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. 2021 Dec 1;11:23233. doi: 10.1038/s41598-021-02373-1

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Chromosomal interaction between MSX1 promoter and its promoter interacting region (PIR) mediated by a noncoding RNA, STX18-AS1. (A) Genomic locations of MSX1 and STX18-AS1 genes, CTCF and YY1 binding sites in H1 human embryonic stem cells (hESCs), GTEx expression quantitative trait loci (eQTLs) targeting MSX1 gene, guide RNA (gRNA) sequences for deleting the first two exons of STX18-AS1 gene and part of MSX1 PIR using CRISPR-Cas9, and PIRs associated with RNAs (the MSX1 promoter-PIR interaction was represented by an arc line). (B) Effects of STX18-AS1 down-regulation by deleting part of STX18-AS1 gene using CRISPR-Cas9 on MSX1 expression and MSX1 promoter-PIR interaction. (C) Effects of STX18-AS1 down-regulation by a specific GapmeR on STX18-AS1 and MSX1 expression levels. (D) Effects of downregulated MSX1 promoter-PIR interaction by deleting part of MSX1 RNA-PIR using CRISPR-Cas9 on expression levels of STX18-AS1 and MSX1. E) Effects of STX18-AS1 and MSX1 RNA-PIR CRISPR-Cas9 deletions, and STX18-AS1 GapmeR on expression levels of STX18, SOX2 and OCT4.*P < 0.05; **P < 0.01. All p-values were obtained from T tests with Bonferroni correction if multiple comparisons apply.

Chromosomal interaction between MSX1 promoter and its promoter interacting region (PIR) mediated by a noncoding RNA, STX18-AS1. (A) Genomic locations of MSX1 and STX18-AS1 genes, CTCF and YY1 binding sites in H1 human embryonic stem cells (hESCs), GTEx expression quantitative trait loci (eQTLs) targeting MSX1 gene, guide RNA (gRNA) sequences for deleting the first two exons of STX18-AS1 gene and part of MSX1 PIR using CRISPR-Cas9, and PIRs associated with RNAs (the MSX1 promoter-PIR interaction was represented by an arc line). (B) Effects of STX18-AS1 down-regulation by deleting part of STX18-AS1 gene using CRISPR-Cas9 on MSX1 expression and MSX1 promoter-PIR interaction. (C) Effects of STX18-AS1 down-regulation by a specific GapmeR on STX18-AS1 and MSX1 expression levels. (D) Effects of downregulated MSX1 promoter-PIR interaction by deleting part of MSX1 RNA-PIR using CRISPR-Cas9 on expression levels of STX18-AS1 and MSX1. E) Effects of STX18-AS1 and MSX1 RNA-PIR CRISPR-Cas9 deletions, and STX18-AS1 GapmeR on expression levels of STX18, SOX2 and OCT4.*P < 0.05; **P < 0.01. All p-values were obtained from T tests with Bonferroni correction if multiple comparisons apply.