Chromatin compacts DNA to an extreme extent and allows the eukaryotic genome to fit the size of the nucleus. On the other hand, however, it must process the ability to untighten DNA and to permit the cellular machinery access to the genome. Chromatin consists of nucleosomes in which a protein core is composed of four canonical histones H2A, H2B, H3, H4, 147 bp of DNA wrapped around them. Histone variants, and the chromatin remodeling machinery, can reorganize the compaction of chromatin and thus be important for epigenetic regulation of gene expression. 

Histone variant H2A.Z is a universal mark of dynamic nucleosomes. H2A.Z is essential for the growth, development and viability of a number of species including mammals. H2A.Z plays critical roles in multiple biological processes including gene transcription and replication, DNA repair, and genome integrity. The chromatin incorporation of H2A.Z is catalyzed by SRCAP, an ATP-dependent, multi-component chromatin remodeling complex. The YL1 subunit of SRCAP is essential for securing H2A.Z recognition. 

A new study published online by Nature Structural and Molecular Biology on March 14, revealed a mechanism by which the histone variant H2A.Z is preferentially recognized by the SRCAP chromatin-remodeling subunit YL1. A combination of biochemical, biophysical and yeast genetic analyses reveals the mechanism by which YL1 protein specifically interacts with histone variant H2A.Z rather than canonical histone H2A. The study elucidates a novel mechanism for histone variant recognition that is essential to the H2A.Z replacement pathway. 

LIANG Xiaoping and his colleagues from the research group led by Prof. ZHOU Zheng at the Institute of Biophysics of the Chinese Academy of Sciences solved the structure of the H2A.Z-H2B dimer in complex with YL1. The 1.9-Å resolution complex structure reveals that an YL1-Z domain located at the N-terminal YL1 clasps over H2A.Z–H2B. Three specific residues in H2A.Z confer the preference for YL1-Z and are essential to H2A.Z functions. 

This study was conducted in collaboration with Prof. Carl Wu at the HHMI Janelia Institute. It was supported by grants from the Ministry of Science and Technology of China and the National Natural Science Foundation of China. 

The structure of YL1-Z in complex of H2A.Z-H2B (left) and the graphic model of H2A.Z recognition and transfer mediated by SRCAP (right). (Image by IBP)