title: DNA breaks and chromatin structural changes enhance the transcription of autoimmune regulator target genes.
abstract: The autoimmune regulator (AIRE) protein is the key factor in thymic negative selection of autoreactive T cells by promoting the ectopic expression of tissue-specific genes in the thymic medullary epithelium. Mutations in AIRE cause a monogenic autoimmune disease called autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy. AIRE has been shown to promote DNA breaks via its interaction with topoisomerase 2 (TOP2). In this study, we investigated topoisomerase-induced DNA breaks and chromatin structural alterations in conjunction with AIRE-dependent gene expression. Using RNA sequencing, we found that inhibition of TOP2 religation activity by etoposide in AIRE-expressing cells had a synergistic effect on genes with low expression levels. AIRE-mediated transcription was not only enhanced by TOP2 inhibition but also by the TOP1 inhibitor camptothecin. The transcriptional activation was associated with structural rearrangements in chromatin, notably the accumulation of γH2AX and the exchange of histone H1 with HMGB1 at AIRE target gene promoters. In addition, we found the transcriptional up-regulation to co-occur with the chromatin structural changes within the genomic cluster of carcinoembryonic antigen-like cellular adhesion molecule genes. Overall, our results suggest that the presence of AIRE can trigger molecular events leading to an altered chromatin landscape and the enhanced transcription of low-expressed genes.
authors.affiliation: From the Molecular Pathology, Institute of Biomedical and Translational Medicine.
authors.forename: Mithu
authors.initials: M
authors.lastname: Guha
authors.affiliation: From the Molecular Pathology, Institute of Biomedical and Translational Medicine.
authors.forename: Mario
authors.initials: M
authors.lastname: Saare
authors.affiliation: From the Molecular Pathology, Institute of Biomedical and Translational Medicine.
authors.forename: Julia
authors.initials: J
authors.lastname: Maslovskaja
authors.affiliation: From the Molecular Pathology, Institute of Biomedical and Translational Medicine.
authors.forename: Kai
authors.initials: K
authors.lastname: Kisand
authors.affiliation: From the Molecular Pathology, Institute of Biomedical and Translational Medicine.
authors.forename: Ingrid
authors.initials: I
authors.lastname: Liiv
authors.affiliation: From the Molecular Pathology, Institute of Biomedical and Translational Medicine.
authors.forename: Uku
authors.initials: U
authors.lastname: Haljasorg
authors.affiliation: Institute of Computer Science.
authors.forename: Tõnis
authors.initials: T
authors.lastname: Tasa
authors.affiliation: Estonian Genome Center, and.|Institute of Molecular and Cell Biology, University of Tartu, Tartu 50411, Estonia.
authors.forename: Andres
authors.initials: A
authors.lastname: Metspalu
authors.affiliation: Estonian Genome Center, and.
authors.forename: Lili
authors.initials: L
authors.lastname: Milani
authors.affiliation: From the Molecular Pathology, Institute of Biomedical and Translational Medicine, part.peterson@ut.ee.
authors.forename: Pärt
authors.initials: P
authors.lastname: Peterson
mesh_terms: D017398:Alternative Splicing; D000951:Antigens, Neoplasm / Q000378:metabolism*; D002166:Camptothecin / Q000737:chemistry; D002272:Carcinoembryonic Antigen / Q000235:genetics; D002843:Chromatin / Q000737:chemistry*; D004249:DNA Damage; D004250:DNA Topoisomerases, Type II / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D005047:Etoposide / Q000737:chemistry; D058851:GPI-Linked Proteins / Q000235:genetics; D020869:Gene Expression Profiling; D057809:HEK293 Cells; D024243:HMGB1 Protein / Q000378:metabolism; D006657:Histones / Q000378:metabolism; D006801:Humans; D005810:Multigene Family; D009154:Mutation; D000075223:Poly-ADP-Ribose Binding Proteins; D011401:Promoter Regions, Genetic; D000072417:Protein Domains; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic; D015533:Transcriptional Activation; D000096927:AIRE Protein
chemical_list: D000951:Antigens, Neoplasm; D002166:Camptothecin; D002272:Carcinoembryonic Antigen; D002843:Chromatin; D004250:DNA Topoisomerases, Type II; D004268:DNA-Binding Proteins; D005047:Etoposide; D058851:GPI-Linked Proteins; D024243:HMGB1 Protein; D006657:Histones; D000075223:Poly-ADP-Ribose Binding Proteins; D014157:Transcription Factors; D000096927:AIRE Protein; C527875:CEACAM5 protein, human; C468783:H2AX protein, human; C585491:HMGB1 protein, human; C000618811:TOP2A protein, human
keywords: DNA sequencing; DNA topoisomerase; RNA splicing; autoimmune disease; chromatin structure; immunology; tolerance; transcription