Faculty

Erik J. Sontheimer, PhD

Associate Professor
Biochemistry, Molecular Biology and Cell Biology
PhD, Yale

Email: erik@northwestern.edu
Phone: 847) 467-6880
Fax: (847) 491-4461
Room: Cook Rm 3137

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Research Interests

Ribonucleoproteins and Eukaryotic Gene Expression

RNA molecules are essential participants in many aspects of cellular function. We aim to understand the mechanisms of RNA-mediated steps during eukaryotic gene expression. Our current research is focused on two critically important pathways: pre-mRNA splicing and RNA silencing.

The machinery that removes introns from mRNA precursors is a large macromolecular machine called the spliceosome. Five small nuclear RNAs (snRNAs) are essential for spliceosome function, and establish a dynamic network of interactions that mediate spliceosome assembly, activation, and catalysis. The spliceosome protein Prp8 is very large (~280 kDa) and highly conserved, and genetic analyses suggest that it regulates the RNA structural rearrangements that underlie spliceosome catalysis. Despite its prominent role, little is known about its precise mechanism of action. We have recently established a link between Prp8 and another conserved protein called ubiquitin (a 76 amino acid protein that modulates the fates and functions of numerous target proteins via covalent attachment). We have found that an essential domain in Prp8 is homologous to other proteins that cleave ubiquitin from target proteins. In Prp8, this domain appears to serve a ubiquitin-binding function. In addition, we have obtained biochemical evidence that ubiquitin can regulate a specific step in spliceosome assembly. We are currently investigating the mechanistic basis for this regulation.

Over the past several years, a new role for RNA has been uncovered in eukaryotic gene expression: double-stranded RNA (dsRNA) molecules trigger the silencing of homologous genes in a phenomenon known as RNA interference (RNAi). RNAi is an important control pathway that regulates the expression of cellular genes and protects cells from viruses and transposons; it has also emerged as a broadly applicable experimental approach to determine the functions of novel genes. In collaboration with Professor Richard Carthew, we are investigating the mechanism of RNAi. The Carthew lab has initiated a genetic screen for RNAi-defective mutants in Drosophila, and we are using extracts from the mutants to characterize the mechanistic basis for the RNAi defects in vitro. In the course of our studies, we have delineated the assembly pathway for the RNA-induced silencing complex (RISC), and identified an ATP-dependent ~80S complex that mediates mRNA target cleavage in response to dsRNA. We are continuing our biochemical analysis of the RNAi pathway in Drosophila. In addition, we are using the biochemical tools developed in the Drosophila model system to examine the mechanism of RISC assembly and RNAi in human cell extracts.

Selected Publications

Silencing by small RNAs is linked to endosomal trafficking. Lee YS, Pressman S, Andress AP, Kim K, White JL, Cassidy JJ, Li X, Lubell K, Lim do H, Cho IS, Nakahara K, Preall JB, Bellare P, Sontheimer EJ, Carthew RW. 

Invasive DNA, chopped and in the CRISPR. Marraffini LA, Sontheimer EJ. Structure. 2009 Jun 10;17(6):786-8. 

Origins and Mechanisms of miRNAs and siRNAs. Carthew RW, Sontheimer EJ. Cell. 2009 Feb 20;136(4):642-55. Review. 

CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Marraffini LA, Sontheimer EJ. Science. 2008 Dec 19;322(5909):1843-5. 

An inside job for siRNAs. Golden DE, Gerbasi VR, Sontheimer EJ. Mol Cell. 2008 Aug 8;31(3):309-12. Review. 

A role for ubiquitin in the spliceosome assembly pathway. Bellare P, Small EC, Huang X, Wohlschlegel JA, Staley JP, Sontheimer EJ. Nat Struct Mol Biol. 2008 May;15(5):444-51. Epub 2008 Apr 20. 

A fork in the road for microRNAs. Bellare P, Sontheimer EJ. Nat Struct Mol Biol. 2007 Aug;14(8):684-6. No abstract available. 

View all publications by Erik J. Sontheimer listed in the National Library of Medicine (PubMed). Past and current IBiS students in blue