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mRNA Splicing-Mediated Gene Expression Regulation in Innate Immunity


Frankiw, Luke Steven (2019) mRNA Splicing-Mediated Gene Expression Regulation in Innate Immunity. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/NBQG-BS67.


At the heart of an inflammatory response lies a tightly regulated gene expression program. Perturbations to this finely tuned response can result in unchecked or inappropriately scaled inflammation, shifting the balance from protective to destructive immunity. A variety of post-transcriptional mechanisms play a role in the fine-tuning of an inflammatory gene expression program. One such mechanism involves unproductive RNA splicing, whereby alternative splicing can frameshift the transcript or introduce a premature termination codon (PTC). These effects render the transcript nonfunctional and/or subject it to nonsense-mediated decay.

We observed such an event in Irf7, the master regulator of the type I interferon response. We found a single intron was consistently retained at a level much greater than other introns in the Irf7 transcript. In an effort to understand trans-acting factors that regulate this retention, we used RNA-antisense purification followed by mass spectrometry (RAP-MS) to identify the factor BUD13 as a highly enriched protein on Irf7 transcripts. Deficiency in BUD13 was associated with increased retention, decreased mature Irf7 transcript and protein levels, and consequently a dampened type I interferon response, which compromised the ability of BUD13-deficient macrophages to withstand vesicular stomatitis virus (VSV) infection.

Beyond this intron retention event in Irf7, we identified a variety of other unproductive splicing events in a number of important genes involved with the innate immune response. This unproductive splicing was not restricted to intron retention events. For example, we identified a frequently used alternative splice site in the crucial murine antiviral response gene, oligoadenylate synthetase 1g (Oas1g) that led to both a frameshift and incorporation of a PTC. Genome editing was used to remove the alternative splice site in a macrophage cell line, which led to both increased Oas1g expression and improved viral clearance. We hypothesize these events exist as a means of mitigation for what might otherwise be an inappropriately scaled response. In doing so, they represent a previously underappreciated layer of gene expression regulation in innate immunity.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Bud13; Irf7; RES complex; inflammation; intron retention; spliceosome; type I interferons; AS-NMD; Oas1g
Degree Grantor:California Institute of Technology
Division:Biology and Biological Engineering
Major Option:Molecular Biology and Biochemistry
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Baltimore, David L.
Thesis Committee:
  • Guttman, Mitchell (chair)
  • Baltimore, David L.
  • Elowitz, Michael B.
  • Mazmanian, Sarkis K.
Defense Date:17 May 2019
Funding AgencyGrant Number
Raymond and Beverly Sackler FoundationUNSPECIFIED
NIH 5R21AI126344
Record Number:CaltechTHESIS:06052019-122355847
Persistent URL:
Related URLs:
URLURL TypeDescription adapted for chapter 2 adapted for chapter 3
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:11687
Deposited By: Luke Frankiw
Deposited On:06 Jun 2019 19:50
Last Modified:04 Oct 2019 00:26

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