Prediction of nucleosome rotational positioning in yeast and human genomes based on sequence-dependent DNA anisotropy

Table 1 Rotational positioning of in vitro nucleosomes predicted by the two computational schemes

Number	Nucleosome positioning fragment	Exp. dyad position	Exp. method	W/S scheme	KS-2009 model	Reference
1	'601'	134	SDHR/FHR	+	+	[18, 19]
2	'603'	153	FHR	+	+	[19]
3	'605'	131	FHR	+	+	[19]
4	X. borealis somatic 5S rDNA	−24	SDHR	+	–	[20]
5	"	−3	SDHR	+	+	[20]
6	"	+7	SDHR	+	+	[20]
7	"	+48	SDHR	+	+	[20]
8	"	+58	SDHR	+	–	[20]
9	X. borealis oocyte 5S rDNA	−2	SDHR	+	+	[20]
10	"	+20	SDHR	+	+	[20]
11	"	+34	SDHR	–	+	[20]
12	"	+58	SDHR	+	–	[20]
13	Sea urchin 5S rDNA	−11/–12	SDHR	+	+	[17]
14	"	+8	SDHR	+	–	[17]
15	MMTV	−127	SDHR	+	+	[22]
16	"	+70	SDHR	+	+	[22]
17	pGUB	84	SDHR	–	–	[23]
18	"	104	SDHR	–	–	[23]
19	Fragment 67	113	FHR	–	+	[24]
20	Chicken β^A-globin	−281	MNase + DNase I	–	–	[21]
			Total correct predictions	15/20	13/20

FHR: free hydroxyl radical method; SDHR: site-directed hydroxyl radical method. The experimental dyad positions and methods used are given according to the references.
The extent of agreement between the experimental data and the predictions: the symbol ‘+’ indicates that the discrepancy between the predicted maximal score and experimental dyad position does not exceed 2 bp. The symbol ‘–’ indicates that the predicted and experimental positions are separated by 3–6 bp (that is, about a half helical turn of DNA duplex).

ISSN: 1471-2105