. Author manuscript; available in PMC: 2008 Jun 18.

Published in final edited form as: FASEB J. 2007 Apr 24;21(10):2622–2632. doi: 10.1096/fj.07-8227com

TABLE 2.

Human and mouse conserved promoter motifs

Human Transcript	Evolutionarily Conserved Region	Motifs¹	Position	Sequence
	ECR 1	PPARA	⁻13233	TGATCT
	[⁻13399−⁻13206]	SP1	⁻13118	CCACAGCCCC
		ERE	⁻11388	TT-GGTCA-GGC-TGGTC-TT
	ECR 2	MYB	⁻10839	GGCCAGTTC
	[⁻10919−⁻10748]	ERE	⁻10266	TT-AGTCA-CGC-TGGTC-TC
		Pol II binding site	⁻9038	(bp 17,435,552−17,436,153)
	ECR 3	CpG island	⁻8774	CpG Repeat
	[⁻9246−⁻9038]	Exon 1	⁻9151
Transcript A: NM_148172		TSS A	⁻9205	TTCCGGGGG (bp 17,435,719)
		ERE	⁻7647	GG-GGTCA-TGA-TCACC-TC
	Consensus	ERE	⁻7401	CG-GGTCA-GGG-TGACC-CT
		ERE	⁻6707	GA-GACCA-GCC-TGACC-AA
		ERE	⁻5879	CG-GGGTA-TCT-TGACT-GC
		FOXA1	⁻3309	AAGTTGTTTCCATT
	ECR 4	MYB	⁻3264	AAACTGCCA
	[⁻3324−⁻2994]	SOX6	⁻3190	TGCATTGTTATCA
		GATA	⁻3186	TGTTATCATT
		SP1	⁻862	GTGGCGTGAT
		AP1	⁻386	CTGACTCCT
		AP1	⁻206	CCCGAGTCAGC
Transcript B: NM_007169		TSS⁺¹	⁺1	TTGTCCATG (bp 17,426,514)
		TSS B	⁺40	GACCACAA (bp 17,426,470)
	ECR 5	Exon 2	⁺50
	[⁻35−⁺1073]	C/EBP	⁺175	AAATTACCA
		AP1	⁺631	CATTAGTCATT
		ERE	⁺725	TG-AGACA-GGC-TGACC-TG
		ERE	⁺741	GA-GGCCA-TTG-GGACC-TG
Transcript C: NM_148173	ECR 6	TSS C	⁺5010	TGTGGGCGA (bp 17,421,504)
	[⁺5192−⁺5579]	GATA	⁺5284	TTTTATCTTC
		ERE	⁺5476	TG-GGCTA-CGT-GGACC-CC

Mouse	Evolutionarily Conserved Region	Motifs¹	Position	Sequence
	ECR 1	Ppar-α	⁻12980	AGATCA
	[⁻12997−⁻12808]	Sp1	⁻12884	CCCACC
	ECR 2	Ppar-α	⁻11788	AGGTCA
	[⁻11874−⁻11709	TSS A	⁻9602	CATCAGATA (bp 59,659,083)
	ECR 3	CpG island	⁻9622−⁻9169	CpG repeats
	[⁻9592−⁻9382]	ERE	⁻7919	TA-GGTCA-GGA-TGACC-TT
Consensus
Transcript A
	ECR 5	TSS B (⁺1)	⁺1	CCCAGTGTG (bp 59,649,481)
	(⁻190−⁺884)
Transcript B: NM_008819		TSS B	⁺110	TTCCTTCTG (bp 59,649,379)
		Ap1	⁺429	CGTTAGTCACT
		ERE	⁺790	TG-AGGCA-GGC-TGACC-AG
		ERE	⁺813	CA-GGGCA-CGG-GGACC-TG
		ERE	⁺5150	TT-AGTCA-TGT-TGGCT-GC
	ECR 6
	(⁺4848−⁺5243)	Gata	⁺5441	CTTTTATCTTC
Transcript C		TSS C	⁺5147	GCTGATCTC (bp 59,644,334)
		ERE	⁺5192	TG-GGTTA-CAT-GGACC-CC
		ERE	⁺5780	GG-TGTCA-AGG-TGACC-TA
		ERE	⁺5860	AA-GACCA-CTG-TGACC-TC
		ERE	⁺7961	CA-GGTGG-GCC-TGACC-CT

For both human and mouse PEMT genes motif chromosomal position is displayed relative to transcription start site B (+1) based on the literature defined major TSS for each (36, 37); +/− indicates upstream or downstream orientation, respectively. For the human +1 site, this corresponds to bp 17,426,514 of ch17. For mouse this corresponds to bp 59,649,481 on ch11 (UCSC May 2004 Release of the Mus musculus genome, mm5), which corresponds to bp 59,853,136 in the current release of the M. musculus genome (mm8). The mouse and human PEMT gene promoters are highly conserved in six distinct evolutionarily conserved regions (ECR 1-ECR 6). ECR 4 in mouse Pemt has been translocated to a different chromosome (data not shown). There are conserved estrogen response elements and transcription factor binding sites within ECR 5 and 6 in mouse and human proximal promoter regions. The human and murine PEMT gene contains additional EREs, including a consensus ERE in a distal promoter/enhancer region approximately 7.5kb from TSS B. The human promoter A region contains a CpG island and an experimentally validated 600 bp RNA polymerase II binding site (Pol 9419, P<0.00001) (Figure 3, Table 2) (38). ECR browser, rVista TFBS search engine, Dragon ERE Finder, and TRANSFAC were used to identify ECRs, EREs, and TFBS, respectively. Underline indicates nucleotides that differ from the estrogen response element consensus sequence. Italicized letters indicate transcription start sites for each proximal promoter region denoted A, B, C.

Motif Abbrevations for gene names are from LocusLink (www.ncbi.nlm.nih.gov/LocustLink/list.cgi; last accessed 01/02/07).