Reader domain specificity and lysine demethylase-4 family function

Area of Science:

• Epigenetics
• Molecular Biology
• Structural Biology

Background:

• KDM4 histone demethylases are crucial epigenetic regulators involved in development, spermatogenesis, and cancer.
• The precise mechanisms by which KDM4 family members target specific chromatin regions remain largely unknown.

Purpose of the Study:

• To investigate the histone trimethyl-lysine binding preferences of KDM4 double tudor domains (DTDs).
• To elucidate the structural basis for H3K23me3 recognition by KDM4A and KDM4B.
• To understand the functional implications of H3K23me3 binding by KDM4B in chromatin regulation.

Main Methods:

• Histone peptide microarray analysis to determine binding specificities.
• Co-crystallography of KDM4A-DTD and KDM4B-DTD with H3K23me3 peptides.
• In vivo co-localization studies in mammalian meiotic spermatocytes.
• In vitro demethylation assays.

Main Results:

• KDM4A and KDM4B DTDs exhibit strong binding to H3K23me3.
• Crystal structures reveal key interactions for H3K23me3 recognition and specificity.
• KDM4B and H3K23me3 co-localize in heterochromatin of meiotic and postmeiotic spermatocytes.
• H3K23me3 binding by KDM4B enhances its H3K36 demethylation activity.

Conclusions:

• H3K23me3 is a specific binding target for KDM4A/B DTDs.
• Structural insights explain the exclusive H3K23me3 specificity of KDM4B.
• KDM4B-mediated H3K36 demethylation is directed by H3K23me3 binding, providing a mechanism for epigenetic regulation during meiosis and spermatogenesis.