Jeremy E Wilusz, Ph.D.

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Assistant Professor of Biochemistry and Biophysics
Department: Biochemistry and Biophysics

Contact information
Department of Biochemistry & Biophysics
University of Pennsylvania Perelman School of Medicine
363 Clinical Research Building
415 Curie Boulevard
Philadelphia, PA 19104-6059
Office: 215-898-8862
Lab: 215-898-8863
Education:
B.S. (Molecular and Cellular Biology)
Johns Hopkins University, 2005.
Ph.D. (Biological Sciences)
Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 2009.
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Description of Research Expertise

The sequencing of the human genome provided quite a surprise to many when it was determined that there are only ~20,000 protein-coding genes, representing less than 2% of the total genomic sequence. Since other less complex eukaryotes like the nematode C. elegans have a very similar number of genes, it quickly became clear that the developmental and physiological complexity of humans probably can not be solely explained by proteins. We now know that most of the human genome is transcribed, yielding a complex repertoire of RNAs that includes tens of thousands of individual noncoding RNAs with little or no protein-coding capacity. Among these are well-studied small RNAs, such as microRNAs, as well as many other classes of small and long transcripts whose functions and mechanisms of biogenesis are less clear – but likely no less important. This is because many of these poorly characterized RNAs exhibit cell type-specific expression or are associated with human diseases, including cancer and neurological disorders. Our goal is to characterize the mechanisms by which noncoding RNAs are generated, regulated, and function, thereby revealing novel fundamental insights into RNA biology and developing new methods to treat diseases.

Much of our recent work has focused on circular RNAs, which are generated from thousands of protein-coding genes. At some genes, the abundance of the circular RNA exceeds that of the associated linear mRNA by a factor of 10, raising the interesting possibility that the function of some protein-coding genes may be to produce circular noncoding RNAs, not proteins. These circular RNAs are generated when the pre-mRNA splicing machinery “backsplices” and joins a splice donor to an upstream splice acceptor. We showed that repetitive elements, e.g. SINE elements, in the flanking introns are critical determinants of whether the intervening exon(s) circularize. When repeat sequences from the flanking introns base pair to one another, the splice sites are brought into close proximity and backsplicing occurs. This knowledge allowed us to generate plasmids that efficiently produce any circular RNA in species ranging from humans to flies. Using high-throughput screening, we have further shown that the ratio of linear to circular RNA produced from a given gene is modulated by a number of factors, including hnRNPs, SR proteins, core spliceosome, and transcription termination proteins. Surprisingly, when spliceosome components were depleted or inhibited pharmacologically, the steady-state levels of circular RNAs increased while expression of their associated linear mRNAs concomitantly decreased. Inhibition or slowing of canonical pre-mRNA processing events thus shifts the steady-state output of protein-coding genes towards circular RNAs, which likely helps explain why and how circular RNAs show tissue-specific expression profiles. Once generated, we showed that most circular RNAs are exported to the cytoplasm using a length-dependent and evolutionarily conserved pathway. It still remains largely unclear what most circular RNAs do, although two are known to efficiently modulate the activity of microRNAs. Ongoing efforts aim to further elucidate the mechanisms by which circular RNAs are produced, regulated, and function to control cell physiology and impact human diseases.

Besides focusing on circular RNAs that have no 5’ or 3’ end, my lab has also provided important insights into how the 3’ ends of linear RNAs are generated and regulated. We showed that the MALAT1 locus, which is over-expressed in many human cancers, produces a long nuclear-retained noncoding RNA as well as a tRNA-like cytoplasmic small RNA (known as mascRNA). Despite being an RNA polymerase II transcript, the 3’ end of MALAT1 is produced not by canonical cleavage/polyadenylation but instead by recognition and cleavage of the tRNA-like structure by RNase P. Mature MALAT1 thus lacks a poly(A) tail, yet is expressed at a level higher than many protein-coding genes due to a highly conserved triple helical structure protecting its 3’ end. We continue to identify and characterize additional RNAs whose 3’ ends are generated via unexpected mechanisms, thereby revealing novel paradigms for how RNAs are processed and, most importantly, new classes of RNAs with important biological functions.

Selected Publications

Huang C, Liang D, Tatomer DC, Wilusz JE: A length-dependent evolutionarily conserved pathway controls nuclear export of circular RNAs. Genes Dev 32: 639-644, May 2018.

Wilusz JE: A 360 degree view of circular RNAs: From biogenesis to functions. Wiley Interdiscip Rev RNA Page: e1478, Apr 2018.

Liang D, Tatomer DC, Luo Z, Wu H, Yang L, Chen LL, Cherry S, Wilusz JE: The output of protein-coding genes shifts to circular RNAs when the pre-mRNA processing machinery is limiting. Mol Cell 68: 940-954, Nov 2017.

Kearse MG, Wilusz JE: Non-AUG translation: a new start for protein synthesis in eukaryotes. Genes Dev 31: 1717-1731, Sept 2017.

Tatomer DC, Liang D, Wilusz JE : Inducible expression of eukaryotic circular RNAs from plasmids. Methods Mol Biol 1648: 143-154, Aug 2017.

Chen YG, Kim MV, Chen X, Batista PJ, Aoyama S, Wilusz JE, Iwasaki A, Chang HY : Sensing self and foreign circular RNAs by intron identity. Mol Cell 67: 228-238, Jun 2017.

Tatomer DC, Wilusz JE: An unchartered journey for ribosomes: Circumnavigating circular RNAs to produce proteins Mol Cell 66: 1-2, Apr 2017.

Wilusz JE: Circular RNAs: Unexpected outputs of many protein-coding genes. RNA Biol 14: 1007-1017, Aug 2016.

Molleston JM, Sabin LR, Moy RH, Menghani SV, Rausch K, Gordesky-Gold B, Hopkins KC, Zhou R, Jensen TH, Wilusz JE, Cherry S: A conserved virus-induced cytoplasmic TRAMP-like complex recruits the exosome to target viral RNA for degradation. Genes Dev 30: 1658-1670, July 2016.

Liang D, Wilusz JE: Short intronic repeat sequences facilitate circular RNA production. Genes Dev 28: 2233-2247, Oct 2014.

Kuhn CD, Wilusz JE, Zheng Y, Beal PA, Joshua-Tor L: On-enzyme refolding permits small RNA and tRNA surveillance by the CCA-adding enzyme. Cell 160: 644-658, Jan 2015.

Wilusz JE: Long noncoding RNAs: Re-writing dogmas of RNA processing and stability. Biochim Biophys Acta 1859: 128-138, Jan 2016.

Kramer MC, Liang D, Tatomer DC, Gold B, March ZM, Cherry S, Wilusz JE: Combinatorial control of Drosophila circular RNA expression by intronic repeats, hnRNPs, and SR proteins. Genes Dev 29: 2168-2182, Oct 2015.

Doucet AJ, Wilusz JE, Miyoshi T, Liu Y, Moran JV: A 3' poly(A) tract is required for LINE-1 retrotransposition. Mol Cell 60: 728-741, Dec 2015.

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Last updated: 05/28/2018
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