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Discovery of novel tumor suppressor p53 response elements using information theory

An accurate method for locating genes under tumor suppressor p53 control that is based on a well-established mathematical theory and built using naturally occurring, experimentally proven p53 sites is essential in understanding the complete p53 network. We used a molecular information theory approac...

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Detalles Bibliográficos
Autores principales: Lyakhov, Ilya G., Krishnamachari, Annangarachari, Schneider, Thomas D.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2441790/
https://www.ncbi.nlm.nih.gov/pubmed/18495754
http://dx.doi.org/10.1093/nar/gkn189
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author Lyakhov, Ilya G.
Krishnamachari, Annangarachari
Schneider, Thomas D.
author_facet Lyakhov, Ilya G.
Krishnamachari, Annangarachari
Schneider, Thomas D.
author_sort Lyakhov, Ilya G.
collection PubMed
description An accurate method for locating genes under tumor suppressor p53 control that is based on a well-established mathematical theory and built using naturally occurring, experimentally proven p53 sites is essential in understanding the complete p53 network. We used a molecular information theory approach to create a flexible model for p53 binding. By searching around transcription start sites in human chromosomes 1 and 2, we predicted 16 novel p53 binding sites and experimentally demonstrated that 15 of the 16 (94%) sites were bound by p53. Some were also bound by the related proteins p63 and p73. Thirteen of the adjacent genes were controlled by at least one of the proteins. Eleven of the 16 sites (69%) had not been identified previously. This molecular information theory approach can be extended to any genetic system to predict new sites for DNA-binding proteins.
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spelling pubmed-24417902008-07-02 Discovery of novel tumor suppressor p53 response elements using information theory Lyakhov, Ilya G. Krishnamachari, Annangarachari Schneider, Thomas D. Nucleic Acids Res Molecular Biology An accurate method for locating genes under tumor suppressor p53 control that is based on a well-established mathematical theory and built using naturally occurring, experimentally proven p53 sites is essential in understanding the complete p53 network. We used a molecular information theory approach to create a flexible model for p53 binding. By searching around transcription start sites in human chromosomes 1 and 2, we predicted 16 novel p53 binding sites and experimentally demonstrated that 15 of the 16 (94%) sites were bound by p53. Some were also bound by the related proteins p63 and p73. Thirteen of the adjacent genes were controlled by at least one of the proteins. Eleven of the 16 sites (69%) had not been identified previously. This molecular information theory approach can be extended to any genetic system to predict new sites for DNA-binding proteins. Oxford University Press 2008-06 2008-05-21 /pmc/articles/PMC2441790/ /pubmed/18495754 http://dx.doi.org/10.1093/nar/gkn189 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Molecular Biology
Lyakhov, Ilya G.
Krishnamachari, Annangarachari
Schneider, Thomas D.
Discovery of novel tumor suppressor p53 response elements using information theory
title Discovery of novel tumor suppressor p53 response elements using information theory
title_full Discovery of novel tumor suppressor p53 response elements using information theory
title_fullStr Discovery of novel tumor suppressor p53 response elements using information theory
title_full_unstemmed Discovery of novel tumor suppressor p53 response elements using information theory
title_short Discovery of novel tumor suppressor p53 response elements using information theory
title_sort discovery of novel tumor suppressor p53 response elements using information theory
topic Molecular Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2441790/
https://www.ncbi.nlm.nih.gov/pubmed/18495754
http://dx.doi.org/10.1093/nar/gkn189
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