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. 2021 Mar 4;12(3):234. doi: 10.1038/s41419-020-03313-z

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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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — a ChIP-qPCR analysis of Gcm1, β-catenin and TCF4 enrichment in Wnt-responsive element (WREs) of Axin2 in control and folate-deficient mESCs. NEG negative control, TSS transcription start site. Right panel: the locations of the WRE and NEG in the promoter. b ChIP-qPCR analysis of Gcm1, β-catenin, and TCF4 enrichment in the WREs of Bcl9l in control and folate-deficient mESCs. Right panel: the locations of the WREs and NEG in the promoter. c ChIP-qPCR analysis of Gcm1, β-catenin, and TCF4 enrichment in the WREs of Isl1 in control and folate-deficient mESCs. Right panel: the locations of the WREs and NEG in the promoter. d Functional clustering of genes associated with Gcm1 ChIP-peaks in mESCs with folate deficiency (the top 10 categories are shown). The X-axis represents the log10 value of the binomial raw P value. e Pathway analysis of Gcm1 ChIP-peaks in mESCs with folate deficiency (the top 10 categories are shown). Gcm1 binding pathway enrichment was determined using PANTHER analysis. The X-axis represents the enrichment factor, the Y-axis represents the binomial raw P value, and the size of each circle represents the number of genes. f Representative examples of Ctla4 and Edn1 chromatin binding. A segment of chromosome 1 demonstrates the decreased binding of Clta4 to a TBE in folate-deficient compared to normal mESCs. A segment of chromosome 13 demonstrates the decreased binding of Edn1 to a TBE in folate-deficient group compared to normal mESCs. g ChIP-qPCR analysis of Clta4 and Edn1 in mESCs with folate deficiency. *P = 0.015 (Clta4) and *P = 0.022 (Edn1). h The mRNA expression of Clta4 (J) and Edn1 (K) in mESCs with folate deficiency. *P = 0.015 (Clta4) and *P = 0.04 (Edn1). i Correlation analysis between ChIP density and the mRNA expression of Clta4 and Edn1. The correlation coefficients for Clta4 is 0.739 (P = 0.003), and for Edn1 is 0.45 (P = 0.002). j Correlation of the tag densities (Y-axis) with the transcription levels of genes from −3 kb to +3 kb (X-axis). All the genes were divided into five groups based on their transcription levels from high (dark blue) to low (orange). The mean-normalized ChIP-seq densities with 1-bp resolution are plotted within a 6-kb region flanking the TSS or the TTS (transcription termination site). Data a–c, g–i represent the mean ± SEM (n = 3). The p value was calculated by Student’s t-test, ns was for no significance, *P < 0.05, **P < 0.01, ***P < 0.001.