title: Genome-wide CIITA-binding profile identifies sequence preferences that dictate function versus recruitment.
abstract: The class II transactivator (CIITA) is essential for the expression of major histocompatibility complex class II (MHC-II) genes; however, the role of CIITA in gene regulation outside of MHC-II biology is not fully understood. To comprehensively map CIITA-bound loci, ChIP-seq was performed in the human B lymphoblastoma cell line Raji. CIITA bound 480 sites, and was significantly enriched at active promoters and enhancers. The complexity of CIITA transcriptional regulation of target genes was analyzed using a combination of CIITA-null cells, including a novel cell line created using CRISPR/Cas9 tools. MHC-II genes and a few novel genes were regulated by CIITA; however, most other genes demonstrated either diminished or no changes in the absence of CIITA. Nearly all CIITA-bound sites were within regions containing accessible chromatin, and CIITA's presence at these sites was associated with increased histone H3K27 acetylation, suggesting that CIITA's role at these non-regulated loci may be to poise the region for subsequent regulation. Computational genome-wide modeling of the CIITA bound XY box motifs provided constraints for sequences associated with CIITA-mediated gene regulation versus binding. These data therefore define the CIITA regulome in B cells and establish sequence specificities that predict activity for an essential regulator of the adaptive immune response.
authors.affiliation: Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA.
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Scharer
authors.affiliation: Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA.
authors.forename: Nancy M
authors.initials: NM
authors.lastname: Choi
authors.affiliation: Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA.
authors.forename: Benjamin G
authors.initials: BG
authors.lastname: Barwick
authors.affiliation: Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA.
authors.forename: Parimal
authors.initials: P
authors.lastname: Majumder
authors.affiliation: Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA.
authors.forename: Sarah
authors.initials: S
authors.lastname: Lohsen
authors.affiliation: Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA jmboss@emory.edu.
authors.forename: Jeremy M
authors.initials: JM
authors.lastname: Boss
mesh_terms: D056704:Adaptive Immunity / Q000235:genetics; D001402:B-Lymphocytes / Q000276:immunology / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D064113:CRISPR-Cas Systems; D002460:Cell Line; D047369:Chromatin Immunoprecipitation; D017124:Conserved Sequence; D005786:Gene Expression Regulation; D005802:Genes, MHC Class II; D015894:Genome, Human; D006657:Histones / Q000378:metabolism; D006801:Humans; D009687:Nuclear Proteins / Q000172:deficiency / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015534:Trans-Activators / Q000172:deficiency / Q000235:genetics / Q000378:metabolism*
chemical_list: D006657:Histones; C083728:MHC class II transactivator protein; D009687:Nuclear Proteins; D012333:RNA, Messenger; D015534:Trans-Activators