Transcriptional Properties of RNA Polymerase II within Triplet Repeat-containing DNA from the Human Myotonic Dystrophy and Fragile X Loci

Expansion of a (CTG)n segment within the 3′-untranslated region of the myotonic dystrophy protein kinase gene alters mRNA production. The inherent ability of RNA polymerase II to transcribe (CTG)17–255 tracts corresponding to DNA from normal, unstable, and affected individuals, and the normal (CGG)54 fragile X repeat tract, was analyzed using a synchronized in vitro transcription system. Core RNA polymerase II transcribed all repeat units irrespective of repeat length or orientation. However, approximately 50% of polymerases transiently halted transcription (with a half-life of approximately 10 ± 1 s) within the first and second CTG repeat unit and a more transient barrier to elongation was observed roughly centered within repeats 6–9. Transcription within the remainder of the CTG tracts and within the CCG, CGG, and CAG tracts appeared uniform with average transcription rates of 170, 250, 300, and 410 nucleotides/min, respectively. These differences correlated with changes in the sequence-specific transient pausing pattern within the CNG repeat tracts; individual incorporation rates were slower after incorporation of pyrimidine residues. Unexpectedly, approximately 4% of the run-off transcripts were, depending on the repeat sequence, either 15 or 18 nucleotides longer than expected. However, these products were not produced by transcriptional slippage within the repeat tract.