title: Binding loci of RelA-containing nuclear factor-kappaB dimers in promoter regions of PHM1-31 myometrial smooth muscle cells.
abstract: Human parturition is associated with many pro-inflammatory mediators which are regulated by the nuclear factor-kappaB (NF-κB) family of transcription factors. In the present study, we employed a ChIP-on-chip approach to define genomic loci within chromatin of PHM1-31 myometrial cells that were occupied by RelA-containing NF-κB dimers in response to a TNF stimulation of 1 h. In TNF-stimulated PHM1-31 cells, anti-RelA serum enriched 13 300 chromatin regions; importantly, 11 110 regions were also enriched by anti-RelA antibodies in the absence of TNF. DNA sequences in these regions, from both unstimulated or TNF-stimulated PHM1-31 cultures, were associated with genic regions including IκBα, COX-2, IL6RN, Jun and KCNMB3. TNF-induced binding events at a consensus κB site numbered 1667; these were represented by 112 different instances of the consensus κB motif. Of the 1667 consensus κB motif occurrences, 770 (46.2%) were identified within intronic regions. In unstimulated PHM1-31 cells, anti-RelA-serum-enriched regions were associated with sequences corresponding to open reading frames of ion channel subunit genes including CACNB3 and KCNB1. Moreover, in unstimulated cells, the consensus κB site was identified 2116 times, being defined by 103 different sequence instances of this motif. Of these 2116 consensus κB motifs, 1089 (51.5%) were identified within intronic regions. Parallel expression array analyses in PHM1-31 cultures demonstrated that TNF stimulated a >2-fold induction in 51 genes and a fold repression of >1.5 in 18 others. We identified 14 anti-RelA-serum-enriched genomic regions that correlated with 17 TNF-inducible genes, such as COX2, Egr-1, Jun, IκBα and IL6, as well as five regions associated with TNF-mediated gene repression, including Col1A2.
authors.affiliation: Academic Unit of Reproductive and Developmental Medicine, Department of Human Metabolism, University of Sheffield, Level 4, Jessop Wing, Tree Root Walk, Sheffield S10 2SF, UK Present address: Academic Unit of Clinical Oncology, University of Sheffield, Medical School, Beech Hill Road, Sheffield S10 2RX, UK.
authors.forename: Victoria J
authors.initials: VJ
authors.lastname: Cookson
authors.affiliation: Academic Unit of Reproductive and Developmental Medicine, Department of Human Metabolism, University of Sheffield, Level 4, Jessop Wing, Tree Root Walk, Sheffield S10 2SF, UK.
authors.forename: Sarah L
authors.initials: SL
authors.lastname: Waite
authors.affiliation: Sheffield Institute for Translational Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK.
authors.forename: Paul R
authors.initials: PR
authors.lastname: Heath
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Hurd
authors.affiliation: Department of Obstetrics and Gynaecology, Sheffield Teaching Hospitals NHS Foundation Trust, Level 4, Jessop Wing, Tree Root Walk, Sheffield S10 2SF, UK.
authors.forename: Saurabh V
authors.initials: SV
authors.lastname: Gandhi
authors.affiliation: Academic Unit of Reproductive and Developmental Medicine, Department of Human Metabolism, University of Sheffield, Level 4, Jessop Wing, Tree Root Walk, Sheffield S10 2SF, UK n.r.chapman@sheffield.ac.uk.
authors.forename: Neil R
authors.initials: NR
authors.lastname: Chapman
mesh_terms: D015220:Calcium Channels / Q000235:genetics / Q000378:metabolism; D005260:Female; D006801:Humans; D032389:Myocytes, Smooth Muscle / Q000187:drug effects / Q000378:metabolism*; D009215:Myometrium / Q000166:cytology*; D016328:NF-kappa B / Q000235:genetics / Q000378:metabolism*; D011247:Pregnancy; D011401:Promoter Regions, Genetic / Q000235:genetics*; D055503:Protein Multimerization; D051669:Shab Potassium Channels / Q000235:genetics / Q000378:metabolism; D051996:Transcription Factor RelA / Q000235:genetics / Q000378:metabolism*; D015533:Transcriptional Activation / Q000187:drug effects; D014409:Tumor Necrosis Factor-alpha / Q000494:pharmacology
chemical_list: C096073:CACNB3 protein, human; D015220:Calcium Channels; C496988:KCNB1 protein, human; D016328:NF-kappa B; D051669:Shab Potassium Channels; D051996:Transcription Factor RelA; D014409:Tumor Necrosis Factor-alpha
keywords: NF-kappaB; chromatin; labour; microarray; preterm birth