In prokaryotes a large fraction of the genome contains coding sequences, hence large sections are copied into RNA. Thus the transcriptome of a bacterium will reflect the base composition of its respective genome. However, only one strand of DNA is copied at any one time, and some sequences are copied far more often than others. The promoter regions, although quite short in bacteria, are rich in A and T and these regions are not copied into RNA. These factors could alter the measured base composition so the relative proportions of the bases of RNA do deviate from the relative proportions of the bases in the genome.
Much of the eukaryotic genome is noncoding, although a large proportion of it is still transcribed. The promoter regions, which are characteristically more A-T rich and much larger than their prokaryotic equivalents, are not transcribed, so this can alter the base composition of the transcriptome relative to the genome.
Some of the noncoding RNA has a short lifetime in the cell, and this can become an important factor when considering the base composition of the transcriptome under steady-state conditions.
