Figure 2. Ectopic expression of PLZF modulates H3K27ac at enhancer regions in myeloid cells. (A) Box plots showing ... Figure 2. Ectopic expression of.

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Figure 2. Ectopic expression of PLZF modulates H3K27ac at enhancer regions in myeloid cells. (A) Box plots showing ... Figure 2. Ectopic expression of PLZF modulates H3K27ac at enhancer regions in myeloid cells. (A) Box plots showing H3K27ac enrichment (% H3K27ac bound/Input) in Empty vector and PLZF-Flag conditions at promoter, enhancer and active enhancer regions. *P < 0.05, **P < 0.01, ***P < 0.001 (Welch's t.test); NS not significant. (B) Venn diagrams showing the overlap of active enhancers (Active) between Empty vector and PLZF-Flag conditions. ***P < 0.001 (hypergeometric test). (C) Venn diagrams showing the overlap between PLZF peaks and active enhancers (Active) in PLZF-Flag condition. ***P < 0.001 (hypergeometric test). (D) Density plot profiles of H3K27ac normalized signal at PLZF-bound active enhancers in PLZF-Flag and Empty vector conditions. ***P < 0.001 (paired Welch's t test). (E) Spike-in ChIP-qPCR validation of H3K27ac variation at Cd47, Furin and Mef2c enhancers. Hoxd10 is used as a negative control. Percentage of bound DNA over input are shown as a mean ±SD of two independent experiments (n = 3, for each experiment). *P < 0.05 (Mann–Whitney test), NS not significant. (F) Venn diagrams showing the overlap between PLZF peaks and active enhancers with decreased H3K27ac level (K27ac Down Active) in PLZF-Flag condition. PBDA: PLZF-Bound Down Active. In figures B and E, ***P < 0.001 (hypergeometric test); NS not significant. (G) Gene Ontology (GO) enrichment analysis on PBDA (intersect Figure E) using g:Profiler. Red scale indicates the P-value (–log<sub>10</sub>) and grey scale represents gene % (i.e. % of genes observed/total number of genes within each GO term). Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. 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 License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz174, https://doi.org/10.1093/nar/gkz174 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 1. PLZF restricts active epigenetic marks in myeloid cells Figure 1. PLZF restricts active epigenetic marks in myeloid cells. (A) Experimental protocol design for engineering ... Figure 1. PLZF restricts active epigenetic marks in myeloid cells. (A) Experimental protocol design for engineering PLZF-Flag 416b cell line and immunoblot showing PLZF expression (using anti-Flag or anti-PLZF antibodies). Alpha-Tubulin was used as loading control. (B) Genomic distribution of PLZF obtained from PLZF-Flag transduced 416b cell line (TSS: transcription start site defined from -1kb to +100bp; TES: transcription ending site defined from –100 bp to +1 kb; UTR: untranslated region. (C) Gene Ontology (GO) analysis using GREAT tools of PLZF-peaks nearby genes (CC: cell cycle; DD: DNA damage; EP: epigenetics; CM: chemical modifications; IM: immunology). Gray scale values illustrate gene enrichment (i.e. number of genes observed/expected) for each GO term. (D) Venn diagrams showing the overlap between PLZF and histone marks.***P < 0.001 (hypergeometric test); NS not significant. (E) Scatter plots showing histone mark profiles in PLZF-Flag versus Empty vector conditions. (F) Venn diagrams showing the percentage of H3K27ac (upper) and H3K4me3 (lower) peaks modulated and/or bound by PLZF. (G) Integrative Genomic Viewer (IGV) screenshots of PLZF and H3K27ac in PLZF-Flag (PLZF) and Empty vector conditions (Empty). Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. 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 License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz174, https://doi.org/10.1093/nar/gkz174 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 3. PLZF binding restrains enhancer activity Figure 3. PLZF binding restrains enhancer activity. (A) Density plot profiles illustrating ATAC-seq normalized signal ... Figure 3. PLZF binding restrains enhancer activity. (A) Density plot profiles illustrating ATAC-seq normalized signal on PLZF-bound active enhancers in absence (Empty vector) or presence of PLZF (PLZF-Flag). ***P < 0.001 (paired Welch's t test). (B) Representative Integrative Genomics Viewer (IGV) tracks of ATAC-seq, PLZF, signals at Cd47, Furin and Mef2c enhancers in PLZF-Flag versus Empty vector conditions. The grey box underlines the enhancers. (C) Box plots showing gene expression in PLZF-Flag condition of all genes and genes associated with PBDA with low (PLZF low) or strong PLZF (PLZF high) signals. PBDA: PLZF-Bound Down Active. *P < 0.05 (Welch's t test), NS not significant. (D) MA plot showing gene expression (RNA-seq) fold changes in PLZF-Flag versus Empty vector conditions (grey dots). Blue dots represent genes associated with PBDA. Yellow dots represent genes associated with PBDA with strong PLZF binding. (E) Luciferase assay performed in 416b cells in absence (Empty vector) or presence of PLZF (PLZF-Flag) with control-LUC (Mock) or with CD47-enhancer-LUC (CD47 Enhancer) reporters. Luciferase activity (FIREFLY: FF) was measured 8 h after transfection. FF values are normalized to RENILLA and expressed as a mean ± SD of three independent experiments. *P < 0.05 (Mann–Whitney test), NS not significant. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. 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 License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz174, https://doi.org/10.1093/nar/gkz174 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 4. PLZF-mutation induced H3K27ac at enhancer regions in GMPs Figure 4. PLZF-mutation induced H3K27ac at enhancer regions in GMPs. (A) Experimental design used for generating ... Figure 4. PLZF-mutation induced H3K27ac at enhancer regions in GMPs. (A) Experimental design used for generating histone mark ChIP-seq in wild type (WT) and PLZF mutant (Zbtb16<sup>lu/lu</sup>) Granulocyte-Monocyte Progenitors (GMPs). Lin-: Lineage negative, LK: Lin-, c-kit<sup>+</sup> and Sca-1<sup>−</sup>. (B) Scatter plots showing H3K27ac, H3K27me3, H3K4me1 and H3K4me3 signal in Zbtb16<sup>lu/lu</sup> versus WT GMP. (C) Box plots showing H3K27ac enrichment (% H3K27ac bound/input) in WT and Zbtb16<sup>lu/lu</sup> GMPs at promoter, enhancer and active enhancer regions. **P < 0.01 (Welch's t test), NS not significant. (D) Venn diagrams showing the numbers of active enhancers in the Zbtb16<sup>lu/lu</sup> GMPs. K27ac Up: upregulated compared to the WT condition, K27ac de novo: not detected in the WT condition. (E) Volcano plot representing differential gene expression (RNA-seq) in Zbtb16<sup>lu/lu</sup>compared to WT. Yellow dots represent genes significantly modulated (false discovery rate (FDR) < 8%, fold change (FC) > 1 or < 1). Up Active enhancers are highlighted in blue. The 12 Up-Active associated genes with FDR <8% that appear in blue are circled in blue. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. 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 License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz174, https://doi.org/10.1093/nar/gkz174 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 5. Aging of GMPs is marked by an accumulation of H3K27ac at enhancer regions. (A) Scatter plots showing H3K27ac ... Figure 5. Aging of GMPs is marked by an accumulation of H3K27ac at enhancer regions. (A) Scatter plots showing H3K27ac profiles in Old versus Young GMPs. (B) Box plot showing H3K27ac level at active enhancers in Old versus Young GMPs. ***P < 0.001 (Welch's t test). (C) Venn diagrams showing the numbers of active enhancers in Old WT GMPs. K27ac Up: upregulated compared to the Young condition, K27ac de novo: not detected in the Young condition. (D) Venn diagram showing the overlap (common) between genes associated with active enhancers upregulated during aging (Old Up Active associated genes) and genes associated with active enhancers upregulated in Zbtb16<sup>lu/lu</sup> GMPs (Zbtb16<sup>lu/lu</sup> Up Active associated genes) ***P < 0.001 (hypergeometric test). (E) Gene Ontology (GO) analysis and associated human phenotype of ‘common’ enhancers that change in aged and Zbtb16<sup>lu/lu</sup> conditions (intersect Figure D) using g:Profiler. Red scale indicates the P-value (–log<sub>10</sub>) and grey scale represents gene % (i.e. % of genes observed /total number of genes within each GO/KEGG term). (F) De novo binding motif analysis at ‘common’ enhancers associated with metabolic processes. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. 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 License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz174, https://doi.org/10.1093/nar/gkz174 The content of this slide may be subject to copyright: please see the slide notes for details.