MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones

El Kennani, Sara; Adrait, Annie; Shaytan, Alexey K.; Khochbin, Saadi; Bruley, Christophe; Panchenko, Anna R.; Landsman, David; Pflieger, Delphine; Govin, Jérôme

doi:10.1186/s13072-016-0109-x

Epigenetics & Chromatin

Table 2 Manually curated list of mouse histones

From: MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones

Histone	Protein name	Entry name for MS analysis	Gene name	UniProtKB	References
H1	H1.1	H1.1	Hist1h1a	P43275	[41, 91]
	H1.2	H1.2	Hist1h1c	P15864	[41, 92]
	H1.3	H1.3	Hist1h1d	P43277	[41]
	H1.4	H1.4	Hist1h1e	P43274	[41]
	H1.5	H1.5	Hist1h1b	P43276	[41]
	H1.0 (H1°)	H1.0 (H1°)	H1f0	P10922	[93]
	TS H1.6 (H1T)	TS H1.6 (H1T)	Hist1h1t	Q07133	[54]
	TS H1.7 (H1T2, HANP1)	TS H1.7 (H1T2, HANP1)	H1fnt	Q8CJI4	[55, 56]
	OO H1.8 (H1oo)	OO H1.8.s1 (H1oo)	H1foo	Q8VIK3	[59]
		OO H1.8.s2	H1foo	Q8VIK3-2	[60]
		OO H1.8.s3 (putative spliced isoform)	H1foo	E0CZ52	*
		OO H1.8.s4 (putative spliced isoform)	H1foo	E0CYL2	Short**
		OO H1.8.s5 (putative spliced isoform)	H1foo	A0A0N4SV54	Short*
	TS H1.9 (HILS1)	TS H1.9 (HILS1)	Hils1	Q9QYL0	[57, 58]
	H1.10	H1.10	H1fx	Q80ZM5	*
	H1.11	H1.11 gene: Gm6970	Gm6970	F7DCP6	*
H2A	Canonical H2A	Canonical H2A genes: Hist1h2ab, Hist1h2ac, Hist1h2ad, Hist1h2ae, Hist1h2ag, Hist1h2ai, Hist1h2an, Hist1h2ao, Hist1h2ap	Hist1h2ab	P22752	[41]
			Hist1h2ac	P22752	[41]
			Hist1h2ad	P22752	[41]
			Hist1h2ae	P22752	[41]
			Hist1h2ag	P22752	[41]
			Hist1h2ai	P22752	[41]
			Hist1h2an	P22752	[41]
			Hist1h2ao	P22752	[41]
			Hist1h2ap	P22752	[41]
		Canonical H2A gene: Hist1h2af	Hist1h2af	Q8CGP5	[41]
		Canonical H2A gene: Hist1h2ah	Hist1h2ah	Q8CGP6	[41]
		Canonical H2A gene: Hist1h2ak	Hist1h2ak	Q8CGP7	[41]
		Canonical H2A gene: Hist1h2al	Hist1h2al	F8WIX8	*
		Canonical H2A genes: Hist2h2aa1, Hist2h2aa2	Hist2h2aa1	Q6GSS7	[41]
			Hist2h2aa2	Q6GSS7	[41]
		Canonical H2A gene: Hist2h2ab	Hist2h2ab	Q64522	[41]
		Canonical H2A gene: Hist2h2ac	Hist2h2ac	Q64523	[41]
		Canonical H2A gene: Hist3h2a	Hist3h2a	Q8BFU2	[41]
	H2A.J (putative variant)	H2A.J.s1 (putative variant)	H2afj	Q8R1M2	*
		H2A.J.s2 (putative variant, putative spliced isoform)	H2afj	A0A0N4SV66	*
	H2A.X	H2A.X	H2afx	P27661	[61, 62, 94]
	H2A.Z.1	H2A.Z.1.s1	H2afz	P0C0S6	[43]
		H2A.Z.1.s2 (putative spliced isoform)	H2afz	Q3UA95	*
		H2A.Z.1.s3 (putative spliced isoform)	H2afz	G3UWL7	Short*
		H2A.Z.1.s4 (putative spliced isoform)	H2afz	G3UX40	Short**
	H2A.Z.2	H2A.Z.2.s1	H2afv	Q3THW5	[43]
		H2A.Z.2.s2 (putative spliced isoform)	H2afv	Q8R029	Short*
	Macro-H2A.1	Macro-H2A.1.s1	H2afy	Q9QZQ8	[95]
		Macro-H2A.1.s2	H2afy	Q9QZQ8-2	[45]
	Macro-H2A.2	Macro-H2A.2	H2afy2	Q8CCK0	[96, 97]
	Macro-H2A.3	Macro-H2A.3 (pseudogene) gene: H2afy3	H2afy3	Q9D3V6	***
	TS H2A.1	TS H2A.1 (TH2A)	Hist1h2aa	Q8CGP4	[41]
	H2A.L.1 (H2A.Lap2)	H2A.L.1 (H2A.Lap2) genes: H2al1a, GH2al1c,H2al1d, H2al1f,H2al1g, H2al1h,H2al1i	H2al1a	Q5M8Q2	[38, 39]
			H2al1c	Q5M8Q2	[38, 39]
			H2al1d	Q5M8Q2	[38, 39]
			H2al1f	Q5M8Q2	[38, 39]
			H2al1g	Q5M8Q2	[38, 39]
			H2al1h	Q5M8Q2	[38, 39]
			H2al1i	Q5M8Q2	[38, 39]
		H2A.L.1 gene: H2al1b	H2al1b	A0A087WP11	*
		H2A.L.1 gene: H2al1e	H2al1e	Q810S6	*
		H2A.L.1 gene: H2al1j	H2al1j	A2BFR3	*
		H2A.L.1 gene: H2al1k	H2al1k	J3QP08	*
		H2A.L.1 gene: H2al1m	H2al1m	Q9DAD9	*
		H2A.L.1 gene: H2al1n	H2al1n	Q497L1	*
		H2A.L.1 gene: H2al1o	H2al1o	L7MU04	*
	H2A.L.2 (H2A.Lap3, H2A.B.1)	H2A.L.2 (H2A.Lap3, H2A.B.1) gene: H2afb1	H2afb1	Q9CQ70	[38, 39]
	Y-chr H2A.L.3	Y-chr H2A.L.3 genes: H2al2b, H2al2c	H2al2b	A9Z055	[98]
			H2al2c	A9Z055	[98]
	H2A.P (H2A.L3, H2A.Lap4)	H2A.P (H2A.L3, H2A.Lap4) gene: Hypm	Hypm	Q9CR04	[38, 39]
	H2A.B.2	H2A.B.2 gene: H2afb2	H2afb2	S4R1M3	[40, 99]
	H2A.B.3	H2A.B.3 gene: H2afb3	H2afb3	S4R1G7	[40, 99]
		H2A.B.3 (H2A.Lap1) gene: Gm14920	Gm14920	S4R1E0	[39, 40, 99]
H2B	Canonical H2B	Canonical H2B gene: Hist1h2bb	Hist1h2bb	Q64475	[41]
		Canonical H2B genes: Hist1h2bc, Hist1h2be, Hist1h2bg	Hist1h2bc	Q6ZWY9	[41]
			Hist1h2be	Q6ZWY9	[41]
			Hist1h2bg	Q6ZWY9	[41]
		Canonical H2B genes: Hist1h2bf, Hist1h2bj, Hist1h2bl, Hist1h2bn, Hist1h2bq, Hist1h2br	Hist1h2bf	P10853	[41]
			Hist1h2bj	P10853	[41]
			Hist1h2bl	P10853	[41]
			Hist1h2bn	P10853	[41]
			Hist1h2bq	P10853	[41]
			Hist1h2br	P10853	[41]
		Canonical H2B genes: Hist1h2bq, Hist1h2br (putative spliced isoform)	Hist1h2bq	Q8CBB6	*
			Hist1h2br	Q8CBB6	*
		Canonical H2B gene: Hist1h2bh	Hist1h2bh	Q64478	[41]
		Canonical H2B gene: Hist1h2bk	Hist1h2bk	Q8CGP1	[41]
		Canonical H2B gene: Hist1h2bm	Hist1h2bm	P10854	[41]
		Canonical H2B gene: Hist1h2bp Spliced isoform 1 (main)	Hist1h2bp	Q8CGP2	[41]
		Canonical H2B gene: hist1h2bp (putative spliced isoform)	Hist1h2bp	Q8CGP2-2	[41]
		Canonical H2B gene: Hist2h2bb	Hist2h2bb	Q64525	[41]
		Canonical H2B gene: Hist2h2be	Hist2h2be	Q64524	[41]
		Canonical H2B gene: Hist3h2ba	Hist3h2ba	Q9D2U9	[41]
		Canonical H2B gene: Hist3h2bb	Hist3h2bb	Q8CGP0	*
	TS H2B.1 (TH2B)	TS H2B.1 (TH2B)	Hist1h2ba	P70696	[41, 79]
	subH2B (H2BL.1)	subH2B (H2BL.1)	1700024p04rik	Q9D9Z7	[38, 100]
	H2B.L.2	H2B.L.2	H2bfm	Q9DAB5	[38]
H3	Canonical H3.1	Canonical H3.1	Hist1h3a	P68433	[41]
			Hist1h3g	P68433	[41]
			Hist1h3h	P68433	[41]
			Hist1h3i	P68433	[41]
	Canonical H3.2	Canonical H3.2	Hist1h3b	P84228	[41]
			Hist1h3c	P84228	[41]
			Hist1h3d	P84228	[41]
			Hist1h3e	P84228	[41]
			Hist1h3f	P84228	[41]
			Hist2h3b	P84228	[41]
			Hist2h3c1	P84228	[41]
			Hist2h3c2	P84228	[41]
	H3.3	H3.3 genes: H3f3a, H3f3b	H3f3a	P84244	[101, 102]
			H3f3b	P84244	[101, 102]
		H3.3 gene: Gm6421	Gm6421	EDL18362.1	[103]
		H3.3 gene: Gm10257	Gm10257	XP_003084990.1	[103]
	cenH3-CENPA	cenH3-CENPA.s1	Cenpa	O35216	[104]
		cenH3-CENPA.s2 (putative spliced isoform)	Cenpa	D6RCV6	Short**
		cenH3-CENPA.s3 (putative spliced isoform)	Cenpa	D6RJ71	**
		cenH3-CENPA.s4 (putative spliced isoform)	Cenpa	A0A0G2JEV0	*
		cenH3-CENPA.s5 (putative spliced isoform)	Cenpa	A0A0G2JGI2	*
		cenH3-CENPA.s6 (putative spliced isoform)	Cenpa	A0A0G2JEV2	**
	H3.5	H3.5	H3f3c	P02301	***
	TS H3.4 (H3T)	TS H3.4 (H3T)	Gm12260	NP_001304932.1	[74]
H4	H4	H4	Hist1h4a	P62806	[41, 105]
			Hist1h4b	P62806	[41, 105]
			Hist1h4c	P62806	[41, 105]
			Hist1h4d	P62806	[41, 105]
			Hist1h4f	P62806	[41, 105]
			Hist1h4h	P62806	[41, 105]
			Hist1h4i	P62806	[41, 105]
			Hist1h4j	P62806	[41, 105]
			Hist1h4k	P62806	[41, 105]
			Hist1h4m	P62806	[41, 105]
			Hist1h4n	P62806	[41, 105]
			Hist2h4	P62806	[41, 105]
			Hist4h4	P62806	[41, 105]

Their protein names have been adapted to improve their identification and analysis by mass spectrometry. Indeed, the column “Entry name for MS analysis” represents the information present in the FASTA file (Additional file 1) used as a database to identify peptides and proteins after an MS analysis. The last column indicates studies on histones that described evidence of transcript and/or protein existence. For the sake of completeness, histone entries lacking a related publication were retained and the classification currently proposed by the Ensembl database was specified, as follows
* “Protein coding”, genes and/or transcript that contains an open reading frame (ORF)
** “Nonsense mediated decay”, transcript is thought to undergo nonsense mediated decay
*** “Pseudogene”, genes containing frameshift and/or stop codon(s) that disrupt the ORF
The term “Short” indicates that the putative protein is significantly smaller than conventional histones; its incorporation into chromatin and its biological function is then doubtful. Additional file 4 presents links to gene, transcripts and protein entries to Ensembl and UniProtKB databases

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