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

Naoki Osato
doi: https://doi.org/10.1101/290825
Naoki Osato
Osaka University
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  • For correspondence: naokiosato@gmail.com
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Abstract

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. 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 functions. To find DNA binding motif sequences of transcription factors (TF), such as CTCF, affecting the interaction between enhancers and promoters of genes and their expression, first I predicted TF bound in enhancers and promoters using DNA motif sequences of TF and experimental data of open chromatin regions in monocytes, T 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). EPA was shortened at the genomic locations of FR or reverse-forward (RF) orientation of DNA motif sequence of a TF, which were supposed to be at chromatin interaction anchors and acted as insulator sites like CTCF. Then, the expression levels of the 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. For 44 (69%) FR and 28 (54%) RF of 64 FR and 52 RF orientations of DNA motif sequences in CD4+ T cells, EPI predicted from EPA that was shortened at the genomic locations of the biased orientation of DNA motif sequence were overlapped with chromatin interaction data significantly more than other types of EPAs. Moreover, 43 (72%) FR and 40 (80%) RF of 64 FR and 52 RF orientations of DNA motifs found in the four cell types in common showed significantly reduced correlation in expression level of nearby genes separated by the motif sites, implying that the DNA motifs were associated with insulator functions.

Footnotes

  • Mainly Results, Discussion, Materials and methods and supplemental material were updated. Background and References were slightly modified. Some figures that do not receive permission to reuse were replaced with web links to the figures.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 02, 2020.
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Discovery of biased orientations of human DNA motif sequences affecting enhancer-promoter interactions and transcription of genes
Naoki Osato
bioRxiv 290825; doi: https://doi.org/10.1101/290825
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Discovery of biased orientations of human DNA motif sequences affecting enhancer-promoter interactions and transcription of genes
Naoki Osato
bioRxiv 290825; doi: https://doi.org/10.1101/290825

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