Table 2.
Manually curated list of 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