HIRA complex presets transcriptional potential through coordinating depositions of the histone variants H3.3 and H2A.Z on the poised genes in mESCs

Abstract

Histone variants have been implicated in regulating chromatin dynamics and genome functions. Previously, we have shown that histone variant H3.3 actively marks enhancers and cooperates with H2A.Z at promoters to prime the genes into a poised state in mouse embryonic stem cells (mESCs). However, how these two important histone variants collaboratively function in this process still remains elusive. In this study, we found that depletion of different components of HIRA complex, a specific chaperone of H3.3, results in significant decreases of H2A.Z enrichment at genome scale. In addition, CUT&Tag data revealed a genomic colocalization between HIRA complex and SRCAP complex. In vivo and in vitro biochemical assays verified that HIRA complex could interact with SRCAP complex through the Hira subunit. Furthermore, our chromatin accessibility and transcription analyses demonstrated that HIRA complex contributed to preset a defined chromatin feature around TSS region for poising gene transcription. In summary, our results unveiled that while regulating the H3.3 incorporation in the regulatory regions, HIRA complex also collaborates with SRCAP to deposit H2A.Z onto the promoters, which cooperatively determines the transcriptional potential of the poised genes in mESCs.

Histone H3.3 deposition in seed is essential for the post-embryonic developmental competence in Arabidopsis

“…In human cells, the presence of H3.3 destabilizes nucleosome, especially when co-existed with H2A.Z, leading to a nucleosome-free region at the 5′ gene end for transcription factor binding 49,72 . In mouse embryonic stem cell, H3.3 and H2A.Z collaborate around gene transcription start sites to set up a poised chromatin state for gene activation during cell differentiation 73 . Despite a predominant localization of H3.3 at the 3′ gene end in Arabidopsis vegetative tissues 32,33,35 , our findings show that at certain developmental stages it is highly enriched around the 5′ gene end and facilitates chromatin opening.…”

The Role of the Histone Variant H2A.Z in Metazoan Development

“…Through this collaboration between SRCAP and HIRA, hybrid H3.3–H2A.Z nucleosomes can be assembled to prime a promoter for subsequent activation ( Figure 3 ). Notably in mESCs, such priming is important for the activation of genes required for neuronal development [ 75 ].…”

“…Knockout of components in the SRCAP complex has been shown to cause defects in the differentiation of different lineages, including neurons [ 75 ], muscle tissue [ 26 ], and prenatal heart cells [ 124 ]. Mutations in SRCAP cause defects in craniofacial development [ 87 ] and are associated with the mental illness bipolar disorder [ 125 ].…”

“…In mESCs, SRCAP loss causes a global reduction in H2A.Z occupancy in chromatin [ 75 ]. In contrast, the loss of p400 does not induce the same effect, which suggests that SRCAP is the key remodeler responsible for depositing H2A.Z in mESCs [ 107 ].…”

“…In contrast, the loss of p400 does not induce the same effect, which suggests that SRCAP is the key remodeler responsible for depositing H2A.Z in mESCs [ 107 ]. As described above, SRCAP has been shown to associate with the H3.3 deposition complex HIRA to assemble hybrid H3.3–H2A.Z nucleosomes to prime promoters required for neuronal differentiation for subsequent activation ( Figure 3 ) [ 75 ].…”