Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays.
Microarrays traditionally have been used to analyze the expression behavior of large numbers of coding transcripts. Here we present a comprehensive approach for high-throughput transcript discovery in Escherichia coli focused mainly on intergenic regions which, together with analysis of coding transcripts, provides us with a more complete insight into the organism's transcriptome. Using a whole genome array, we detected expression for 4052 coding transcripts and identified 1102 additional transcripts in the intergenic regions of the E.coli genome. Further classification reveals 317 novel transcripts with unknown function. Our results show that, despite sophisticated approaches to genome annotation, many cellular transcripts remain unidentified. Through the experimental identification of all RNAs expressed under a specific condition, we gain a more thorough understanding of all cellular processes.
Tjaden
Brian
B
Department of Computer Science, University of Washington, Seattle, WA 98195, USA.
Saxena
Rini Mukherjee
RM
Stolyar
Sergey
S
Haynor
David R
DR
Kolker
Eugene
E
Rosenow
Carsten
C
D020413:3' Untranslated Regions / Q000235:genetics; D020121:5' Untranslated Regions / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009876:Operon / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014158:Transcription, Genetic / Q000235:genetics*
D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D012329:RNA, Bacterial