Selected Publications - Zahler Lab at UCSC

Neeb, Z.T., Hogan, D.J., Katzman, S. and Zahler, A.M. 2017. Preferential expression of scores of functionally and evolutionarily diverse DNA and RNA-binding proteins during Oxytricha trifallax macronuclear development. PLoS ONE 12(2):e0170870.

Ragle, J.M., Katzman, S., Akers, T.F., Barberan-Soler, S. and Zahler, A.M. 2015. Coordinated tissue-specific regulation of alternative adjacent 3' splice sites in C. elegans. Genome Research 25: 982-94.

Neeb, Z.T. and Zahler, A.M. 2014. An expanding world of small RNAs. Developmental Cell 28:111-2.

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 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.

Zahler, A.M. 2005. Alternative splicing in C. elegans. WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.31.1.

Zahler, A.M., Tuttle, J.D. and Chisholm, A.D. 2004. Genetic suppression of intronic +1G mutations by compensatory U1 snRNA changes in Caenorhabditis elegans. Genetics 167:1689-1696.

Zahler, A.M., Damgaard, C.K., Kjems, J. and Caputi, M. 2004. SC35 and heterogeneous nuclear ribonucleoprotein A/B proteins bind to a juxtaposed exonic splicing enhancer/exonic splicing silencer element to regulate HIV-1 tat exon 2 splicing. J. Biol. Chem. 279:10077-10084.

Farrer, T., Roller, A.B., Kent, W.J. and Zahler, A.M. 2002. Analysis of the role of C. elegans GC-AG introns in regulated splicing. Nucleic Acids Research 30:3360-3367.

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.

Caputi, M. and Zahler, A.M. 2002. SR proteins and hnRNP H regulate the splicing of the HIV-1 tev-specific exon 6D. EMBO J. 21:845-855.

Caputi, M. and Zahler, A.M. 2001. Determination of the RNA-binding specificity of the heterogeneous nuclear ribonucleoprotein (hnRNP) H/H'/F/2H9 family. J. Biol. Chem. 276:43850-43859.

Zahler, A.M. 2001. Tale of a tail kinase. Nature Structural Biology 8:104-106.

Kent, W.J. and Zahler, A.M. 2000. Conservation, regulation, synteny, and introns in a large scale C. briggsae/C. elegans genomic alignment. Genome Research 10:1115-1125.

Roller, A.B., Hoffman, D.C., and Zahler, A.M. 2000. The allele-specific suppressor sup-39 alters use of cryptic splice sites in C. elegans. Genetics 154:1169-1179.

Kent, W.J. and Zahler, A.M. 2000. The Intronerator: exploring introns and alternative splicing in C.elegans. Nucleic Acids Research 28:91-93.

Caputi, M., Mayeda, A., Krainer, A.R., and Zahler, A.M. 1999. hnRNP A/B proteins are required for inhibition of HIV-1 pre-mRNA splicing. EMBO J. 18:4060-4067.

Zahler, A.M. 1999. Purification of SR protein splicing factors. Methods in Molecular Biology 118:419-432.

Nagel, R.J., Lancaster, A.M., and Zahler, A.M. 1998. Specific binding of an exonic splicing enhancer by the pre-mRNA splicing factor SRp55. RNA 4:11-23.

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