Additional file 1: of Enhancers reside in a unique epigenetic environment during early zebrafish development

Figures S1–S6. (ZIP 3593 kb

Additional file 3: of Enhancers reside in a unique epigenetic environment during early zebrafish development

An excel file listing the primers used to clone the enhancers in the transgenic assays. (XLSX 47 kb

Boletín de la Estadística Municipal de Cuenca: - 1918 enero 1

Copia digital. Madrid : Ministerio de Cultura. Subdirección General de Coordinación Bibliotecaria, 200

Additional file 6: Table S5. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

(a) Summary of df DIRs overlap with CTCF, Mediator, and cohesin binding sites. Column 1, Region, refers to the viewpoint assessed. Column 2, diffsites, refers to df DIRs. Column 4, no. sites and feature name corresponds to the number of DIRs that contain the specified genomic feature. Column 6, bp sites feature, presents the sum of DIRs bp which contain the specified feature. Column 8, no. features, indicates the number of features included inside DIRs. Percentages in columns 5, 7, and 9 are calculated based on the total number of regions or features in the preceding column. (b) Summary of df DIRs overlap with CTCF, Mediator, and cohesin binding sites. Column 1, Region, refers to the viewpoint assessed. Column 2, diffsites, refers to df DIRs. Column 4, no. sites and feature name corresponds to the number of DIRs that contain the specified genomic feature. Column 6, bp sites feature, presents the sum of DIRs bp which contain the specified feature. Column 8, no. features, indicates the number of features included inside the DIRs. Percentages in columns 5, 7, and 9 are calculated based on the total number of regions or features in the preceding column. (c) Summary of +  D Bl6 DIRs overlap for viewpoints 1, 2, 11, and 12 with CTCF, Mediator, and Smc1 binding sites. Column identities are as described in (a). (d) Summary of Monte Carlo simulations for assessing statistical significance of protein binding overlaps for +  D Bl6 DIRs for viewpoints 1, 2, 11, and 12. Column identities are as described in (b). Notice the significant p-values obtained for CTCF and Smc1 binding (p-val < 0.001, rounded down to zero in table). (XLSX 31 kb

Boletín de Segovia: Número 116 - 1868 septiembre 25

Copia digital. Madrid : Ministerio de Cultura. Subdirección General de Coordinación Bibliotecaria, 200

Additional file 2: Table S1. of Local compartment changes and regulatory landscape alterations in histone H1-depleted cells

The number of loci at which changes are observed for various combinations of epigenetic marks. (XLS 13 kb

Additional file 1: Figure S1. of Local compartment changes and regulatory landscape alterations in histone H1-depleted cells

DNA methylation changes per chromosome in histone H1-depleted ES cells. Figure S2. Hypomethylation in TKO cells occurs preferentially in gene-dense TADs regardless of GC content. Figure S3. ChIP-seq of four different histone marks in wild-type and TKO mouse ES cells. Figure S4. Large-scale changes in H3K4me1 and H3K4me3 sites upon depletion of histone H1. Figure S5. Analysis of DNA binding motifs at de novo formed DHSs in TKO cells. Figure S6. Over 10 % of de novo formed DHSs also show loss in CpG methylation in H1 TKO cells. Figure S7. Active chromatin marks accumulate in the most gene-dense TADs. Figure S8. Higher-order genome topology is very similar between wild-type and histone H1 TKO cells. Figure S9. Changes in compartment organization are not related to gene content, TAD size or differential expression. (PDF 4637 kb