PT - JOURNAL ARTICLE AU - Naoki Osato TI - Discovery of directional chromatin-associated regulatory motifs affecting human gene transcription AID - 10.1101/290825 DP - 2020 Jan 01 TA - bioRxiv PG - 290825 4099 - http://biorxiv.org/content/early/2020/10/06/290825.short 4100 - http://biorxiv.org/content/early/2020/10/06/290825.full AB - Background Chromatin interactions are essential in enhancer-promoter interactions (EPIs) and transcriptional regulation. CTCF and cohesin proteins located at chromatin interaction anchors and other DNA-binding proteins such as YY1, ZNF143, and SMARCA4 are involved in chromatin interactions. However, there is still no good overall understanding of proteins associated with chromatin interactions and insulator functions.Results Here, I describe a systematic and comprehensive approach for discovering DNA-binding motifs of transcription factors (TFs) that affect EPIs and gene expression. This analysis identified 96 biased orientations [64 forward-reverse (FR) and 52 reverse-forward (RF)] of motifs that significantly affected the expression level of putative transcriptional target genes in monocytes, T cells, HMEC, and NPC and included CTCF, cohesin (RAD21 and SMC3), YY1, and ZNF143; some TFs have more than one motif in databases; thus, the total number is smaller than the sum of FRs and RFs. KLF4, ERG, RFX, RFX2, HIF1, SP1, STAT3, and AP1 were associated with chromatin interactions. Many other TFs were also known to have chromatin-associated functions. The predicted biased orientations of motifs were compared with chromatin interaction data. Correlations in expression level of nearby genes separated by the motif sites were then examined among 53 tissues.Conclusion One hundred FR and RF orientations associated with chromatin interactions and functions were discovered. Most TFs showed weak directional biases at chromatin interaction anchors and were difficult to identify using enrichment analysis of motifs. These findings contribute to the understanding of chromatin-associated motifs involved in transcriptional regulation, chromatin interactions/regulation, and histone modifications.Competing Interest StatementThe authors have declared no competing interest.TFTranscription factorsTFBSTranscription factor binding sitesTSSTranscriptional start sitesEPA domainPromoter and extended regions for enhancer-promoter associationEPIEnhancer-promoter interactionFFForward-forwardFRForward-reverseRFReverse-forwardRRReverse-reverseChIP-seqChIP-sequencing, chromatin immunoprecipitation followed by massively parallel DNA sequencingDNase-seqDNase I hypersensitive sites sequencingRNA-seqRNA sequencingENCODEEncyclopedia of DNA elements