Table 6

NFκB binding sites confirmed by chromatin immunoprecipitation.

Gene

Binding site position

TRANSFAC 8.4

TRANSFAC 11.1

Primer Position


AMIGO2

-721

V$NFKAPPAB_01

-795


BDNF

-223

V$CREL_01

V$NFKAPPAB_01

-586


BIRC3/cIAP2

-92

V$CREL_01

-75

-115

V$NFKAPPAB65_01

-178

V$NFKAPPAB65_01

V$NFKAPPAB_01


CCL2

-2602

V$NFKAPPAB65_01

V$NFKAPPAB_01

-2763

-2631

V$NFKAPPAB_01

V$NFKAPPAB_01

-2804

V$CREL_01

V$NFKAPPAB_01


CCND1

-698

V$CREL_01

-701


EDN1

-225 (II)

V$CREL_01

-241

-293 (II)

V$CREL_01

-2263 (I)

V$CREL_01

-2252


F3

-188 (II)

V$NFKAPPAB65_01

V$CREL_01

-351

-482 (II)

V$CREL_01

V$NFKAPPAB_01

-2373 (I)

V$NFKAPPAB65_01

V$NFKAPPAB_01

-2358


FST

-1335

V$CREL_01

-1341


GABPB2

-13

V$CREL_01

-145


G0S2

-1832

V$CREL_01

-1914


IGFBP5

-176

V$NFKAPPAB_01

-135


IL7R

-184 (II)

V$NFKB_C

-184

-2348 (I)

V$NFKAPPAB65_01

V$NFKAPPAB_01

-2344


MAT2A

-343 (II)

V$NFKAPPAB_01

-312

-1249 (I)

V$CREL_01

-1248


PLAU

-1598

V$CREL_01

-1942

-1838

V$NFKAPPAB65_01

-1872

V$NFKAPPAB65_01

V$NFKAPPAB_01


PTX3

-64

V$NFKAPPAB_01

V$NFKAPPAB_01

-147


RGS20

-179

V$NFKAPPAB_01

-345


STC2

-642

V$NFKAPPAB65_01

-587


TNFRSF11B/osteoprotegerin

-128

V$CREL_01

-258


The predicted NFκB binding sites that were confirmed by chromatin immunoprecipitation are indicated by the most 5' nucleotide. When multiple matrices predicted overlapping sites, the position indicates the most 5' nucleotide of the consensus sequence (see Additional file 4 for all sequences). Both over-represented (Table 4) and 7 additional (Additional file 4) NFκB matrices were used for the predictions. The TRANSFAC matrices shown are those that predicted the indicated sites with the lowest p-values. ChIP assays were considered to confirm binding sites located within 500 bp of the primer position. The site in the promoter region of GABPB2 was predicted using the alignment of the hg17 and mm5 genomes. Multiple binding sites for a gene are designated I and II, where appropriate. Primer positions are indicated by the most 5' nucleotide of the forward primer; all amplicons were 50–55 bp.

Terragni et al. BMC Cell Biology 2008 9:6   doi:10.1186/1471-2121-9-6

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