Regulation of Toll-like Receptor Signaling by the SF3a mRNA Splicing Complex

O’Connor, Brian P.; Danhorn, Thomas; Arras, Lesly De; Flatley, Brenna R.; Marcus, Randall E.; Farias-Hesson, Eveline; Leach, Sonia M.; Alper, Scott

doi:10.1371/journal.pgen.1004932

Cited by 46 publications

(51 citation statements)

References 145 publications

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“…Alternative splicing can impact cellular function by creating distinct mRNA transcripts from the same gene, which may encode unique proteins that have distinct or opposing functions. For instance, in human and mouse cells, several alternatively spliced forms of genes involved in the TLR pathway have been shown to function as negative regulators of TLR signaling in order to prevent uncontrolled inflammation [9][10][11]. Additionally, several in-depth studies of individual genes suggest that alternative splicing plays an important role in increasing the diversity of transcripts encoding MHC molecules [12] and in modulating intracellular signaling and intercellular interactions through the expression of various isoforms of key cytokines [13,14], cytokine receptors [9,15,16], kinases [17] and adaptor proteins [18][19][20].…”

Section: Introductionmentioning

confidence: 99%

Widespread shortening of 3’ untranslated regions and increased exon inclusion are evolutionarily conserved features of innate immune responses to infection

Pai

Baharian

Sabourin

et al. 2015

Preprint

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The contribution of pre-mRNA processing mechanisms to the regulation of immune responses remains poorly studied despite emerging examples of their role as regulators of immune defenses. We sought to investigate the role of mRNA processing in the cellular responses of human macrophages to live bacterial infections. Here, we used mRNA sequencing to quantify gene expression and isoform abundances in primary macrophages from 60 individuals, before and after infection with Listeria monocytogenes and Salmonella typhimurium. In response to both bacteria we identified thousands of genes that significantly change isoform usage in response to infection, characterized by an overall increase in isoform diversity after infection. In response to both bacteria, we found global shifts towards (i) the inclusion of cassette exons and (ii) shorter 3' UTRs, with near-universal shifts towards usage of more upstream polyadenylation sites. Using complementary data collected in non-human primates, we show that these features are evolutionarily conserved among primates. Following infection, we identify candidate RNA processing factors whose expression is associated with individual-specific variation in isoform abundance. Finally, by profiling microRNA levels, we show that 3' UTRs with reduced abundance after infection are significantly enriched for target sites for particular miRNAs. These results suggest that the pervasive usage of shorter 3' UTRs is a mechanism for particular genes to evade repression by immune-activated miRNAs. Collectively, our results suggest that dynamic PLOS Genetics |

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Section: Introductionmentioning

confidence: 99%

Widespread shortening of 3’ untranslated regions and increased exon inclusion are evolutionarily conserved features of innate immune responses to infection

Pai

Baharian

Sabourin

et al. 2015

Preprint

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“…Our prior studies indicated that inhibiting SF3A1 altered splicing of many genes in the TLR signaling pathway, 5 including the signaling adaptor MyD88. The MyD88 gene encodes two isoforms: a long isoform (MyD88L, an NFκB activator), and a shorter isoform in which exon two is skipped (MyD88S, an NFκB inhibitor).…”

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confidence: 99%

Myelodysplastic syndrome-associated spliceosome gene mutations enhance innate immune signaling

et al. 2019

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Myelodysplastic syndrome-associated spliceosome gene mutations enhance innate immune signaling Genes encoding spliceosome components including SF3B1, U2AF1, and SRSF2, are frequently somatically mutated in myelodysplastic syndromes (MDS), other hematologic malignancies, and solid tumors. 1 Typically these are mutually exclusive, heterozygous, missense, hotspot mutations that result in neomorphic or gain-offunction splicing phenotypes. These mutations alter splicing of many genes; however, overlap among the different splicing factors is limited. Thus, a common mechanism by which spliceosome mutations contribute to disease is suspected but has remained elusive. We previously demonstrated that inhibiting any of five different spliceosome genes (SF3B1, SF3A1, SF3A2, SF3A3, EFTUD2) in mouse or human macrophages reduces inflammatory cytokine production induced by multiple Toll-like receptor (TLR) agonists including the TLR4 agonist lipopolysaccharide (LPS). 2-5 Although these genes encode essential spliceosome components, partial gene knockdown (approx. 80%) reduces LPS-induced inflammatory cytokine production without affecting viability or phagocytosis. 2-5 Hence, innate immunity may be particularly sensitive to spliceosome perturbation. These observations suggest that MDS-associated spliceosome mutations might enhance innate immunity,

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“…The PCR products 4 were then resolved using agarose gel electrophoresis. This also allowed us to determine the relative levels of the two isoforms, as there is substantially more MyD88-L than MyD88-S in unstimulated cells (12,33). In the absence of LPS, only a single PCR product of 369 bp corresponding to MyD88-L was amplified (Fig.…”

Section: Lps Induces Myd88-s Expression In Mouse Macrophagesmentioning

confidence: 99%

“…MyD88-L was assessed using a forward primer that annealed to the exon 2-3 boundary and a reverse primer that annealed to exon 3; MyD88-S was assessed using a primer that annealed to the unique exon 1-3 boundary and a reverse primer that annealed exon 3. These MyD88 isoform-specific primers as well as primers used to analyze cytokines and housekeeping genes have been validated extensively by us previously (12,33,71). RT-PCR to analyze MyD88-L and MyD88-S simultaneously was performed by first reverse transcribing RNA with the iScript cDNA synthesis kit (Biorad) and subsequently performing PCR using primers that bracket exon 2 (Table S1).…”

Section: Qpcr Rt-pcr and Elisa Analysismentioning

confidence: 99%

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NF-κB mediates lipopolysaccharide-induced alternative pre-mRNA splicing of MyD88 in mouse macrophages

Lee

Davidson

Harris

et al. 2020

Journal of Biological Chemistry

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Although a robust inflammatory response is needed to combat infection, this response must ultimately be terminated to prevent chronic inflammation. One mechanism that terminates inflammatory signaling is the production of alternative mRNA splice forms in the Toll-like receptor (TLR) signaling pathway. Whereas most genes in the TLR pathway encode positive mediators of inflammatory signaling, several, including that encoding the MyD88 signaling adaptor, also produce alternative spliced mRNA isoforms that encode dominant-negative inhibitors of the response. Production of these negatively acting alternatively spliced isoforms is induced by stimulation with the TLR4 agonist lipopolysaccharide (LPS); thus, this alternative pre-mRNA splicing represents a negative feedback loop that terminates TLR signaling and prevents chronic inflammation. In the current study, we investigated the mechanisms regulating the LPS-induced alternative pre-mRNA splicing of the MyD88 transcript in murine macrophages. We found that 1) the induction of the alternatively spliced MyD88 form is due to alternative pre-mRNA splicing and not caused by another RNA regulatory mechanism, 2) MyD88 splicing is regulated by both the MyD88- and TRIF-dependent arms of the TLR signaling pathway, 3) MyD88 splicing is regulated by the NF-κB transcription factor, and 4) NF-κB likely regulates MyD88 alternative pre-mRNA splicing per se rather than regulating splicing indirectly by altering MyD88 transcription. We conclude that alternative splicing of MyD88 may provide a sensitive mechanism that ensures robust termination of inflammation for tissue repair and restoration of normal tissue homeostasis once an infection is controlled.

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Regulation of Toll-like Receptor Signaling by the SF3a mRNA Splicing Complex

Cited by 46 publications

References 145 publications

Widespread shortening of 3’ untranslated regions and increased exon inclusion are evolutionarily conserved features of innate immune responses to infection

Widespread shortening of 3’ untranslated regions and increased exon inclusion are evolutionarily conserved features of innate immune responses to infection

Myelodysplastic syndrome-associated spliceosome gene mutations enhance innate immune signaling

NF-κB mediates lipopolysaccharide-induced alternative pre-mRNA splicing of MyD88 in mouse macrophages

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