Key Functional Regions in the Histone Variant H2A.Z C-Terminal Docking Domain

Abstract

The incorporation of histone variants into nucleosomes represents one way of altering the chromatin structure to accommodate diverse functions. Histone variant H2A.Z has specific roles in gene regulation, heterochromatin boundary formation, and genomic integrity. The precise features required for H2A.Z to function and specify an identity different from canonical H2A remain to be fully explored. Analysis of the C-terminal docking domain of H2A.Z in Saccharomyces cerevisiae using epistatic miniarray profile (E-MAP) uncovered nuanced requirements of the H2A.Z C-terminal region for cell growth when additional genes were compromised. Moreover, the H2A.Z(1-114) truncation, lacking the last 20 amino acids of the protein, did not support regular H2A.Z functions, such as resistance to genotoxic stress, restriction of heterochromatin in its native context, GAL1 gene activation, and chromatin anchoring. The corresponding region of H2A could fully rescue the strong defects caused by loss of this functionally essential region in the C terminus of H2A.Z. Despite the dramatic reduction in function, the H2A.Z(1-114) truncation still bound the H2A.Z deposition complex SWR1-C, the histone chaperone Chz1, and histone H2B. These data are consistent with a model in which retaining the variant in chromatin after its deposition by SWR1-C is a crucial determinant of its function.

Histone H2A variants in nucleosomes and chromatin: more or less stable?

“…In the past 2 years, the importance of the H2A.Z C-terminus for nucleosome stability and chromatin association has been explored in S. cerevisiae and humans (20,21,178). Two studies in S. cerevisiae revealed that C-terminal deletions, depending on the extent of truncation, decrease or completely abolish chromatin association (23,178).…”

“…Two studies in S. cerevisiae revealed that C-terminal deletions, depending on the extent of truncation, decrease or completely abolish chromatin association (23,178). As expected, loss of chromatin association leads to phenotypes similar to the complete knock-out of the H2A.Z gene in S. cerevisiae , such as reduced resistance to genotoxic stress and spreading of heterochromatin into euchromatic regions, indicating that chromatin association is essential for H2A.Z function.…”

High-resolution network biology: connecting sequence with function

“…Although such approaches are valuable for exploring the functionality of essential genes, they usually address the problem at the whole-protein level and do not identify the parts of proteins that are responsible for specific interactions or functions. However, a few studies have shown that genetic and chemogenetic interaction profiling can be extremely useful in this context 98–100 , particularly for investigating the functional consequences of PTMs 98–102 that may not be detectable in the protein–protein interaction network. This can be achieved by mutating the specific residues that are subject to PTM, such that they mimic either their modified or unmodified state.…”

“…These results indicate that genetic interaction screening can be used not only to identify the consequences of mutating specific residues but also to identify how combinatorial perturbations of the same gene can result in unique outcomes. Genetic interaction screening has also been used to study H2A.Z using truncations of varying lengths in S. cerevisiae 102 or using targeted mutation in Schizosaccharomyces pombe 103 .…”

Unexplored Potentials of Epigenetic Mechanisms of Plants and Animals–-Theoretical Considerations

“…Each of the histones has an N-terminal tail with a specific sequence of amino acids, but the H2A also has a C-terminal tail 12. The C-terminus forms a globular docking domain that is packaged into the core 13. Several studies have demonstrated the importance of the histone tails for nucleosome remodeling by ATP-dependent chromatin remodeling factors 14,15…”