SAFB1 mediates repression of immune regulators and apoptotic genes in breast cancer cells.
The scaffold attachment factors SAFB1 and SAFB2 are paralogs, which are involved in cell cycle regulation, apoptosis, differentiation, and stress response. They have been shown to function as estrogen receptor corepressors, and there is evidence for a role in breast tumorigenesis. To identify their endogenous target genes in MCF-7 breast cancer cells, we utilized a combined approach of chromatin immunoprecipitation (ChIP)-on-chip and gene expression array studies. By performing ChIP-on-chip on microarrays containing 24,000 promoters, we identified 541 SAFB1/SAFB2-binding sites in promoters of known genes, with significant enrichment on chromosomes 1 and 6. Gene expression analysis revealed that the majority of target genes were induced in the absence of SAFB1 or SAFB2 and less were repressed. Interestingly, there was no significant overlap between the genes identified by ChIP-on-chip and gene expression array analysis, suggesting regulation through regions outside the proximal promoters. In contrast to SAFB2, which shared most of its target genes with SAFB1, SAFB1 had many unique target genes, most of them involved in the regulation of the immune system. A subsequent analysis of the estrogen treatment group revealed that 12% of estrogen-regulated genes were dependent on SAFB1, with the majority being estrogen-repressed genes. These were primarily genes involved in apoptosis, such as BBC3, NEDD9, and OPG. Thus, this study confirms the primary role of SAFB1/SAFB2 as corepressors and also uncovers a previously unknown role for SAFB1 in the regulation of immune genes and in estrogen-mediated repression of genes.
Hammerich-Hille
Stephanie
S
From the Lester and Sue Smith Breast Center, Department of Medicine and Molecular and Cellular Biology, Texas Children's Cancer Center, Houston, Texas 77030.
Kaipparettu
Benny A
BA
From the Lester and Sue Smith Breast Center, Department of Medicine and Molecular and Cellular Biology, Texas Children's Cancer Center, Houston, Texas 77030.
Tsimelzon
Anna
A
From the Lester and Sue Smith Breast Center, Department of Medicine and Molecular and Cellular Biology, Texas Children's Cancer Center, Houston, Texas 77030.
Creighton
Chad J
CJ
From the Lester and Sue Smith Breast Center, Department of Medicine and Molecular and Cellular Biology, Texas Children's Cancer Center, Houston, Texas 77030.
Jiang
Shiming
S
From the Lester and Sue Smith Breast Center, Department of Medicine and Molecular and Cellular Biology, Texas Children's Cancer Center, Houston, Texas 77030.
Polo
Jose M
JM
the Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York 10461.
Melnick
Ari
A
the Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York 10461.
Meyer
Rene
R
Department of Pediatric Hematology/Oncology, Texas Children's Cancer Center, Houston, Texas 77030 and.
Oesterreich
Steffi
S
From the Lester and Sue Smith Breast Center, Department of Medicine and Molecular and Cellular Biology, Texas Children's Cancer Center, Houston, Texas 77030; Department of Pediatric Hematology/Oncology, Texas Children's Cancer Center, Houston, Texas 77030 and. Electronic address: steffio@breastcenter.tmc.edu.
D000595:Amino Acid Sequence; D017209:Apoptosis / Q000235:genetics*; D001665:Binding Sites / Q000235:genetics; D001943:Breast Neoplasms / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation; D056970:Co-Repressor Proteins / Q000235:genetics / Q000378:metabolism; D004967:Estrogens / Q000494:pharmacology; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D006801:Humans; D007109:Immunity / Q000235:genetics*; D015151:Immunoblotting; D036961:Matrix Attachment Region Binding Proteins / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D034521:Nuclear Matrix-Associated Proteins / Q000235:genetics* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D011401:Promoter Regions, Genetic / Q000235:genetics; D034622:RNA Interference; D011960:Receptors, Estrogen / Q000235:genetics* / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction
D056970:Co-Repressor Proteins; D004967:Estrogens; D036961:Matrix Attachment Region Binding Proteins; D034521:Nuclear Matrix-Associated Proteins; D011960:Receptors, Estrogen; C109132:SAFB protein, human; C486369:SAFB2 protein, human