Histone variant H3.3 residue S31 is essential for Xenopus gastrulation regardless of the deposition pathway

Abstract

Vertebrates exhibit specific requirements for replicative H3 and non-replicative H3.3 variants during development. To disentangle whether this involves distinct modes of deposition or unique functions once incorporated into chromatin, we combined studies in Xenopus early development with chromatin assays. Here we investigate the extent to which H3.3 mutated at residues that differ from H3.2 rescue developmental defects caused by H3.3 depletion. Regardless of the deposition pathway, only variants at residue 31-a serine that can become phosphorylated-failed to rescue endogenous H3.3 depletion. Although an alanine substitution fails to rescue H3.3 depletion, a phospho-mimic aspartate residue at position 31 rescues H3.3 function. To explore mechanisms involving H3.3 S31 phosphorylation, we identified factors attracted or repulsed by the presence of aspartate at position 31, along with modifications on neighboring residues. We propose that serine 31-phosphorylated H3.3 acts as a signaling module that stimulates the acetylation of K27, providing a chromatin state permissive to the embryonic development program.

Surprising phenotypic diversity of cancer-associated mutations of Gly 34 in the histone H3 tail

“…H3.3 only differs from H3.2 by four residues: Ser31 in the tail, and three substitutions within the core of H3 which dictate chaperone selectivity ( Ahmad and Henikoff, 2002 ; Elsässer et al, 2012 ; Liu et al, 2012 ). Phosphorylation of Ser31 in H3.3 is important for regulation of cell fate during gastrulation and for enhancer activation ( Martire et al, 2019 ; Sitbon et al, 2020 ) and Ser31P influences H3.3 K27 trimethylation and acetylation ( Martire et al, 2019 ; Sitbon et al, 2020 ), and so phosphoregulation via S31 may provide an additional mechanistic link as to why the Gly 34 mutations are only found in H3.3.…”

H3.3S31 phosphorylation: linking transcription elongation to stimulation responses

“…Studies from two laboratories recently showed that H3.3S31ph stimulates the catalytic activity of histone acetyltransferase p300, thus maintaining enhancers at an open, acetylated chromatin state permissive to the embryonic development program. 4,5 In the current study, Armache et al 2 discovered a novel role of H3.3S31ph in transcription elongation. It not only augments the catalytic activity of SETD2, but also ejects negative regulator ZMYND11.…”

Establishment and function of chromatin modification at enhancers

“…Several recent studies also demonstrate a link between H3.3 phosphorylation and p300 activity at enhancers [ 57 , 164 ]. Interestingly, the N-terminal tails of canonical H3 and H3.3 differ by only one amino acid.…”

“…While H3.1 and H3.2 contain an alanine at position 31, H3.3 has a unique and highly conserved serine that has been reported to be phosphorylated by both checkpoint kinase 1 (Chk1) and Aurora B [165][166][167]. A study from the Almouzni lab demonstrates that a phosphomimetic mutant of H3.3 at this position (H3.3S31D) results in increased H3K27ac in cis in both human cell lines and Xenopus embryos [164]. Our own work demonstrates that phosphorylation of H3.3 Ser31 (H3.3S31ph) facilitates p300 activity not only on phosphorylated tails, but also in trans on canonical H3 substrates in mESCs (figure 2b) [57].…”