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. 2018 Sep 21;9:3837. doi: 10.1038/s41467-018-06347-2

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© The Author(s) 2018

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 — Stage-specific SRF chromatin occupancy determines its maturation-specific regulation of gene expression. a SRF bioChIP-Seq at P14 and adult stages identified chromatin regions bound by endogenous SRF in hearts. These regions were grouped into maturation-specific elements (MEs) uniquely present at P14, and constitutive elements (CEs) found at both P14 and adult stages, and adult-only elements. b SRF bioChIP-seq signal on CEs and MEs. Each row shows SRF signal of a genomic region centered on a CE or ME and extending 1 kb upstream and downstream. Plots below show average signal at these regions. c GO term analysis of genes associated with CEs or MEs. d Distance of SRF-bound regions to the nearest transcriptional start site (TSS) for peaks found at P14 only (ME), P14 and adult (CE), or adult only. e Analysis of TF motifs enriched in the central 200 bp of CEs and MEs at proximal (TSS ±1 kb) or distal regions. The 1000 regions with the greatest SRF signal in each group was used for this analysis. Non-redundant motifs with P < 10^–5 are shown. Left and right panels show enrichment compared to randomly permuted background or the indicated set of comparison sequences, respectively. P values were calculated by Homer⁶⁵ using a negative binomial distribution. f SRF bioChIP-seq signal at P14 at four SRF-dependent mature myofibrillar genes (magenta) and their immature paralogs (green). Called peak regions are labeled as bars below the signal plot. g Relationship between peak distance to TSS, peak SRF occupancy signal, and likelihood of gene down-regulation on SRF knockout. SRF-occupied regions were divided into deciles by SRF bioChIP-seq signal. Color represents the ratio of down-regulated to unchanged genes. One-tailed Fisher's exact test: *P < 0.05