Recognition of non-canonical DNA structures in genomic DNA
sequences by p53 proteins

a 2009

Recognition of non-canonical DNA structures in genomic DNA sequences by p53 proteins

NAVRATILOVA, L.; Marie BRAZDOVA; V. TICHY; Miroslav FOJTA; Matej LEXA et. al.

Základní údaje

Originální název

Recognition of non-canonical DNA structures in genomic DNA sequences by p53 proteins

Název česky

Ropoznávání nekanonických DNA struktur v genomových sekvencích DNA proteiny p53

Autoři

NAVRATILOVA, L. (203 Česká republika); Marie BRAZDOVA (203 Česká republika); V. TICHY (203 Česká republika); Miroslav FOJTA (203 Česká republika); Matej LEXA (703 Slovensko, domácí); I. KYJOVSKY (203 Česká republika); W. DEPPERT (276 Německo) a E. PALEČEK (203 Česká republika, garant)

Vydání

34th Congress of the Federation-of-European-Biochemical-Societies Prague, 2009

Další údaje

Jazyk

angličtina

Typ výsledku

Konferenční abstrakt

Obor

Genetika a molekulární biologie

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 3.042

Kód RIV

RIV/00216224:14330/09:00048866

Organizační jednotka

Fakulta informatiky

ISSN

UT WoS

000267069900306

Klíčová slova anglicky

p53; triplex DNA; DNA-binding; gene regulation

Změněno: 23. 9. 2013 21:49, doc. Ing. Matej Lexa, Ph.D.

Anotace

V originále

In our analyses we combined molecular and computational approaches to understand the mutant p53 function in specific gene regulation via binding to non-canonical DNA structures in chromatin DNA. We used two glioblastoma cell lines U251 (R273H) and Onda11 (R273C) expressing endogenous mutp53 proteins to isolate natural mutant p53 binding sites (mutp53BS) by genome- wide ChIP-cloning. In our computational work, we developed tools for rapid identification of DNA sequences (among the isolated mutp53BS) tending to form non-B structures (hairpins and triplex DNA) as well as for mapping their genomic locations. These sites are frequently localized in the regulatory first introns of genes and are enriched in repetitive elements. Potential to form triplex and cruciform structures was predicted by developed computational tools and detected by enzymatic and chemical probing. The role of topological status of studied DNA and p53 domains in mutp53BS recognition was investigated by recombinant mutp53 proteins in vitro and reporter assays in vivo. Our data suggest that the mutant p53 proteins bind selectively non-B DNA structures not only in vitro but also with functional consequences in vivo.

Návaznosti

GA204/08/1560, projekt VaV

Název: Bioinformatická a experimentální identifikace nekanonických struktur v genomové DNA

Investor: Grantová agentura ČR, Bioinformatická a experimentální identifikace nekanonických struktur v genomové DNA

Citovat

NAVRATILOVA, L.; Marie BRAZDOVA; V. TICHY; Miroslav FOJTA; Matej LEXA; I. KYJOVSKY; W. DEPPERT a E. PALEČEK. Recognition of non-canonical DNA structures in genomic DNA sequences by p53 proteins. In 34th Congress of the Federation-of-European-Biochemical-Societies Prague. 2009. ISSN 1742-464X.

@proceedings{899413,
   author = {Navratilova, L. and Brazdova, Marie and Tichy, V. and Fojta, Miroslav and Lexa, Matej and Kyjovsky, I. and Deppert, W. and Paleček, E.},
   booktitle = {34th Congress of the Federation-of-European-Biochemical-Societies Prague},
   keywords = {p53; triplex DNA; DNA-binding; gene regulation},
   language = {eng},
   title = {Recognition of non-canonical DNA structures in genomic DNA sequences by p53 proteins},
   year = {2009}
}

TY  - CONF
ID  - 899413
AU  - Navratilova, L. - Brazdova, Marie - Tichy, V. - Fojta, Miroslav - Lexa, Matej - Kyjovsky, I. - Deppert, W. - Paleček, E.
PY  - 2009
TI  - Recognition of non-canonical DNA structures in genomic DNA sequences by p53 proteins
KW  - p53
KW  - triplex DNA
KW  - DNA-binding
KW  - gene regulation
N2  - In our analyses we combined molecular and computational approaches to understand the mutant p53 function in specific gene regulation via binding to non-canonical DNA structures in chromatin DNA. We used two glioblastoma cell lines U251 (R273H) and Onda11 (R273C) expressing endogenous mutp53 proteins to isolate natural mutant p53 binding sites (mutp53BS) by genome- wide ChIP-cloning. In our computational work, we developed tools for rapid identification of DNA sequences (among the isolated mutp53BS) tending to form non-B structures (hairpins and triplex DNA) as well as for mapping their genomic locations. These sites are frequently localized in the regulatory first introns of genes and are enriched in repetitive elements. Potential to form triplex and cruciform structures was predicted by developed computational tools and detected by enzymatic and chemical probing. The role of topological status of studied DNA and p53 domains in mutp53BS recognition was investigated by recombinant mutp53 proteins in vitro and reporter assays in vivo. Our data suggest that the mutant p53 proteins bind selectively non-B DNA structures not only in vitro but also with functional consequences in vivo.
ER  -

NAVRATILOVA, L.; Marie BRAZDOVA; V. TICHY; Miroslav FOJTA; Matej LEXA; I. KYJOVSKY; W. DEPPERT a E. PALEČEK. Recognition of non-canonical DNA structures in genomic DNA sequences by p53 proteins. In \textit{34th Congress of the Federation-of-European-Biochemical-Societies Prague}. 2009. ISSN~1742-464X.

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