Genome-wide CIITA-binding profile identifies sequence preferences that dictate function versus recruitment

Area of Science:

• Immunology
• Molecular Biology
• Genetics

Background:

• The class II transactivator (CIITA) is crucial for major histocompatibility complex class II (MHC-II) gene expression.
• The broader role of CIITA in gene regulation beyond MHC-II is not fully understood.

Purpose of the Study:

• To comprehensively map CIITA-bound DNA sites in B cells.
• To analyze the complexity of CIITA's transcriptional regulation.
• To identify sequence specificities for CIITA-mediated gene regulation.

Main Methods:

• Chromatin immunoprecipitation sequencing (ChIP-seq) in Raji B lymphoblastoma cells.
• Utilized CIITA-null cells, including a novel CRISPR/Cas9-generated line.
• Computational genome-wide modeling of CIITA-bound motifs.

Main Results:

• CIITA bound 480 loci, enriched at active promoters and enhancers.
• CIITA regulated MHC-II genes and a few novel genes; most other genes showed minimal changes in CIITA-null cells.
• CIITA binding sites were in accessible chromatin and associated with increased histone acetylation, suggesting a role in poising regions for regulation.

Conclusions:

• Defined the CIITA regulome in B cells.
• Identified sequence specificities predicting CIITA activity.
• Established CIITA as an essential regulator with roles beyond MHC-II gene expression.