title: Role of lysine methylation of NF-κB in differential gene regulation.
abstract: Lysine methylation of the p65 subunit of nuclear factor κB (NF-κB) on K218 and K221 together or K37 alone strongly enhances gene expression in response to cytokines. We analyzed the effects of K-to-Q mutations in the REL homology domain of p65 on the response to IL-1β in 293 cells with low levels of p65. The K218/221Q mutation greatly reduced the expression of 39 of 82 genes, whereas the K37Q mutation reduced the expression of 23 different genes. Enhanced expression of the lysine demethylase FBXL11, which catalyzes the demethylation of K218 and K221 specifically, inhibited the expression of most of the genes that were inhibited by the DKQ mutation. CHIP-Seq analysis showed that the K218/221Q mutation greatly reduces the affinity of p65 for many promoters and that the K37Q mutation does not. Structural modeling showed that the newly introduced methyl groups of K218 and K221 interact directly with DNA to increase the affinity of p65 for specific κB sites. Thus, the K218/221Q and K37Q mutations have dramatically different effects because methylations of these residues affect different genes by distinct mechanisms.
authors.affiliation: Department of Molecular Genetics, Cleveland Clinic, Cleveland, OH 44195, USA. lut@iupui.edu
authors.forename: Tao
authors.initials: T
authors.lastname: Lu
authors.forename: Maojing
authors.initials: M
authors.lastname: Yang
authors.forename: De-Bin
authors.initials: DB
authors.lastname: Huang
authors.forename: Han
authors.initials: H
authors.lastname: Wei
authors.forename: Gulcin H
authors.initials: GH
authors.lastname: Ozer
authors.forename: Gourisankar
authors.initials: G
authors.lastname: Ghosh
authors.forename: George R
authors.initials: GR
authors.lastname: Stark
mesh_terms: D015153:Blotting, Western; D047369:Chromatin Immunoprecipitation; D016207:Cytokines / Q000494:pharmacology; D017931:DNA Primers / Q000235:genetics; D044783:F-Box Proteins / Q000378:metabolism*; D005786:Gene Expression Regulation / Q000187:drug effects / Q000276:immunology*; D057809:HEK293 Cells; D006801:Humans; D053583:Interleukin-1beta / Q000494:pharmacology; D056484:Jumonji Domain-Containing Histone Demethylases; D008239:Lysine / Q000378:metabolism*; D008745:Methylation; D046228:Microarray Analysis; D016297:Mutagenesis, Site-Directed; D009154:Mutation / Q000235:genetics; D016328:NF-kappa B / Q000235:genetics / Q000378:metabolism*; D010089:Oxidoreductases, N-Demethylating / Q000378:metabolism*; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
chemical_list: D016207:Cytokines; D017931:DNA Primers; D044783:F-Box Proteins; D053583:Interleukin-1beta; D016328:NF-kappa B; D056484:Jumonji Domain-Containing Histone Demethylases; C534524:KDM2A protein, human; D010089:Oxidoreductases, N-Demethylating; D008239:Lysine
keywords: histone modifying enzyme; protein methylation
references.citation: EMBO J. 2009 Apr 22;28(8):1055-66
references.pmid: 19262565
references.citation: Nature. 2007 Sep 6;449(7158):105-8
references.pmid: 17805299
references.citation: Cell Death Differ. 2006 May;13(5):759-72
references.pmid: 16410803
references.citation: Nature. 2006 Nov 30;444(7119):629-32
references.pmid: 17108971
references.citation: J Biol Chem. 2005 Jan 7;280(1):244-52
references.pmid: 15516339
references.citation: Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):18972-7
references.pmid: 19864627
references.citation: Mol Cell Biol. 2007 Oct;27(19):6756-69
references.pmid: 17646389
references.citation: Nature. 1998 Jan 22;391(6665):410-3
references.pmid: 9450761
references.citation: Proc Natl Acad Sci U S A. 2009 Oct 27;106(43):18207-12
references.pmid: 19820169
references.citation: Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21499-504
references.pmid: 21098664
references.citation: Cell. 2008 Feb 8;132(3):344-62
references.pmid: 18267068
references.citation: Cell Res. 2011 Mar;21(3):375-80
references.pmid: 21151202
references.citation: Oncogene. 2006 Oct 30;25(51):6717-30
references.pmid: 17072324
references.citation: Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16339-44
references.pmid: 19805303
references.citation: Nat Immunol. 2011 Jan;12(1):29-36
references.pmid: 21131967
references.citation: Nat Rev Drug Discov. 2004 Jan;3(1):17-26
references.pmid: 14708018
references.citation: Nat Commun. 2013;4:2062
references.pmid: 23797602
references.citation: Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):46-51
references.pmid: 20080798