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| RNA expression analysis using a 30 base pair resolution Escherichia coli genome array |
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| Author(s): Selinger DW, Cheung KJ, Mei R, Johansson EM, Richmond CS, Blattner FR, Lockhart DJ, Church GM |
| Source: NATURE BIOTECHNOLOGY Volume: 18 Issue: 12 Pages: 1262-1268 Published: DEC 2000 |
| Times Cited: 174 References: 40 |
| Abstract: We have developed a high-resolution "genome array" for the study of gene expression and regulation in Escherichia coli. This array contains on average one 25-mer oligonucleotide probe per 30 base pairs over the entire genome, with one every 6 bases for the intergenic regions and every 60 bases for the 4,290 open reading frames (ORFs). Twofold concentration differences can be detected at levels as low as 0.2 messenger RNA (mRNA) copies per cell, and differences can be seen over a dynamic range of three orders of magnitude. In rich medium we detected transcripts for 97% and 87% of the ORFs in stationary and log phases, respectively. We found that 1,529 transcripts were differentially expressed under these conditions. As expected, genes involved in translation were expressed at higher levels in log phase, whereas many genes known to be involved in the starvation response were expressed at higher levels in stationary phase. Many previously unrecognized growth phase-regulated genes were identified, such as a putative receptor (b0836) and a 30S ribosomal protein subunit (S22), both of which are highly upregulated in stationary phase. Transcription of between 3,000 and 4,000 predicted ORFs was observed from the antisense strand, indicating that most of the genome is transcribed at a detectable level. Examples are also presented for high-resolution array analysis of transcript start and stop sites and RNA secondary structure. |
| Document Type: Article |
| Language: English |
| Reprint Address: Church, GM (reprint author), Harvard Univ, Sch Med, Dept Genet, 200 Longwood Ave, Boston, MA 02115 USA |
Addresses:
1. Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA
2. Harvard Coll, Cambridge, MA 02138 USA
3. Affymetrix Inc, Santa Clara, CA USA
4. Novartis Res Fdn, Genom Inst, San Diego, CA 92121 USA
5. Univ Wisconsin, Genet Lab, Madison, WI 53706 USA |
| Publisher: NATURE AMERICA INC, 345 PARK AVE SOUTH, NEW YORK, NY 10010-1707 USA |
| Subject Category: Biotechnology & Applied Microbiology |
| IDS Number: 379TR |
| ISSN: 1087-0156 |
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