Supplemental Data Combinatorial Analysis of Transcription Factor Partners Reveals Recruitment of c-MYC to Estrogen Receptor-α Responsive Promoters

Supplemental Methods and Results Computational Analysis of Putative ERα Targets Of the 92 ERα target genes identified by ChIP-chip, 72 have orthologous mouse counterparts, and their promoter sequences can be retrieved from the OMGProm database (Palaniswamy et al., 2005). When these promoter sequences were scanned by the ERTargetDB, a database for mammalian ERα target promoters previously constructed by our group (Jin et al., 2004; Jin et al., 2005), we found that 53/72 (74%) of the target genes have estrogen response elements (EREs). This result was consistent with the previous finding that one third of known target genes associate indirectly with ERα through intermediary transcription factors (O’Lone et al., 2004). Thirty-four of 92 (37%) identified target genes have altered transcription levels upon estrogen stimulation in breast cancer cells, based on gene expression microarray experiments described elsewhere (Inoue et al., 2002; Frasor et al., 2003; Lin et al., 2004; Fan et al., unpublished data). This value was possibly underestimated, because different microarray platforms were used in these experiments. Seventy-four identified ERα target genes had known biological functions covering diverse metabolic and cell regulatory pathways, consistent with the multiple roles of estrogen (Table S1). Interestingly, 20/74 (27%) were transcription factors or coregulators directly involved in transcriptional control (Figure S4). Collectively, these results suggest that the direct ERα target genes identified in this study are consistent with the existing knowledge of estrogen and ERα.