title: Whole-genome tiling array analysis of Mycobacterium leprae RNA reveals high expression of pseudogenes and noncoding regions.
abstract: Whole-genome sequence analysis of Mycobacterium leprae has revealed a limited number of protein-coding genes, with half of the genome composed of pseudogenes and noncoding regions. We previously showed that some M. leprae pseudogenes are transcribed at high levels and that their expression levels change following infection. In order to clarify the RNA expression profile of the M. leprae genome, a tiling array in which overlapping 60-mer probes cover the entire 3.3-Mbp genome was designed. The array was hybridized with M. leprae RNA from the SHR/NCrj-rnu nude rat, and the results were compared to results from an open reading frame array and confirmed by reverse transcription-PCR. RNA expression was detected from genes, pseudogenes, and noncoding regions. The signal intensities obtained from noncoding regions were higher than those from pseudogenes. Expressed noncoding regions include the M. leprae unique repetitive sequence RLEP and other sequences without any homology to known functional noncoding RNAs. Although the biological functions of RNA transcribed from M. leprae pseudogenes and noncoding regions are not known, RNA expression analysis will provide insights into the bacteriological significance of the species. In addition, our study suggests that M. leprae will be a useful model organism for the study of the molecular mechanism underlying the creation of pseudogenes and the role of microRNAs derived from noncoding regions.
authors.affiliation: Department of Bioregulation, Leprosy Research Center, National Institute of Infectious Diseases, 4-2-1 Aoba-cho, Higashimurayama-shi, Tokyo 189-0002, Japan.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Akama
authors.forename: Koichi
authors.initials: K
authors.lastname: Suzuki
authors.forename: Kazunari
authors.initials: K
authors.lastname: Tanigawa
authors.forename: Akira
authors.initials: A
authors.lastname: Kawashima
authors.forename: Huhehasi
authors.initials: H
authors.lastname: Wu
authors.forename: Noboru
authors.initials: N
authors.lastname: Nakata
authors.forename: Yasunori
authors.initials: Y
authors.lastname: Osana
authors.forename: Yasubumi
authors.initials: Y
authors.lastname: Sakakibara
authors.forename: Norihisa
authors.initials: N
authors.lastname: Ishii
mesh_terms: D009166:Mycobacterium leprae / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016366:Open Reading Frames; D016133:Polymerase Chain Reaction; D011544:Pseudogenes / Q000235:genetics*; D012329:RNA, Bacterial / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*
chemical_list: D012329:RNA, Bacterial; D022661:RNA, Untranslated