Erik J. Sontheimer
Soretta and Henry Shapiro Research Professor
Noncoding RNAs in Gene Regulation
RNA molecules are essential participants in many aspects of cellular function. We aim to understand the roles and mechanisms of regulatory RNAs in gene expression, with an emphasis on genetic interference pathways.
Although genetic interference pathways [in particular, RNA interference (RNAi)] were reported in eukaryotes more than a decade ago, analogous RNA-guided silencing phenomena were thought to be largely absent in bacteria and archaea. In 2007, however, genetic elements known as clustered, regularly interspaced, short palindromic repeat (CRISPR) loci were revealed as sequence-based specificity determinants of an adaptive immune system that defends against bacteriophage infection. Shortly thereafter, CRISPR interference was found to be directed by small RNAs that are transcribed from CRISPR loci. Although this pathway has functional parallels with RNAi in eukaryotes, the mechanisms of RNAi and CRISPR interference are completely distinct. We are working to understand the roles and mechanisms of CRISPR interference in bacteria. Thus far our work has provided three fundamental advances in our understanding of the CRISPR pathway. (i) CRISPR interference is not confined to phage defense but functions more broadly to limit horizontal gene transfer. (ii) The CRISPR RNAs (crRNAs) that specify interference can target DNA rather than RNA, establishing a fundamental distinction between CRISPR interference and RNAi. (iii) The mode of crRNA/target interaction includes a built-in mechanism for distinguishing “self” DNA (the encoding CRISPR locus) from “non-self” DNA (phage or plasmid sequences), leading to selective targeting of the latter. We are now employing biochemical approaches to identify the molecular events that lead to crRNA-directed silencing.
We have also continued our work on eukaryotic silencing pathways by identifying novel factors that associate with the short interfering RNAs (siRNAs) that direct RNAi. Most notably, we identified a protein called Blanks that is expressed in the male germline of Drosophila melanogaster and is essential for spermiogenesis and male fertility. Blanks is localized to the nucleus and associates with additional proteins in a particle that is distinct from canonical forms of the RNA-induced silencing complex (RISC). Our current focus is on defining the regulatory targets and mechanisms of Blanks as well as an apparent Blanks paralog.
Our third research avenue is an analysis of the roles of non-coding RNAs (ncRNAs), as well as non-coding portions of mRNAs, in the budding yeast Saccharomyces cerevisiae. Unlike most other eukaryotes, this model organism lacks the signature components of the RNAi machinery, indicating that it uses other RNA-based systems to regulate gene expression. Our genome-wide analyses of RNAs expressed during meiosis and sporulation has revealed large numbers of ncRNAs, as well as an unanticipated degree of dynamism in transcript architecture. We are now using this dataset as a springboard to identify and characterize novel modes of eukaryotic gene regulation.
Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Hou Z, Zhang Y, Propson NE, Howden SE, Chu L-F, Sontheimer EJ, and Thomson JA. PNAS. 2013 September 24;110(39):15644-15649.
Processing-Independent CRISPR RNAs Limit Natural Transformation in Neisseria meningitidis. Zhang Y, Heldrich N, Ampattu BJ, Gunderson CW, Seifert HS, Schoen C, Vogel J, and Sontheimer EJ. Molecular Cell. 2013 May 23;50(4):488-503.
Quit Stalling or You’ll Be Silenced. Kim Guisbert KS and Sontheimer EJ. Cell. 2013 February 28;152(5):938-939.
Small RNAs of Opposite Sign… but Same Absolute Value. Sontheimer EJ. Cell. 2012 December 7;151(6):1157-1158.
Meiosis-induced alterations in transcript architecture and noncoding RNA expression in S. cerevisiae. Kim Guisbert KS, Zhang Y, Flatow J, Hurtado S, Staley JP, Lin S, and Sontheimer EJ. RNA. 2012 June;18(6):1142-1153.
Blanks, a nuclear siRNA/dsRNA-binding complex component, is required for Drosophila spermiogenesis. Gerbasi VR, Preall JB, Golden DE, Powell DW, Cummins TD, and Sontheimer EJ. PNAS. 2011 February 22;108(8):3204-3209.
Microbiology: Slicer for DNA. Sontheimer EJ and Marraffini LA. Nature. 2010 November 4;468(7320):45-46.
CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Marraffini LA and Sontheimer EJ. Nature Reviews Genetics. 2010 March;11(3):181-190.
Self versus non-self discrimination during CRISPR RNA-directed immunity. Marraffini LA and Sontheimer EJ. Nature. 2010 January 28;463(7280):568-571.
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 DH, Cho IS, Nakahara K, Preall JB, Bellare P, Sontheimer EJ, and Carthew RW. Nature Cell Biology. 2009 September;11(9):1150-1156.
Origins and Mechanisms of miRNAs and siRNAs. Carthew RW and Sontheimer EJ. Cell. 2009 February 20;136(4):642-655.
CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA. Marraffini LA and Sontheimer EJ. Science. 2008 December 19;322(5909):1843-1845.
A role for ubiquitin in the spliceosome assembly pathway. Bellare P, Small EC, Huang X, Wohlschlegel JA, Staley JP, and Sontheimer EJ. Nature Structural & Molecular Biology. 2008 May;15(5):444-451.
Short Interfering RNA Strand Selection Is Independent of dsRNA Processing Polarity during RNAi in Drosophila. Preall JB, He Z, Gorra JM, and Sontheimer EJ. Current Biology. 2006 March 7;16(5):530-535.
A Dicer-2-Dependent 80S Complex Cleaves Targeted mRNAs during RNAi in Drosophila. Pham JW, Pellino JL, Lee YS, Carthew RW, and Sontheimer EJ. Cell. 2004 April 2;117(1):83-94.
Distinct Roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA Silencing Pathways. Lee YS, Nakahara K, Pham JW, Kim K, He Z, Sontheimer EJ, and Carthew RW. Cell. 2004 April 2;117(1):69-81.
View all publications by Erik J. Sontheimer listed in the National Library of Medicine (PubMed). Current and former IBiS students in blue.