Computational prediction and experimental validation of novel Hedgehog-responsive enhancers linked to genes of the Hedgehog pathway

Table 1 Assessment of predicted Hh enhancer regions

Annotated gene	Genomic coordinates (mm9)	Hh responsive	LD	CD	MB	NP
Ptch2	chr4:116,767,757-116,769,455	+	+	+	+	+
Boc	chr16:44,502,136-44,503,346	+	-	+	+	-
Dpp6	chr5:27,248,056-27,249,266	+	+	-	-	-
Gli3	chr13:15,764,694-15,765,904	-	-	-	-	-
Hhip	chr8:82,838,195-82,839,405	+	+	-	-	+
Hipk2	chr6:38,614,001-38,615,211	+	-	-	-	-
Ptch1	chr13:63669992-63671202	+	+	-	+	+
Scube1	chr15:83503053-83504263	+	-	-	-	-
Shh	chr5:28832033-28833243	-	-	-	-	-
Tgfbr2	chr9:116,151,184-116,152,394	+	-	-	-	-

Seven of the nine regions predicted to be GLI-driven enhancers were indeed determined to be Hh responsive and GLI binding site dependent in a cell culture assay. Overlap of the predicted regions with peaks from the GLI^FLAG ChIP datasets (LD, CD, MB, NP) is indicated by the plus sign. Boc, Hipk2, Scube1 and Tgfbr2 were predicted by kmer-SVM and found to be positive, even though those regions do not overlap any of the peaks identified in the LD or NP datasets used to generate the kmer-SVM classifier

ISSN: 1471-213X