Spatial distribution of histone methylation during MHC class II expression

Area of Science:

• Immunology
• Epigenetics
• Molecular Biology

Background:

• Major Histocompatibility Complex (MHC) class II expression is crucial for immune responses.
• Class II transactivator (CIITA) is a key regulator of MHC class II gene expression.
• Histone deacetylase inhibitors (HDACi) can induce MHC class II expression independently of CIITA.

Purpose of the Study:

• To characterize histone modifications in CIITA-dependent (IFN-gamma induced) and -independent (HDACi induced) MHC class II expression.
• To compare the epigenetic patterns associated with different MHC class II induction pathways.
• To investigate the role of specific histone marks in regulating MHC class II transcription.

Main Methods:

• Chromatin immunoprecipitation (ChIP) to analyze histone modifications (acetylation, H3K4me3, H3K9me3, H3K36me3, H3K79me2).
• Treatment of B cell lines with IFN-gamma and HDACi.
• Stable transfection of a CIITA-deficient B cell line to restore CIITA expression.

Main Results:

• Both IFN-gamma and HDACi treatments enhanced H3, H4 acetylation and H3K4me3 at the MHC class II promoter, while decreasing H3K9me3.
• High levels of H3K36me3 were found in exons 3 and 5, but not the promoter or LCR.
• H3K79me2 was enriched at the promoter and exon 3 in B cells, and its levels were restored by CIITA expression.

Conclusions:

• IFN-gamma and HDACi induce similar histone modification patterns at the MHC class II locus.
• HDACi treatment leads to both histone methylation and acetylation.
• The distinct localization of lysine methylation marks suggests roles in different stages of transcription.