ChIP-seq reveals cell type-specific binding patterns of BMP-specific Smads and a novel binding motif

Abstract

Dysregulated bone morphogenetic protein (BMP) signaling in endothelial cells (ECs) and pulmonary arterial smooth muscle cells (PASMCs) are implicated in human genetic disorders. Here, we generated genome-wide maps of Smad1/5 binding sites in ECs and PASMCs. Smad1/5 preferentially bound to the region outside the promoter of known genes, and the binding was associated with target gene upregulation. Cell-selective Smad1/5 binding patterns appear to be determined mostly by cell-specific differences in baseline chromatin accessibility patterns. We identified, for the first time, a Smad1/5 binding motif in mammals, and termed GC-rich Smad binding element (GC-SBE). Several sequences in the identified GC-SBE motif had relatively weak affinity for Smad binding, and were enriched in cell type-specific Smad1/5 binding regions. We also found that both GC-SBE and the canonical SBE affect binding affinity for the Smad complex. Furthermore, we characterized EC-specific Smad1/5 target genes and found that several Notch signaling pathway-related genes were induced by BMP in ECs. Among them, a Notch ligand, JAG1 was regulated directly by Smad1/5, transactivating Notch signaling in the neighboring cells. These results provide insights into the molecular mechanism of BMP signaling and the pathogenesis of vascular lesions of certain genetic disorders, including hereditary hemorrhagic telangiectasia.

The Proto-oncogene Transcription Factor Ets1 Regulates Neural Crest Development through Histone Deacetylase 1 to Mediate Output of Bone Morphogenetic Protein Signaling

“…5, M-P). The ETS binding motif is enriched in Smad1/5 binding regions in the human genome (51). In this study, we found that endogenous human ETS1 directly bound to the promoter of ID3 in HEK293T cells (Fig.…”

Transcriptional Control by the SMADs

“…1B). The best-defined SMAD1/5-binding site is GGCGCC, which is present in the enhancers of well-characterized BMP-responsive genes, such as the ID and VENTX genes (Korchynskyi and ten Dijke 2002;Blitz and Cho 2009;Nakahiro et al 2010;Morikawa et al 2011). A lower affinity variant of this sequence, GGAGCC, was also identified in a ChIP-seq experiment investigating BMP-responsive elements in endothelial cells and pulmonary arterial smooth muscle cells .…”

Prostate Cancer Cells and Bone Stromal Cells Mutually Interact with Each Other through Bone Morphogenetic Protein-mediated Signals

“…Cells-Numerous BMP target genes have been identified in many types of cells (4,5). Among them, HH family genes, which are targets of BMPs in certain types of cells, play a crucial role in skeletal development (19 -21).…”

“…Phosphorylated Smad1/5/8 form a heteromeric Smad complex with the common-partner Smad (CoSmad), Smad4. This Smad complex translocates into the nucleus, regulates the transcription of various target genes, and exerts a broad range of biological activities (5).…”