Journal: bioRxiv

Article Title: Noncoding function of super enhancer derived mRNA in modulating neighboring gene expression and TAD interaction

doi: 10.1101/2023.12.05.570115

Figure Lengend Snippet: Heatmap shows the distribution of p300, H3K27ac and H3K27me3 signals around +/-5kb region of p300 only peak and p300/H3K27ac common peaks. B. Pie chart shows the distributions of annotated features around p300 only peaks in MEL cell. C. Homer motif analysis identifies significant enrichment of transcription factors binding sites at p300 only peaks. D. Binding profiles of transcription factors at p300 only peak in MEL cells. E. Distribution of different types of interaction observed at TAD boundary(blue) and chromatin loops(red). X axis represents number of different types of interactions. “Gene” represents genes that do not overlap with H3K27me3 and p300 only peak. “Intergenic” represents intergenic regions that do not overlap with H3K27me3 and p300 only peak. F and G. Aggregated peak analysis (APA) of chromatin loops anchored by p300 only peaks (F) and p300 only peak-H3K27me3 peaks (G) in G1ER late G1 cell. HiC matrix was normalized with VC_SQRT, window = 6. H. ECDF plot shows the comparison of the expression level of H3K27me3 non-overlapping and overlapping genes looped to p300 only peaks at TAD boundary or Chromatin loops. MEL cell RNA-seq processed expression quantification data was obtained from ENCODE. Wilcoxon test was used to compare the log2(TPM+1) value of H3K27me3 genes and non-H3K27me3 genes, P values ≤ 0.05 indicating a significant difference.

Article Snippet: For p300 ChIP experiment, undifferentiated MEL cells were used, p300 antibody (Santa Cruz Biotechnology, sc-48343).

Techniques: Binding Assay, Comparison, Expressing, RNA Sequencing

Journal: bioRxiv

Article Title: Noncoding function of super enhancer derived mRNA in modulating neighboring gene expression and TAD interaction

doi: 10.1101/2023.12.05.570115

Figure Lengend Snippet: A. Location of primers used for ChIP-qPCR in C and D. B. Cpox intron 5 TFBS KO gel image. C. Cpox intron 5 TFBS KO BLAST result, MEL p300 ChIP seq data from ENCODE. D. Sanger sequencing data, black line shows the deletion site.

Article Snippet: For p300 ChIP experiment, undifferentiated MEL cells were used, p300 antibody (Santa Cruz Biotechnology, sc-48343).

Techniques: ChIP-qPCR, ChIP-sequencing, Sequencing

Journal: bioRxiv

Article Title: Noncoding function of super enhancer derived mRNA in modulating neighboring gene expression and TAD interaction

doi: 10.1101/2023.12.05.570115

Figure Lengend Snippet: UCSC genome browser tracks shows p300, H3K27ac, H3K27me3, and H3K4me1 pattern at Dcbld2 promoter and Cpox intron 5. ChIP-seq data from ENCODE. p300 only peak was highlighted in grey. B. qRT-PCR result shows the expression of Dcbld2-2 , St3gal6-2 and CpoxeRNA after Cpox intron 5 TFBS deletion in UMEL cells. Three biological replicates. Data are mean ± s.d., unpaired one-tailed t-test. C. ChIP-qPCR result shows p300 binding at the Cpox intron 5 region after Cpox knock down by shRNA in UMEL cells. Two biological replicates. Data are mean ± s.d., unpaired one-tailed t-test. D. Model of Cpox mRNA loss activate neighboring gene and enhancer. Left graph shows in normal situation, right graph shows Cpox mRNA knock down situation. Colored arrows represent the genomic locus of the protein genes and enhancer. Colored curves represent the corresponding RNA transcribed. Blue dots represent p300, orange dots represent PRC2. Rectangles on genes represent the promoters.

Article Snippet: For p300 ChIP experiment, undifferentiated MEL cells were used, p300 antibody (Santa Cruz Biotechnology, sc-48343).

Techniques: ChIP-sequencing, Quantitative RT-PCR, Expressing, One-tailed Test, ChIP-qPCR, Binding Assay, Knockdown, shRNA