Description

This 139pb sequence, located upstream of DDR1/DDR2/MUSK (KH.C9.371), drives reporter gene expression in notochord, head epidermis and tail muscles. It contains a cluster of Fox and Brachyury putative binding sites and can be considered as a minimal enhancer.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.C9:5648367-5648757|DDR1; DDR2; MUSK by deletion

Regulated gene(s)

KH2012:KH.C9.371 (DDR1; DDR2)

Construct(s) made to test this region

CONS00001250: p.Cirobu.REG.KH2012.C9:5648367-5648505>LacZ

Overview of functional TF binding sites in this region

5,648,3675,648,505

	Motif Name	Binding Factor(s)	Sequence	Position in Region	Comment
1	T-Box	n/a	tctcac	[5,648,369 / 5,648,375]	First Brachyury binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer.
2	T-Box	n/a	gtgaca	[5,648,387 / 5,648,393]	Second Brachyury binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of all four Brachyury sites strongly reduces enhancer activity in the notochord.
3	T-Box	n/a	gtgtga	[5,648,400 / 5,648,406]	Third Brachyury binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of all four Brachyury sites strongly reduces enhancer activity in the notochord.
4	Fox	n/a	tatttac	[5,648,424 / 5,648,431]	First Fox binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of this site alone does not affect enhancer activity in the notochord, but creates new activity in central nervous system and tail muscle. Mutation of this site and of the fourth Brachyury site strongly reduces enhancer activity in the notochord. Mutation of three Fox sites and of the fourth Brachyury site abolishes enhancer activity in the notochord.
5	T-Box	n/a	gtgtaa	[5,648,439 / 5,648,445]	Fourth Brachyury binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of this site alone does not affect enhancer activity in the notochord, but creates new mesenchyme activity. Mutation of this site and of the first Fox site strongly reduces enhancer activity in the notochord. Mutation of all four Brachyury sites strongly reduces enhancer activity in the notochord.
6	Fox	n/a	gtaaata	[5,648,441 / 5,648,448]	Second Fox binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of three Fox sites and of the fourth Brachyury site abolishes enhancer activity in the notochord.
7	Fox	n/a	ataaaca	[5,648,445 / 5,648,452]	Third Fox binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of three Fox sites and of the fourth Brachyury site abolishes enhancer activity in the notochord.
8	Fox	n/a	acaaata	[5,648,449 / 5,648,456]	Fourth Fox binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of the three other three Fox sites and of the fourth Brachyury site abolishes enhancer activity in the notochord.
9	Helix Turn Helix / Tryptophane clusters	n/a	attgaa	[5,648,477 / 5,648,483]	This Myb#2 binding site is located in the notochord-active enhancer of KH.C9.371.
10	ZnF_(C2H2)	n/a	ccacc	[5,648,492 / 5,648,497]	Sp1/Klf binding site located next to the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer.

Sequence

Aniseed Coordinates: [5,648,367 / 5,648,505] on scaffold KhC9

This sequence was retrieved using ANISEED Blast tool, thanks to the information provided in FigS2.a and TableS5 of Jose-Edwards et al. 2015.

Reference(s)

José-Edwards et al. (2015). Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord. PLoS Genet. 11(12):e1005730