Crystal Structure and DNA Binding of the Homeodomain of the Stem Cell Transcription Factor Nanog

Ralf Jauch, Calista Keow Leng Ng, Kumar Singh Saikatendu, Raymond C. Stevens, Prasanna Kolatkar

Research output: Contribution to journalArticle

62 Citations (Scopus)

Abstract

The transcription factor Nanog is an upstream regulator in early mammalian development and a key determinant of pluripotency in embryonic stem cells. Nanog binds to promoter elements of hundreds of target genes and regulates their expression by an as yet unknown mechanism. Here, we report the crystal structure of the murine Nanog homeodomain (HD) and analysis of its interaction with a DNA element derived from the Tcf3 promoter. Two Nanog amino acid pairs, unique among HD sequences, appear to affect the mechanism of nonspecific DNA recognition as well as maintain the integrity of the structural scaffold. To assess selective DNA recognition by Nanog, we performed electrophoretic mobility shift assays using a panel of modified DNA binding sites and found that Nanog HD preferentially binds the TAAT(G/T)(G/T) motif. A series of rational mutagenesis experiments probing the role of six variant residues of Nanog on its DNA binding function establish their role in affecting binding affinity but not binding specificity. Together, the structural and functional evidence establish Nanog as a distant member of a Q50-type HD despite having considerable variation at the sequence level.

Original languageEnglish
Pages (from-to)758-770
Number of pages13
JournalJournal of Molecular Biology
Volume376
Issue number3
DOIs
Publication statusPublished - 22 Feb 2008
Externally publishedYes

Fingerprint

Stem Cell Factor
Transcription Factors
DNA
Electrophoretic Mobility Shift Assay
Embryonic Stem Cells
Mutagenesis
Binding Sites
Amino Acids
Genes

Keywords

  • DNA binding
  • homeodomain
  • Nanog
  • pluripotency
  • transcription factor

ASJC Scopus subject areas

  • Virology

Cite this

Crystal Structure and DNA Binding of the Homeodomain of the Stem Cell Transcription Factor Nanog. / Jauch, Ralf; Ng, Calista Keow Leng; Saikatendu, Kumar Singh; Stevens, Raymond C.; Kolatkar, Prasanna.

In: Journal of Molecular Biology, Vol. 376, No. 3, 22.02.2008, p. 758-770.

Research output: Contribution to journalArticle

Jauch, Ralf ; Ng, Calista Keow Leng ; Saikatendu, Kumar Singh ; Stevens, Raymond C. ; Kolatkar, Prasanna. / Crystal Structure and DNA Binding of the Homeodomain of the Stem Cell Transcription Factor Nanog. In: Journal of Molecular Biology. 2008 ; Vol. 376, No. 3. pp. 758-770.
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