Transcriptomics

Dataset Information

5

SAFB1 mediates repression of immune regulators and apoptotic genes in breast cancer cells


ABSTRACT: 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 co-repressors, and there is evidence for a role in breast tumorigenesis. To identify their endogenous target genes in MCF-7 breast cancer cells, we utilized gene expression array analysis, which was set up in a two-by-four design, with vehicle and estrogen treatment, and control, SAFB1, SAFB2, and SAFB1/SAFB2 siRNA as variables. Using custom chips containing 1.5 kb upstream regulatory region, we identified 541 SAFB1/SAFB2 binding sites in promoters of known genes, with significant enrichment on chromosome 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. In contrast to SAFB2, which shared most of its target genes with SAFB1, SAFB1 had many unique target genes, most of them involved in regulation of the immune system. A subsequent analysis of the estrogen treatment group revealed that twelve percent 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 SAFB1/SAFB2’s primary role as co-repressors, and also uncovers a previously unknown role for SAFB1 in regulation of immune genes, and in estrogen-mediated repression of genes. To identify transcripts which were altered upon decrease of SAFB1 or SAFB2 expression we performed gene expression array analysis in MCF-7 cells. A secondary goal was to identify ERα-target genes for which estrogen regulation was dependent upon SAFB expression. We also added an experimental group in which we co-transfected siRNAs targeting both SAFB1 and SAFB2, which allowed us to address the question of interactions between the two paralogs. We therefore set up an experiment reflecting a 2x4 design, with a total of eight experimental groups.

ORGANISM(S): Homo sapiens  

SUBMITTER: Chad Creighton   Steffi Oesterreich  Stephanie Hammerich-Hille  Anna Tsimelzon 

PROVIDER: E-GEOD-15548 | ArrayExpress | 2010-02-21

SECONDARY ACCESSION(S): GSE15548PRJNA115987

REPOSITORIES: GEO, ArrayExpress

altmetric image

Publications

SAFB1 mediates repression of immune regulators and apoptotic genes in breast cancer cells.

Hammerich-Hille Stephanie S   Kaipparettu Benny A BA   Tsimelzon Anna A   Creighton Chad J CJ   Jiang Shiming S   Polo Jose M JM   Melnick Ari A   Meyer Rene R   Oesterreich Steffi S  

The Journal of biological chemistry 20091109 6


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 m  ...[more]

Similar Datasets

2013-06-16 | E-GEOD-47763 | ArrayExpress
2015-09-16 | E-GEOD-62854 | ArrayExpress
2010-01-28 | GSE15548 | GEO
2013-09-01 | E-GEOD-47803 | ArrayExpress
2013-02-23 | E-GEOD-41786 | ArrayExpress
2016-04-22 | E-GEOD-62854 | ExpressionAtlas
2012-11-28 | E-GEOD-42538 | ArrayExpress
2015-12-31 | E-MTAB-2515 | ArrayExpress
2013-08-01 | E-GEOD-49390 | ArrayExpress
2017-07-05 | E-MTAB-4570 | ArrayExpress