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

Matthew Murtha, Zeynep Tokcaer-Keskin, Zuojian Tang, Francesco Strino, Xi Chen, Yatong Wang, Xiangmei Xi, Claudio Basilico, Stuart Brown, Richard Bonneau, Yuval Kluger, Lisa Dailey

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)559-565
Number of pages7
JournalNature Methods
Volume11
Issue number5
DOIs
StatePublished - 2014

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Embryonic Stem Cells
Stem cells
Chromatin
Genes
Cells
Throughput
SOXB1 Transcription Factors
Genome Size
Nucleosomes
Gene Regulatory Networks
Transcription
Cultured Cells
Assays
Transcription Factors
Binding Sites
Genome
DNA

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Biochemistry
  • Cell Biology

Cite this

Murtha, M., Tokcaer-Keskin, Z., Tang, Z., Strino, F., Chen, X., Wang, Y., ... Dailey, L. (2014). FIREWACh: High-throughput functional detection of transcriptional regulatory modules in mammalian cells. Nature Methods, 11(5), 559-565. https://doi.org/10.1038/nmeth.2885

FIREWACh : High-throughput functional detection of transcriptional regulatory modules in mammalian cells. / Murtha, Matthew; Tokcaer-Keskin, Zeynep; Tang, Zuojian; Strino, Francesco; Chen, Xi; Wang, Yatong; Xi, Xiangmei; Basilico, Claudio; Brown, Stuart; Bonneau, Richard; Kluger, Yuval; Dailey, Lisa.

In: Nature Methods, Vol. 11, No. 5, 2014, p. 559-565.

Research output: Contribution to journalArticle

Murtha, M, Tokcaer-Keskin, Z, Tang, Z, Strino, F, Chen, X, Wang, Y, Xi, X, Basilico, C, Brown, S, Bonneau, R, Kluger, Y & Dailey, L 2014, 'FIREWACh: High-throughput functional detection of transcriptional regulatory modules in mammalian cells', Nature Methods, vol. 11, no. 5, pp. 559-565. https://doi.org/10.1038/nmeth.2885
Murtha, Matthew ; Tokcaer-Keskin, Zeynep ; Tang, Zuojian ; Strino, Francesco ; Chen, Xi ; Wang, Yatong ; Xi, Xiangmei ; Basilico, Claudio ; Brown, Stuart ; Bonneau, Richard ; Kluger, Yuval ; Dailey, Lisa. / FIREWACh : High-throughput functional detection of transcriptional regulatory modules in mammalian cells. In: Nature Methods. 2014 ; Vol. 11, No. 5. pp. 559-565.
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