Common distal elements orchestrate CIITA isoform-specific expression in multiple cell types

• Authors: Sarah Lohsen, Emory University; Parimal Majumder, Emory University; Christopher Scharer, Emory University; Benjamin G. Barwick, Emory University; James W. Austin, Emory University; Wendy Zinzow-Kramer, Emory University; Jeremy Boss, Emory University
• Journal Title: Genes and Immunity
• Volume: Volume 15, Number 8
• Publisher: Springer Nature [academic journals on nature.com]: Hybrid Journals | 2014-12-01, Pages 543-555
• Type of Work: Article | Post-print: After Peer Review
• Publisher DOI: http://doi.org/10.1038/gene.2014.49
• Subjects: Biology, Genetics; Health Sciences, Immunology
• Keywords: Science & Technology; Life Sciences & Biomedicine; Genetics & Heredity; Immunology; CLASS-II TRANSACTIVATOR; REGULATORY ELEMENTS; GENE-EXPRESSION; IFN-GAMMA; MHC; PROMOTER; TRANSCRIPTION; ENHANCERS; DIFFERENTIATION; DISTINCT

Abstract

Major histocompatibility class II (MHC-II) expression is critical for immune responses and is controlled by the MHC-II transactivator CIITA. CIITA is primarily regulated at the transcriptional level and is expressed from three main promoters with myeloid, lymphoid and interferon (IFN)-γ-treated non-hematopoietic cells using promoters pI, pIII and pIV, respectively. Recent studies in non-hematopoietic cells suggest that a series of distal regulatory elements may be involved in regulating CIITA transcription. To identify distal elements in B cells, a DNase I hypersensitivity screen was performed, revealing a series of potential novel regulatory elements. These elements were analyzed computationally and biochemically. Several regions displayed active histone modifications and/or enhanced expression of a reporter gene. Four of the elements interacted with pIII in B cells. These same four regions were also found to interact with pI in splenic dendritic cells (spDC). Intriguingly, examination of the above interactions in pI-knockout-derived spDC showed a switch to the next available promoter, pIII. Extensive DNA methylation was found at the pI region in B cells, suggesting that this promoter is not accessible in B cells. Thus, CIITA expression is likely mediated in hematopoietic cells by common elements with promoter accessibility having a part in promoter choice.