CGGBP1 from higher amniotes restricts cytosine methylation and drives a GC-bias in transcription factor binding sites at repressed promoters [MeDIP-Seq]

Human CGGBP1 has been attributed multiple function related to the regulation of gene expression, cytosine methylation (including non-CpG methylation), related epigenetic states of target gene promoter regions and somatic mutation rates. CGGBP1 has also been shown to be a prominent transcription repressor of protein coding genes as well as repetitive elements, mainly Alu-SINEs. There is a possibility that CGGBP1-regulated cytosine methylation affects base mutation rates (C-T transitions) thereby directing TFBS evolution in the human genome. Some recent data suggest that the DNA-binding activity of human CGGBP1 prevents TFBS from cytosine methylation and preserves their GC content. The DNA-binding domain of CGGBP1 is conserved more than its other segments which contain no identifiable domains. In this study we assay global cytosine methylation using MeDIP-seq on human cells (HEK293T) over-expressing only representative vertebrate species (Latimeria chalumnae (Lc), Anolis carolinenesis (Ac), Gallus gallus (Gg), Homo sapiens (Hs)) and perform comparative analyses. Our analyses encompass a parallel global expression profiling (using Agilent arrays, submitted separately to NCBI GEO) and a large-scale estimation of TFBS C-T transition mutation rates from orthologs of genes repressed by the various forms of CGGBP1 used in this study. We report that cytosine methylation restriction by CGGBP1 promotes GC retention in some GC-rich TFBSs. Overall design: MeDIP-seq was performed on genomic DNA from HEK293T KD cells over-expressing vertebrate representative forms of CGGBP1 namely (Latimeria chalumnae Lc, Anolis carolinensis Ac, Gallus gallus Gg) and HEK293T CT cells over-expressing human CGGBP1 Hs and, HEK293T CT cells over-expressing empty pcDNA3.1(+) vector Ev as control.