title: A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells.
abstract: We report the immediate effects of estrogen signaling on the transcriptome of breast cancer cells using global run-on and sequencing (GRO-seq). The data were analyzed using a new bioinformatic approach that allowed us to identify transcripts directly from the GRO-seq data. We found that estrogen signaling directly regulates a strikingly large fraction of the transcriptome in a rapid, robust, and unexpectedly transient manner. In addition to protein-coding genes, estrogen regulates the distribution and activity of all three RNA polymerases and virtually every class of noncoding RNA that has been described to date. We also identified a large number of previously undetected estrogen-regulated intergenic transcripts, many of which are found proximal to estrogen receptor binding sites. Collectively, our results provide the most comprehensive measurement of the primary and immediate estrogen effects to date and a resource for understanding rapid signal-dependent transcription in other systems.
authors.affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Nasun
authors.initials: N
authors.lastname: Hah
authors.forename: Charles G
authors.initials: CG
authors.lastname: Danko
authors.forename: Leighton
authors.initials: L
authors.lastname: Core
authors.forename: Joshua J
authors.initials: JJ
authors.lastname: Waterfall
authors.forename: Adam
authors.initials: A
authors.lastname: Siepel
authors.forename: John T
authors.initials: JT
authors.lastname: Lis
authors.forename: W Lee
authors.initials: WL
authors.lastname: Kraus
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics*; D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods*; D047628:Estrogen Receptor alpha / Q000378:metabolism; D004967:Estrogens / Q000378:metabolism*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D005821:Genetic Techniques; D006801:Humans; D022661:RNA, Untranslated / Q000235:genetics; D017422:Sequence Analysis, DNA; D015398:Signal Transduction
chemical_list: D047628:Estrogen Receptor alpha; D004967:Estrogens; D022661:RNA, Untranslated