Profiling RNA Polymerase II Using the Fast Chromatin Immunoprecipitation Method

Methods in Molecular Biology

Volumn 703, Issue , 2011, Pages 219-234

  Nelson, Joel ^a   Denisenko, Oleg ^b   Bomsztyk, Karol ^a,c  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

ChIP chip; Chromatin immunoprecipitation; RNA polymerase II; tissue ChIP; transcription

Indexed keywords

RNA POLYMERASE II;

ARTICLE; CHROMATIN IMMUNOPRECIPITATION; GENE EXPRESSION PROFILING; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; METHODOLOGY;

CHROMATIN IMMUNOPRECIPITATION; GENE EXPRESSION PROFILING; RNA POLYMERASE II; TRANSCRIPTION, GENETIC;

MLCS; MLOWN;

EID: 79952587706     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-59745-248-9_15     Document Type: Chapter

References (22)

1. Gariglio, P., Bellard, M., Chambon, P. (1981) Clustering of RNA polymerase-B molecules in the 5’ moiety of the adult beta-globin gene of hen erythrocytes. Nucleic Acids Res 9, 2589–2598.
2. Srivastava, R. A., Schonfeld, G. (1998) Measurements of rate of transcription in isolated nuclei by nuclear “run-off” assay. Methods Mol Biol 86, 201–207.
3. Kuo, M. H., Allis, C. D. (1999) In vivo cross-linking and immunoprecipitation for studying dynamic Protein:DNA associations in a chromatin environment. Methods 19, 425–433.
4. Orlando, V., Strutt, H., Paro, R. (1997) Analysis of chromatin structure by in vivo formaldehyde cross-linking. Methods 11, 205–214.
5. Sandoval, J., Rodriguez, J. L., Tur, G., Serviddio, G., Pereda, J., Boukaba, A., Sas-tre, J., Torres, L., Franco, L., Lopez-Rodas, G. (2004) RNAPol-ChIP: a novel application of chromatin immunoprecipitation to the analysis of real-time gene transcription. Nucleic Acids Res 32, e88.
6. Core, L. J., Lis, J. T. (2008) Transcription regulation through promoter-proximal pausing of RNA polymerase II. Science 319, 1791–1792.
7. Saunders, A., Core, L. J., Lis, J. T. (2006) Breaking barriers to transcription elongation. Nat Rev Mol Cell Biol 7, 557–567.
8. Muse, G. W., Gilchrist, D. A., Nechaev, S., Shah, R., Parker, J. S., Grissom, S. F., Zeitlinger, J., Adelman, K. (2007) RNA polymerase is poised for activation across the genome. Nat Genet 39, 1507–1511.
9. Barski, A., Cuddapah, S., Cui, K., Roh, T. Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., Zhao, K. (2007) High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837.
10. Kouzarides, T. (2007) Chromatin modifications and their function. Cell 128, 693–705.
11. Shilatifard, A. (2004) Transcriptional elongation control by RNA polymerase II: a new frontier. Biochim Biophys Acta 1677, 79–86.
12. Solomon, M. J., Varshavsky, A. (1985) Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures. Proc Natl Acad Sci USA 82, 6470–6474.
13. Thorne, A. W., Myers, F. A., Hebbes, T. R. (2004) Native chromatin immunoprecipitation. Methods Mol Biol 287, 21–44.
14. Solomon, M. J., Larsen, P. L., Varshavsky, A. (1988) Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell 53, 937–947.
15. Nelson, J. D., Denisenko, O., Sova, P., Bomsztyk, K. (2006) Fast chromatin immunoprecipitation assay. Nucleic Acids Res 34, e2.
16. Huebert, D. J., Kamal, M., O‘Donovan, A., Bernstein, B. E. (2006) Genome-wide analysis of histone modifications by ChIP-on-chip. Methods 40, 365–369.
17. Johnson, D. S., Mortazavi, A., Myers, R. M., Wold, B. (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497–1502.
18. Chen, R., Weng, L., Sizto, N. C., Osorio, B., Hsu, C. J., Rodgers, R., Litman, D. J. (1984) Ultrasound-accelerated immunoassay, as exemplified by enzyme immunoas- say of choriogonadotropin. Clin Chem 30, 1446–1451.
19. Nelson, J. D., Flanagin, S., Kawata, Y., Denisenko, O., Bomsztyk, K. (2008) Transcription of laminin {gamma}1 chain gene in rat mesangial cells: constitutive and inducible RNA polymerase II recruitment and chromatin states. Am J Physiol Renal Physiol 294, F525–F533.
20. Zager, R. A., Johnson, A. C., Naito, M., Bomsztyk, K. (2008) Maleate nephrotoxic-ity: mechanisms of injury and correlates with ischemic/hypoxic tubular cell death. Am J Physiol Renal Physiol 294, F187–F197.
21. Denisenko, O., Bomsztyk, K. (2008) Epistatic interaction between the K-homology domain protein HEK2 and SIR1 at HMR and telomeres in yeast. J Mol Biol 375, 1178–1187.
22. Glover-Cutter, K., et al. (2008) RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes. Nat Struct Mol Biol 15(1), 71.