Candidate SNP markers of reproductive potential are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters

Chadaeva, Irina V.; Ponomarenko, Petr M.; Rasskazov, Dmitry A.; Sharypova, Ekaterina B.; Kashina, Elena V.; Zhechev, Dmitry A.; Drachkova, Irina A.; Arkova, Olga V.; Savinkova, Ludmila K.; Ponomarenko, Mikhail P.; Kolchanov, Nikolay A.; Osadchuk, Ludmila V.; Osadchuk, Alexandr V.

doi:10.1186/s12864-018-4478-3

Table 1 Known and candidate SNP markers of tumors in reproductive organs

From: Candidate SNP markers of reproductive potential are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters

Gene	dbSNP [6] rel. 147 or see [Ref]	5′ flank	wt mut	3′ flank	K_D, nM					Known diseases (SNP markers) or hypothetical disease (candidate SNP markers)	[Ref] or [this work]
Gene	dbSNP [6] rel. 147 or see [Ref]	5′ flank	wt mut	3′ flank	wt mut	Δ	Z	α	ρ		[Ref] or [this work]
ESR2	rs35036378	cctctcggtc	t g	ttaaaaggaa	6 8	↓	5	10^-3	B	ESR2-deficient pT1 breast tumor needing tamoxifen prophylaxis against cancer	[61]
ESR2	rs766797386	ttaaaaggaa	g t	aaggggctta	6 7	↓	3	10^-2	C	(hypothetically) the same disease	[this work]
HSD17B1	rs201739205	aggtgatatc	a c	agcccagagc	13 18	↓	5	10^-6	A	higher risk of breast cancer	[64]
	rs201739205	agcaggtgat	a t	tcaagcccag	13 35	↓	18	10^-6	A	(hypothetically) the same disease	[this work]
	rs748743528	gcaggtgata	t c	caagcccaga	13 28	↓	13	10^-6	A	(hypothetically) the same disease	[this work]
	rs755636251	ggcgaagcag	g t	tgatatcaag	13 11	↑	2	0.05	D	(hypothetically) higher risk of breast cancer	[68]
PGR	rs10895068	gggagataaa	g a	gagccgcgtg	10 6	↑	8	10^-6	A	endometrial cancer caused by the spurious TATA box and its TSS disbalancing both α and β isoforms of progesterone receptor	[65]
PGR	rs544843047	agtcgggaga	t c	aaaggagccg	10 22	↓	14	10^-6	A	(hypothetically) health as the norm without the above-mentioned spurious TATA box	[this work]
GSTM3	rs1332018	ccccttatgt	c a	gggtataaag	4 3	=	2	1	E	maternal “c” (Wb: TF-binding site damaged, not TATA box), elevates risk of a brain tumor in her child, renal cancer, and Alzheimer’s disease	[66, 67]
	rs200209906	gtataaagcc	c t,a	ctcccgctca	3.6 4.3	↓	2	1	E	(hypothetically) the same disease and low risks of breast cancer in those who never drink alcohol and lesser Hg-resistance during reproduction	[this work], [69]
	rs750789679	cgggtataaa	g c	cccctcccgc	3.6 4.5	↓	3	10^-2	C		[this work], [69]
	rs748231432	cccttatgtc	g c,t	ggtataaagc	3.6 3.0	↑	3	0.05	D	(hypothetically) lower risk of a brain tumor in a child whose mother has “c”-allele of rs1332018	[this work], [66]
	rs763859166	gggtataaag	c t	ccctcccgct	3.6 2.9	↑	3	10^-2	C		[this work], [66]

Hereinafter, ancestral (wt) and minor (mut) alleles; K_D, dissociation constant of TBP–DNA interaction; Δ, a change: overexpression (↑), deficit (↓), norm (=); α = 1 – p, significance {where p value is shown in Fig. 1; α = 1 denotes insignificance}; ρ, heuristic rank of candidate SNP markers varying in alphabetical order from the “best” (A) to the “worst” (E); the CETP gene: 18bp, the 18-bp deletion 5’-gggcggacatacatatac-3’; the F3 gene: 30bp, 17bp, and 18bp as the insertions 5’-agaccttcataagaaataatcctgatccaa-3’, 5’-tgctgcgtactggcaaa-3’, and 5’-acggcgtagagactggga-3’ of 30 bp, 17 bp, and 18 bp in length, respectively; EMSA, electrophoretic mobility shift assay; Hg, mercury; LUC, luciferase reporter assay; TF, transcription factor; Wb: western blot.

Back to article page

ISSN: 1471-2164

Contact us

Submission enquiries: bmcgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com

BMC Genomics

Contact us