TLRs sense a variety of microbial products. Cell surface TLRs, including TLR4/MD-2, TLR1/TLR2, and TLR6/TLR2, recognize microbial membrane lipids, whereas TLR3, TLR7, TLR8, and TLR9 localize to intracellular organelles and recognize microbial nucleic acids [1][2][3]. TLR9 recognizes single-stranded DNA. Selfversus-pathogen discrimination by TLR9 is primarily dependent on structural differences between self and microbial DNA such as unmethylated CpG motifs in viral DNA [4][5][6]. CpG motifs are more often found in microbial genomes than in mammalian genomes, enabling pathogen-specific DNA recognition by TLR9. However, several studies reveal that mammalian DNA also activates TLR9Correspondence: Dr. Kensuke Miyake e-mail: kmiyake@ims.u-tokyo.ac.jp [7]. Self-versus-pathogen discrimination by TLR9 is thus error prone and one way to make this process more robust is by compartmentalizing DNA sensing in endolysosomes, rather than it taking place on the cell surface. While self-derived DNA is rapidly degraded by DNase II, microbial DNA is resistant to degradation because it is encased in bacterial cell walls or viral particles. Microbial DNA, but not self-derived DNA, therefore reaches TLR9 by way of endocytosis and trafficking through endolysosomes. In autoimmune diseases such as systemic lupus erythematosus or psoriasis, self-DNA released from dead cells is complexed with autoantibodies or the cationic antimicrobial peptide LL37. These complexes are resistant to degradation, and are delivered into endosomal compartments by endocytosis, and activate TLR9, leading to DC activation and production of .To compartmentalize DNA sensing, two mechanisms are proposed. The first mechanism depends on the proteolytic cleavagewww.eji-journal.eu Eur. J. Immunol. 2013. 43: 2006 HIGHLIGHTS 2007 of the TLR9 ectodomain in endolysosomes [11,12], on which DNA sensing is thought to depend. The ectodomain of TLR9 is cleaved by asparagine endopeptidase and cathepsins in endolysosomes [13,14]. The C-terminal TLR9 fragment (TLR9C) starting at 461T or 467F [15] is essential for triggering an activation signal. Requirement for the N-terminal TLR9 fragment in DNA sensing, however, has been controversial. Although N-terminal TLR9 fragment (TLR9N) is reported to be cleaved off and not required for DNA sensing [11,12], newly established monoclonal antibodies (mAbs) to mouse endogenous TLR9 have revealed that the TLR9N remains associated with TLR9C in DCs [15]. Furthermore, this study [15] showed that TLR9C alone fails to respond to DNA, and that TLR9N coexpression is required for DNA sensing, thus demonstrating DNA sensing by both TLR9N + TLR9C. The second mechanism compartmentalizing DNA sensing is based on TLR9 transportation. Trafficking of TLR9 out of the ER is dependent on a TLR-specific chaperone, protein associated with TLR4 A (PRAT4A), and Unc93B1, a multiple transmembrane protein [16][17][18]. Without Unc93B1, nucleic acid-sensing TLRs fail to respond to nucleic acid, because all the nucleic acid-sensing TLRs remain uncleaved in the ER [16,...