title: Comparative genomics on SLIT1, SLIT2, and SLIT3 orthologs.
abstract: SLIT1 gene at human chromosome 10q24.1, SLIT2 gene at 4p15.31, and SLIT3 gene at 5q34-q35.1 encode large secreted proteins functioning as ligands for Roundabout (Robo) receptors. SLIT-ROBO signaling pathway is implicated in neurogenesis, angiogenesis, and immune response through the regulation of axonal guidance, endothelial cell migration, and denderitic cell migration, respectively. GREMLIN (CKTSF1B1 or GREM1) and DANTE (CKTSF1B3 or GREM3) are secreted antagonists for BMPs and SLITs. Here, comparative integromics analyses on SLIT1, SLIT2, and SLIT3 orthologs were performed by using bioinformatics. Rat Slit2 gene, consisting of 36 exons, was located within rat genome sequences AC098362.4 and AC111627.6. Mouse Slit3 complete coding sequence was determined by assembling BB634238 EST, AF144629 cDNA, and AK129223 cDNA. Leucine-rich repeats with nine conserved cysteine (LRRCC) domains and SLIT C-terminal cysteine-rich (SLITCCR) domain were identified in this study. CPxxCxCxxxxVxCxxxxLxxxPxxxPx(10~58) Nx(19,20)LxxNx(9)Fx(8)LxLxxNxxxCxxxxxFxxLxxx xxLxLxxNx(9)Fx(13)NxxxCxCxxxWLx(15)CxxPx(17)C was the consensus sequence of LRRCC domain. Mammalian SLIT1, SLIT2 and SLIT3 orthologs were large secreted proteins with four LRRCC domains, nine EGF domains, Laminin G (LamG) domain, and SLITCCR domain. SLIT1 mRNA was expressed in fetal brain, infant brain, anaplastic oligodendroglioma, and Jurkat T cells. SLIT2 and SLIT3 mRNAs were co-expressed in embryonic stem (ES) cells with embryoid body formation, and diffuse type gastric cancer with signet ring cell features. Double TCF/LEF and bHLH-binding sites were conserved among mammalian SLIT1 promoters. FOXJ2, E47, ETS1, and FOXA2-binding sites and CCAAT box were conserved among mammalian SLIT3 promoters. Mammalian SLIT1 orthologs were identified as evolutionarily conserved targets of the WNT/beta-catenin signaling pathway.
authors.affiliation: M&M Medical BioInformatics, Hongo 113-0033, Japan.
authors.forename: Yuriko
authors.initials: Y
authors.lastname: Katoh
authors.forename: Masaru
authors.initials: M
authors.lastname: Katoh
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D001921:Brain / Q000166:cytology; D019295:Computational Biology; D019143:Evolution, Molecular; D023281:Genomics; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins; D019169:Jurkat Cells; D008565:Membrane Proteins / Q000096:biosynthesis / Q000235:genetics*; D051379:Mice; D008969:Molecular Sequence Data; D009419:Nerve Tissue Proteins / Q000096:biosynthesis / Q000235:genetics*; D011401:Promoter Regions, Genetic; D051381:Rats; D017385:Sequence Homology; D015398:Signal Transduction; D013234:Stem Cells; D013274:Stomach Neoplasms / Q000473:pathology; D000098552:Slit Homolog 2 Protein
chemical_list: D036341:Intercellular Signaling Peptides and Proteins; D008565:Membrane Proteins; D009419:Nerve Tissue Proteins; C492289:SLIT1 protein, human; C498990:SLIT3 protein, human; C432251:Slit3 protein, mouse; C498991:Slit3 protein, rat; D000098552:Slit Homolog 2 Protein