A unified phylogeny-based nomenclature for histone variants

Table 3 Sequence variation in ‘H3.3’ and ‘H2A.X’ variants

Kingdom	Organism	Histone Variant	Residue 31 -	Residues (85)86-89
Animals	Homo	H3.3	S	A AIG
	Homo	H3.2	A	S AVM
Fungi	Saccharomyces	H3	S	SAIG
Plants	Arabidopsis	H3.3	T	H AVL
	Arabidopsis	H3.1	A	S AVA
Rhodophytes	Porphyra	H3.3?	S-	T AVL
	Porphyra	H3.1?	VG	S AVL
Alveolates	Tetrahymena	H3.3	VS	Q AI L
	Tetrahymena	H3.1	AT	S AV L
Heterokonts	Thalassiosira	H3.3?	TA	ST AVL
	Thalassiosira	H3.1?	AT	GS AVL
Amoebozoa	Dictyostelium	H3.3?	STQP	AAIQ
	Dictyostelium	H3.1?	VNEV	AAIE
Excavates	Euglena	H3	A	NAIL
			Residues 109-
Animals	Homo	H2A.X	PNIQAVLLPKKSATVGPKAPSGGKKATQASQEY
	Homo	H2A.2.2	PNIQAVLLPKKTSHKPGKNK
Fungi	Saccharomyces	H2A.X	PNIHQNLLPKKSAKATKASQEL
Plants	Arabidopsis	H2A.X.3	PNIHQTLLPSKVGKNKGDIGSASQEF
	Arabidopsis	H2A.1	PNIHNLLLPKKAGASKPQED
Rhodophytes	Griffithsia	H2A.X	PNIHQVLMPRKKTKGDASQEV
	Cyanidioschyzon	H2A	PNIHAVLLPKKKAKGE
Alveolates	Tetrahymena	H2A.X	PNINPMLLPSKSKKTESRGGASQDL
	Tetrahymena	H2A.1	PNINPMLLPSKTKKSTEPEH
Heterokonts	Phaeodactylum	H2A.X	PNIHAILLPKKTIKTKGPSQDY
	Phaeodactylum	H2A.3	PNIHAILLPKKSGPTK
Amoebozoa	Dictyostelium	H2A.X?	PTPQQSTGEKKKKPSKKAAEGSSQIY
	Dictyostelium	H2A	PTPQSNTEGKKKKATSKKS
Excavates	Giardia	H2A.X	RSAKEGREGKGSHRSQDL
	Trypanosoma	H2A	PSLNKALAKKQKSGKHAKATPSV

RI ‘H3.3’ variants and ‘H2A.X’ variants are paraphyletic or polyphyletic, but have recognizable sequence features. Upper panel: Divergence between RI and RC H3 variants usually involves differences at residue 31 and residues 86 to 89. Lower panel: ‘H2A.X’ variants are distinguished from related H2A variants by bearing a consensus SQ(E/D)Φ phosphorylation motif at the C-terminus. Residue numbers refer to the human H3.3 and H2A.X protein sequences, and to orthologous positions in other variants.