Abstract
As development proceeds, inductive cues are interpreted by competent tissues in a spatially and temporally restricted manner. While key inductive signaling pathways within competent cells are well-described at a molecular level, the mechanisms by which tissues lose responsiveness to inductive signals are not well understood. Localized activation of Wnt signaling before zygotic gene activation in Xenopus laevis leads to dorsal development, but competence to induce dorsal genes in response to Wnts is lost by the late blastula stage. We hypothesize that loss of competence is mediated by changes in histone modifications leading to a loss of chromatin accessibility at the promoters of Wnt target genes. We use ATAC-seq to evaluate genome-wide changes in chromatin accessibility across several developmental stages. Based on overlap with p300 binding, we identify thousands of putative cis-regulatory elements at the gastrula stage, including sites that lose accessibility by the end of gastrulation and are enriched for pluripotency factor binding motifs. Dorsal Wnt target gene promoters are not accessible after the loss of competence in the early gastrula while genes involved in mesoderm and neural crest development maintain accessibility at their promoters. Inhibition of histone deacetylases increases acetylation at the promoters of dorsal Wnt target genes and extends competence for dorsal gene induction by Wnt signaling. Histone deacetylase inhibition, however, is not sufficient to extend competence for mesoderm or neural crest induction. These data suggest that chromatin state regulates the loss of competence to inductive signals in a context-dependent manner.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 20-35 |
| Number of pages | 16 |
| Journal | Developmental Biology |
| Volume | 462 |
| Issue number | 1 |
| DOIs | |
| State | Published - Jun 1 2020 |
Funding
We greatly appreciate Zhijun Duan for providing technical guidance with ATAC-seq library construction. We thank Parisha Shah, Gert Veenstra, Douglas Epstein, Daniel Kessler, Mary Mullins, Montserrat Anguera, Melinda Snitow, and David Klein for helpful advice and Linyang Ju for advice and generously supplying Tn5 transposase. M.E. was supported in part by the Medical Scientist Training Program at the Perelman School of Medicine at the University of Pennsylvania . This work was supported by grants from the National Institutes of Health including 1R01GM115517 and 1R01HL141759 (PSK); R01GM111816 and R35GM131810 (JY); R01GM132438 (KZ); T32GM007170 , F31GM116588 , and T32HL007439 (ME). Chromatin accessibility is mediated by post-translational modifications of histones, and increased histone acetylation contributes to openness of chromatin and a generally favorable environment for transcription (Shahbazian and Grunstein, 2007). As HDAC inhibition extends the window of competence to induce dorsal development in response to Wnt signaling, we propose that HDACs mediate the loss of competence at dorsal Wnt target genes. The T-cell factor/lymphoid enhancer factor (TCF/LEF) family of transcription factors are downstream mediators of canonical Wnt/?-catenin signaling that in the absence of Wnt signaling bind diverse corepressors, including Groucho/transducin-like enhancer of split (Gro/TLE) family, C-terminal binding protein (CtBP), Silencing Mediator for Retinoid and Thyroid hormone receptor (SMRT) and Nuclear receptor Co-Repressor (NCoR), and others, all of which recruit HDACs (Cadigan, 2012; Ramakrishnan et al., 2018). In addition, the transcription repressor Kaiso binds to both TCF3 and Wnt-response elements and represses sia1 expression (Cadigan, 2012; Park et al., 2005; Ramakrishnan et al., 2018). Thus, although the mechanisms of repression by Kaiso are controversial (Cadigan, 2012; Park et al., 2005; Ramakrishnan et al., 2018; Ruzov et al., 2009), the repressive function of Kaiso may also contribute to the loss of competence at dorsal Wnt target genes. We speculate that TCFs bind to Wnt responsive elements throughout competent tissues and could serve two opposing functions. Localized Wnt signaling in future dorsal blastomeres causes ?-catenin accumulation and displacement of corepressors, but in the absence of a Wnt signal, TCF may recruit HDACs that would deaceylate Wnt target gene promoters leading to loss of responsiveness to Wnt signaling. This proposed model is consistent with reports showing that knockdown of maternal Tcf3 increases sia1 expression in ventral blastomeres (Houston et al., 2002) and deletion of TCF binding sites in the sia1 promoter-reporter enhances reporter activity in ventral blastomeres (Brannon et al., 1997), further supporting a repressive function for maternal Tcf3. A novel 11 base-pair negative regulatory element (NRE) has recently been identified upstream of multiple Wnt-responsive genes including sia1 and nodal3.1 (Kim et al., 2017) and could contribute to loss of competence for dorsal induction.We greatly appreciate Zhijun Duan for providing technical guidance with ATAC-seq library construction. We thank Parisha Shah, Gert Veenstra, Douglas Epstein, Daniel Kessler, Mary Mullins, Montserrat Anguera, Melinda Snitow, and David Klein for helpful advice and Linyang Ju for advice and generously supplying Tn5 transposase. M.E. was supported in part by the Medical Scientist Training Program at the Perelman School of Medicine at the University of Pennsylvania. This work was supported by grants from the National Institutes of Health including 1R01GM115517 and 1R01HL141759 (PSK); R01GM111816 and R35GM131810 (JY); R01GM132438 (KZ); T32GM007170, F31GM116588, and T32HL007439 (ME).
Keywords
- ATAC-seq
- Chromatin
- Competence
- Dorsal development
- Induction
- Xenopus
ASJC Scopus subject areas
- Molecular Biology
- Developmental Biology
- Cell Biology