Figure 3.

Alignment of the ESTs generated from skeletal muscle 3′-end cDNA libraries along the human mitochondrial genome. One hundred ESTs for each gene encoded by the mitochondrial H strand were selected and assembled with the corresponding full-length RNA transcript (Table S2), using the program SeqMan II (DNAStar). We chose the 100 longest ESTs produced for each mitochondrial gene, after trimming the poor quality regions, but only 92 sequences were available for the NADH 5 gene. It is conceivable that the scattered ESTs identify real RNA terminations, since the cDNA libraries were constructed from poly(A)⁺ RNA; actually many of the selected ESTs have long poly(A) stretches at their 3′-end. From the alignment we conclude that a premature termination of transcription occurs frequently in mitochondria from skeletal muscle. The phenomenon is clearly evident for longer genes and reaches extreme proportions in a few cases. Note that the figure does not reflect the relative abundance of mitochondrial RNAs in human skeletal muscle, reported in Table S2. We also note that the most 3′-terminal ESTs selected for the NADH 5 gene identified a different 3′-end compared to that annotated in the reference sequence (Table S2). Further information on the alignments shown is available upon request.