The identification and localization of 33 pea chloroplast transcription initiation sites

We have used a novel approach to produce a comprehensive transcription initiation map of the pea chloroplast genome. Sites were mapped by measuring the ability of DNA probes to protect 5′ ends of transcripts that have been capped in vitro. Using this approach, at least 33 probes appear to contain one or more transcription start sites. A more precise location of some of these sites was obtained by hybrid selecting certain of these RNAs and determining their size both before and after RNase treatment. We have found at least one initiation site in front of every chloroplast gene cluster for which appropriate clones were available. In addition, we have found initiation sites within gene clusters previously shown to be co-transcribed. In one such case, we were able to locate a transcription start site for psbC within the coding sequence of psbD.