Characterization of genome-wide binding of NF-κB in TNFα-stimulated HeLa cells

Gene

Volumn 526, Issue 2, 2013, Pages 142-149

  Xing, Yujun ^a   Yang, Yang ^a   Zhou, Fei ^a   Wang, Jinke ^a  

^a SOUTHEAST UNIVERSITY   (China)

Author keywords

Genome wide binding; NF B

Indexed keywords

IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; TUMOR NECROSIS FACTOR ALPHA;

ARTICLE; BINDING SITE; CHROMOSOME 2; CHROMOSOME 5; CONTROLLED STUDY; DNA MICROARRAY; DOWN REGULATION; FEMALE; GENE CONTROL; GENE EXPRESSION; GENE LOCATION; GENE TARGETING; GENETIC TRAIT; GENETIC TRANSCRIPTION; HELA CELL; HUMAN; HUMAN CELL; HUMAN GENOME; IN VITRO STUDY; INTRON; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION; UPREGULATION; X CHROMOSOME;

4-(2-HYDROXYETHYL) PIPERAZINE-1-ETHANESULFONIC ACID; CHIP; CHIP IN COMBINATION WITH DNA MICROARRAY; CHIP IN COMBINATION WITH PAIRED END TAG; CHIP IN COMBINATION WITH POLYMERASE CHAIN REACTION; CHIP IN COMBINATION WITH SEQUENCING; CHIP-CHIP; CHIP-PCR; CHIP-PET; CHIP-SEQ; CHROMATIN IMMUNOPRECIPITATION; DBP; DIRECT TARGET GENES; DITHIOTHREITOL; DMEM; DNA BINDING PROFILE; DTG; DTT; DULBECCO'S MODIFIED EAGLE MEDIUM; EDTA; ELECTROPHORESIS MOBILITY SHIFT ASSAY IN COMBINATION WITH SEQUENCING; EMSA-SEQ; ETHYLENEDIAMINETETRAACETIC ACID; FBS; FC; FE; FETAL BOVINE SERUM; FOLD CHANGE; FOLD ENRICHMENT; GENOME-WIDE BINDING; HC-PEAK; HEPES; HIGH-CONFIDENCE PEAK; LIPOPOLYSACCHARIDE; LPS; NF-ΚB; NUCLEAR FACTOR KAPPA B; PCR; PHENYLMETHYLSULFONYL FLUORIDE; PIC; PMSF; POLYMERASE CHAIN REACTION; PROTEASE INHIBITOR COCKTAIL; SIRNA; SMALL INTERFERING RNA; TES; TNFΑ; TRANSCRIPTION END SITE; TRANSCRIPTION START SITE; TSS; TUMOR NECROSIS FACTOR-ALPHA;

BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN; DNA; GENE EXPRESSION REGULATION; GENOME, HUMAN; HELA CELLS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; NF-KAPPA B; NUCLEOTIDE MOTIFS; PROTEIN BINDING; TRANSCRIPTION INITIATION SITE; TUMOR NECROSIS FACTOR-ALPHA;

EID: 84880740252     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2013.05.001     Document Type: Article

References (36)

1. Antonaki A., Demetriades C., Polyzos A., Banos A., Vatsellas G., Lavigne M.D., et al. Genomic analysis reveals a novel nuclear factor-kappaB (NF-kappaB)-binding site in Alu-repetitive elements. J. Biol. Chem. 2011, 286:38768-38782.
2. Beg A.A., Baldwin A.S. The I kappa B proteins: multifunctional regulators of Rel/NF-kappa B transcription factors. Genes Dev. 1993, 7:2064-2070.
3. Euskirchen G.M., Rozowsky J.S., Wei C.L., Lee W.H., Zhang Z.D., Hartman S., et al. Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res. 2007, 17:898-909.
4. Ghosh S., May M.J., Kopp E.B. NF-kappa B and Rel proteins: evolutionarily conserved mediators of immune responses. Annu. Rev. Immunol. 1998, 16:225-260.
5. Gilbert N., Boyle S., Fiegler H., Woodfine K., Carter N.P., Bickmore W.A. Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers. Cell 2004, 118:555-566.
6. Giorgetti L., Siggers T., Tiana G., Caprara G., Notarbartolo S., Corona T., et al. Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs. Mol. Cell 2010, 37:418-428.
7. Karin M. The beginning of the end: IkappaB kinase (IKK) and NF-kappaB activation. J. Biol. Chem. 1999, 274:27339-27342.
8. Kasowski M., Grubert F., Heffelfinger C., Hariharan M., Asabere A., Waszak S.M., et al. Variation in transcription factor binding among humans. Science 2010, 328:232-235.
9. Lee S.T., Li Z., Wu Z., Aau M., Guan P., Karuturi R.K., et al. Context-specific regulation of NF-kappaB target gene expression by EZH2 in breast cancers. Mol. Cell 2011, 43:798-810.
10. Lim C.A., Yao F., Wong J.J., George J., Xu H., Chiu K.P., et al. Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation. Mol. Cell 2007, 27:622-635.
11. Linnell J., Mott R., Field S., Kwiatkowski D.P., Ragoussis J., Udalova I.A. Quantitative high-throughput analysis of transcription factor binding specificities. Nucleic Acids Res. 2004, 32:e44.
12. Martone R., Euskirchen G., Bertone P., Hartman S., Royce T.E., Luscombe N.M., et al. Distribution of NF-kappaB-binding sites across human chromosome 22. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:12247-12252.
13. Matys V., Fricke E., Geffers R., Gossling E., Haubrock M., Hehl R., et al. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 2003, 31:374-378.
14. Natoli G. Control of NF-kappaB-dependent transcriptional responses by chromatin organization. Cold Spring Harb. Perspect. Biol. 2009, 1:a000224.
15. Natoli G., Saccani S., Bosisio D., Marazzi I. Interactions of NF-kappaB with chromatin: the art of being at the right place at the right time. Nat. Immunol. 2005, 6:439-445.
16. Natoli G., Saccani S., Bosisio D., Marazzi I. Interactions of NF-kappa B with chromatin: the art of being at the right place at the right time. Nat. Immunol. 2005, 6:439-445.
17. Nijnik A., Mott R., Kwiatkowski D.P., Udalova I.A. Comparing the fine specificity of DNA binding by NF-kappaB p50 and p52 using principal coordinates analysis. Nucleic Acids Res. 2003, 31:1497-1501.
18. Ning Z., Cox A.J., Mullikin J.C. SSAHA: a fast search method for large DNA databases. Genome Res. 2001, 11:1725-1729.
19. Nowak D.E., Tian B., Brasier A.R. Two-step cross-linking method for identification of NF-kappaB gene network by chromatin immunoprecipitation. Biotechniques 2005, 39:715-725.
20. Pahl H.L. Activators and target genes of Rel/NF-kappaB transcription factors. Oncogene 1999, 18:6853-6866.
21. Ponts N., Harris E.Y., Lonardi S., Le Roch K.G. Nucleosome occupancy at transcription start sites in the human malaria parasite: a hard-wired evolution of virulence?. Infect. Genet. Evol. 2011, 11:716-724.
22. Rozowsky J., Euskirchen G., Auerbach R.K., Zhang Z.D., Gibson T., Bjornson R., et al. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat. Biotechnol. 2009, 27:66-75.
23. Saccani S., Pantano S., Natoli G. Two waves of nuclear factor kappaB recruitment to target promoters. J. Exp. Med. 2001, 193:1351-1359.
24. Schmitz M.L., Baeuerle P.A. The p65 subunit is responsible for the strong transcription activating potential of NF-kappa B. EMBO J. 1991, 10:3805-3817.
25. Schreiber J., Jenner R.G., Murray H.L., Gerber G.K., Gifford D.K., Young R.A. Coordinated binding of NF-kappaB family members in the response of human cells to lipopolysaccharide. Proc. Natl. Acad. Sci. U.S.A. 2006, 103:5899-5904.
26. Sen R. Control of B lymphocyte apoptosis by the transcription factor NF-kappaB. Immunity 2006, 25:871-883.
27. Sen R., Baltimore D. Multiple nuclear factors interact with the immunoglobulin enhancer sequences. Cell 1986, 46:705-716.
28. Sen R., Baltimore D. Inducibility of kappa immunoglobulin enhancer-binding protein Nf-kappa B by a posttranslational mechanism. Cell 1986, 47:921-928.
29. Sen R., Smale S.T. Selectivity of the NF-{kappa}B response. Cold Spring Harb. Perspect. Biol. 2010, 2:a000257.
30. Smale S.T. Hierarchies of NF-kappaB target-gene regulation. Nat. Immunol. 2011, 12:689-694.
31. Udalova I.A., Mott R., Field D., Kwiatkowski D. Quantitative prediction of NF-kappa B DNA-protein interactions. Proc. Natl. Acad. Sci. U.S.A. 2002, 99:8167-8172.
32. Vallabhapurapu S., Karin M. Regulation and function of NF-kappaB transcription factors in the immune system. Annu. Rev. Immunol. 2009, 27:693-733.
33. Wan F., Anderson D.E., Barnitz R.A., Snow A., Bidere N., Zheng L., et al. Ribosomal protein S3: a KH domain subunit in NF-kappaB complexes that mediates selective gene regulation. Cell 2007, 131:927-939.
34. Wang J.K., Li T.X., Bai Y.F., Lu Z.H. Evaluating the binding affinities of NF-kappaB p50 homodimer to the wild-type and single-nucleotide mutant Ig-kappaB sites by the unimolecular dsDNA microarray. Anal. Biochem. 2003, 316:192-201.
35. Wong D., Teixeira A., Oikonomopoulos S., Humburg P., Lone I.N., Saliba D., et al. Extensive characterization of NF-kappaB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits. Genome Biol. 2011, 12:R70.
36. Xing Y., Zhou F., Wang J. Subset of genes targeted by transcription factor NF-kappaB in TNFalpha-stimulated human HeLa cells. Funct. Integr. Genomics 2013, 13:143-154.