Functional evolution of the p53 regulatory network through its target response elements

Proceedings of the National Academy of Sciences of the United States of America
Anil G JeggaMichael A Resnick

Abstract

Transcriptional network evolution is central to the development of complex biological systems. Networks can evolve through variation of master regulators and/or by changes in regulation of genes within networks. To gain insight into meaningful evolutionary differences in large networks, it is essential to address the functional consequences of sequence differences in response elements (REs) targeted by transcription factors. Using a combination of custom bioinformatics and multispecies alignment of promoter regions, we investigated the functional evolution of REs in terms of responsiveness to the sequence-specific transcription factor p53, a tumor suppressor and master regulator of stress responses. We identified REs orthologous to known p53 targets in human and rodent cells or alternatively REs related to the established p53 consensus. The orthologous REs were assigned p53 transactivation capabilities based on rules determined from model systems, and a functional heat map was developed to visually summarize conservation of sequence and relative level of responsiveness to p53 for 47 REs in 14 species. Individual REs exhibited marked differences in transactivation potentials and widespread evolutionary turnover. Functional diffe...Continue Reading

References

Jun 1, 1995·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Y Sanchez, S J Elledge
Jan 1, 1996·Nucleic Acids Research·E WingenderR Knüppel
Apr 25, 1996·Biochemical and Biophysical Research Communications·S J SchererS Dooley
Apr 10, 1997·Nature·M Ptashne, A Gann
Dec 23, 1998·Proceedings of the National Academy of Sciences of the United States of America·C S ShashikantF H Ruddle
Jan 16, 1999·Molecular and Cellular Biology·C J Di ComoC Prives
Oct 21, 2000·Genes & Development·B Lemon, R Tjian
Jan 5, 2002·Proceedings of the National Academy of Sciences of the United States of America·M D Kaeser, R D Iggo
Jan 31, 2002·Trends in Genetics : TIG·Annie YangFrank McKeon
Apr 2, 2002·Neoplasia : an International Journal for Oncology Research·Kensuke OchiHirofumi Arakawa
Apr 25, 2002·Molecular and Cellular Biology·Thomas Tan, Gilbert Chu
Jun 26, 2002·Molecular Biology and Evolution·Emmanouil T Dermitzakis, Andrew G Clark
Sep 21, 2002·Proceedings of the National Academy of Sciences of the United States of America·Shanthi Adimoolam, James M Ford
Jan 10, 2003·Nucleic Acids Research·D KarolchikUNKNOWN University of California Santa Cruz
Aug 12, 2003·Proceedings of the National Academy of Sciences of the United States of America·Michael A Resnick, Alberto Inga
Aug 29, 2003·Development·Ilya Ruvinsky, Gary Ruvkun
Dec 4, 2003·Mutation Research·Philip C HanawaltDaniel R Lloyd
Apr 3, 2004·Genome Research·Mathieu BlanchetteWebb Miller
Aug 11, 2004·Proceedings of the National Academy of Sciences of the United States of America·Osnat Ashur-FabianGideon Rechavi
Nov 10, 2004·PLoS Biology·Audrey P GaschMichael B Eisen
Mar 11, 2005·PLoS Biology·Michael Z LudwigMartin Kreitman
Apr 22, 2005·Proceedings of the National Academy of Sciences of the United States of America·Daniel J TomsoMichael A Resnick
Jul 1, 2005·Molecular and Cellular Biology·Motonobu OsadaDavid Sidransky
Jan 25, 2006·Proceedings of the National Academy of Sciences of the United States of America·Daniel MenendezGilbert Schönfelder
Aug 7, 2007·PLoS Genetics·Monica M HorvathDouglas A Bell

❮ Previous
Next ❯

Citations

Jan 1, 1979·Journal of Immunological Methods·S MihaescuV Gheţie
Sep 25, 2009·European Journal of Cancer : Official Journal for European Organization for Research and Treatment of Cancer (EORTC) [and] European Association for Cancer Research (EACR)·Yosef Buganim, Varda Rotter
Sep 20, 2008·Cancer Gene Therapy·M OlivierP Hainaut
Sep 25, 2009·Nature Reviews. Cancer·Daniel MenendezMichael A Resnick
Jan 19, 2010·Proceedings of the National Academy of Sciences of the United States of America·Daniel MenendezMichael A Resnick
Apr 5, 2012·Proceedings of the National Academy of Sciences of the United States of America·Abdul S EthayathullaHector Viadiu
Nov 15, 2012·Genes & Cancer·Ian M Love, Steven R Grossman
Jul 16, 2009·BMC Bioinformatics·Sivakumar Gowrisankar, Anil G Jegga
Aug 21, 2008·PLoS Genetics·Jennifer J JordanMichael A Resnick
Apr 13, 2011·PLoS Genetics·Daniel MenendezMichael A Resnick
Dec 4, 2013·Proceedings of the National Academy of Sciences of the United States of America·Yang ZhaoJi-Zeng Du
Aug 31, 2014·Clinica Chimica Acta; International Journal of Clinical Chemistry·Chuck C-K Chao
Jan 23, 2016·Cellular and Molecular Life Sciences : CMLS·Sonja Matt, Thomas G Hofmann
Jul 21, 2015·Tumour Biology : the Journal of the International Society for Oncodevelopmental Biology and Medicine·K Rekha DeviKanwar Narain
Dec 23, 2008·Trends in Genetics : TIG·Tomasz ZemojtelMartin Vingron
Sep 25, 2008·Biochemical Pharmacology·Ella KimWolfgang Deppert
Apr 2, 2016·Nucleic Acids Research·Sinéad KearnsAndrei L Okorokov
Jun 12, 2012·Cell·Shu XiaoSheng Zhong
Nov 22, 2013·BMC Cancer·Alessandra BisioYari Ciribilli
Sep 2, 2016·Scientific Reports·Barbara MandrianiLucia Micale
Sep 30, 2016·FEMS Yeast Research·Vasundhara SharmaAlberto Inga
Mar 5, 2019·Nucleic Acids Research·Lucia HaronikovaRobin Fåhraeus
Feb 13, 2018·Nature Biotechnology·Antonio CasiniAnna Cereseto
May 23, 2018·Journal of Neuropathology and Experimental Neurology·Lee J Martin, Qing Chang
Sep 15, 2019·BMC Cancer·Konstantinos Karakostis, Robin Fåhraeus
Aug 17, 2020·Nucleic Acids Research·Morgan A SammonsMartin Fischer

❮ Previous
Next ❯

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