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Brachyury controls Ciona notochord fate as part of a feedforward network [I]

ABSTRACT: Brachyury controls Ciona notochord fate as part of a feedforward network [I]

PROVIDER: PRJNA673505 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12956963.fastq.gz	Fastqsanger.gz
	SRR12956964.fastq.gz	Fastqsanger.gz
	SRR12956965.fastq.gz	Fastqsanger.gz
	SRR12956966.fastq.gz	Fastqsanger.gz
	SRR12956967.fastq.gz	Fastqsanger.gz

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Brachyury controls Ciona notochord fate as part of a feedforward network [I]

Project description:The notochord is a defining feature of the chordates. The transcription factor Brachyury (Bra) is a key regulator of notochord fate but here we show that it is not a unitary master regulator in the model chordate Ciona. Ectopic Bra expression only partially reprograms other cell types to a notochord-like transcriptional profile and a subset of notochord-enriched genes are unaffected by CRISPR Bra disruption. We identify Foxa.a and Mnx as potential co-regulators and find that combinatorial cocktails are more effective at reprograming other cell types than Bra alone. We reassess the network relationships between Foxa.a, and other components of the notochord gene regulatory network and find that Foxa.a expression in the notochord is regulated by vegetal FGF signaling. It is a direct activator of Bra expression and has a binding motif that is significantly enriched in the regulatory regions of notochord-enriched genes. These and other results indicate that Bra and Foxa.a act together in a regulatory network dominated by positive feed-forward interactions, with neither being a classically-defined master regulator.

2020-10-31 | GSE160544 | GEO

Brachyury controls Ciona notochord fate as part of a feedforward network [IV]

2020-10-31 | GSE160547 | GEO

Brachyury controls Ciona notochord fate as part of a feedforward network [III]

2020-10-31 | GSE160546 | GEO

Brachyury controls Ciona notochord fate as part of a feedforward network [II]

2020-10-31 | GSE160545 | GEO

Brachyury controls Ciona notochord fate as part of a feedforward network

Project description:Brachyury controls Ciona notochord fate as part of a feedforward network

| PRJNA673503 | ENA

Brachyury controls Ciona notochord fate as part of a feedforward network [II]

Project description:Brachyury controls Ciona notochord fate as part of a feedforward network [II]

| PRJNA673506 | ENA

Brachyury controls Ciona notochord fate as part of a feedforward network [III]

Project description:Brachyury controls Ciona notochord fate as part of a feedforward network [III]

| PRJNA673507 | ENA

Brachyury controls Ciona notochord fate as part of a feedforward network [IV]

Project description:Brachyury controls Ciona notochord fate as part of a feedforward network [IV]

| PRJNA673508 | ENA

Ectopic expression of the Brachyury transcription factor upregulates only a subset of notochord expressed genes

Project description:The key notochord transcription factor Brachyury was ectopically expressed in Ciona embryos under the control of the FoxAa cis-regulatory region (which drives expression in neural, endodermal and mesenchymal lineages in addition to notochord). Misexpression of Brachyury induced 925 genes compared to a control reporter plasmid (Bra>GFP). There was only modest overlap with a set of notochord-enriched genes previously identified by RNAseq of flow-sorted notochord cells, indicating that Brachyury is not a notochord master regulator gene as strictly defined.

2017-09-19 | GSE102142 | GEO

Brachyury controls Ciona notochord fate as part of a feedforward network

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-10-31 | GSE160548 | GEO