in controlling development, stem cell fates and neuronal differentiation, and mutations in human miRNA genes have been linked to oncogenic and other disease states.    The Pasquinelli lab couples C. elegans genetics with molecular and biochemical techniques to understand the basic mechanisms of miRNA expression and function and to elucidate the biological roles of specific miRNAs in cellular differentiation programs.


figure 1
   How is the expression of miRNAs regulated?  MiRNA genes typically encode long primary transcripts (pri-miRNAs) that undergo multiple processing steps to generate the mature ~22 nucleotide miRNA (Figure 2).  Many miRNA genes are expressed at precise times in development and in specific tissues.  To understand how these temporal and spatial expression patterns are achieved, we study the transcriptional and processing events that cooperate to produce specific miRNAs at the right time and in the right place.


figure 2
   How do miRNAs regulate gene expression?  The miRNAs regulate specific genes by partially base-pairing to complementary sequences in the messenger RNAs (mRNAs) of protein-coding genes (Figure 2).  The human genome contains over 700 different miRNA genes, each of which may directly regulate hundreds of protein coding genes.  To help elucidate how miRNAs find and regulate targets with limited sequence complementarity, we have focused on specific miRNA genes and have performed genome wide analyses to identify potential targets. Regulation by miRNAs can result in degradation or translational repression of the target mRNA (Figure 2), but the molecular mechanisms behind these inhibitory strategies are not entirely understood.  By studying defined miRNA and target pathways in C. elegans, my lab aims to elucidate how miRNAs control gene expression in the endogenous context.

   What is the biological function of miRNA regulatory pathways?  Some miRNA genes, like let-7, are essential for normal development (Figure 1).  The let-7 miRNA and its temporally regulated expression pattern are widely conserved across animal phylogeny and misexpression of this miRNA has been linked to cancer in humans.  A goal of our studies on the worm let-7 gene is to understand the broad role let-7 plays in cellular differentiation events across species.


Van Wynsberghe PM, Kai ZS, Massirer KB, Burton VH, Yeo GW, Pasquinelli AE. Co-transcriptional association of LIN-28 with let-7 primary transcripts regulates miRNA maturation in C. elegans. Nat Struct Mol Biol. 2011 18:302-308.

Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo GW. Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nat Struct Mol Biol. 2010 17:173-179.

Bracht JR, Van Wynsberghe PM, Mondol V, Pasquinelli AE. Regulation of lin-4 miRNA Expression, Organismal Growth and Development by a Conserved RNA Binding Protein in C. elegans. Dev Biol. 2010 348:201-221.

Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, Eachus R, Pasquinelli AE. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell. 2005 122:553-563.

Bracht J, Hunter S, Eachus R, Weeks P, Pasquinelli AE.  Trans-splicing and polyadenylation of let-7 microRNA primary transcripts. RNA. 2004 10:1586-1594.

Reviews & Book Chapters
Zisoulis DG, Yeo GW, Pasquinelli AE. Comprehensive identification of miRNA target sites in live animals. Methods Mol Biol. 2011 732:169-185.

Kai ZS, Pasquinelli AE. MicroRNA assassins: factors that regulate the disappearance of miRNAs. Nat Struct Mol Biol. 2010 17:5-10.

Massirer K, Pasquinelli AE. The evolving role of microRNAs in animal gene expression. BioEssays 2006 28:449-452.

Pasquinelli AE, Hunter S, Bracht J. MicroRNAs: a developing story. Curr Opin Genet Dev. 2005 15:200-205.

    Amy Pasquinelli received her Ph.D. in Biomolecular Chemistry from the University of Wisconsin-Madison and was a Helen Hay Whitney Postdoctoral Fellow in the Genetics Department at Harvard Medical School.  Since joining the faculty in 2003, she has been named a Keck Distinguished Young Scholar in Medical Research, a Searle Scholar, a V Foundation for Cancer Research Scholar, an Emerald Foundation Scholar and a Rosalind Franklin Young Investigator.