title: Genomic analysis reveals a novel nuclear factor-κB (NF-κB)-binding site in Alu-repetitive elements.
abstract: The transcription factor NF-κB is a critical regulator of immune responses. To determine how NF-κB builds transcriptional control networks, we need to obtain a topographic map of the factor bound to the genome and correlate it with global gene expression. We used a ChIP cloning technique and identified novel NF-κB target genes in response to virus infection. We discovered that most of the NF-κB-bound genomic sites deviate from the consensus and are located away from conventional promoter regions. Remarkably, we identified a novel abundant NF-κB-binding site residing in specialized Alu-repetitive elements having the potential for long range transcription regulation, thus suggesting that in addition to its known role, NF-κB has a primate-specific function and a role in human evolution. By combining these data with global gene expression profiling of virus-infected cells, we found that most of the sites bound by NF-κB in the human genome do not correlate with changes in gene expression of the nearby genes and they do not appear to function in the context of synthetic promoters. These results demonstrate that repetitive elements interspersed in the human genome function as common target sites for transcription factors and may play an important role in expanding the repertoire of binding sites to engage new genes into regulatory networks.
authors: Institute of Molecular Biology, Genetics and Biotechnology, Biomedical Research Foundation, Academy of Athens, 4 Soranou Efesiou Street, Athens 11527, Greece.
authors: Athina
authors: A
authors: Antonaki
authors: Department of Biology, Aristotle University of Thessaloniki, University Campus, Thessaloniki 54124, Greece.
authors: Constantinos
authors: C
authors: Demetriades
authors: Institute of Molecular Biology, Genetics and Biotechnology, Biomedical Research Foundation, Academy of Athens, 4 Soranou Efesiou Street, Athens 11527, Greece.
authors: Alexander
authors: A
authors: Polyzos
authors: Institute of Molecular Biology, Genetics and Biotechnology, Biomedical Research Foundation, Academy of Athens, 4 Soranou Efesiou Street, Athens 11527, Greece.
authors: Aggelos
authors: A
authors: Banos
authors: Institute of Molecular Biology, Genetics and Biotechnology, Biomedical Research Foundation, Academy of Athens, 4 Soranou Efesiou Street, Athens 11527, Greece.
authors: Giannis
authors: G
authors: Vatsellas
authors: Institute of Molecular Biology, Genetics and Biotechnology, Biomedical Research Foundation, Academy of Athens, 4 Soranou Efesiou Street, Athens 11527, Greece.
authors: Matthieu D
authors: MD
authors: Lavigne
authors: Institute of Molecular Biology, Genetics and Biotechnology, Biomedical Research Foundation, Academy of Athens, 4 Soranou Efesiou Street, Athens 11527, Greece.
authors: Effie
authors: E
authors: Apostolou
authors: Institute of Molecular Biology, Genetics and Biotechnology, Biomedical Research Foundation, Academy of Athens, 4 Soranou Efesiou Street, Athens 11527, Greece.
authors: Eva
authors: E
authors: Mantouvalou
authors: Institute of Molecular Biology, Genetics and Biotechnology, Biomedical Research Foundation, Academy of Athens, 4 Soranou Efesiou Street, Athens 11527, Greece.
authors: Deppie
authors: D
authors: Papadopoulou
authors: Department of Biology, Aristotle University of Thessaloniki, University Campus, Thessaloniki 54124, Greece. Electronic address: gmosialo@bio.auth.gr.
authors: George
authors: G
authors: Mosialos
authors: Institute of Molecular Biology, Genetics and Biotechnology, Biomedical Research Foundation, Academy of Athens, 4 Soranou Efesiou Street, Athens 11527, Greece. Electronic address: thanos@bioacademy.gr.
authors: Dimitris
authors: D
authors: Thanos
mesh_terms: D020087:Alu Elements / Q000235:genetics*; D000818:Animals; D001665:Binding Sites; D002843:Chromatin / Q000737:chemistry; D047369:Chromatin Immunoprecipitation; D004247:DNA / Q000737:chemistry / Q000235:genetics; D016678:Genome; D015894:Genome, Human; D006367:HeLa Cells; D006801:Humans; D051379:Mice; D016328:NF-kappa B / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D011323:Primates; D011485:Protein Binding; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D016328:NF-kappa B; D004247:DNA