Table 2.

List of all transcript initiation sites for the 3 genes in mouse (A) and human (B) samples with their shapes and association with TATA-box and CpG islands

A Mouse promoters
Promoter	TATA	CpG	Shape
pA@Foxg1	TATA-less	CpG	Broad
pB@Foxg1	TATA-less	CpG-less	Broad
p1@Foxg1	TATA-less	CpG-less	Sharp
p2@Foxg1	TATA-less	CpG	Broad
p3@Foxg1	TATA-less	CpG	Broad
p4@Foxg1	TATA-less	CpG	Broad
p1@Mecp2	TATA-less	CpG	Broad
p2@Mecp2	TATA-less	CpG	Broad
p1@Cdkl5	TATA-less	CpG	Broad
p2@Cdkl5	TATA-less	CpG	Sharp
B Human promoters
Promoter	TATA	CpG	Shape
p1@FOXG1	TATA-less	CpG	Broad
p2@ FOXG1	TATA-less	CpG-less	Sharp
p3@ FOXG1	TATA-less	CpG-less	Sharp
p4@ FOXG1	TATA-less	CpG	Broad
p5@ FOXG1	TATA-less	CpG-less	Broad
p6 @FOXG1	TATA-less	CpG-less	Broad
p7@ FOXG1	TATA-less	CpG	Broad
p9@ FOXG1	TATA-less	CpG-less	Sharp
p1@MECP2	TATA-less	CpG	Broad
p2@ MECP2	TATA-less	CpG	Broad
p5@MECP2	TATA-less	CpG-less	Broad
p1@CDKL5	TATA-less	CpG	Broad
p2@CDKL5	TATA-less	CpG	Sharp

Promoters were listed as TATA-less if a TATA-box was absent 500 bp upstream of the promoter. Similarly in the absence of a CpG island within 500 bp of the TSS, the promoter was classified as CpG-less.