Developmental enhancers are marked independently of zygotic Nodal signals in Xenopus

Gupta, Ritu; Wills, Andrea E.; Ucar, Duygu; Baker, Julie C.

doi:10.1016/j.ydbio.2014.08.034

Cited by 31 publications

(46 citation statements)

References 49 publications

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“…Each experiment was performed in duplicate except ChIP-Seq of Smad2/3 in E2a-depleted embryos, which was performed in triplicate. For ChIP-Seq, each library was made using 1000 embryos, according to published methods (Wills et al, 2014), and our existing control Smad2/3 library data was used as one replicate (Gupta et al, 2014). For RNA-Seq, each library was made using 20μg of total starting RNA, according to published methods (Tan et al, 2013).…”

Section: Resultsmentioning

confidence: 99%

E2a Is Necessary for Smad2/3-Dependent Transcription and the Direct Repression of lefty during Gastrulation

Wills

Baker

2015

Developmental Cell

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Summary 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 investigated 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.

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Section: Resultsmentioning

confidence: 99%

E2a Is Necessary for Smad2/3-Dependent Transcription and the Direct Repression of lefty during Gastrulation

Wills

Baker

2015

Developmental Cell

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“…Multiple growth factor signals, including activin/nodal, BMP, Wnt, and fibroblast growth factor (FGF), have been shown to modulate organizer formation and/or activities. The downstream targets of these signals have also been investigated, including at the genomic scale (Wessely et al, 2004; Perffer et al, 2005; Hufton et al, 2006; Chiu et al, 2014; Gupta et al, 2014). However, most of the functional studies are focused on genes with the ability to induce or pattern embryonic tissues, and some large scale studies also employ techniques that are biased toward abundant genes.…”

Section: Discussionmentioning

confidence: 99%

Identification of new regulators of embryonic patterning and morphogenesis in Xenopus gastrulae by RNA sequencing

Popov

Kwon

Crossman

et al. 2017

Developmental Biology

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During early vertebrate embryogenesis, cell fate specification is often coupled with cell acquisition of specific adhesive, polar and/or motile behaviors. In Xenopus gastrulae, tissues fated to form different axial structures display distinct motility. The cells in the early organizer move collectively and directionally toward the animal pole and contribute to anterior mesendoderm, whereas the dorsal and the ventral-posterior trunk tissues surrounding the blastopore of mid-gastrula embryos undergo convergent extension and convergent thickening movements, respectively. While factors regulating cell lineage specification have been described in some detail, the molecular machinery that controls cell motility is not understood in depth. To gain insight into the gene battery that regulates both cell fates and motility in particular embryonic tissues, we performed RNA sequencing (RNA-seq) to investigate differentially expressed genes in the early organizer, the dorsal and the ventral marginal zone of Xenopus gastrulae. We uncovered many known signaling and transcription factors that have been reported to play roles in embryonic patterning during gastrulation. We also identified many uncharacterized genes as well as genes that encoded extracellular matrix (ECM) proteins or potential regulators of actin cytoskeleton. Co-expression of a selected subset of the differentially expressed genes with activin in animal caps revealed that they had distinct ability to block activin-induced animal cap elongation. Most of these factors did not interfere with mesodermal induction by activin, but an ECM protein, EFEMP2, inhibited activin signaling and acted downstream of the activated type I receptor. By focusing on a secreted protein kinase PKDCC1, we showed with overexpression and knockdown experiments that PKDCC1 regulated gastrulation movements as well as anterior neural patterning during early Xenopus development. Overall, our studies identify many differentially expressed signaling and cytoskeleton regulators in different embryonic regions of Xenopus gastrulae and imply their functions in regulating cell fates and/or behaviors during gastrulation.

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“…Interestingly, Pitx2 is one of the 53 genes (Supplementary Table 3) that has HEB/PRC2 promoter in ESCs and HEB/SMAD2/3 element in ME and the mouse ARE precisely overlaps with this HEB/SMAD2/3 element. Further, all three of these AREs also can be found in X. tropicalis where they are associated with H3K4me1 and H3K27ac chromatin-enhancer marks, suggesting evolutionarily conserved function 42 . Overall, this strongly suggests that the HEB/SMAD2/3 enhancers are indeed functional.…”

Section: Heb Occupies Bivalent Domainsmentioning

confidence: 93%

HEB associates with PRC2 and SMAD2/3 to regulate developmental fates

2015

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In embryonic stem cells, extracellular signals are required to derepress developmental promoters to drive lineage specification, but the proteins involved in connecting extrinsic cues to relaxation of chromatin remain unknown. We demonstrate that the helix-loop-helix (HLH) protein, HEB, directly associates with the Polycomb repressive complex 2 (PRC2) at a subset of developmental promoters, including at genes involved in mesoderm and endoderm specification and at the Hox and Fox gene families. While we show that depletion of HEB does not affect mouse ESCs, it does cause premature differentiation after exposure to Activin. Further, we find that HEB deposition at developmental promoters is dependent upon PRC2 and independent of Nodal, whereas HEB association with SMAD2/3 elements is dependent of Nodal, but independent of PRC2. We suggest that HEB is a fundamental link between Nodal signalling, the derepression of a specific class of poised promoters during differentiation, and lineage specification in mouse ESCs.

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Developmental enhancers are marked independently of zygotic Nodal signals in Xenopus

Cited by 31 publications

References 49 publications

E2a Is Necessary for Smad2/3-Dependent Transcription and the Direct Repression of lefty during Gastrulation

E2a Is Necessary for Smad2/3-Dependent Transcription and the Direct Repression of lefty during Gastrulation

Identification of new regulators of embryonic patterning and morphogenesis in Xenopus gastrulae by RNA sequencing

HEB associates with PRC2 and SMAD2/3 to regulate developmental fates

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