Alan M. Zahler

Professor of Molecular, Cell and Developmental Biology
B.S., Carnegie-Mellon University
Ph.D., University of Colorado, Boulder
Postdoctorate, Fred Hutchinson Cancer Research Center, Seattle, WA

Regulation of Pre-mRNA Splicing and Analysis of Small RNA Function and Biogenesis

Alternative Splicing Regulation and mRNA Stability
Research in our laboratory is focused on the alternative splicing code; the sequences on the pre-mRNA and the protein factors that bind to them which regulate alternative splicing. We have focused on the identification of the cis splicing-regulatory elements, the trans-acting protein factors that bind them, and the mechanisms by which splicing is regulated. Our laboratory is using the powerful genetic, molecular biology and bioinformatics tools available for the nematode Caenorhabditis elegans to tackle this problem. A recent area of focus is the connection between alternative splicing and message stability. In about 1/3 of cases, alternative splicing yields an isoform with a premature stop codon; this isoform is unstable and subject to nonsense-mediated mRNA decay. We have identified many examples of alternative splicing factors whose own expression is regulated by alternative splicing coupled to nonsense-mediated decay. We are characterizing this process in C. elegans where we have uncovered a phenomenon in which the efficiency of nonsense-mediated decay can be developmentally regulated.

Small RNA Function in Ciliated Protozoans
Ciliated protozoans possess two types of nuclei; a transcriptionally silent micronucleus, which serves as the germ line nucleus, and a transcriptionally active macronucleus, which serves as the somatic nucleus. The macronucleus is derived from a new diploid micronucleus after mating, with epigenetic information contributed by the parental macronucleus serving to guide the formation of the new macronucleus. In the stichotrichous ciliate Oxytricha trifallax, the macronuclear DNA is highly processed to yield gene-sized nanochromosomes with an average length of 2200bp - most nanochromosomes encode only one gene and there are ~20,000 genes in the organism. We recently started to use this system to study the role of small RNAs in the regulation of chromatin. We found that soon after mating of Oxytricha is initiated, abundant 27nt small RNAs are produced that are not present prior to mating. We performed next generation sequencing of these small RNAs and found that the 27nt RNA class derives from the parental macronucleus. These small RNAs are produced equally from both strands of macronuclear nanochromosomes, but in a non-uniform distribution along the length of the nanochromosome, with a particular depletion in the 30 nt telomere-proximal positions. We are currently studying the mechanism by which the entire macronuclear genome is transcribed and processed into short RNAs and the role of these "27macRNAs" in macronuclear development.

Selected Publications

Zahler, A.M., Neeb, Z.T., Lin, A. and Katzman, S. 2012. Mating of the Stichotrichous Ciliate Oxytricha trifallax Induces Production of a Class of 27nt Small RNAs Derived from the Parental Macronucleus. PLoS One 7:e42371.

Zahler, A.M. 2012. Pre-mRNA splicing and its regulation in Caenorhabditis elegans, WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.31.2, Wormbook.

Lambert, N.J., Gu, S.G. and Zahler, A.M. 2011. The conformation of microRNA seed regions in native microRNPs is prearranged for presentation to mRNA targets. Nucleic Acids Research Nucleic Acids Res. 39: 4827-35.

Barberan-Soler, S., Medina, P., Estella, J., Williams, J. and Zahler, A.M. 2011. Co-regulation of alternative splicing by diverse splicing factors in Caenorhabditis elegans. Nucleic Acids Research 39: 666-674.

Kabat, J.L., Barberan-Soler, S. and Zahler, A.M. 2009. HRP-2, the C. elegans homolog of mammalian HNRNP Q and R, is an alternative splicing factor that binds to UCUAUC splicing regulatory elements. J. Biol. Chem. 284:28490-7.

Barberan-Soler, S., Lambert, N.J. and Zahler, A.M. 2009. Global analysis of alternative splicing uncovers developmental regulation of nonsense-mediated decay in C. elegans. RNA 15: 1652-1660.

Dassah, M., Patzek, S., Hunt, V.M., Medina, P.E. and Zahler A.M. 2009. A genetic screen for suppressors of a mutated 5' splice site identifies factors associated with later steps of spliceosome assembly. Genetics 182: 725-734.

Barberan-Soler, S. and Zahler, A.M. 2008. Alternative splicing and the steady-state ratios of mRNA isoforms generated by it are under strong stabilizing selection in C. elegans. Mol. Biol. Evol. 25:2341-2347.

Barberan-Soler, S. and Zahler, A.M. 2008. Alternative splicing regulation during C. elegans development: splicing factors as regulated targets. PLoS Genetics 4:e1000001.

Gu, S.G., Pak, J., Barberan-Soler, S., Ali, M., Fire, A., and Zahler, A.M. 2007. Distinct ribonucleoprotein reservoirs for microRNA and siRNA populations in C. elegans. RNA 13:1492-1504.

Kabat, J.L., Barberan-Soler, S., McKenna, P., Clawson, H., Farrer, T. and Zahler, A.M. 2006. Intronic alternative splicing regulators identified by comparative genomics in nematodes. PLoS Computational Biology 2:e86.

Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M. and Haussler, D. 2002. The human genome browser at UCSC. Genome Research 12:996-1006.

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