Global remodeling of nucleosome positions in C. elegans

BMC Genomics

Table 1 Ranked dinucleotide energies predicted by position-independent models

Rank	In vitro(Rsa I)		*In vitro*(Hinc II)		In vivo(Gu & Fire)		In vivo(Valouev et al.)		S. cerevisiae in vitro(Zhang et al.)		In vivo (Embryos)		In vivo(Adults)		In vivo(Germlineless Adults)
1	TT	1.53	AT	1.39	GC	1.74	TT	1.52	TT	1.82	TA	1.39	TA	1.61	TA	1.69
2	AA	1.53	TT	1.23	CG	1.62	AA	1.52	AA	1.82	TT	1.29	TT	1.40	TT	1.64
3	AT	1.45	AA	1.23	GG	1.51	CG	1.48	TA	1.14	AA	1.29	AA	1.40	AA	1.64
4	TA	1.08	TA	0.88	CC	1.51	GC	1.05	AT	1.01	AT	1.22	AT	1.18	AT	1.22
5	GT	0.24	TC	0.36	TT	0.4	TA	0.68	AG	0.28	CT	0.23	AG	0.23	CT	0.04
6	AC	0.24	GA	0.36	AA	0.4	CC	0.52	CT	0.28	AG	0.23	CT	0.23	AG	0.04
7	GA	0.11	CA	0.26	TA	-0.31	GG	0.52	GA	0.2	GA	0.04	TC	-0.09	GA	-0.25
8	TC	0.11	TG	0.26	CT	-0.64	AT	0.02	TC	0.2	TC	0.04	GA	-0.09	TC	-0.25
9	TG	-0.06	GT	0.19	AG	-0.64	CT	-0.73	GT	-0.51	TG	-0.04	GT	-0.14	AC	-0.37
10	CA	-0.06	AC	0.19	AC	-0.69	AG	-0.73	AC	-0.51	CA	-0.04	AC	-0.14	GT	-0.37
11	AG	-0.55	AG	-0.08	GT	-0.69	AC	-0.76	TG	-0.56	AC	-0.06	CA	-0.26	TG	-0.55
12	CT	-0.55	CT	-0.08	AT	-0.73	GT	-0.76	CA	-0.56	GT	-0.06	TG	-0.26	CA	-0.55
13	CC	-0.94	GG	-1.33	CA	-0.84	GA	-0.85	CC	-0.84	GG	-1.08	CC	-0.96	GG	-0.65
14	GG	-0.94	CC	-1.33	TG	-0.84	TC	-0.85	GG	-0.84	CC	-1.08	GG	-0.96	CC	-0.65
15	CG	-1.12	CG	-1.58	TC	-0.90	TG	-1.31	GC	-1.45	GC	-1.59	GC	-1.48	GC	-1.26
16	GC	-2.08	GC	-1.95	GA	-0.9	CA	-1.31	CG	-1.48	CG	-1.80	CG	-1.68	CG	-1.37

Dinucleotide energies E_w predicted by N = 2 position-independent models fit on the indicated datasets are shown ranked from highest (least favorable) to lowest (most favorable). The energy of a dinucleotide w is defined as $E_{w} = ϵ_{w_{1} w_{2}} + ϵ_{w_{1}} + ϵ_{w_{2}}$ , where w₁ and w₂ are the first and second nucleotides in w, and the ϵ’s are the fitting parameters of the model (see Methods). Energy contributions are shown in arbitrary units, scaled so that each set of sixteen energies has zero mean and unit variance. A/T dinucleotides, composed only of A and T, are bolded, and G/C dinucleotides, composed only of G and C, are bolded and italicized.

ISSN: 1471-2164