p53 Specifically Binds Triplex DNA In Vitro and in Cells

J 2016

p53 Specifically Binds Triplex DNA In Vitro and in Cells

BRÁZDOVÁ, Marie, Vlastimil TICHÝ, Robert HELMA, Pavla BAŽANTOVÁ, Alena POLÁŠKOVÁ et. al.

Basic information

Original name

p53 Specifically Binds Triplex DNA In Vitro and in Cells

Authors

BRÁZDOVÁ, Marie (203 Czech Republic, guarantor), Vlastimil TICHÝ (203 Czech Republic), Robert HELMA (203 Czech Republic), Pavla BAŽANTOVÁ (203 Czech Republic), Alena POLÁŠKOVÁ (203 Czech Republic), Aneta KREJČÍ (203 Czech Republic), Marek PETR (203 Czech Republic), Lucie NAVRÁTILOVÁ (203 Czech Republic), Olga TICHÁ (203 Czech Republic), Karel NEJEDLÝ (203 Czech Republic), Martin L BENNINK (528 Netherlands), Vinod SUBRAMANIAM (528 Netherlands), Zuzana BÁBKOVÁ (203 Czech Republic), Tomáš MARTÍNEK (203 Czech Republic), Matej LEXA (703 Slovakia, belonging to the institution) and Matej ADÁMIK (703 Slovakia)

Edition

PLOS ONE, Public Library of Science, 2016, 1932-6203

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL URL

Impact factor

Impact factor: 2.806

RIV identification code

RIV/00216224:14330/16:00088595

Organization unit

Faculty of Informatics

DOI

http://dx.doi.org/10.1371/journal.pone.0167439

UT WoS

000389482700156

Keywords in English

cancer; H-DNA; non-B DNA; gene regulation; DNA binding;

Abstract

V originále

Triplex DNA is implicated in a wide range of biological activities, including regulation of gene expression and genomic instability leading to cancer. The tumor suppressor p53 is a central regulator of cell fate in response to different type of insults. Sequence and structure specific modes of DNA recognition are core attributes of the p53 protein. The focus of this work is the structure-specific binding of p53 to DNA containing triplex-forming sequences in vitro and in cells and the effect on p53-driven transcription. This is the first DNA binding study of full-length p53 and its deletion variants to both intermolecular and intramolecular T.A.T triplexes. We demonstrate that the interaction of p53 with intermolecular T.A.T triplex is comparable to the recognition of CTG-hairpin non-B DNA structure. Using deletion mutants we determined the C-terminal DNA binding domain of p53 to be crucial for triplex recognition. Furthermore, strong p53 recognition of intramolecular T.A.T triplexes (H-DNA), stabilized by negative superhelicity in plasmid DNA, was detected by competition and immunoprecipitation experiments, and visualized by AFM. Moreover, chromatin immunoprecipitation revealed p53 binding T.A.T forming sequence in vivo. Enhanced reporter transactivation by p53 on insertion of triplex forming sequence into plasmid with p53 consensus sequence was observed by luciferase reporter assays. In-silico scan of human regulatory regions for the simultaneous presence of both consensus sequence and T.A.T motifs identified a set of candidate p53 target genes and p53-dependent activation of several of them (ABCG5, ENOX1, INSR, MCC, NFAT5) was confirmed by RT-qPCR. Our results show that T.A.T triplex comprises a new class of p53 binding sites targeted by p53 in a DNA structure-dependent mode in vitro and in cells. The contribution of p53 DNA structure-dependent binding to the regulation of transcription is discussed.

Links

GA15-02891S, research and development project

Name: Rostlinné transpozony a konformace DNA

Investor: Czech Science Foundation

Citovat

BRÁZDOVÁ, Marie, Vlastimil TICHÝ, Robert HELMA, Pavla BAŽANTOVÁ, Alena POLÁŠKOVÁ, Aneta KREJČÍ, Marek PETR, Lucie NAVRÁTILOVÁ, Olga TICHÁ, Karel NEJEDLÝ, Martin L BENNINK, Vinod SUBRAMANIAM, Zuzana BÁBKOVÁ, Tomáš MARTÍNEK, Matej LEXA and Matej ADÁMIK. p53 Specifically Binds Triplex DNA In Vitro and in Cells. PLOS ONE. Public Library of Science, 2016, vol. 11, No 12, p. "e0167439", 25 pp. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0167439.

@article{1369148,
   author = {Brázdová, Marie and Tichý, Vlastimil and Helma, Robert and Bažantová, Pavla and Polášková, Alena and Krejčí, Aneta and Petr, Marek and Navrátilová, Lucie and Tichá, Olga and Nejedlý, Karel and Bennink, Martin L and Subramaniam, Vinod and Bábková, Zuzana and Martínek, Tomáš and Lexa, Matej and Adámik, Matej},
   article_number = {12},
   doi = {http://dx.doi.org/10.1371/journal.pone.0167439},
   keywords = {cancer; H-DNA; non-B DNA; gene regulation; DNA binding;},
   language = {eng},
   issn = {1932-6203},
   journal = {PLOS ONE},
   title = {p53 Specifically Binds Triplex DNA In Vitro and in Cells},
   url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0167439},
   volume = {11},
   year = {2016}
}

TY  - JOUR
ID  - 1369148
AU  - Brázdová, Marie - Tichý, Vlastimil - Helma, Robert - Bažantová, Pavla - Polášková, Alena - Krejčí, Aneta - Petr, Marek - Navrátilová, Lucie - Tichá, Olga - Nejedlý, Karel - Bennink, Martin L - Subramaniam, Vinod - Bábková, Zuzana - Martínek, Tomáš - Lexa, Matej - Adámik, Matej
PY  - 2016
TI  - p53 Specifically Binds Triplex DNA In Vitro and in Cells
JF  - PLOS ONE
VL  - 11
IS  - 12
SP  - "e0167439"
EP  - "e0167439"
PB  - Public Library of Science
SN  - 19326203
KW  - cancer
KW  - H-DNA
KW  - non-B DNA
KW  - gene regulation
KW  - DNA binding;
UR  - http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0167439
L2  - http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0167439
N2  - Triplex DNA is implicated in a wide range of biological activities, including regulation of gene expression and genomic instability leading to cancer. The tumor suppressor p53 is a central regulator of cell fate in response to different type of insults. Sequence and structure specific modes of DNA recognition are core attributes of the p53 protein. The focus of this work is the structure-specific binding of p53 to DNA containing triplex-forming sequences in vitro and in cells and the effect on p53-driven transcription. This is the first DNA binding study of full-length p53 and its deletion variants to both intermolecular and intramolecular T.A.T triplexes. We demonstrate that the interaction of p53 with intermolecular T.A.T triplex is comparable to the recognition of CTG-hairpin non-B DNA structure. Using deletion mutants we determined the C-terminal DNA binding domain of p53 to be crucial for triplex recognition. Furthermore, strong p53 recognition of intramolecular T.A.T triplexes (H-DNA), stabilized by negative superhelicity in plasmid DNA, was detected by competition and immunoprecipitation experiments, and visualized by AFM. Moreover, chromatin immunoprecipitation revealed p53 binding T.A.T forming sequence in vivo. Enhanced reporter transactivation by p53 on insertion of triplex forming sequence into plasmid with p53 consensus sequence was observed by luciferase reporter assays. In-silico scan of human regulatory regions for the simultaneous presence of both consensus sequence and T.A.T motifs identified a set of candidate p53 target genes and p53-dependent activation of several of them (ABCG5, ENOX1, INSR, MCC, NFAT5) was confirmed by RT-qPCR. Our results show that T.A.T triplex comprises a new class of p53 binding sites targeted by p53 in a DNA structure-dependent mode in vitro and in cells. The contribution of p53 DNA structure-dependent binding to the regulation of transcription is discussed.
ER  -

BRÁZDOVÁ, Marie, Vlastimil TICHÝ, Robert HELMA, Pavla BAŽANTOVÁ, Alena POLÁŠKOVÁ, Aneta KREJČÍ, Marek PETR, Lucie NAVRÁTILOVÁ, Olga TICHÁ, Karel NEJEDLÝ, Martin L BENNINK, Vinod SUBRAMANIAM, Zuzana BÁBKOVÁ, Tomáš MARTÍNEK, Matej LEXA and Matej ADÁMIK. p53 Specifically Binds Triplex DNA In Vitro and in Cells. \textit{PLOS ONE}. Public Library of Science, 2016, vol.~11, No~12, p.~''e0167439'', 25 pp. ISSN~1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0167439.

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