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. 2020 Nov 10;48(21):12116–12134. doi: 10.1093/nar/gkaa1003

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© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 4. — Reduced promoter DNA methylation correlates with increased transcripts. (A) Volcano plot for differentially expressed genes between control and LSH KO HeLa cells. (B) Heatmap visualization of differentially expressed genes. (C) Enriched GO terms for the LSH-KO up- and down-regulated genes. (D) Correlation of DNA methylation changes at promoter and gene expression levels. Changes of DNA methylation represent the mean difference of CpGs in the TSS region. (E) Examples of genes with significantly decreased DNA methylation in CpG islands and up-regulated RNA transcripts in LSH-KO HeLa cells. (F) Expression changes at transposable regions for all TEs (left), ERV1 family (middle) and SVA family (right). Repeats of ERV1 and SVA families were selected as they had significant decrease of mean CpG methylations (KO-WT ≥ 30%). (G) qRT-PCR analysis of specific transposable elements. *** P< 0.0005.