RNA Expression Analysis Using an Antisense Bacillus subtilis Genome Array

• DOI: 10.1128/jb.183.24.7371-7380.2001
• Publication Date: 2002-07-27T10:01:09Z
• Authors: Jian-Ming Lee; Shehui Zhang; Soumitra Saha; Sonia Santa Anna; Can Jiang; John Perkins
• Keywords: DNA, Bacterial; 0303 health sciences; Base Sequence; Gene Expression Profiling; Riboflavin; Molecular Sequence Data; Biotin; Gene Expression Regulation, Bacterial; Regulon; DNA, Antisense; RNA, Bacterial; 03 medical and health sciences; Amino Acid Sequence; RNA, Messenger; Thiamine; Cell Division; Genome, Bacterial; Bacillus subtilis; Oligonucleotide Array Sequence Analysis

ABSTRACT

We have developed an antisense oligonucleotide microarray for the study of gene expression and regulation in Bacillus subtilis by using Affymetrix technology. Quality control tests of the B. subtilis GeneChip were performed to ascertain the quality of the array. These tests included optimization of the labeling and hybridization conditions, determination of the linear dynamic range of gene expression levels, and assessment of differential gene expression patterns of known vitamin biosynthetic genes. In minimal medium, we detected transcripts for approximately 70% of the known open reading frames (ORFs). In addition, we were able to monitor the transcript level of known biosynthetic genes regulated by riboflavin, biotin, or thiamine. Moreover, novel transcripts were also detected within intergenic regions and on the opposite coding strand of known ORFs. Several of these novel transcripts were subsequently correlated to new coding regions.