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. 2023 May 10;16:16. doi: 10.1186/s13072-023-00491-w

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© The Author(s) 2023

Open AccessThis 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/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 8 — MMP-2 mediated H3NT proteolysis alters the histone code at TSSs a ChIP was performed in U2OS wild type (WT, blue) and MMP-2 depleted cells (MMP2sh1, red) using the H3.cs1 antibody, that detects cleaved H3NT, and a C-terminal H3 antibody to normalize for nucleosome occupancy. qPCR was performed at the indicated ProMMP2-3xHA positive gene loci and a negative control locus (gene desert, x-axis). Enrichment of cleaved H3NT at each locus was plotted as fold change relative to H3 control (y-axis), with the average and standard deviation between three independent biological replicates shown. Statistically significant differences between WT and MMP2sh1 at each locus were determined by a Student T-test (p-value: ns > 0.05, * < 0.05, ** < 0.005, *** < 0.0005, **** < 0.00005). b ChIP-qPCR analysis of histone H3 lysine 4 trimethyl (H3K4me3, top), lysine 9 acetyl (H3K9ac, middle) and lysine 18 acetyl (H3K18ac, bottom) as described in a. c Western analysis of chromatin purified from U2OS pLKO.1 control cells and the 2 different U2OS pLKO.1-MMP2 shRNA cell lines (sh1 and sh2) using the indicated antibodies. Amido black stain (AB) of the membrane shows equivalent loading of chromatin between samples. d Western analysis of chromatin purified from U2OS subconfluent (− 2) and overconfluent (+ 2) cells, as described in c. e Quantitative analysis of band intensities from c for each antibody (x-axis) was performed using ImageStudio (BioRad) and plotted as fold change relative to the pLKO.1 control, with the average and standard deviation of three independent biological replicates shown. f Quantitative analysis of band intensities from d, as described in e, plotted as fold change relative to U2OS subconfluent cells (− 2)