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. 2020 Jul 14;11:3506. doi: 10.1038/s41467-020-17206-4

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© The Author(s) 2020

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. 1 — a Schematic of the strategy to detect repeat families associated with open chromatin in AML (hematopoietic cells’ credit: A. Rad and M. Häggström; CC-BY-SA-3.0 licence). b Heatmap of the observed/expected enrichment for DHSs in selected repeat families. Cell lines are presented in the following order: HL-60, MOLM-13 and OCI-AML3. c DNase-seq profile across all elements of each AML DHS-associated repeat (A-DAR) families in OCI-AML3. d Gene expression average across all Blueprint AML samples for genes within 50 kb of A-DARs with or without a DHS in AML and/or in differentiated cells (boxes indicate first, second (median) and third quartiles; whiskers indicate data within 1.5× of the interquartile range). e For each gene lying near an A-DAR element, we compared its expression in AML samples (n = 26) where the respective ERV has a DHS, versus AML samples where the DHS is absent. Expression values were normalised using the variance-stabilising transformation (vst, log2 scale) in DESeq2. Highlighted are genes with >4-fold difference and vst > 0. f Example of a gene (SCIN) that displays a strict correlation between its expression (orange) and the presence of a DHS peak (blue) at a nearby LTR12C element in different AML samples.