Identification of the promoter, genomic structure, and mouse ortholog of LGI1

The human LGI1 gene is a leucine-rich, repeat-containing gene that was cloned from the t(10:19) breakpoint of the T98G glioblastoma cell line. The LGI1 gene maps to 10q24, a region of peak LOH in malignant gliomas, and is inactivated during the transition from low to high-grade brain tumors. Here we report detailed studies of the genomic structure of the LGI1 gene and its promoter. We have also cloned and characterized the mouse lgil gene, which is 97% homologous to the human gene at the amino acid level and 91% homologous at the nucleotide level. LGI1 contains 8 exons, when each of the four leucine-rich repeat units is contained in an individual 72-bp exon. The cysteine-rich regions flanking the LRR and the single trans-membrane domain do not occupy individual exons. Approximately 5-kb of the genomic region 5' to LGI1 was sequenced, but conventional CAAT and TATA motifs were not present within this sequence. A 597-bp fragment of this 5' sequence was cloned upstream of a promoterless luciferase gene and was shown to be sufficient to drive transcription. SSCP analysis of the coding region of LGI1 in 20 glioblastomas and five cell lines did not reveal any mutations. Because LGI1 expression is considerably downregulated in gliomas, we also investigated whether this was owing to changes in the methylation status of the promoter. Southern blot analysis and 5-azacytidine treatment did not show any appreciable difference in methylation status between normal brain and glioblastomas.