Charting Brachyury-mediated developmental pathways during early mouse embryogenesis

Abstract

To gain insights into coordinated lineage-specification and morphogenetic processes during early embryogenesis, here we report a systematic identification of transcriptional programs mediated by a key developmental regulator-Brachyury. High-resolution chromosomal localization mapping of Brachyury by ChIP sequencing and ChIP-exonuclease revealed distinct sequence signatures enriched in Brachyury-bound enhancers. A combination of genomewide in vitro and in vivo perturbation analysis and cross-species evolutionary comparison unveiled a detailed Brachyury-dependent gene-regulatory network that directly links the function of Brachyury to diverse developmental pathways and cellular housekeeping programs. We also show that Brachyury functions primarily as a transcriptional activator genome-wide and that an unexpected gene-regulatory feedback loop consisting of Brachyury, Foxa2, and Sox17 directs proper stem-cell lineage commitment during streak formation. Target gene and mRNA-sequencing correlation analysis of the T c mouse model supports a crucial role of Brachyury in up-regulating multiple key hematopoietic and musclefate regulators. Our results thus chart a comprehensive map of the Brachyury-mediated gene-regulatory network and how it influences in vivo developmental homeostasis and coordination.primitive streak | early development | mesoendoderm differentiation I n the past decade, significant insights have been gained in understanding gene-regulatory programs responsible for embryonic stem (ES) cell pluripotency and self-renewal. However, transcriptional control mechanisms underlying finely balanced lineage-segregation and morphogenetic processes during early mammalian embryogenesis remained elusive. During early mouse gastrulation, Brachyury (T), a classical enhancer-binding transcription factor (TF), has been reported to be required for the proper development of primitive streak, allantois, axial, and posterior mesoderm (reviewed in ref. 1).Specifically, mouse embryos that are homozygous for the Brachyury (T) deletion die at midgestation (2). T −/− mutant epiblast cells are compromised in their ability to migrate away from the primitive streak and, therefore, are unable to undergo the morphogenetic movements carried out by their wild-type (WT) counterparts during gastrulation. In addition to defects in the primitive streak, the notochord is absent in posterior portions of the embryo. Although the anterior portions of T mutant mice contain notochordal precursor-like cells, they fail to undergo normal terminal differentiation (3, 4). The embryonic pattern posterior to the forelimb region of T −/− animals is also disturbed, with somites posterior to the seventh pair absent or abnormal. Although neural folds fuse to form the neural tube, they are severely kinked in the caudal region, and the surface ectoderm tends to form fluid-filled blisters (2, 4, 5). In addition to these well-documented defects, numerous other phenotypic abnormalities have been reported in T −/− and T mutant embryos, including left-right pattern...

The T-box gene family: emerging roles in development, stem cells and cancer

“…A screen to identify targets of zebrafish ntl (also known as ta), which is one of two zebrafish orthologs of T (Martin and Kimelman, 2008), identified a transcription factor gene, flh, the homolog of the mouse Noto gene, which is necessary for normal node and cilia formation. In addition, a large number of other genes involved in the formation of primary germ layers, mesoderm formation and mesoderm cell migration were identified by genomewide binding site mapping as potential targets of T orthologs in zebrafish (Morley et al, 2009), Xenopus (Gentsch et al, 2013) and mouse (Lolas et al, 2014), indicating the existence of gene regulatory networks directed by brachyury and providing a treasure trove of candidate genes to elucidate the additional roles of this T-box gene.…”

Signaling Control of Differentiation of Embryonic Stem Cells toward Mesendoderm

“…For instance, Brachyury (T), which is expressed throughout the primitive streak [7], and loss of function studies indicate its essential role in primitive streak formation and ME differentiation [8]. As a T-box transcription factor, Brachyury controls the expression of many developmental related genes.…”

Genomic Control Processes in Adult Body Part Formation

“…ChIP measurements on zebrafish and mouse embryos reveal a large array of mesodermal Bra targets associated with these functions (Fig. 4.10(B); Morley et al, 2009;Lolas et al, 2014).…”