Journal: Communications biology

Article Title: H3K27ac nucleosomes facilitate HMGN localization at regulatory sites to modulate chromatin binding of transcription factors.

doi: 10.1038/s42003-022-03099-0

Figure Lengend Snippet: Fig. 3 Loss of HMGN alters H3K27modifications and H1 occupancy at chromatin regulatory sites of MEFs. a Box plot showing decreased H3K27ac but increased H3K27me3 levels at enhancers and promoters of DKO mice. b MA plots showing differences between WT and DKO cells in H3K27ac or H3K27me3 levels at enhancers and promoters. Statistically significant differences (FDR < 0.05) are shown in red. Blue dots and blue density cloud represents all points corresponding to the nonchanging regions. c Aggregate plots showing the distribution of the average H3K27ac, H3K27me3 and histone H1 levels in WT and DKO MEFs. Left panels: throughout the genome (regulatory sites subtracted). “Center” indicates a location of the middle point of each 6kbp bin. Center panels: at enhancers. In these panels all cellular enhancers were aligned at their center. RPGC: reads per genomic coverage. Right panels: at promoters, Arrows point to promoter regions where H1 occupancy differs between WT and DKO cells. All ChIP analyses from two biological replicates. Regulatory sites identification is based on UCSC genome annotation (NCBI37/mm9).

Article Snippet: Mono and oligo nucleosomes devoid of protein (salt stripped chromatin particles) were prepared from mouse embryonic fibroblasts (MEFs) derived in our laboratory and from chicken erythrocytes (Rockland R401-0050) as described57,58.

Techniques:

Journal: Communications biology

Article Title: H3K27ac nucleosomes facilitate HMGN localization at regulatory sites to modulate chromatin binding of transcription factors.

doi: 10.1038/s42003-022-03099-0

Figure Lengend Snippet: Fig. 4 Decreased p300 and Brd3 chromatin binding in DKO MEFs. a Equal P300 expression in WT and DKO MEFs. b Box plots showing decrease P300 chromatin occupancy at enhancers and promoters of DKO cells. c MA plots showing differences in P300 chromatin binding between DKO and WT cells. Sites showing statistically significant differences (FDR < 0.05) are in red. Blue dots and blue density cloud represents all points corresponding to the non- changing regions. Note that most altered sites show decrease binding in DKO cells. d Profile plots showing decreased P300 occupancy at promoters and enhancers of DKO cells. e Equal Brd3 expression in WT and DKO MEFs. f Box plots showing decrease Brd3 chromatin occupancy at enhancer and promoters of DKO MEFs. g MA plot showing differences in Brd3 chromatin binding between DKO and WT cells. Sites showing significant differences (FDR < 0.05) are in red. Blue dots and blue density cloud represents all points corresponding to the non-changing regions. h Profile plots showing decreased Brd3 occupancy at promoters and enhancers of DKO cells. i IGV tracks showing reduced H3K27ac levels, and reduced P300 or Brd3 chromatin occupancy in DKO cells. All ChIP analyses from two biological replicates.

Article Snippet: Mono and oligo nucleosomes devoid of protein (salt stripped chromatin particles) were prepared from mouse embryonic fibroblasts (MEFs) derived in our laboratory and from chicken erythrocytes (Rockland R401-0050) as described57,58.

Techniques: Binding Assay, Expressing

Journal: Communications biology

Article Title: H3K27ac nucleosomes facilitate HMGN localization at regulatory sites to modulate chromatin binding of transcription factors.

doi: 10.1038/s42003-022-03099-0

Figure Lengend Snippet: Fig. 5 Decreased CEBPB chromatin binding in DKO MEFs. a Equal levels of CEBPB transcript and protein in WT and DKO MEFs. b Scatter plot comparing intensities of CEBPB peaks between biological replicates of WT (left), and of DKO cells (center). Right scatter plot shows reduced CEBPB chromatin binding in DKO cells. c Decreased CEBPB binding at TSS and enhancers of DKO cells. d Venn diagram showing CEBPB chromatin binding sites in WT and DKO MEFs. e Top DNA sequence motif underlying the CEBPB binding sites in WT and DKO cells, compared with the CEBPB motif in database. f Top and unique motifs in retained and lost CEBPB binding sites. Lost CEBP sites are defined as present in WT but not in DKO cells. The diagrams to the right show the location of the DNA binding motifs relative to the center of the CEBPB binding motif. g H3K27ac levels at lost or retained CEBPB sites in WT cells. h Overlap between CEBPB, H3K27ac and HMGN occupancy. i IGV snapshots showing loss of CEBPB binding in DKO cells at regions overlapping with H3K27ac. All ChIP analyses from two biological replicates.

Article Snippet: Mono and oligo nucleosomes devoid of protein (salt stripped chromatin particles) were prepared from mouse embryonic fibroblasts (MEFs) derived in our laboratory and from chicken erythrocytes (Rockland R401-0050) as described57,58.

Techniques: Binding Assay, Sequencing