My chief scientific interest is post-transcriptional regulation otgene expression. In particular, I am fascinated by the diversity and complexity of RNA-dependent mechanisms of translational control. In the future, I hope to make my own lab an outstanding center for research into the fundamental mechanisms of gene expression, and the defects in gene expression that lead to human diseases. Pursuing my training in Jennifer Doudna's lab at UC Berkeley will provide an outstanding technical education in biochemical dissection of RNA-protein interactions relevant to translation, as well as a diverse and stimulating intellectual environment. I will also develop the professional skills I will need to thrive as an independent investigator in the future, through numerous opportunities to supervise students with diverse scientific strengths and interests. Translation initiation is a crucial point of regulation of eukaryotic gene expression. In response to a variety of environmental insults, cells down-regulate the primary (cap-dependent) mechanism of translation while favoring expression of a select group of genes via alternative initiation mechanisms including direct recruitment of the translation machinery to internal ribosome entry sites (IRESs). Little is known about the molecular basis for cellular IRES activity or for message-specific regulation of these mechanisms. I have identified 24 yeast cellular IRES elements with strong activity both in vitro and in vivo, creating a unique opportunity to combine molecular genetics and biochemistry to determine the molecular basis for, and physiological significance of IRES-dependent gene expression.
My aim i s to define the molecular functions of cellular IRES RNA sequences and their associated RNA-binding proteins and ultimately, to identify the mechanisms linking stress-related signaling pathways to global and message-specific translational regulation using a combination of biochemical, molecular genetic, and bioinformatic approaches. Results from this work will provide detailed molecular insight into the mechanisms and regulation of internal initiation of translation by diverse cellular IRESs, which is expected to have wide-ranging implications for translational control of eukaryotic gene expression.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Transition Award (R00)
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Special Emphasis Panel (NSS)
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Bender, Michael T
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Massachusetts Institute of Technology
Schools of Arts and Sciences
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Zinshteyn, Boris; Rojas-Duran, Maria F; Gilbert, Wendy V (2017) Translation initiation factor eIF4G1 preferentially binds yeast transcript leaders containing conserved oligo-uridine motifs. RNA 23:1365-1375
Carlile, Thomas M; Rojas-Duran, Maria F; Gilbert, Wendy V (2015) Transcriptome-Wide Identification of Pseudouridine Modifications Using Pseudo-seq. Curr Protoc Mol Biol 112:4.25.1-24
Carlile, Thomas M; Rojas-Duran, Maria F; Gilbert, Wendy V (2015) Pseudo-Seq: Genome-Wide Detection of Pseudouridine Modifications in RNA. Methods Enzymol 560:219-45
Saha, Agniva; Mitchell, Jessica A; Nishida, Yuri et al. (2015) A trans-dominant form of Gag restricts Ty1 retrotransposition and mediates copy number control. J Virol 89:3922-38
Carlile, Thomas M; Rojas-Duran, Maria F; Zinshteyn, Boris et al. (2014) Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 515:143-6
Zinshteyn, Boris; Gilbert, Wendy V (2013) Loss of a conserved tRNA anticodon modification perturbs cellular signaling. PLoS Genet 9:e1003675
Arribere, Joshua A; Gilbert, Wendy V (2013) Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing. Genome Res 23:977-87
Rojas-Duran, Maria F; Gilbert, Wendy V (2012) Alternative transcription start site selection leads to large differences in translation activity in yeast. RNA 18:2299-305
Arribere, Joshua A; Doudna, Jennifer A; Gilbert, Wendy V (2011) Reconsidering movement of eukaryotic mRNAs between polysomes and P bodies. Mol Cell 44:745-58
Gilbert, Wendy V (2011) Functional specialization of ribosomes? Trends Biochem Sci 36:127-32

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