Histone variants: the artists of eukaryotic chromatin

The eukaryotic genome is packaged into a complex nucleoprotein structure named chromatin, balancing the compactness of genome and the accessibility of regulatory proteins and RNA polymerases to DNA. The mechanisms of the regulation of chromatin dynamics include the post-translational modification of histones, alteration of nucleosome positions by chromatin remodelers, replacement of canonical histones by histone variants with the aid of histone chaperones, and dynamic organization of the three-dimensional genome in the small nucleus. Histone variants are different from canonical histones by substitution of several amino acid residues or changes in amino acid sequence. Histone variants perform specialized functions such as altering nucleosome stability, dynamics, structure, as well as playing critical roles in a range of biological processes like transcriptional regulation, DNA repair and recombination, development and immune responses. Here we discuss how histone variants, their modification and specific loading to chromatin are involved in transcriptional regulation, DNA repair and plant development.

Histone Variants in Development and Diseases

Eukaryotic genomic DNA is highly packaged into chromatin by histones to fit inside the nucleus. Other than the bulk packaging role of canonical histones with an expression peak at S phase and replication-coupled deposition, different histone variants have evolved distinct regulatory mechanisms for their expression, deposition and functional implications. The diversity of histone variants results in structural plasticity of chromatin and highlights functionally distinct chromosomal domain, which plays critical roles in development from a fertilized egg into a complex organism, as well as in aging and diseases. However, the mechanisms of this fundamental process are poorly understood so far. It is of particular interest to investigate how the variants are incorporated into chromatin and mark specific chromatin states to regulate gene expression, and how they are involved in development and diseases. In this review, we focus on recent progress in studies of epigenetic regulation of three extensively investigated variants including H2A.Z, macroH2A and H3.3, and their functional implications in development and diseases.

Histone Variant H3.3:A versatile H3 variant in health and in disease

Histones are the main protein components of eukaryotic chromatin. Histone variants and histone modifications modulate chromatin structure, ensuring the precise operation of cellular processes associated with genomic DNA. H3.3, an ancient and conserved H3 variant, differs from its canonical H3 counterpart by only five amino acids, yet it plays essential and specific roles in gene transcription, DNA repair and in maintaining genome integrity. Here, we review the most recent insights into the functions of histone H3.3, and the involvement of its mutant forms in human diseases.

H2A Variants in Arabidopsis: Versatile Regulators of Genome Activity

The eukaryotic nucleosome prevents access to the genome.Convergently evolving histone isoforms,also called histone variants,form diverse families that are enriched over distinct features of plant genomes.Among the diverse families of plant histone variants,H2A.Z exclusively marks genes.Here we review recent research progress on the genome-wide distribution patterns and deposition of H2A.Z in plants as well as its association with histone modifications and roles in plant chromatin regulation.We also discuss some hypotheses that explain the different findings about the roles of H2A.Z in plants.

Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis

Temperature influences the distribution, range, and phenology of plants. The key transcriptional activators of heat shock response in eukaryotes, the heat shock factors （HSFs）, have undergone large-scale gene amplification in plants. While HSFs are central in heat stress responses, their role in the response to ambient temperature changes is less well understood. We show here that the warm ambient temperature transcriptome is dependent upon the HSFA1 clade ofArabidopsis HSFs, which cause a rapid and dynamic eviction of H2A.Z nucleosomes at target genes. A transcriptional cascade results in the activation of multiple downstream stress-responsive transcription factors, triggering large-scale changes to the transcriptome in response to elevated temperature. H2A.Z nucleosomes are enriched at temperature-responsive genes at non-inducible temperature, and thus likely confer inducibility of gene expression and higher responsive dynamics. We propose that the antagonistic effects of H2A.Z and HSF1 provide a mechanism to activate gene expression rapidly and precisely in response to temperature, while preventing leaky transcription in the absence of an activation signal.

Epigenetic regulation of thermomorphogenesis in Arabidopsis thaliana

Temperature is a key factor in determining plant growth and development,geographical distribution,and seasonal behavior.Plants accurately sense subtle changes in ambient temperature and alter their growth and development accordingly to improve their chances of survival and successful propagation.Thermomorphogenesis encompasses a variety of morphological changes that help plants acclimate to warm environmental temperatures.Revealing the molecular mechanism of thermomorphogenesis is important for breeding thermo-tolerant crops and ensuri ng food security under global climate change.Plant adaptation to elevated ambient temperature is regulated by multiple signaling pathways and epigenetic mechanisms such as histone modifications,histone variants,and non-coding RNAs.In this review,we summarize recent advances in the mechanism of epigenetic regulation during thermo-morphogenesis with a focus on the model plant Arabidopsis thaliana and briefly discuss future pro-spects for this field.