SMAD3 ChIPseq in HCASMC identifies targeted genes in developmental and disease pathways and regions of SMAD3 and TCF21 colocalization.

A) SMAD3 motifs from HOMER de novo analysis of SMAD3 peaks. Aln sequence is the aligned HCASMC SMAD3 peak sequence and Ref indicates the reference binding sequence. B) DAVID Gene Ontology analysis of all SMAD3 target genes identified by GREAT in “basal plus extension” mode, including KEGG pathways and GAD disease enrichment analysis. C) Homer “known” motif analysis of intersected SMAD3 and TCF21 peaks identified the TCF21 binding sequence as the top motif, and also found enrichment of the binding sequence for the TCF21 partner TCF12. D) Venn diagram showing the overlapped gene number between filtered SMAD3 peak (fold change>5, -logQ>10) target genes and filtered TCF21 peak (fold change>15, -logQ>200) target genes, as identified with GREAT. E) Venn diagram showing the number of filtered TCF21 peaks (fold change>5, -logQ>60) located within the intervals of all SMAD3 peaks extended by ±1 kilobase. F) Overlapping peaks identified in E were extended ±1 kb from SMAD3 peak summits, and a density plot created for enrichment levels of SMAD3, TCF21, and control transcription factor HNF1A, along with HCASMC ATACseq open chromatin. G) Pattern of SMAD3 and TCF21 overlapping binding at the human SERPINE1 locus. In addition to SMAD3 and TCF21 ChIPseq data, also shown are additional HCASMC genomic profiling, including ATACseq mapping of open chromatin and H3K27Ac ChIPseq mapping of enhancer marks. Published SMAD3 ChIPseq data from A549 cells [52], and ENCODE H3K27Ac data are shown as well. H) Similar SMAD3 ChIPseq data in the COL1A1 locus.