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Enhancer Transcripts Mark Active Estrogen Receptor Binding Sites

ABSTRACT: In this study, we used Global Run-On sequencing (GRO-seq), a method that assays the genome-wide location and orientation of all active RNA polymerases. We generated a global profile of active transcription at ERM-NM-1 binding sites in MCF-7 human breast cancer cells in response to short time course of E2 treatment. This method enabled us to detect active transcription at enhancers and define a class of primary transcripts transcribed uni- or bidirectionally from the ERM-NM-1 binding sites. The raw data used in this study is from GSE27463 but sequenced to a greater depth. Using GRO-seq over a time course (0, 10, 40 min) of estrogen signaling in ER-alpha positive MCF-7 human breast cancer cells.

ORGANISM(S): Homo sapiens

SUBMITTER: W. Lee Kraus

PROVIDER: E-GEOD-43835 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Enhancer transcripts mark active estrogen receptor binding sites.

Hah Nasun N Murakami Shino S Nagari Anusha A Danko Charles G CG Kraus W Lee WL

Genome research 20130501 8

We have integrated and analyzed a large number of data sets from a variety of genomic assays using a novel computational pipeline to provide a global view of estrogen receptor 1 (ESR1; a.k.a. ERα) enhancers in MCF-7 human breast cancer cells. Using this approach, we have defined a class of primary transcripts (eRNAs) that are transcribed uni- or bidirectionally from estrogen receptor binding sites (ERBSs) with an average transcription unit length of ∼3-5 kb. The majority are up-regulated by shor ...[more]

PMID: 23636943

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