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Table 1 List of studied gene regions and number of CpGs covered, Breast Cancer Care in Chicago study (2005-2008)

From: Exploring DNA methylation changes in promoter, intragenic, and intergenic regions as early and late events in breast cancer formation

Gene/RNA isoforma

Test region

Test region coordinates (hg19)

Distance from TSS (bp)b

CGIc

# CpGsd

TSGe

Promoter region

     

  BRCA1

Exon 1 (extended promoter)

chr17: 41277463-41277365

+37 to +135

No

11

Yes

  CD44

Promoter

chr11: 35160374-35160443

-43 to +26

Yes

8

No

  ESR1

Exon 2 (extended promoter)

chr6: 152129110 - 152129167

+656 to +713

Yes

5

Unclear

  GSTM2

Promoter

chr1: 110210582-110210641

-62 to -3

Yes

8

No

  GSTP1

Exon 1 (extended promoter)

chr11: 67351205-67351215

+139 to +149

Yes

4

Yes

  MAGEA1f

Promoter

chrX: 152486180-152486129

-13 to -64

No

6

No

  MSI1

Promoter

chr12: 120807571-120807474

-588 to -491

No

5

 

  NFE2L3

Exon 1 (Extended promoter)

chr7: 26192663-26192744

+816 to +897

Yes

14

No

  RASSF1A

Exon 1 (extended promoter)

chr3: 50378293-50378233

+74 to +134

Yes

9

Yes

  RUNX3

Exon 1 (extended promoter)

chr1: 25256198-25256306

+464 to +572

Yes

28

Yes

  SIX3

Exon 1 (extended promoter)

chr2: 45169609-45169529

+492 to +572

Yes

12

Unclear

  TFF1

Promoter

chr21: 43786664-43786628

-20 to +16

No

5

Unclear

Upstream of promoter

     

  EN1

Upstream of promoter

chr2: 119611385-119611338

-5579 to -5626

Yes

6

No

  PAX3g

Far upstream

chr2: 223170608-223170643

-6928 to -6893

Yes

5

No

  PITX2f,h

Far upstream or intron I

chr4: 111562566-111562677

-18312 to -18413/+602 to +713

No

10

No

  SGK1h

Far upstream/ alt. exon 1

chr6: 134638893-134638831

-14823 to -14761/+303 to +365

Yes

6

Unclear

Introns

      

  APC

Intron 1 or promoter

chr5: 112073426-112073445

+30224 to +30243/-130 to -111

No

4

Yes

  EGFR

intron 1

chr7: 55088080-55088104

+1355 to +1379

Yes

4

No

  LHX2

Intron 3

chr9: 126777854-126777983

+3966 to +4095

Yes

11

No

  RFX1f

Intron 7

chr19: 14089984-14089969

+27150 to +27165

No

4

No

  SOX9

Intron 2

chr17: 70119151-70119195

+1990 to +2034

Yes

4

No

DNA Repeats

      

  LINE-1

N.A.

DNA Repeat

N.A.

 

4

N.A.

  Sat2

N.A.

DNA Repeat

N.A.

 

2

N.A.

  1. aWhere there are multiple RefSeq RNA isoforms and expression in HMEC cells by RNA-seq (ENCODE/Cold Spring Harbor), the RNA isoform closest to the predominant HMEC RNA was used in this table to determine the TSS. The isoforms for calculation of the distance from the TSS are given in Additional file 1: Tables S1 and S2
  2. bTSS, transcription start site for the indicated RefSeq isoform. N.A., not applicable
  3. cCGI, CpG island overlapping the test region
  4. dThe number of CpG dinucleotide pairs in the test region (the amplicon used for pyrosequencing minus the primer regions)
  5. eTSG, Tumor suppressor gene
  6. fAlthough the sequences were in regions that did not make the criteria to be classified as CGI [13], the regions were rich in CpG compared to the average for human DNA
  7. gThere is a little expressed, primate specific gene, CCDC140, between PAX3 and the test region whose 5’ end overlaps the 5’ end of PAX3
  8. hThere are distant alternative 5’ ends of these genes
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BMC Cancer

ISSN: 1471-2407

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