Global mapping of cell type-specific open chromatin by FAIRE-seq reveals the regulatory role of the NFI family in adipocyte differentiation

Hironori Waki, Masahiro Nakamura, Toshimasa Yamauchi, Ken ichi Wakabayashi, Jing Yu, Lisa Hirose-Yotsuya, Kazumi Take, Wei Sun, Masato Iwabu, Miki Okada-Iwabu, Takanori Fujita, Tomohisa Aoyama, Shuichi Tsutsumi, Kohjiro Ueki, Tatsuhiko Kodama, Juro Sakai, Hiroyuki Aburatani, Takashi Kadowaki

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76 Citations (Scopus)

Abstract

Identification of regulatory elements within the genome is crucial for understanding the mechanisms that govern cell type-specific gene expression. We generated genome-wide maps of open chromatin sites in 3T3-L1 adipocytes (on day 0 and day 8 of differentiation) and NIH-3T3 fibroblasts using formaldehyde-assisted isolation of regulatory elements coupled with high-throughput sequencing (FAIRE-seq). FAIRE peaks at the promoter were associated with active transcription and histone modifications of H3K4me3 and H3K27ac. Non-promoter FAIRE peaks were characterized by H3K4me1+/me3-, the signature of enhancers, and were largely located in distal regions. The non-promoter FAIRE peaks showed dynamic change during differentiation, while the promoter FAIRE peaks were relatively constant. Functionally, the adipocyte- and preadipocyte-specific non-promoter FAIRE peaks were, respectively, associated with genes up-regulated and down-regulated by differentiation. Genes highly up-regulated during differentiation were associated with multiple clustered adipocyte-specific FAIRE peaks. Among the adipocyte-specific FAIRE peaks, 45.3% and 11.7% overlapped binding sites for, respectively, PPARγ and C/EBPα, the master regulators of adipocyte differentiation. Computational motif analyses of the adipocyte-specific FAIRE peaks revealed enrichment of a binding motif for nuclear family I (NFI) transcription factors. Indeed, ChIP assay showed that NFI occupy the adipocyte-specific FAIRE peaks and/or the PPARγ binding sites near PPARγ, C/EBPα, and aP2 genes. Overexpression of NFIA in 3T3-L1 cells resulted in robust induction of these genes and lipid droplet formation without differentiation stimulus. Overexpression of dominant-negative NFIA or siRNA-mediated knockdown of NFIA or NFIB significantly suppressed both induction of genes and lipid accumulation during differentiation, suggesting a physiological function of these factors in the adipogenic program. Together, our study demonstrates the utility of FAIRE-seq in providing a global view of cell type-specific regulatory elements in the genome and in identifying transcriptional regulators of adipocyte differentiation.

Original languageEnglish
Article numbere1002311
JournalPLoS Genetics
Volume7
Issue number10
DOIs
Publication statusPublished - 2011 Oct
Externally publishedYes

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Genetics(clinical)
  • Cancer Research

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    Waki, H., Nakamura, M., Yamauchi, T., Wakabayashi, K. I., Yu, J., Hirose-Yotsuya, L., Take, K., Sun, W., Iwabu, M., Okada-Iwabu, M., Fujita, T., Aoyama, T., Tsutsumi, S., Ueki, K., Kodama, T., Sakai, J., Aburatani, H., & Kadowaki, T. (2011). Global mapping of cell type-specific open chromatin by FAIRE-seq reveals the regulatory role of the NFI family in adipocyte differentiation. PLoS Genetics, 7(10), [e1002311]. https://doi.org/10.1371/journal.pgen.1002311