Analysis of the transcriptional control region in progressive multifocal leukoencephalopathy.

Progressive multifocal leukoencephalopathy (PML) is a fatal demyelinating disease caused by the human polyomavirus JCV. The hypervariable noncoding transcriptional control region (TCR) largely regulates replication of JCV in glial cells. Two distinct types of the TCR can be distinguished. Type II is derived from the archetype sequence. All type I TCRs, including the prototypical Mad-1 isolate contain a 23 bp deletion at nucleotide position 36. In a prospective study, TCR-DNA could be amplified and sequenced in 16/29 (55%) suspect cases of PML from the cerebrospinal fluid (CSF) and in 14/28 (50%) urine samples. Sequencing of the CSF-TCR identified Mad-1 like sequences in 5/17 (29.5%) instances and a type II TCR in 12/17 (70.5%) of cases. Of 14 urine TCRs, 12 (86%) displayed the archetype sequence, while two showed complex rearrangements. In all type II TCR sequences, the tst-1/oct-6 binding sites present in regions C and E of Mad-1 were missing. In 11/12 type II TCR sequences the pentanucleotide repeat in region A showed a G to T substitution of one nucleotide at position 36 relative to the Mad-1 TCR. All type II TCRs contained an Sp1 binding site at the beginning of region B. Of the 12 TCR type II sequences, 10 (83%) were of the 'D-retaining' pattern. In eight of these (80%) additional juxtapositioned nuclear factor 1, glial factor 1 and/or AP-1 binding motifs were created by duplications and/or insertions in region D. These findings indicate that type II TCRs are frequently present in PML and suggest to use TCR type II constructs for in vitro and in vivo studies of the evaluation of the functional role of DNA binding motifs.