Defining Differential Genetic Signatures in CXCR4- and the CCR5-Utilizing HIV-1 Co-Linear Sequences
Figure 10
HIV-1 LTR regions and binding sites have differential X4/R5 MGD with Sp binding sites demonstrating altered predicted binding phenotype.
(A) Phylogenetic trees were created based on identified transcription factor binding sites within HIV-1 LTR from a total of 18 final selected samples: nine X4 and nine R5 sequences, using a maximum-likelihood method. A simple Python script was written to automate the process of generating the hundreds of trees. The branch distance was calculated between all pairs of X4 and R5 sequences. These groups of distances were tested for significant differences using a two-tailed student t-test. (B) The JASPAR position weight matrix was utilized to examine the predicted binding scores of the sequences in the X4 and R5 groups for each of the three Sp binding sites. The sequence logos for the JASPAR matrix and each Sp binding site in the X4 and R5 groups are shown. Mean binding scores (MBS) are also presented. p values were calculated using a student t-test with p<0.05 being considered statistically significant.