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 into the mode
of DNA binding and its effect on the regulation of transcription
by SATB1.
National Centre for Cell Science, Ganeshkhind, Pune 411007, India.
journal
Nucleic Acids Res
number
7
pages
2107--2122
volume
36
pmid
18187506
timestamp
2008.09.10
pii
gkm1151
file
:C\:\\Users\\denilw\\Desktop\\Steven Jones Lab\\Papers\\SatB1\\PDZ
domain-mediated dimerization and homeodomain-directed specificity
are required for high-affinity DNA binding by SATB1.pdf:PDF;:C\:\\Users\\denilw\\Desktop\\Steven
Jones Lab\\Papers\\SatB1\\PDZ domain-mediated dimerization and homeodomain-directed
specificity are required for high-affinity DNA binding by SATB1 SUPPLIMENTARY.pdf:PDF
%0 Journal Article
%1 Purbey2008
%A Purbey, Prabhat Kumar
%A Singh, Sunita
%A Kumar, P. Pavan
%A Mehta, Sameet
%A Ganesh, K. N.
%A Mitra, Debashis
%A Galande, Sanjeev
%D 2008
%J Nucleic Acids Res
%K AT Aptamer Attachment Base Binding Binding; Cell Chain; Cloning, Consensus DNA, Dimerization; Domains; Genes, Heavy Homeodomain Humans; Immunoglobulin Line; Matrix Models, Molecular; PDZ Protein Proteins, Region Regions; Repressor Rich SELEX Sequence; Sites; Structure, Technique Tertiary; chemistry/metabolism; chemistry;
%N 7
%P 2107--2122
%R 10.1093/nar/gkm1151
%T PDZ domain-mediated dimerization and homeodomain-directed specificity
are required for high-affinity DNA binding by SATB1.
%U http://dx.doi.org/10.1093/nar/gkm1151
%V 36
%X 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 into the mode
of DNA binding and its effect on the regulation of transcription
by SATB1.
@article{Purbey2008,
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 into the mode
of DNA binding and its effect on the regulation of transcription
by SATB1.},
added-at = {2008-09-25T22:07:47.000+0200},
author = {Purbey, Prabhat Kumar and Singh, Sunita and Kumar, P. Pavan and Mehta, Sameet and Ganesh, K. N. and Mitra, Debashis and Galande, Sanjeev},
biburl = {https://www.bibsonomy.org/bibtex/2e96893da05ab2fee47533ec15a6ce47f/denilw},
doi = {10.1093/nar/gkm1151},
file = {:C\:\\Users\\denilw\\Desktop\\Steven Jones Lab\\Papers\\SatB1\\PDZ
domain-mediated dimerization and homeodomain-directed specificity
are required for high-affinity DNA binding by SATB1.pdf:PDF;:C\:\\Users\\denilw\\Desktop\\Steven
Jones Lab\\Papers\\SatB1\\PDZ domain-mediated dimerization and homeodomain-directed
specificity are required for high-affinity DNA binding by SATB1 SUPPLIMENTARY.pdf:PDF},
institution = {National Centre for Cell Science, Ganeshkhind, Pune 411007, India.},
interhash = {c5c92c318fa4d485c4042970b823da8e},
intrahash = {e96893da05ab2fee47533ec15a6ce47f},
journal = {Nucleic Acids Res},
keywords = {AT Aptamer Attachment Base Binding Binding; Cell Chain; Cloning, Consensus DNA, Dimerization; Domains; Genes, Heavy Homeodomain Humans; Immunoglobulin Line; Matrix Models, Molecular; PDZ Protein Proteins, Region Regions; Repressor Rich SELEX Sequence; Sites; Structure, Technique Tertiary; chemistry/metabolism; chemistry;},
month = Apr,
number = 7,
owner = {denilw},
pages = {2107--2122},
pii = {gkm1151},
pmid = {18187506},
timestamp = {2008-09-25T22:07:48.000+0200},
title = {PDZ domain-mediated dimerization and homeodomain-directed specificity
are required for high-affinity DNA binding by SATB1.},
url = {http://dx.doi.org/10.1093/nar/gkm1151},
volume = 36,
year = 2008
}