Comprehensive analysis of the palindromic motif TCTCGCGAGA: A regulatory element of the HNRNPK promoter

DNA Research

Volumn 17, Issue 4, 2010, Pages 245-260

  Mikula, Michal ^a   Gaj, Pawel ^b   Dzwonek, Karolina ^a   Rubel, Tymon ^a   Karczmarski, Jakub ^a   Paziewska, Agnieszka ^b   Dzwonek, Artur ^a   Bragoszewski, Piotr ^b   Dadlez, Michal ^c   Ostrowski, Jerzy ^a,b  

^a INSTITUTE OF ONCOLOGY   (Poland)

^b MEDICAL CENTER FOR POSTGRADUATE EDUCATION   (Poland)

^c INSTITUTE OF BIOCHEMISTRY AND BIOPHYSICS   (Poland)

Author keywords

chromatin immunoprecipitation; EMSA; HNRNPK promoter; mass spectrometry; palindromic motif

Indexed keywords

HETEROGENOUS NUCLEAR RIBONUCLEOPROTEIN K; LUCIFERASE; NICOTINAMIDE ADENINE DINUCLEOTIDE ADENOSINE DIPHOSPHATE RIBOSYLTRANSFERASE 1; NUCLEAR PROTEIN; TRANS ACTING FACTOR; UNCLASSIFIED DRUG;

ARTICLE; CHROMATIN IMMUNOPRECIPITATION; DNA BINDING MOTIF; DNA PROBE; GEL MOBILITY SHIFT ASSAY; GENE ACTIVITY; GENE EXPRESSION REGULATION; HETEROCHROMATIN; HOUSEKEEPING GENE; MASS SPECTROMETRY; NONHUMAN; NUCLEOSOME; NUCLEOTIDE SEQUENCE; PROMOTER REGION; PROTEIN DNA INTERACTION; REPORTER GENE;

CHROMATIN IMMUNOPRECIPITATION; DNA-BINDING PROTEINS; ELECTROPHORETIC MOBILITY SHIFT ASSAY; ENHANCER ELEMENTS, GENETIC; HELA CELLS; HUMANS; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; POLY(ADP-RIBOSE) POLYMERASES; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; RIBONUCLEOPROTEINS;

EID: 77955873057     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dsq016     Document Type: Article

References (45)

1. Bomsztyk, K.,Denisenko,O.and Ostrowski,J.2004, hnRNP K: one protein multiple processes, Bioessays, 26, 629-638
2. Habelhah, H., Shah, K., Huang, L., et al. 2001, ERK phos-phorylation drives cytoplasmic accumulation of hnRNP-K and inhibition of mRNA translation, Nat. Cell biol., 3, 325-330
3. Michelotti, E.F., Michelotti, G.A., Aronsohn, A.I. and Levens, D. 1996, Heterogeneous nuclear ribonucleopro-tein K is a transcription factor, Mol. Cell. Biol., 16, 2350-2360
4. Moumen, A., Masterson, P., O'Connor, M.J. and Jackson, S.P. 2005, hnRNP K: an HDM2 target and tran-scriptional coactivator of p53 in response to DNA damage, Cell, 123, 1065-1078
5. Carpenter, B., McKay, M., Dundas, S.R., Lawrie, L.C., Telfer, C. and Murray, G.I. 2006, Heterogeneous nuclear ribonucleoprotein K is over expressed, aberrantly localised and is associated with poor prognosis in colorectal cancer, Br. J. Cancer, 95, 921-927
6. Chen, L.C., Hsueh, C., Tsang, N.M., et al. 2008, Heterogeneous ribonucleoprotein k and thymidine phosphorylase are independent prognostic and therapeutic markers for nasopharyngeal carcinoma, Clin. Cancer Res., 14, 3807-3813
7. Hatakeyama, H., Kondo, T., Fujii, K., et al. 2006, Protein clusters associated with carcinogenesis, histological differentiation and nodal metastasis in esophageal cancer, Proteomics, 6, 6300-6316
8. Pino, I., Pio, R., Toledo, G., et al. 2003, Altered patterns of expression of members of the heterogeneous nuclear ribonucleoprotein (hnRNP) family in lung cancer, Lung Cancer, 41, 131-143
9. Roychoudhury, P. and Chaudhuri, K. 2007, Evidence for heterogeneous nuclear ribonucleoprotein K overexpression in oral squamous cell carcinoma, Br. J. Cancer, 97, 574-575 author reply 576.
10. de Hoog, C.L., Foster, L.J. and Mann, M. 2004, RNA and RNA binding proteins participate in early stages of cell spreading through spreading initiation centers, Cell, 117, 649-662
11. Inoue, A., Sawata, S.Y., Taira, K. and Wadhwa, R. 2007, Loss-of-function screening by randomized intracellular antibodies: identification of hnRNP-K as a potential target for metastasis, Proc. Natl. Acad. Sci. USA, 104, 8983-8988
12. Wyrwicz, L.S., Gaj, P., Hoffmann, M., Rychlewski, L. and Ostrowski, J. 2007, A common cis-element in promoters of protein synthesis and cell cycle genes, Acta Biochim. Pol., 54, 89-98.
13. Ostrowski, J., Sims, J.E., Sibley, C.H., et al. 1991, A serine/threonine kinase activity is closely associated with a 65-kDa phosphoprotein specifically recognized by the kappa B enhancer element, J. Biol. Chem., 266, 12722-12733
14. Bakun, M., Karczmarski, J., Poznanski, J., et al. 2009, An integrated LC-ESI-MS platform for quantitation of serum peptide ladders. Application for colon carcinoma study, Proteomics Clin. Appl., 3, 932-946
15. Benjamini, Y. and Hochberg, Y. 1995, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. Roy. Stat. Soc. Ser. B, 50, 289-300.
16. Mikula, M., Hanusek, K., Paziewska, A., et al. 2010, Halogenated imidazole derivatives block RNA polymer-ase II elongation along mitogen inducible genes, BMC Mol. Biol., 11, 4.
17. Flanagin, S., Nelson, J.D., Castner, D.G., Denisenko, O. and Bomsztyk, K. 2008, Microplate-based chromatin immunoprecipitation method, Matrix ChIP: a platform to study signaling of complex genomic events, Nucleic Acids Res., 36, e17.
18. Ostrowski, J., Woszczynski, M., Kowalczyk, P., Trzeciak, L., Hennig, E. and Bomsztyk, K. 2000, Treatment of mice with EGF and orthovanadate activates cytoplasmic and nuclear MAPK, p70S6k, and p90rsk in the liver, J. Hepatol., 32, 965-974
19. Rosenbloom, K.R., Dreszer, T.R., Pheasant, M., et al. 2010, ENCODE whole-genome data in the UCSC Genome Browser, Nucleic Acids Res., 38, D620-D625.
20. Elnitski, L., Jin, V.X., Farnham, P.J. and Jones, S.J. 2006, Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques, Genome Res., 16, 1455-1464
21. Guo, G., Bauer, S., Hecht, J., Schulz, M.H., Busche, A. and Robinson, P.N. 2008, A short ultraconserved sequence drives transcription from an alternate FBN1 promoter, Int. J. Biochem. Cell Biol., 40, 638-650
22. Kanaar, R., Hoeijmakers, J.H. and van Gent, D.C. 1998, Molecular mechanisms of DNA double strand break repair, Trends Cell Biol., 8, 483-489
23. Jiang, D., Jarrett, H.W. and Haskins, W.E. 2009, Methods for proteomic analysis of transcription factors, J. Chromatogr., 1216, 6881-6889
24. Hu, S., Xie, Z., Onishi, A., et al. 2009, Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling, Cell, 139, 610-622
25. Xie, Z., Hu, S., Blackshaw, S., Zhu, H. and Qian, J. 2010, hPDI: a database of experimental human protein-DNA interactions, Bioinformatics, 26, 287-289
26. Yamashita, D., Sano, Y., Adachi, Y., et al. 2007, hDREF regulates cell proliferation and expression of ribosomal protein genes, Mol. Cell. Biol., 27, 2003-2013
27. Kouzarides, T. 2007, Chromatin modifications and their function, Cell, 128, 693-705.
28. Li, B., Carey, M. and Workman, J.L. 2007, The role of chromatin during transcription, Cell, 128, 707-719
29. Mellor, J., Dudek, P. and Clynes, D. 2008, A glimpse into the epigenetic landscape of gene regulation, Curr. Opin. Genet. Dev., 18, 116-122
30. Kraus, W.L. 2008, Transcriptional control by PARP-1: chromatin modulation, enhancer-binding, coregula-tion, and insulation, Curr. Opin. Cell Biol., 20, 294-302.
31. Petesch, S.J. and Lis, J.T. 2008, Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci, Cell, 134, 74-84.
32. Hossain, M.B., Ji, P., Anish, R., Jacobson, R.H. and Takada, S. 2009, Poly(ADP-ribose) polymerase 1 interacts with nuclear respiratory factor 1 (NRF-1) and plays a role in NRF-1 transcriptional regulation, J. Biol. Chem., 284, 8621-8632
33. Ju, B.G., Lunyak, V.V., Perissi, V., et al. 2006, A topoisome-rase IIbeta-mediated dsDNA break required for regulated transcription, Science, 312, 1798-1802
34. Shi, L., Qiu, D., Zhao, G., et al. 2007, Dynamic binding of Ku80, Ku70 and NF90 to the IL-2 promoter in vivo in activated T-cells, Nucleic Acids Res., 35, 2302-2310
35. Potaman, V.N., Shlyakhtenko, L.S., Oussatcheva, E.A., Lyubchenko, Y.L. and Soldatenkov, V.A. 2005, Specific binding of poly(ADP-ribose) polymerase-1 to cruciform hairpins, J. Mol. Biol., 348, 609-615
36. Soldatenkov, V.A., Chasovskikh, S., Potaman, V.N., Trofimova, I., Smulson, M.E. and Dritschilo, A. 2002, Transcriptional repression by binding of poly(ADP-ribose) polymerase to promoter sequences, J. Biol. Chem., 277, 665-670
37. Kim, M.Y., Mauro, S., Gevry, N., Lis, J.T. and Kraus, W.L. 2004, NAD\+-dependent modulation of chromatin structure and transcription by nucleosome binding properties of PARP-1, Cell, 119, 803-814
38. Wacker, D.A., Ruhl, D.D., Balagamwala, E.H., Hope, K.M., Zhang, T. and Kraus, W.L. 2007, The DNA binding and catalytic domains of poly(ADP-ribose) polymerase 1 cooperate in the regulation of chromatin structure and transcription, Mol. Cell. Biol., 27, 7475-7485
39. Schones, D.E., Cui, K., Cuddapah, S., et al. 2008, Dynamic regulation of nucleosome positioning in the human genome, Cell, 132, 887-898
40. Zhang, Y., Shin, H., Song, J.S., Lei, Y. and Liu, X.S. 2008, Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq, BMC Genomics, 9, 537.
41. Wu, C. 1985, An exonuclease protection assay reveals heat-shock element and TATA box DNA-binding proteins in crude nuclear extracts, Nature, 317, 84-87
42. Johnson, D.S., Mortazavi, A., Myers, R.M. and Wold, B. 2007, Genome-wide mapping of in vivo protein-DNA interactions, Science, 316, 1497-1502
43. Valouev, A., Johnson, D.S., Sundquist, A., et al. 2008, Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data, Nat. Methods, 5, 829-834
44. Boyle, A.P., Davis, S., Shulha, H.P., et al. 2008, High-resolution mapping and characterization of open chro-matin across the genome, Cell, 132, 311-322
45. Barski, A., Cuddapah, S., Cui, K., et al. 2007, High-resolution profiling of histone methylations in the human genome, Cell, 129, 823-837