Distinct modes of SMAD2 chromatin binding and remodeling shape the transcriptional response to NODAL/Activin signaling

Abstract

NODAL/Activin signaling orchestrates key processes during embryonic development via SMAD2. How SMAD2 activates programs of gene expression that are modulated over time however, is not known. Here we delineate the sequence of events that occur from SMAD2 binding to transcriptional activation, and the mechanisms underlying them. NODAL/Activin signaling induces dramatic chromatin landscape changes, and a dynamic transcriptional network regulated by SMAD2, acting via multiple mechanisms. Crucially we have discovered two modes of SMAD2 binding. SMAD2 can bind pre-acetylated nucleosome-depleted sites. However, it also binds to unacetylated, closed chromatin, independently of pioneer factors, where it induces nucleosome displacement and histone acetylation. For a subset of genes, this requires SMARCA4. We find that long term modulation of the transcriptional responses requires continued NODAL/Activin signaling. Thus SMAD2 binding does not linearly equate with transcriptional kinetics, and our data suggest that SMAD2 recruits multiple co-factors during sustained signaling to shape the downstream transcriptional program.DOI: http://dx.doi.org/10.7554/eLife.22474.001

An autocrine ActivinB mechanism drives TGF β/Activin signaling in Group 3 medulloblastoma

“…mechanisms. In contrast, we showed that PMEPA1, whose expression is induced by TGFb or Activin signaling in many different contexts (Coda et al, 2017), is also an Activin-regulated gene in Group 3 MB. Indeed, inhibition or activation of the Activin signaling pathway modulated PMEPA1 expression accordingly.…”

“…We did not detect any consistent changes in MYC and OTX2 expression upon modulation of the Activin pathway, suggesting that this signaling pathway does not regulate these two genes in Group 3 tumors and promotes tumor growth through other mechanisms. In contrast, we showed that PMEPA1 , whose expression is induced by TGFβ or Activin signaling in many different contexts (Coda et al , ), is also an Activin‐regulated gene in Group 3 MB. Indeed, inhibition or activation of the Activin signaling pathway modulated PMEPA1 expression accordingly.…”

“…To identify relevant genes downstream of Activin signaling in Group 3 MB, we sorted the top 10 genes, whose expression was correlated with INHBB in Group 3 patient samples (Fig A). PMEPA1 , which scored as the top gene, is a well‐established Smad2/3 target gene in different cell types including P19 cells stimulated by Activin (Coda et al , ). Accordingly, we found that PMEPA1 expression level was enriched in Group 3 MB (Fig B) and correlated with INHBB expression in MB (Fig C).…”

“…In agreement with this pro-mitogenic activity, we found that pathway inhibition decreased cell proliferation in Group 3 MB, while ActivinB stimulation increased it by consistently promoting cell cycle progression. MYC and OTX2, two genes known to promote cell proliferation in Group 3 MB, are target genes of the Smad2/3 pathway in other contexts (Jia et al, 2009;Brown et al, 2011;Coda et al, 2017). In general, this signaling pathway reduces MYC expression (Warner et al, 1999;Seoane et al, 2001), although it can be induced in human embryonic stem cells (Brown et al, 2011).…”

Genomic functions of developmental pluripotency associated factor 4 (Dppa4) in pluripotent stem cells and cancer

“…To define the specific types of chromatin that Dppa4 associates with in each cell type, we examined the genome-wide association of Dppa4 with different histone modifications in P19, E14 mESC, and 3T3 cells using published and publicly available ChIP-Seq data (The ENCODE Project Consortium, 2012; Rosenbloom et al, 2012; Zullo et al, 2012; Schick et al, 2015; Zhu et al, 2012; Serandour et al, 2012; Coda et al, 2017), GSE82314. We observed strong overlap between Dppa4 binding and the active histone marks H3K4me3, H3K4me2, and H3K27ac, in all three cell types.…”