Carnegie Mellon University

C. Joel McManus

Associate Professor


Address: 
255 Mellon Institute
Department of Biological Sciences
Carnegie Mellon University
4400 Fifth Avenue
Pittsburgh, PA 15213

Phone: 412-268-9407
Fax: 412-268-7129

Email

Lab website

Joel McManus

Education

Ph.D., University of Wisconsin, Madison
Postdoctoral Appointment, University of Connecticut Health Center

Research

How does variation in gene expression contribute to phenotypic diversity and disease? Gene expression involves transcription of DNA into mRNA, alternative splicing of mRNA, translation of mRNA into proteins, and regulation of mRNA and protein levels through turnover pathways. Research in the McManus lab focuses on understanding mechanisms that regulate mRNA translation in fungal species, and how variation in RNA sequences and structures affects protein production. Our lab develops and employs novel high-throughput assay systems to identify RNA cis-regulatory elements and structures, and then quantitate their impact on mRNA translation using massively parallel reporter systems. We computationally mine the resulting data to distill features and develop models that predict the functions of mRNA transcript leaders. Our work addresses two major questions regarding translational control.

1. How do uORFs control translation? Upstream Open Reading Frames (uORFs) are short open reading frames found in mRNA transcript leaders that regulate mRNA translation and stability in eukaryotes. These fascinating regulatory elements control the expression of many eukaryotic genes. Intriguingly, many uORFs initiate at non-AUG (“near-cognate”) start codons (e.g. UUG). We use quantitative analysis of ribosome profiling to identify candidate uORFs in the yeast Saccharomyces cerevisiae and its sister species.
This footprinting technique identifies the locations on ribosomes on mRNA genome wide. By computationally assessing the resulting profiles of ribosome occupancy, we have predicted thousands of candidate uORFs in three Saccharomyces species. To test their functions, we have developed massively parallel reporter assays that quantitate the regulatory impacts of thousands of uORFs simultaneously. We use the resulting data to build computational models that predict uORF functions.
 
2. How is translation regulated by a fungal pathogen during infection of a mammalian host? Candida albicans is a deadly fungal pathogen that causes thousands of deaths annually. During infection, the fungal pathogen C. albicans resists numerous stresses imposed by the host immune system, including restriction of heavy metals and exposure to oxidative stress. mRNA translation is highly regulated in response to stress conditions. However, little is known regarding how translational control contributes to virulence. In collaboration with the Mitchell (CMU) and Filler (UCLA) labs, we have developed novel approaches to assay genome-wide changes in mRNA translation during infection in a mouse host. By characterizing the dynamic translatome during infection, we expect to identify novel virulence mechanisms and potential drug targets.

Publications

Huang MY, Woolford CA, May G, McManus CJ, Mitchell AP. Circuit diversification in a biofilm regulatory network. PLoS Pathog. 2019 May 22;15(5):e1007787. doi: 10.1371/journal.ppat.1007787. eCollection 2019 May. PMID: 31116789

Lin Y, Schmidt BF, Bruchez MP, McManus CJ. Structural analyses of NEAT1 lncRNAs suggest long-range RNA interactions that may contribute to paraspeckle architecture. Nucleic Acids Res. 2018 Apr 20;46(7):3742-3752. doi: 10.1093/nar/gky046. PMID: 29394378

Wang H, Kingsford C, McManus CJ. Using the Ribodeblur pipeline to recover A-sites from yeast ribosome profiling data. Methods. 2018 Mar 15;137:67-70. doi: 10.1016/j.ymeth.2018.01.002. Epub 2018 Jan 9. PMID: 29330118

Spealman P, Naik AW, May GE, Kuersten S, Freeberg L, Murphy RF, McManus J. Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data. Genome Res. 2018 Feb;28(2):214-222. doi: 10.1101/gr.221507.117. Epub 2017 Dec 18. PMID: 29254944

Wang H, McManus J, Kingsford C. Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast. J Comput Biol. 2017 Jun;24(6):486-500. doi: 10.1089/cmb.2016.0147. Epub 2016 Oct 11. PMID: 27726445

Wang H, McManus J, Kingsford C. Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap. Bioinformatics. 2016 Jun 15;32(12):1880-2. doi: 10.1093/bioinformatics/btw085. Epub 2016 Feb 15. PMID: 27153676

McManus J, Cheng Z, Vogel C. Next-generation analysis of gene expression regulation--comparing the roles of synthesis and degradation. Mol Biosyst. 2015 Oct;11(10):2680-9. doi: 10.1039/c5mb00310e. Review. PMID: 26259698

Lin Y, May GE, Joel McManus C. Mod-seq: A High-Throughput Method for Probing RNA Secondary Structure. Methods Enzymol. 2015;558:125-52.

Coolon JD, Stevenson KR, McManus CJ, Yang B, Graveley BR, Wittkopp PJ. Molecular mechanisms and evolutionary processes contributing to accelerated divergence of gene expression on the Drosophila X chromosome. Mol Biol Evol. 2015 Jun 2.

McManus CJ, May GE, Spealman P, Shteyman A. Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast. Genome Res. 2014 Mar;24(3):422-30.

Rafiq K, Shashikant T, McManus CJ, Ettensohn CA. Genome-wide analysis of the skeletogenic gene regulatory network of sea urchins. Development. 2014 Feb;141(4):950-61.

Dembowski J.A., Ramesh M, McManus C. J., and Woolford J.L. Jr. (2013) Identification of the binding site of Rlp7 on assembling 60S ribosomal subunits in Saccharomyces cerevisiae. RNA 19:1639-1647.

McManus CJ, Graveley BR. RNA Structure and the mechanisms of alternative splicing. Curr Opin Genet Dev 21(4):373-9,2011.

May GE, Olson S, McManus CJ, and Graveley BR. Competing RNA secondary structures are required for mutually exclusive splicing of the Dscam exon 6 cluster. RNA 17(2):222-229,2011.

McManus CJ, Duff MO, Eipper-Mains J, and Graveley BR. Global analysis of trans-splicing in Drosophila. Proc Natl Acad Sci USA 107(29):12975-12979, 2010.

McManus CJ, Coolon JD, Duff MO, Eipper-Mains J, Graveley BR, and Wittkopp PJ. Regulatory Divergence in Drosophila revealed by mRNA-seq. Genome Res 20(6):816-825, 2010.

McManus CJ, Graveley BR. Getting the message out. Mol Cell. 31(1):4-6, 2008.

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