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Targets of the transcription factor Brachyury in differentiating mouse ES cells

ABSTRACT: Brachyury (or T) is expressed in the primitive streak, tailbud and notochord of the early mouse embryo (Herrmann et al., 1990; Wilkinson et al., 1990). It plays a key role in early development: mouse embryos lacking functional Brachyury protein fail to gastrulate properly, do not form a differentiated notochord, and lack structures posterior to somite seven (Chesley, 1935; Dobrovolskaïa-Zavadskaïa, 1927; Naiche et al., 2005; Wilson et al., 1995; Wilson et al., 1993; Yanagisawa et al., 1981) We apply a ChIP-on-chip approach to identify targets of Brachyury during mouse ES cell differentiation. ES cells provide an abundant source of differentiating cells and the identification of Brachyury targets in such cells will shed light on the mechanisms of ES cell differentiation and, by analyzing the targets in the developing embryo, will reveal to what extent they provide a bone fide model of early mouse development.

ORGANISM(S): Mus musculus

PROVIDER: GSE16646 | GEO | 2012/05/29

SECONDARY ACCESSION(S): PRJNA167613

REPOSITORIES: GEO

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Targets of the transcription factor Brachyury in differentiating mouse ES cells

Project description:Brachyury (or T) is expressed in the primitive streak, tailbud and notochord of the early mouse embryo (Herrmann et al., 1990; Wilkinson et al., 1990). It plays a key role in early development: mouse embryos lacking functional Brachyury protein fail to gastrulate properly, do not form a differentiated notochord, and lack structures posterior to somite seven (Chesley, 1935; DobrovolskaM-CM-/a-ZavadskaM-CM-/a, 1927; Naiche et al., 2005; Wilson et al., 1995; Wilson et al., 1993; Yanagisawa et al., 1981) We apply a ChIP-on-chip approach to identify targets of Brachyury during mouse ES cell differentiation. ES cells provide an abundant source of differentiating cells and the identification of Brachyury targets in such cells will shed light on the mechanisms of ES cell differentiation and, by analyzing the targets in the developing embryo, will reveal to what extent they provide a bone fide model of early mouse development. The brachyury IP expts used 3 independent biological replicates hybridised to design 1 and 2 chips per replicate Design 1 raw file AE_251471610189 + Design 2 raw file AE_251471710182 = replicate 1 Design 1 raw file AE_251471610716 + Design 2 raw file AE_251471710724 = replicate 2 Design 1 raw file AE_251471610717 + Design 2 raw file AE_251471710725 = replicate 3 in all cases IP DNA label was Cy5 and whole chromatin Cy3 Design 1 files GSM417692 Design 2 files GSM417704 Isotype control experiment performed 1 x ie design 1 raw file AE_251471610714 design 2 raw file AE_251471710722 in GSM417714 and GSM417756 IP DNA label was Cy5 and whole chromatin Cy3 as for brachyury data

2012-05-28 | E-GEOD-16646 | biostudies-arrayexpress

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Project description:Oncogenic transformation of individual cell fates by developmental signaling cascades and transcription factors triggers diverse cancer types. Chordoma is a rare, aggressive tumor arising from transformed notochord remnants. Various potentially oncogenic factors have been found deregulated in chordoma and its metastases, yet clear causation remains uncertain. In particular, expression of the notochord-controlling transcription factor Brachyury is hypothesized as key molecular driver in chordoma formation, yet an in vivo model to causally test its oncogenic potential in the notochord is missing. Here, we apply a zebrafish model of chordoma onset to identify the notochord-transforming potential of tumor-implicated candidate genes in vivo. We find that overexpression of human and zebrafish Brachyury, including a version with augmented transcriptional activity, is insufficient to initiate notochord hyperplasia in vivo. In contrast, the repeatedly chordoma-implicated receptor tyrosine kinase (RTK) genes EGFR and KDR/VEGFR2 are sufficient to transform developmental notochord cells, akin to direct activation of Ras. Analysis of transcriptome and sub-cellular organization from transformed notochords suggests that aberrant activation of RTK/Ras signaling attenuates processes required for the differentiation of notochord cells. Taken together, our results provide first in vivo indication for a lack of tumor-initiating potential of Brachyury expression in the notochord, and suggest activated RTK signaling as potent hyperplasia-initiating event in chordoma.

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