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ChIP-sequencing
Expressing
Immunoprecipitation
MANN-WHITNEY
Modification
Over Expression
Purification
Standard Deviation
Incorporation of histone H3.1 suppresses the lineage potential of skeletal muscle 
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Global effects of GFP-H3.1 overexpression on endogenous H3.3 and modifications. (A) H3.3 enrichment in different gene sets. Box plots show H3.3 ChIP-seq signal intensities for the indicated gene sets at TSS ± 2 kb. Mann-Whitney test was used for the statistical analysis. *P < 0.05, **P < 0.01. Related data are shown in Supplementary Tables S4 and 5. (B) GFP-H3.1 or GFP-H3.3 incorporation in different gene sets expressed in box plots. GFP ChIP-seq signal intensities were analyzed at TSS ± 2 kb. Related data are shown in Supplementary Tables S4 and 5. (C) Co-localization of GFP-H3.1 and endogenous H3.3 in nucleosomes. Hydroxyapatite (HAP)-purified chromatin from C2C12 cells expressing GFP-H3.1 and GFP-H3.3 were immunoprecipitated with control IgG and GFP-specific antibody, and the presence of endogenous histones were analyzed by Western blotting. H3.3 was associated with GFP-H3.1-containing nucleosomes to form a bivariant state. (D) Association of H3K4me3 and H3K27m3 with different gene sets expressed as Z-scores from ChIP-seq signal intensities in each gene set at TSS ± 2 kb. GFP-H3.1 expression caused preferential <t>H3K27me3</t> in SKM genes.
Incorporation of histone H3.1 suppresses the lineage potential of skeletal muscle 
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Increases in <t>H3K27me3</t> level and H3.1 incorporation into SKM gene regulatory regions. (A) ChIP-qPCR assay using Ezh2-specific antibody. The regulatory regions of SKM, HK, and silent genes in GFP-H3.1 and GFP-H3.3 expressing cells and in WT cells at growth state were analyzed. Recovery efficiency (mean ± standard deviation of three independent experiments) is expressed as relative enrichment to WT cells (left axis) and ratio to input (right axis). The positions of PCR primers are indicated on top. *P < 0.05, **P < 0.01. (B and C) Association of GFP-H3.1 and Ezh2. Chromatin prepared from GFP-H3.1 expressing cells was immunoprecipitated and probed using antibodies directed against GFP (B) and Ezh2 (C). (D-F) ChIP-qPCR assays. H3K27me3 (D), H3K4me3 (E), and H3.3 (F) were analyzed as in (A). Recovery efficiency (mean ± standard deviation of three independent experiments) is expressed as relative enrichment to WT cells (left axis) and ratio to input (right axis). *P < 0.05, **P < 0.01.
Incorporation of histone H3.1 suppresses the lineage potential of skeletal muscle 
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Bivalenthistone modifications form on H3.3-containing SKM gene loci in mouse embryo. (A) H3.3-enriched regions showed more bivalent modifications than those exhibiting no modifications and tended to colocalize with H3K4me3 and <t>H3K27me3</t> modifications. (B) The quantitatively balanced state of the bivalent modification was associated with H3.3 incorporation. The scatter plot represents the relative ratio of H3K4me3 and H3K27me3 modifications (x-axis) and H3.3 ChIP-seq signal intensities (y-axis) in tissue-specific genes at TSS ± 2 kb. Related data are shown in Supplementary Tables S6-8.
Incorporation of histone H3.1 suppresses the lineage potential of skeletal muscle Nucleic Acids Research, 2015 Jan 30
"Global effects of GFP-H3.1 overexpression on endogenous H3.3 and modifications. (A) H3.3 enrichment in different gene sets. Box plots show H3.3 ChIP-seq signal intensities for the indicated gene sets at TSS ± 2 kb. Mann-Whitney test was used for the statistical analysis. *P < 0.05, **P < 0.01. Related data are shown in Supplementary Tables S4 and 5. (B) GFP-H3.1 or GFP-H3.3 incorporation in different gene sets expressed in box plots. GFP ChIP-seq signal intensities were analyzed at TSS ± 2 kb. Related data are shown in Supplementary Tables S4 and 5. (C) Co-localization of GFP-H3.1 and endogenous H3.3 in nucleosomes. Hydroxyapatite (HAP)-purified chromatin from C2C12 cells expressing GFP-H3.1 and GFP-H3.3 were immunoprecipitated with control IgG and GFP-specific antibody, and the presence of endogenous histones were analyzed by Western blotting. H3.3 was associated with GFP-H3.1-containing nucleosomes to form a bivariant state. (D) Association of H3K4me3 and H3K27m3 with different gene sets expressed as Z-scores from ChIP-seq signal intensities in each gene set at TSS ± 2 kb. GFP-H3.1 expression caused preferential <t>H3K27me3</t> in SKM genes. "
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