RNAPol-ChIP: a novel application of chromatin immunoprecipitation to the analysis of real-time gene transcription

Nucleic Acids Research
Juan SandovalGerardo López-Rodas

Abstract

We describe a procedure, RNAPol-ChIP, to measure actual transcriptional rate. It consists of the detection, by chromatin immunoprecipitation (ChIP), of RNA polymerase II within the coding region of genes. To do this, the DNA immunoprecipitated with polymerase antibodies is analysed by PCR, using an amplicon well within the coding region of the desired genes to avoid interferences with polymerase paused at the promoter. To validate RNAPol-ChIP, we compare our results to those obtained by classical methods in several genes induced during either liver regeneration or acute pancreatitis. When short half-life mRNA genes are studied (e.g. c-fos and egr1), RNAPol-ChIP gives results similar to those of other procedures. However, in genes whose mRNA is more stable (e.g. the hemopexin, hpx, gene) RNAPol-ChIP informs on real-time transcription with results comparable to those of methods such as nuclear run-on or run-off, which require the isolation of highly purified nuclei. Moreover, RNAPol-ChIP advantageously compares with methods based on the analysis of steady-state mRNA (northern blot or RT-PCR). Additional advantages of RNAPol-ChIP, such as the possibility of combining it with classical ChIP analysis to study transcription-associate...Continue Reading

References

Aug 1, 1992·Trends in Genetics : TIG·J H WeisC T Wittwer
Feb 25, 1987·Nucleic Acids Research·H J RahmsdorfP Herrlich
May 1, 1994·Analytical Biochemistry·D EickL J Strobl
Jul 17, 1998·Methods in Molecular Biology·R A Srivastava, G Schonfeld
Mar 23, 2000·Journal of Hepatology·N Fausto
Apr 3, 2001·Nature Reviews. Molecular Cell Biology·C J WiluszS W Peltz
Jun 11, 2002·Methods : a Companion to Methods in Enzymology·Julie Wells, Peggy J Farnham
Aug 1, 2002·Proceedings of the National Academy of Sciences of the United States of America·Jinshui FanMyriam Gorospe
Aug 15, 2002·Proceedings of the National Academy of Sciences of the United States of America·Andrew I SuPeter G Schultz
Sep 27, 2003·European Journal of Biochemistry·Benoît Palancade, Olivier Bensaude
Oct 3, 2003·Journal of the American College of Surgeons·Leonidas G KoniarisTeresa A Zimmers

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Citations

Apr 21, 2009·Nature Genetics·UNKNOWN FANTOM ConsortiumYoshihide Hayashizaki
Sep 9, 2010·Proceedings of the National Academy of Sciences of the United States of America·Joseph J AbrajanoMark F Mehler
Feb 11, 2010·The Journal of Biological Chemistry·Ana Fernández-AlvarezMarta Casado
Jan 18, 2007·The Journal of Experimental Medicine·Diana RonaiMatthew D Scharff
Sep 2, 2010·The Journal of Experimental Medicine·Tim SmallieLynn M Williams
Mar 17, 2006·Nucleic Acids Research·Jinshui FanMyriam Gorospe
Aug 24, 2013·Nucleic Acids Research·Hsiang-Ying ChenPauline H Yen
Nov 17, 2010·Genes & Development·Xuying WangJoseph Heitman
Aug 15, 2012·Molecular and Cellular Biology·Mónica Martínez-MorenoAntonia Ávila-Flores
Dec 8, 2007·The Journal of Clinical Investigation·Laure A Moutouh-de ParsevalKyle Chan
Oct 10, 2013·Biochimica Et Biophysica Acta·Ana MiguelJosé E Pérez-Ortín
Oct 16, 2004·Proceedings of the National Academy of Sciences of the United States of America·Ziqiang LiMatthew D Scharff
Jan 1, 2011·Genetics Research International·Maria Micaela Molina-NavarroSusana Rodriguez-Navarro
May 13, 2009·Cellular and Molecular Life Sciences : CMLS·M Ferrés-MasóE Folch-Puy
Feb 5, 2010·Cellular and Molecular Life Sciences : CMLS·J SandovalG López-Rodas
Jun 29, 2010·Cellular and Molecular Life Sciences : CMLS·Gema TurLuis Franco
Dec 20, 2011·Cellular Physiology and Biochemistry : International Journal of Experimental Cellular Physiology, Biochemistry, and Pharmacology·Luis TorresElena R García-Trevijano
Apr 5, 2007·Nature Protocols·Joel D NelsonKarol Bomsztyk
Jul 23, 2008·The Journal of Cell Biology·Kai-Fu TangCai-Xia He
Dec 20, 2011·Free Radical Biology & Medicine·Javier EscobarJuan Sastre
Nov 17, 2009·Biochimica Et Biophysica Acta·Kai-Fu TangYong-Hua Li
Mar 18, 2009·Free Radical Biology & Medicine·Luis TorresElena R García-Trevijano

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