Aniseed - Cis-regulation

Region 'REG00001231'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.C6:403782-404043(µ_OCb)|Onecut_HNF6

Short name

Onecut/HNF6 (-935/-674)µ_OCb

Region ID

REG00001231

Status

Curated

Origin

engineered region from C. robusta formely Ciona int. type A

Type of Activity

regulatory_region
(enhancer)

Author

Maria Rosa Pezzotti (2017-08-06)

Annotator

Marion Gueroult-Bellone (2017-08-06)

Curator

Delphine Dauga (2017-09-06)

View position in WashU

Description

This sequence derives from the 260pb cis-regulatory sequence of Onecut/HNF6 (REG00001223) which contains 2 Onecut binding sites (-746/-730pb and -705/-689pb from TSS) and one Neurogenin binding site (-847/-835pb from TSS). Mutation of the second onecut binding site weakens the enhancer activity.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.C6:403782-404043|Onecut_HNF6 by substitution

Cirobu.REG.KH2012.C6:403105-405698|Onecut_HNF6 REG00001211 [ regulatory_region (extended_promoter) ]

Regulated gene(s)

KH2012:KH.C6.185 (ONECUT1; ONECUT2; ONECUT3)

Construct(s) made to test this region

CONS00001233: p.Cirobu.REG.KH2012.C6:403782-404043(µ_OCb)>LacZ

Show in situ data

Overview of functional TF binding sites in this region

403,782404,043

	Motif Name	Binding Factor(s)	Sequence	Position in Region	Comment
1	Homeobox	n/a	aattgtagattgtttgaa	[403,838 / 403,856]	This Onecut/HNF6 binding site is one of the three identified binding sites of HNF6/Onecut minimal enhancer (the others are a Neurogenin and another HNF6/Onecut sites). It is located at -746/-730pb from HNF6/Onecut TSS. The mutational analysis not only indicates that all the three identified binding sites (Ngn, OCa and OCb) are necessary for Onecut activation in its endogenous territories but also that a cooperation between the two OC sites for the maintenance of its expression exists.
2	bHLH	n/a	gggccatctgctg	[403,943 / 403,956]	This Neurogenin binding site is one of the three identified binding sites of HNF6/Onecut minimal enhancer (the others are two HNF6/Onecut sites). It is located at -847/-835pb from HNF6/Onecut TSS. At neurula stage, Neurogenin is necessary for enhancer activation in the Onecut territories. Then, neurogenin seems to be the activator only in the visceral ganglion up to larva stage.

Sequence

Aniseed Coordinates: [403,782 / 404,043] on scaffold KhC6

This fragment extending from the position 935 to 674 upstream of the translation start site was prepared by site-directed mutagenesis from the 260pb Onecut/HNF6 enhancer (REG00001223). The second Onecut binding site (-705/-689pb from TSS) was mutated (replaced by tataggggggtattttt).

Show sequence

Length: 262

ctgactaaactgttttataggggggtatttttctttccaaggcttgaacttgtcttaatt
gtagattgtttgaatttaaacaaattttcgatcagtcctttacggttgagctccaagctc
gaatggaagactggtgccgtactcgtatgggagtaagcaatgggccatctgctgcgtttt
tctgttcggcttatatacgagtggttcgcgtcggcgcgcggtttgagcaaaaacaatagg
accgctgtcgaaaacaaggcga

Reference(s)

Pezzotti et al. (2014). Auto and cross regulatory elements control Onecut expression in the ascidian nervous system. Dev. Biol. 390(2):273-87