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Updated: Feb 11, 2026

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions
Published on: June 28, 2018
The interaction between IKKα and LC3 promotes type I interferon production through the TLR9-containing LAPosome
Kachiko Hayashi1, Manabu Taura1, Akiko Iwasaki2,3
1Department of Immunobiology, Yale University, New Haven, CT 06520, USA.
Insights
Toll-like receptor 9 (TLR9) signaling requires LC3-associated phagocytosis (LAP) for type I interferon production. LAP recruits IKKα to endosomes, directly linking autophagy to IFN synthesis via TLR9 activation.
Area of Science:
- Immunology
- Cell Biology
- Molecular Biology
Background:
- Toll-like receptor 9 (TLR9) recognizes DNA in endosomes, initiating immune responses.
- TLR9 signaling activates pathways for proinflammatory cytokines and type I interferons (IFNs).
- Signaling platform assembly on LC3-decorated endosomes is crucial for IFN production, but not IL-12p40.
Purpose of the Study:
- To investigate the mechanism linking TLR9 activation to type I IFN production.
- To elucidate the role of LC3-associated phagocytosis (LAP) in TLR9 signaling.
- To determine the interaction between autophagy proteins and signaling molecules in TLR9-mediated immunity.
Main Methods:
- Stimulation of TLR9 with CpG oligonucleotides in immune cells.
- Recruitment analysis of autophagy protein LC3 and kinase IKKα to TLR9-containing endosomes.
- Investigation of LAP formation requirements (ATG5, FIP200).
- Co-immunoprecipitation assays to study protein complex formation (LC3-IKKα, TRAF3, IRF7).
- Mutagenesis of LC3-interacting regions (LIRs) in IKKα and functional rescue experiments in IKKα-deficient dendritic cells.
Main Results:
- TLR9 stimulation recruited LC3 and IKKα to endosomes.
- LAP formation, requiring ATG5, was involved in this recruitment.
- The LC3-IKKα complex associated with TRAF3 and IRF7.
- Specific LIRs in IKKα were critical for LC3 binding and type I IFN production.
Conclusions:
- LC3-associated phagocytosis (LAP) directly links TLR9 activation to IKKα recruitment.
- This LAP-mediated recruitment is essential for initiating type I IFN production downstream of TLR9.
- The findings reveal a novel mechanism for regulating innate immune responses via noncanonical autophagy.
Abstract:
Toll-like receptor 9 (TLR9) recognizes DNA in endosomes and activates distinct signaling pathways to stimulate the production of proinflammatory cytokines and type I interferons (IFNs). The assembly of signaling platforms on microtubule-associated proteins 1A/1B-light chain 3 (LC3)-decorated endosomal vesicles is required to transduce TLR9 signals that stimulate the production of IFN but not interleukin-12 p40 (IL-12p40). LC3-associated phagocytosis (LAP), a form of noncanonical autophagy, is critical for the activation of interferon regulatory factor 7 (IRF7) and for IFN synthesis. We showed that after the stimulation of TLR9 by CpG oligonucleotides, the autophagy protein LC3 and the kinase IKKα were recruited to endosomes that contained TLR9. The recruitment of IKKα and LC3 to such signaling endosomes was not stimulated by catalysts of classical autophagosome formation but involved LAP formation, which required ATG5 but not FIP200. In addition, we found that the LC3-IKKα complex further associated with both TRAF3 and IRF7. We identified three putative LC3-interacting regions (LIRs) in IKKα, and mutagenesis suggested that two of these were critical for direct binding to LC3. Moreover, mutation of the same LIR sequences failed to rescue type I IFN production in IKKα-deficient dendritic cells upon reconstitution. Together, these data suggest a direct link between LAP formation and IKKα recruitment downstream of TLR9 activation that is necessary to facilitate type I IFN production.
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