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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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