E2a is necessary for Smad2/3-dependent transcription and the direct repression of lefty during gastrulation

Abstract

Transcription factor complexes have varied effects on cell fate and behavior, but how this diversification of function occurs is largely unknown. The Nodal signaling pathway has many biological functions that all converge on the transcription factors Smad2/3. Smad2/3 has many cofactors, and alternative usage of these may provide a mechanism for modulating Smad2/3 function. Here, we investigate how perturbation of the cofactor E2a affects global patterns of Smad2/3 binding and gene expression during gastrulation. We find that E2a regulates early development in two ways. E2a changes the position of Smad2/3 binding at the Nodal inhibitor lefty, resulting in direct repression of lefty that is critical for mesendoderm specification. Separately, E2a is necessary to drive transcription of Smad2/3 target genes, including critical regulators of dorsal cell fate and morphogenesis. Overall, we find that E2a functions as both a transcriptional repressor and activator to precisely regulate Nodal signaling.

Figure 1. E2a is required for subsets of Smad2/3 binding, and for global patterns of Smad2/3 target gene expression

A) Smad2/3 targets 1027 distinct genomic regions in control stage 10.5 embryos (yellow), and 1671 regions in E2a-depleted embryos (blue). 495 regions are targeted in both conditions. B) Categories of Smad2/3 binding behavior in E2a-depleted embryos (blue) relative to controls (yellow). C) DAVID clustering analysis shows enrichment for developmental terms in all Smad2/3 associated genes, and for genes that have stable Smad2/3 binding when E2a is depleted (red box in B), but not other subcategories of Smad2/3 binding. D) Genes that retain Smad2/3 binding at the same genomic coordinates in E2a-depleted embryos (red box in B) are more likely to be downregulated by 2 fold or more in E2a-depleted embryos. E–F) Significant overlap exists between genes that are Smad2/3 targets and genes that are downregulated in E2a depleted embryos. Smad2/3 targets in which binding is at the same genomic position in control and E2a-depleted embryos are more likely to be downregulated in E2a-depleted embryos. These genes maintain enrichment for DAVID terms associated with early development. See also Tables S1, S2.

Figure 2. E2a regulates Samd2/3 positioning at lefty and represses lefty transcription

A) qRT-PCR showing upregulation of lefty in E2a depleted embryos, and downregulation of gsc and xbra. odc is shown as a loading control. Error bars represent standard deviations for three biological replicates. B) In situ hybridization for lefty expression at stage 10 in control, E2a depleted, and e2a mRNA injected embryos (red=lacZ lineage tracer). C) Distribution of key transcription factor binding sites near the lefty locus. There are two regions of observed Smad2/3 binding in control embryos, schematized in blue. D) In E2a-depleted embryos, Smad2/3 binding at region 1 is reduced, while binding at region 2 is increased. Fold enrichment over input is shown along the Y axis. E) Embryos were injected at the 2-cell stage with mE2a-GFP and RFP-tagged histone H2b mRNA and monitored for fluorescence at stage 10.5. F) ChIP-qRT-PCR using anti-GFP antibodies in stage 10.5 embryos following mE2a-GFP injection at the 2-cell stage. Y axis represents fold enrichment over a negative control region near the lefty locus. See also Figure S1.

Figure 3. Lefty is downstream of E2a in mesoderm induction

A) Embryos were injected with E2a MO in specific blatomeres as follows: “All”= both blastomeres at the 2-cell stage (N=72); “Dorsal”=2 dorsal blastomeres at the 4-cell stage (N=51); “Ventral”=both ventral blastomeres at the 4-cell stage (N=63); “Animal”=4 animal blastomeres at the 8-cell stage (N=9). B) Embryos were injected in both blastomeres at the 2 cell stage with e2a MO, and/or at the animal pole at the 4 cell stage with xnr1 mRNA. Animal caps were harvested at stage 8 and cultured to stage 10. qPCRs were normalized to whole embryo expression and to odc expression. Error bars represent standard deviations for three biological replicates. C–J) E2a depleted embryos have reduced expression of gsc (C) and xbra (D) compared with uninjected control embryos (A,B). By contrast, Lefty-depleted embryos show increased expression of gsc (E) and xbra (F). Embryos injected with both E2a and Lefty MOs have moderate expression of gsc (G) and xbra (H). See also Figure S2.

Figure 4. E2a is required for dorsal mesoderm gene expression, and binds directly to these target genes

A) qPCRs comparing expression of xbra, eomes, and epha4 in whole stage 10.5 control or e2a-depleted embryos, and in ectoderm explants. Expression levels are normalized to odc and to control ectoderm explants. Error bars represent the standard deviation for three biological replicates, with two technical replicates per biological replicate. Note: although error bars for eomes expression are large, reflecting biological variation between groups of explants, eomes expression was lower in E2a MO+Xnr1 ectoderm than Xnr1 ectoderm in every biological replicate. B) Regulatory regions for eomes, epha4, and xbra were identified from ChIP-Seq analysis in Figure 1, and regulatory regions that are occupied by Smad2/3 in both control and e2a-depleted embryos were analyzed for E2a occupancy. Primers, Smad, FoxH1, and E2a (SCA) binding sites as well as the positions of Smad2/3 peaks are shown as in Figure 2. C) ChIP-qPCR for mE2a-GFP shows significant enrichment at regulatory regions for eomes, xbra, and epha4. qPCRs are normalized to expression in embryos injected with GFP alone, and to expression of an off-peak primer. See also Figure S3.

Figure 5. E2a fused to the Engrailed repressor domain causes mild blastopore formation defects and loss of axial mesoderm, and synergizes with low doses of lefty mRNA

A) Effects of E2a-EnR injection (both cells at the 2-cell stage) at stage 11. Embryos injected with E2a-EnR have delayed blastopore closure relative to uninjected control embryos, but far better blastopore formation than E2a morphants. Stage 10.5 E2a-EnR embryos express more xbra than E2a morphants, but less than control embryos. E2a-EnR injected embryos express less lefty than E2a morphants. B) Effects of E2a-EnR injection (both cells at the 2-cell stage) at stage 30. E2a-EnR injected embryos show reduced expression of muscle markers (myoD, myf5), and notochord markers (shh, foxA2), but normal expression of the heart marker nkx2.5. C) E2a-Enr and 5pg of lefty mRNA each cause only modest effects on blastopore closure, but embryos injected with both mRNAs show a failure of bottle cell formation similar to E2a morphants. Arrowhead indicates bottle cells.

Figure 6. Model of Smad2/3 and E2a interactions in transcriptional regulation

A) At the lefty locus. In control embryos, Smad2/3 normally occupies region 1, while E2a normally occupies region 2. Transcription of lefty is weak. In the absence of E2a, Smad2/3 moves to preferentially occupy region 2, and transcription of lefty is upregulated. B) At dorsal mesoderm loci. In control embryos, Smad2/3 occupancy at enhancers is coupled by E2a to coactivators, and transcription of the target gene (epha4 is shown as an example) is robust. In the absence of E2a, the coupling of Smad2/3 to transcriptional coactivators is lost, and transcription of the target gene is reduced.