Fig. 6: Evolution of the LTR48B-derived enhancer.

a Multiple alignment across six species (three hominoids: chimpanzee, gorilla, gibbon; rhesus macaque, lemur, and mouse) for the human LTR48B element defining the common XACT and T113.3 enhancer. The multiple alignment was performed using Multiz online from the UCSC browser. Positions on the X chr. are indicated for genome assembly hg38. b Phylogenetic tree of primates, with evolutionary distance between species. The approximate evolutionary time for the appearance of the LTR48B enhancer and the LTR/ERVs giving rise to the promoters of XACT and T113.3 are represented. c Prediction of binding sites for pluripotent transcription factors OCT4, SOX2, and NANOG in the LTR48B enhancer. Using RSAT matrix-scan⁶² and position-specific scoring matrices (PSSMs) of pluripotent transcription factors as input, the most probable binding sites were identified in the human LTR48B XACT/T113.3 enhancer. The PSSMs used to scan the region of interest were the Transfac M01307 for OCT4, M01123 for NANOG, and the Jaspar MA0143.1 for SOX2. Multiple alignment for the putative binding sites was performed on orthologous sequences in chimpanzee, gorilla, gibbon, rhesus, and lemur. P-values for the likelihood of the identified regions being bona-fide binding sites in the different primate species, were determined using RSAT matrix-scan. Logos of the PSSMs used for each transcription factor are represented below.