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

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.

Authors:
; ; ; ;  [1]
  1. GI-Singapore
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
USDOE
OSTI Identifier:
1007149
Resource Type:
Journal Article
Journal Name:
J. Mol. Biol.
Additional Journal Information:
Journal Volume: 376; Journal Issue: (3) ; 02, 2008; Journal ID: ISSN 0022-2836
Country of Publication:
United States
Language:
ENGLISH
Subject:
36 MATERIALS SCIENCE; AFFINITY; AMINO ACIDS; CRYSTAL STRUCTURE; DNA; FUNCTIONALS; GENES; MUTAGENESIS; PROMOTERS; RESIDUES; SPECIFICITY; STEM CELLS; TARGETS; TRANSCRIPTION FACTORS

Citation Formats

Jauch, Ralf, Ng, Calista Keow Leng, Saikatendu, Kumar Singh, Stevens, Raymond C, Kolatkar, Prasanna R, and Scripps). Crystal Structure and DNA Binding of the Homeodomain of the Stem Cell Transcription Factor Nanog. United States: N. p., 2010. Web. doi:10.1016/j.jmb.2007.11.091.
Jauch, Ralf, Ng, Calista Keow Leng, Saikatendu, Kumar Singh, Stevens, Raymond C, Kolatkar, Prasanna R, & Scripps). Crystal Structure and DNA Binding of the Homeodomain of the Stem Cell Transcription Factor Nanog. United States. https://doi.org/10.1016/j.jmb.2007.11.091
Jauch, Ralf, Ng, Calista Keow Leng, Saikatendu, Kumar Singh, Stevens, Raymond C, Kolatkar, Prasanna R, and Scripps). 2010. "Crystal Structure and DNA Binding of the Homeodomain of the Stem Cell Transcription Factor Nanog". United States. https://doi.org/10.1016/j.jmb.2007.11.091.
@article{osti_1007149,
title = {Crystal Structure and DNA Binding of the Homeodomain of the Stem Cell Transcription Factor Nanog},
author = {Jauch, Ralf and Ng, Calista Keow Leng and Saikatendu, Kumar Singh and Stevens, Raymond C and Kolatkar, Prasanna R and Scripps)},
abstractNote = {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.},
doi = {10.1016/j.jmb.2007.11.091},
url = {https://www.osti.gov/biblio/1007149}, journal = {J. Mol. Biol.},
issn = {0022-2836},
number = (3) ; 02, 2008,
volume = 376,
place = {United States},
year = {Mon Feb 08 00:00:00 EST 2010},
month = {Mon Feb 08 00:00:00 EST 2010}
}