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Table 1 Frequency of MNase-preferred tetramers at the cutting sites

From: Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast

Naked DNA

ratio

p-val

Nucleosomal DNA

ratio

p-val

TATA.TATA

13.28

< 10-18

CTAG.CTAG

4.07

< 10-18

ATAG.CTAT

8.45

< 10-18

ATAG.CTAT

3.93

< 10-18

CTAA.TTAG

7.90

< 10-18

CAAG.CTTG

3.57

< 10-18

CTAG.CTAG

6.80

< 10-18

CTTA.TAAG

3.52

< 10-18

ATTA.TAAT

5.74

< 10-18

CATG.CATG

3.42

3.01 × 10-4

CATA.TATG

5.62

< 10-18

CATA.TATG

3.11

< 10-18

ATAA.TTAT

5.14

< 10-18

CTAA.TTAG

3.00

< 10-18

CTTA.TAAG

4.92

< 10-18

CTAC.GTAG

2.98

< 10-18

TTAA.TTAA

4.64

< 10-18

ATTG.CAAT

2.96

< 10-18

ATAT.ATAT

4.52

< 10-18

AAAG.CTTT

2.82

< 10-18

TAAA.TTTA

3.48

< 10-18

CTTC.GAAG

2.79

< 10-18

ATTG.CAAT

3.25

< 10-18

AATG.CATT

2.50

< 10-18

GTAA.TTAC

2.64

1.01 × 10-4

CATC.GATG

2.24

6.03 × 10-4

ATAC.GTAT

2.39

2.01 × 10-4

CAAC.GTTG

2.19

10-3

   

CAAA.TTTG

2.17

< 10-18

  1. Experimentally detected and expected frequency ratios of MNase-preferred tetramers at the cutting sites for naked (left) and nucleosomal (right) DNAs. Displayed tetramers are observed in at least two-fold higher frequency than expected, with a statistically significant difference (p < 10-3) (Supplementary Methods). Ratios for d(TAAA)·d(TTTA) and d(GTAA)·d(TTAC) tetramers in nucleosomal DNA are 1.39 (p < 0.08) and 1.6 (p < 0.03) respectively.
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BMC Genomics

ISSN: 1471-2164

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