Discovery of biased orientation of human DNA motif sequences affecting enhancer-promoter interactions and transcription of genes

Chromatin interactions have important roles for enhancer-promoter interactions (EPI) and regulating the transcription of genes. CTCF and cohesin proteins are located at the anchors of chromatin interactions, forming their loop structures. CTCF has insulator function limiting the activity of enhancers into the loops. DNA binding sequences of CTCF indicate their orientation bias at chromatin interaction anchors - forward-reverse (FR) orientation is frequently observed. DNA binding sequences of CTCF were found in open chromatin regions at about 40% - 80% of chromatin interaction anchors in Hi-C and in situ Hi-C experimental data. It has been reported that long range of chromatin interactions tends to include less CTCF at their anchors. It is still unclear what proteins are associated with chromatin interactions. To find DNA binding motif sequences of transcription factors (TF) such as CTCF affecting the interaction between enhancers and promoters of transcriptional target genes and their expression, here, I predicted human transcriptional target genes of TF bound in open chromatin regions in enhancers and promoters in monocytes and other cell types using experimental data in public database. Transcriptional target genes were predicted based on enhancer-promoter association (EPA). EPA was shortened at the genomic locations of FR orientation of DNA binding motifs of TF, which were supposed to be at chromatin interaction anchors. The expression level of the target genes predicted based on EPA was compared with target genes predicted from only promoters. Total 287 biased orientation of DNA motifs [159 forward-reverse (FR) and 153 reverse-forward (RF) orientation, the reverse complement sequences of some DNA motifs are also registered in databases, so the total number is smaller than the number of FR and RF] affected the expression level of putative transcriptional target genes significantly in CD14+ monocytes of four people in common. The same analysis was conducted in CD4+ T cells of four people. DNA motif sequences of CTCF, cohesin and other transcription factors involved in chromatin interactions were found to be biased orientation. Transposon sequences, which are known to be involved in insulators and enhancers, showed biased orientation. Moreover, EPI predicted using FR or RF orientation of DNA motif sequences were overlapped with chromatin interaction data (Hi-C and HiChIP) more than other EPA.