PDZ domain-mediated dimerization and homeodomain-directed specificity are required for high-affinity DNA binding by SATB1

Nucleic Acids Research
Prabhat Kumar PurbeySanjeev Galande

Abstract

To better understand DNA recognition and transcription activity by SATB1, the T-lineage-enriched chromatin organizer and transcription factor, we have determined its optimal DNA-binding sequence by random oligonucleotide selection. The consensus SATB1-binding sequence (CSBS) comprises a palindromic sequence in which two identical AT-rich half-sites are arranged as inverted repeats flanking a central cytosine or guanine. Strikingly, the CSBS half-site is identical to the conserved element 'TAATA' bound by the known homeodomains (HDs). Furthermore, we show that the high-affinity binding of SATB1 to DNA is dimerization-dependent and the HD also binds in similar fashion. Binding studies using HD-lacking SATB1 and binding target with increased spacer between the two half-sites led us to propose a model for SATB1-DNA complex in which the HDs bind in an antiparallel fashion to the palindromic consensus element via minor groove, bridged by the PDZ-like dimerization domain. CSBS-driven in vivo reporter analysis indicated that SATB1 acts as a repressor upon binding to the CSBS and most of its derivatives and the extent of repression is proportional to SATB1's binding affinity to these sequences. These studies provide mechanistic insights...Continue Reading

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Citations

Jun 20, 2012·Immunology and Cell Biology·Mithila BuruteSanjeev Galande
Nov 30, 2011·The Journal of Biological Chemistry·Kazuo AsanomaM A Karim Rumi
Jul 3, 2010·Journal of the National Cancer Institute·Elizabeth IornsMarc Lippman
Jan 14, 2012·Nucleic Acids Research·Zheng WangJiafu Long
Dec 24, 2008·Molecular and Cellular Biology·Prabhat Kumar PurbeySanjeev Galande
Mar 31, 2010·Molecular and Cellular Biology·Joseph-Anthony T TanLinda K Durrin
May 21, 2011·Journal of Thoracic Oncology : Official Publication of the International Association for the Study of Lung Cancer·Christina I SelingerMaija R J Kohonen-Corish
Mar 18, 2009·Biophysical Journal·Mario Nicodemi, Antonella Prisco
Oct 20, 2012·Developmental Cell·Robert NechanitzkyRudolf Grosschedl
Sep 4, 2016·The Journal of Biological Chemistry·Simran KaurAlain Nepveu
Jul 28, 2016·The Biochemical Journal·Kazuhiko Yamasaki, Tomoko Yamasaki
Feb 17, 2017·Molecular and Cellular Biochemistry·Minying ZhengHao Zhou
May 18, 2018·Biomedicine & Pharmacotherapy = Biomédecine & Pharmacothérapie·Krishna P SunkaraMary Bebawy
Dec 29, 2020·Nucleus·Tomas Zelenka, Charalampos Spilianakis
Feb 11, 2021·Scientific Reports·Praveena L RamanujamSanjeev Galande

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Methods Mentioned

BETA
acetylation
immunoprecipitation
exponential enrichment
PCR
SELEX
X-ray
transfection
two-hybrid
affinity purification
gel filtration

Software Mentioned

SigmaStat
MEME
SPSS
LOGO
Photoshop

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