Carnegie Mellon University

 C. Joel McManus

Associate Professor, Department of Biological Sciences

Address:

255 Mellon Institute
Department of Biological Sciences
Carnegie Mellon University 
4400 Fifth Avenue
Pittsburgh, PA 15213
Work Phone: 412-268-9407

Email

 Administrative Assistant: Ally Ricarte

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 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.

Lab Members

 Christina Akirtava

Ph.D. Student

 Claire Dupont

Undergraduate Researcher

 Tate Mauzy

Undergraduate Researcher

 Gemma May

Researcher and Lab Manager

 Melissa Tosiano

Ph.D. Student

 Derek Wang

Undergraduate Researcher

 Cassia Williams-Rogers

Undergraduate Researcher

Highlighted Publications

Akirtava C, McManus CJ. Control of translation by eukaryotic mRNA transcript leaders-Insights from high-throughput assays and computational modeling. Wiley Interdiscip Rev RNA. 2021 May;12(3):e1623. doi: 10.1002/wrna.1623. Epub 2020 Aug 31. PMID: 32869519

Lagree K, Woolford CA, Huang MY, May G, McManus CJ, Solis NV, Filler SG, Mitchell AP. Roles of Candida albicans Mig1 and Mig2 in glucose repression, pathogenicity traits, and SNF1 essentiality. PLoS Genet. 2020 Jan 21;16(1):e1008582. doi: 10.1371/journal.pgen.1008582. PMID: 31961865

Lin Y, May GE, Kready H, Nazzaro L, Mao M, Spealman P, Creeger Y, McManus CJ. Impacts of uORF codon identity and position on translation regulation. Nucleic Acids Res. 2019 Sep 26;47(17):9358-9367. doi: 10.1093/nar/gkz681. PMID: 31392980

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

All Publications

Software

Assemblies of the resequenced genomes of the Drosophila strains described in McManus, C.J., Coolon, J.D., Eipper-Mains, J., Wittkopp, P.J. and Graveley, B.R. (2014) Evolution of Splicing Regulatory networks inDrosophilaGenome Research, in press.

The files included in this tar.gz contain the resequenced versions of the D. simulans (Tsimbazaza strain; Hollocher et al. 2000) and D. sechellia (Reference strain; 14021-0231.36) genomes, as well as genome from D. melanogaster strains zhr and z30 (McManus et al., 2014 (accepted)) in fasta format. Chain files are also included to convert coordinates on these genomes to those of the D. melanogaster reference version 3 (dm3), using the liftOver tool available on the UCSC genome browser website (http://hgdownload.soe.ucsc.edu/admin/exe/). Custom perl scripts are also included to convert coordinates from the D. simulans and D. sechellia genomes into dm3 coordinates (as this is a multi-step process). You must have the liftOver tool installed in your path to use these perl scripts. (Download here -> SplicingRegDivGenomes.zip).

Mod-seeker data analysis pipeline for high-throughput probing of RNA chemical modification, as described in Talkish, J, May, GE, Lin, Y, Woolford JL, Jr, and McManus CJ. (2014). Mod-seq: High-throughput sequencing for chemical probing of RNA structure. RNA (accepted).

The files included in this tar.gz contain mod-seeker analysis pipeline and test data (Download here ->Mod-seeker.tar ).