Aniseed - Cis-regulation

Region 'REG00001094'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.C2.4475337-4475581_μTcf7(b,c)|Fgf9/16/20

Short name

Fgf9/16/20 (-219pb)_μTcf7(b,c)

Region ID

REG00001094

Status

Curated

Origin

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

Type of Activity

inactive_region

Author

Izumi Oda-Ishii (2017-01-17)

Annotator

Marion Gueroult-Bellone (2017-09-03)

Curator

Marion Gueroult-Bellone (2018-03-13)

View position in WashU

Description

Mutation of the more 3' Tcf7 binding sites (called Tcf7(b) and (c) in the article). This mutation completely abolishes the enhancer activity.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.C2.4475337-4475581|Fgf9/16/20 by substitution

Cirobu.REG.KH2012.C2.4472575-4475581|Fgf9/16/20 REG00001083 [ regulatory_region (extended_promoter) ]
- Cirobu.REG.KH2012.C2.4474936-4475581|Fgf9/16/20 REG00001082 [ regulatory_region (extended_promoter) ]
  - Cirobu.REG.KH2012.C2.4475137-4475581|Fgf9/16/20 REG00001081 [ regulatory_region (extended_promoter) ]
    - Cirobu.REG.KH2012.C2.4475337-4475581|Fgf9/16/20 REG00001080 [ regulatory_region (extended_promoter) ]

Regulated gene(s)

KH2012:KH.C2.125 (FGF16; FGF20; FGF9)

Construct(s) made to test this region

CONS00001064: p.Cirobu.REG.KH2012.C2.4475337-4475581_μTcf7(b,c)>GFP

Show in situ data

Overview of functional TF binding sites in this region

4,475,3374,475,581

	Motif Name	Binding Factor(s)	Sequence	Position in Region	Comment
1	TCF/LEF	n/a	ttta	[4,475,341 / 4,475,345]	First of the 3 Tcf7 binding site located in FGF9/16/20 enhancer. Its mutation alone does not affect a lot the 219pb enhancer activity, but when both first and second Tcf7 binding sites are mutated, the enhancer is inactivated.

Sequence

Aniseed Coordinates: [4,475,337 / 4,475,581] on scaffold KhC2

The second and third Tcf7 binding sites (AAAG and TTTC) were respectively replaced by GGGA (bases #132 to 135 of this sequence) and CCCT (bases # 179 to 182).

Show sequence

Length: 245

gttgtttacagcaattaagccgccatatagataactgtgcgcactggtcgtctgcccatt
tttagatagccttcccagtgcttctgttctcgagattacgatcacaagcgtaagacgtca
agttcaccgacgggaataagaatcgcgacccacacaagtcactgccgccccttcttcgcc
cttcgtcgtacacaaaagcagcgggaatcttgactcggaGCATCACTCTTGAATCGCCAC
TCAGC

Reference(s)

Oda-Ishii et al. (2016). A Maternal System Initiating the Zygotic Developmental Program through Combinatorial Repression in the Ascidian Embryo. PLoS Genet. 12(5):e1006045