Additional file 2 of Multiple epigenetic factors co-localize with HMGN proteins in A-compartment chromatin
Creators: name: He, Bing
name: Zhu, Iris
name: Postnikov, Yuri
name: Furusawa, Takashi
name: Jenkins, Lisa
name: Nanduri, Ravikanth
name: Bustin, Michael
name: Landsman, David
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Fig. S1. Stratum correlation coefficients (SCCs) between Hi–C data samples. There are two or three replicates for WT and DKO MEF and rBs. There is one sample for WT and DKO iPSCs. The SCC among all WT and DKO replicates ranges from 0.985 to 0.995 for MEF or rBs. The SCC between WT and DKO iPSC is 0.977. The SCCs between samples from different cell types are about 0.5 (MEF vs. rB or iPSC vs. rB) and 0.62 (MEF vs. iPSC). Fig. S2 .A) 75 bp mappability scores (2 mismatches allowed) was computed for the mm10 genome using GenMap ( https://github.com/cpockrandt/genmap ). The average mappability across all the compartment B- &gt; A boundaries are calculated for MEF, rB, ESC and iPS cell types. B) An illustration of how, Fig. 2A, was made. The whole genome is divided into bins of 25 kb. A C-score ranging from -1.0 to 1.0 is calculated for each bin. The C-scores of WT cells is plotted against DKO cells for all the bins. C) Two genomic regions, one at chr4 and the other at chr13, show a switch from B compartment to A compartment (marked with red frames) upon depletion of HMGN proteins. No correlations with gene expression was found. The RNA-seq data of WT and DKO MEFs is shown in the bottom two rows. Fig. S3. Comparison of TAD-calling results between WT and DKO cells. (A) Proportion of TADs according to the size range in three different cell types. (B) TADs size distribution in three different cell types. Fig. S4. Snapshots of cell type-specific interactions identified with CHiCAGO in rBs, and iPSCs, lined with ChIP-seq signals of HMGN1, HMGN2 and H3K27ac in the same regions, similar to Fig. 3. (A) Genomic regions around the promoter of an rB-specific gene Foxp1. (B) Genomic regions around the promoter of a pluripotency-specific gene Nanog. Fig. S5. Regions of differential interactions between MEF WT and DKO cells identified with Chicdiff. A total of 131 differential interactions are from regions related to six genes: U1.119 on Chr16, Fgfbp3, Btaf1, U6.858, Ide, and Kif11 on Chr19. For each gene, significant interactions detected with CHiCAGO are represented with color-coded dots (blue: 3 &lt; Chicago score ≤ 5; red: Chicago score &gt; 5). The upper panel contains the WT MEF cells and lower panel contains the DKO cells. Between the upper and lower panels are differentially interacting regions detected by Chicdiff, depicted as color-coded blocks with the color as representing a p value range. Interactions beyond 1 Mb each way were cropped. Fig. S6: Validation of the ChIP–MS procedure by ChIP-Western analysis. Western blot analyses of Smarca5, Atrx and Hspa8 proteins in immunoprecipitated chromatin fractions. The proteins from 0.1% input chromatin and the proteins, purified by ChIP with antibodies to either HMGN1 (A) or HMGN2 (B) was loaded on the gel, and probed with mouse Smarca5 (ThermoFisher Scientific MA3-055), Atrx (ThermoFisher Scientific CL0537) and Hspa8 (ThermoFisher Scientific 13D3) antibodies. Input and ChIP preparations are indicated at the top. The antibodies used for the Western blot analyses are in the middle. The abundance values for indicated proteins (from Additional file 1) were used to calculate a standardized Z-score. Obtained Z-scores were further color-coded.