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Table 1 List of oligonucleotides

From: Regulation of UGT1A1 and HNF1 transcription factor gene expression by DNA methylation in colon cancer cells

Transcient transfection experiement

Transcription factora

OCT1

5'

GGTCTGTGGAAATACTGGCC TAATGGATCCTGAGGTTC

3'

CDX2

5'

GTGGACTGACAGCTTTTCGCC GTCACGTGACACAGTC

3'

USF

5'

GCTTTTTATAGTCAAT TGACACAGTCAAAC

3'

HNF1

5'

CACAGTCAAACATGAG CTTGGTGTATCGA

3'

NF-Y

5'

CTTGGTGTATCGACCT GTTTTTGCCATAT

3'

Electrophoretic mobility shift assays

Putative TFs binding motif in UGT1A1 proximal promotera

OCT1

5'

GTGGAAATACTAATT TAATGGA

3'

CDX2

5'

GACTGACAGCTTTTTA TAGTCA

3'

CREB/USF/SREBP1

5'

TTTTTATAGTCACGTG ACACAGTC

3'

HNF1

5'

CACAGTCAAACATTAAC TTG

3'

NF-Y

5'

CTTGGTGTATCGATTGG TTTTTGCCAT

3'

PBX

5'

TGTATCGATT GGTTTTTGCCATATAT

3'

Consensus oligonucleotide probes used in competition assaysa

OCT1 consensus oligo

5'

TGTCGAATGCAAATC ACTAGAA

3'

CDX2 consensus oligo

5'

GTGCAATAAAACTTTA TGAGTA

3'

USF consensus oligo

5'

CACCCGGTCACGTG GCCTACACC

3'

HNF1 consensus oligo

5'

CCAGGTTAATGATTAAC CCA

3'

NF-Y consensus oligo

5'

AGACCGTACGTGATTGG TTAATCTCTT

3'

PBX consensus oligo

5'

CGAATTGATT GATGCACTAATTGCAG

3'

Oligonucleotide probes of the UGT1A1 promoter with CpG sitesb

CpG-4/USF

5'

AGCTTTTTATAGTCACG TGACACAGTCAAACAT

3'

CpG-4/USF-HNF1

5'

TCACG TGACACAGTCAAACATTAACTTGGT

3'

Reverse transcription (RT)-PCR

Target gene

HNF-1α Forward

5'

GGTCATGAGCTTCGTCAACC

3'

HNF-1α Reverse

5'

GCAGGAAGAGATCCGATTCC

3'

USF-1 Forward

5'

GGCAGCTGAGACGGCCTTGG

3'

USF-1 Reverse

5'

TGGCCCCCATTCTCAGTTCGGA

3'

USF-2 Forward

5'

CTGCCTCTGTGCCCCCAGGT

3'

USF-2 Reverse

5'

TTGTCCCTCCGCCTCCGCTC

3'

GAPDH Forward

5'

TTGGTATCGTGGAAGGACTCA

3'

GAPDH Reverse

5'

TGTCATCATATTTGGCAGGTTT

3'

  1. a TF recognition core sequence is underlined.
  2. b UGT1A1 promoter CpG sites are underlined.