Description

This 313bp sequence, located in the upstream region of KH.S345.4, drives reporter gene expression in notochord, mesenchyme and endoderm. It contains 3 E-box, 4 Sp1/Klf and 1 Myb#2 putative binding sites. Compared to the active WT enhancer, it lacks one Brachyury binding site.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.S345:68522-68829|KH.S345.4 by substitution

Regulated gene(s)

KH2012:KH.S345.4 (KH.S345.4)

Construct(s) made to test this region

CONS00001357: p.Cirobu.REG.KH2012.S345:68522-68829_BraMut>LacZ

Overview of functional TF binding sites in this region

68,52268,829

	Motif Name	Binding Factor(s)	Sequence	Position in Region	Comment
1	ZnF_(C2H2)	n/a	ggtgg	[68,529 / 68,534]	This the first of the 4 Sp1/Klf binding sites located in the notochord-active enhancer of KH.S345.4. Deletion of the region containing this binding site, or its mutation inhibits enhancer activity in the notochord.
2	bHLH	n/a	caagtg	[68,545 / 68,551]	This the first of the 3 E-box binding sites located in the notochord-active enhancer of KH.S345.4.
3	ZnF_(C2H2)	n/a	ccacc	[68,600 / 68,605]	This is one of the 4 Sp1/Klf binding sites located in the notochord-active enhancer of KH.S345.4.
4	bHLH	n/a	caaatg	[68,617 / 68,623]	This is one of the 3 E-box binding sites located in the notochord-active enhancer of KH.S345.4.
5	ZnF_(C2H2)	n/a	ggtgg	[68,702 / 68,707]	This is one of the 4 Sp1/Klf binding sites located in the notochord-active enhancer of KH.S345.4.
6	Helix Turn Helix / Tryptophane clusters	n/a	attgaa	[68,786 / 68,792]	This Myb#2 binding site is located in the notochord-active enhancer of KH.S345.4. Its deletion does not affect enhancer activity in the notochord.
7	ZnF_(C2H2)	n/a	ggtgg	[68,808 / 68,813]	This is one of the 4 Sp1/Klf binding sites is located in the notochord-active enhancer of KH.S345.4. Its deletion does not affect enhancer activity in the notochord.

Sequence

Aniseed Coordinates: [68,522 / 68,829] on scaffold KhS345

The Brachyury binding site is mutated. TGGCAC replaced by TGGAGT This sequence was retrieved using ANISEED Blast tool, thanks to the information provided in FigS1.c 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