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CIS-REGULATION

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  1. Clone 'cign024e23' > 
  2. Region 'REG00001080'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.C2.4475337-4475581|Fgf9/16/20

Short name

Fgf9/16/20 (-219pb)

Region ID

REG00001080

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Izumi Oda-Ishii ()

Annotator

Marion Gueroult-Bellone (2017-09-03)

Curator

Marion Gueroult-Bellone (2018-03-13)

View position in WashU

Description

A series of deletion constructs showed that 219 bp upstream sequence of the transcription start site of Fgf9/16/20 was sufficient to drive expression of the reporter gene specifically in the entire vegetal hemisphere domain. This region contains three Tcf7-binding sites that are critical for expression in the vegetal hemisphere domain.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.C2.4475137-4475581|Fgf9/16/20 by deletion

Regulated gene(s)

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

Construct(s) made to test this region

CONS00001053: pCirobu.REG00001080>GFP

CONS00001051: Cirobu.REG.KH2012.C2.4475337-4475522

CONS00001107: p.Cirobu.REG.KH2012.C2.4475337-4475581_(Cirobu.REG.KH2012.S654:27045-27068)x4>GFP

CONS00001052: Cirobu.REG.KH2012.C2.4475337-4475522

CONS00001058: p.Cirobu.REG.KH2012.C2.4475337-4475581>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.
2 TCF/LEF n/a aaag [4,475,468 / 4,475,472] Second of the 3 Tcf7 binding site located in FGF9/16/20 enhancer. Its mutation alone does nearly anihilates the 219pb enhancer activity, and when associated to the mutation of another Tcf7 binding site, the enhancer is inactivated.
3 TCF/LEF n/a tttc [4,475,515 / 4,475,519] Third of the 3 Tcf7 binding site located in FGF9/16/20 enhancer. Its mutation alone does not affect the 219pb enhancer activity, but when it is associated with the mutation of the second Tcf7 binding site, the enhancer is inactivated.

Sequence

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

Sequence retrieved in the supporting information of the article (S4 Fig.) Cap letters correspond to nucleotides located downstream the TSS. Transcription start site is based on the start of the first exon of KH.C2.125.v1.A.nonSL4-1 transcript model.

Show sequence

Length: 245


gttgtttacagcaattaagccgccatatagataactgtgcgcactggtcgtctgcccatt
tttagatagccttcccagtgcttctgttctcgagattacgatcacaagcgtaagacgtca
agttcaccgacaaagataagaatcgcgacccacacaagtcactgccgccccttcttcgtt
tctcgtcgtacacaaaagcagcgggaatcttgactcggaGCATCACTCTTGAATCGCCAC
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

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