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Nat Methods. 2014 May;11(5):559-65. doi: 10.1038/nmeth.2885. Epub 2014 Mar 23.

FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells.

Author information

  • 1Department of Microbiology, New York University School of Medicine, New York, New York, USA.
  • 2Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York, USA.
  • 3Department of Biology and Biological Sciences, Yale University, New Haven, Connecticut, USA.
  • 4Department of Biology, New York University, New York, New York, USA.
  • 51] Department of Biology, New York University, New York, New York, USA. [2] Department of Computer Science, Courant Institute of Mathematical Sciences, New York, New York, USA.

Abstract

Promoters and enhancers establish precise gene transcription patterns. The development of functional approaches for their identification in mammalian cells has been complicated by the size of these genomes. Here we report a high-throughput functional assay for directly identifying active promoter and enhancer elements called FIREWACh (Functional Identification of Regulatory Elements Within Accessible Chromatin), which we used to simultaneously assess over 80,000 DNA fragments derived from nucleosome-free regions within the chromatin of embryonic stem cells (ESCs) and identify 6,364 active regulatory elements. Many of these represent newly discovered ESC-specific enhancers, showing enriched binding-site motifs for ESC-specific transcription factors including SOX2, POU5F1 (OCT4) and KLF4. The application of FIREWACh to additional cultured cell types will facilitate functional annotation of the genome and expand our view of transcriptional network dynamics.

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PMID:
24658142
[PubMed - indexed for MEDLINE]
PMCID:
PMC4020622
Free PMC Article
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