Abstract
Chromatin interactions have important roles for enhancer-promoter interactions (EPIs) 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. Other DNA binding proteins such as YY1, ZNF143 and SMARCA4 are also reported to be associated with chromatin interactions. It is still unclear what proteins are associated with chromatin interactions and insulator function.
To find DNA binding motif sequences of transcription factors (TFs) like CTCF, affecting the interaction between enhancers and promoters of genes and their expression by the insulator function of the TFs, first, I predicted TF bound in enhancers and promoters using DNA motif sequences of TFs and experimental data of open chromatin regions in monocytes, T, Th17, Treg, GM12878 cells, HMEC and NPC, which were obtained from public and commercial databases. Second, transcriptional target genes of each TF were predicted based on enhancer-promoter association (EPA). An EPA was shortened at the FR or reverse-forward (RF) orientation of DNA motif sites of a TF, which were supposed to be at chromatin interaction anchors and acted as insulator sites. Then, the expression levels of transcriptional target genes predicted based on the EPA were compared with those predicted from closed chromatin regions.
Total 96 biased orientations of DNA motifs (64 FR and 52 RF orientations, the reverse complement sequences of some DNA motifs were also registered in databases, so the total number was smaller than the number of FR and RF) affected the expression level of putative transcriptional target genes significantly in monocytes, T cells, HMEC and NPC in common, including known TFs associated with chromatin interaction and insulator function such as CTCF, cohesin (RAD21 and SMC3), YY1 and ZNF143. Compared with chromatin interaction data, for 44 (69%) FR and 28 (54%) RF orientations of DNA motif sequences in CD4+ T cells, EPIs predicted from EPAs that were shortened at the biased orientations of DNA motif sites, overlapped with chromatin interactions significantly more than other types of EPAs. Using gene expression data among 53 tissues, 43 (72%) FR and 40 (80%) RF orientations of DNA motifs showed significantly reduced correlation in expression level of nearby genes separated by the motif sites. These analyses suggest that the DNA motifs are associated with insulator functions.
Footnotes
Abstract, Background, Results, Discussion, Materials and methods were slightly modified. Supplemental material is unchanged. Some figures that do not receive permission to reuse were replaced with web links to the figures.