Role of the DR/DQ super enhancer in MHC-II expression

Major histocompatibility complex class-II (MHC-II) proteins are encoded by HLA-DR, -DQ, and -DP α/β gene
pairs and function by presenting processed antigenic peptides to CD4+ T cells thereby initiating and/or sustaining
adaptive immune responses. MHC-II expression is transcriptionally regulated and expressed constitutively in
antigen-presenting cells, such as B cells, but may be induced in non-immune cells by IFNγ. Thus, MHC-II-
mediated immune responses and adaptive immunity is controlled primarily at the level of transcription. All MHC-
II genes are coregulated by a common set of proximal promoter transcription elements and factors of which only
CIITA is cell type limiting and induced by IFNγ. Several years ago, we showed that MHC-II gene expression was
also modulated by a series of transcriptional insulator elements that bound CTCF and cohesin and that these
elements were the focal points of long-range chromatin interactions between each other and MHC-II promoter
regions. Together these elements formed a three-dimensional chromatin architecture that favored gene
expression. Indeed, as B cells differentiated into plasma cells and lost MHC-II expression, this architecture was
also lost. While this model is correct and has stood for the last 5 years, we now provide exciting new evidence
that it is incomplete. New data presented herein identifies a super enhancer (SE) located between the HLA-
DRB1 and -DQA1 genes (termed the DR/DQ-SE) that is required for maximal expression of the system and for
its “3D” architecture. CRISPR/Cas9 mediated deletion of the DR/DQ-SE in Raji B cells resulted in decreased
expression of HLA-DR and -DQ, reduced ability to stimulate an allogenic CD4 T cell response, and loss of
promoter associated histone modifications and all local CTCF-insulator interactions. Additionally, while it is
accepted that MHC proteins are highly polymorphic, non-coding polymorphisms within cis-regulatory regions of
the MHC-II locus are more extensive and strongly linked to MHC-II expression and disease, suggesting that
transcriptional regulation of MHC-II expression by the DR/DQ-SE is a key component of immunity and disease.
Aside from what we present, nothing else is known about this region and how it works. To fill this gap in
knowledge, this application seeks to understand how this SE functions to control MHC-II expression and
immunity. Aim 1 will elucidate fundamental molecular and biochemical components of the DR/DQ-SE and
determine how polymorphisms affect its function. Aim 2 will determine the range of the SE’s influence and test
a model of how it may operate. Aim 3 will examine how the SE is established, and decommissioned. Together,
our studies will provide insight into how human (SNP) diversity influences immunity, and ultimately how this
critically important set of immune system genes are regulated. The knowledge gained will have broad
implications on gene regulation and will provide new insight into how the initial steps of adaptive immune
responses may be controlled. Our results could have important implications for future immune-based therapies
and vaccinations, and for treatments of infectious disease, autoimmunity, cancer, and transplantation.

Grant Number: 5R01AI153102-05
NIH Institute/Center: NIH
Principal Investigator: JEREMY BOSS