Figure 2

DNA sequence blocks of NCCR rearrangement obtained in this study in comparison to archetype reference sequence: Upper case letters A, B, C, D, E, F indicate sequence blocks. Transcriptional binding sites are labelled on each block. Clear blocks indicate sequence blocks similar to archetype. Black colored blocks with Δ indicates truncated regions with the loss of one or more transcriptional binding sites. Black colored blocks without Δ indicates mutations or one to three nucleotide deletion which does not affect the transcriptional binding sites. Grey colored blocks indicate insertions with their base pairs. Additional transcriptional binding formed at the rearranged junctions are highlighted in bold. TATA (TATA box), TBP (TATA binding proteins), Oct6/Tst-1A, Tst-1B (POU domain protein or Octamer binding protein 6), SP-1 (Specificity protein 1), p53 (cellular tumor antigen p53), CEBPB (CCAAT/enhancer binding protein beta), AP-1 (Activating protein 1), NF-1 (Nuclear factor 1), EGR-1 (Early growth response protein-1), GF-1 (Glial factor 1), CRE-TAR (cyclic AMP response element, Transactivating response element), NFkB (Nuclear factor NF-kappa-B subunit). ** Indicates 2nt deletion and/or 1nt substitution observed in this study and retains all the binding sites in F block. * Indicates 1nt substitution or deletion observed in this study and results in the loss of binding sites for AP-1, SP-1 and/or NF-1. (A) Type IIS archetype like sequence: (a) NNV-JCV-NCCR-CSF15 with truncated D; (b) NNV-JCV-NCCR-CSF22 with complete deletion of block D and 1 bp insertion between C and F retains transcriptional binding site for NF-1, AP-1 and SP-1; (c) NNV-JCV-NCCR-CSF01 with truncated D and F, 18bp insertion between truncated D and E with two copies of p53. (B) Type IIR NCCR rearrangement with deletions: Deletions and repeats of different blocks. Rearrangements are frequently targeted in the junction of blocks-p53 between F/C (e); NF-1 between E/C (f); p53 between C/D (h); NF-1, SP-1 and/or AP-1 between C/E (i,j); p53 between F/B (i); AP-1 between A/C (k); Truncated D with second copy of NF-1 and TATA box (k). Complete loss of D block (i,j) and complete loss of B block (k). (C) Type IIR NCCR rearrangement with deletions and insertions: (l) 69bp insertion between two E blocks with two copies of TBP, two copies of p53 and single copy of Tst-1, CEBPB, AP-1 and SP-1; (m) SP-1 in the junction of E/F, 18bp insertion between F/D with SP-1, AP-1 and NF-1; (n) Complete loss of D block, 6bp insertion between C/F with SP-1 and p53, 20bp insertion between F/E with SP-1, AP-1 and NF-1.