Nature Biotechnology
18, 1262 - 1268 (2000)
doi:10.1038/82367
RNA expression analysis using a 30 base pair resolution Escherichia
coli genome arrayDouglas W. Selinger1, Kevin J. Cheung2, Rui Mei3, Erik M. Johansson3, Craig S. Richmond5, Frederick R. Blattner5, David J. Lockhart3, 4
& George M. Church11
Department of Genetics, Harvard Medical School,
200 Longwood Avenue Boston, MA 02115. 2
Harvard College, Cambridge, MA 02138. 3
Affymetrix Inc., 3380 Central Expressway,
Santa Clara, CA. 4
Genomics Institute of the Novartis Research Foundation,
3115 Merryfield Row, San Diego, CA 92121. 5
Laboratory of Genetics, University of Wisconsin,
Madison, WI 53706.
Correspondence should be addressed to George M. Church church@arep.med.harvard.eduEscherichia colistationary phasegene expressionfunctional genomicsDNA chipsoligonucleotide arraysmicroarraysWe 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.
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