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. 2021 Feb 16;12:1072. doi: 10.1038/s41467-021-21227-y

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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. 1 — a Aggregate plot for pH2A.X enrichment within the gene body ±2 kb of UCSC Known Genes in Hmga2+/+ and Hmga2−/− MEF. ChIP-seq reads were normalized using reads per kilobase per million (RPKM) measure and are represented as log2 enrichment over their corresponding inputs. TSS, transcription start site; TTS, transcription termination site. Dotted square, ±750 bp region around the TSS. b Top, schematic representation of the genomic region highlighted in a. Bottom, box plot of pH2A.X enrichment in the genomic regions showed as squares at the top in Hmga2+/+ and Hmga2−/− MEF. RPKM of the pH2A.X ChIP-seq were binned within each of these genomic regions and represented as log2. Box plots indicate median (middle line), 25th, 75th percentile (box) and 5th and 95th percentile (whiskers); n = 9522 genes enriched with pH2A.X; asterisks P-values after two-tailed Wilcoxon–Mann–Whitney test, ***P ≤ 0.001. c Heat map for pH2A.X enrichment at the TSS + 0.25 kb of UCSC Known Genes in Hmga2 + /+ and Hmga2−/− MEF. Genes were ranked by pH2A.X enrichment in Hmga2 + /+ MEF. Doted square, the top 15% ranked genes, as well as Gata6, Mtor, Igf1 and Rptor were selected for further analysis. d Visualization of selected HMGA2 target genes using UCSC Genome Browser showing HMGA2 (black), pH2A.X (turquoise), H2A.X (yellow) and H3 (blue) enrichment in Hmga2+/+ and −/− MEF. ChIP-seq reads were normalized using RPKM measure and are represented as log2 enrichment over their corresponding inputs. Images show the indicated gene loci with their genomic coordinates. Arrows, direction of the genes; black boxes, exons; dotted squares, regions selected for single gene analysis. See also Supplementary Fig. 1. Source data are provided as a Source Data files 01 and 04.