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Linker histone H1 variants

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Diagram showing the linker histone H1 binding to the nucleosome

In molecular biology, the linker histone H1 is a protein family forming a critical component of eukaryotic chromatin. H1 histones bind to the linker DNA exiting from the nucleosome core particle, while the core histones (H2A, H2B, H3 and H4) form the octamer core of the nucleosome around which the DNA is wrapped.[1]

H1 forms a complex family of related proteins with distinct specificity for tissues, developmental stages, and organisms in which they are expressed.[2] Individual H1 proteins are often referred to as isoforms or variants.

The discovery of H1 variants in calf thymus preceded the discovery of core histone variants.[3][4]

Evolutionary tree of eukaryotes showing in brackets the number of known linker histone H1 variants in a given species (see original data in [2])

Human linker histone variants

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In human and mouse cells 11 H1 variants have been described and are encoded by single genes. Six of the variants are mainly expressed during the S phase and hence replication-dependent. They are encoded by genes within histone cluster 1 located in human cells on chromosome 6. The five further variants are expressed over the whole cell cycle and their encoding genes are scattered in the genome.

Human gene symbol Unified phylogeny-based nomenclature[5]
H1 variants within histone gene cluster 1 (replication dependent)
HIST1H1A H1.1
HIST1H1B H1.5
HIST1H1C H1.2
HIST1H1D H1.3
HIST1H1E H1.4
HIST1H1T (TS) H1.6
H1 variants encoded by orphan genes (replication independent)
H1F0 H1.0
H1FNT (TS) H1.7
H1FOO (OO) H1.8
HILS1 (TS) H1.9
H1FX H1.10

TS - testis specific, OO - oocyte specific variants

Evolution

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Histone H1 differs strongly from the core histones. Rather than originating from archaeal histones, it probably evolved from a bacterial protein.[6] Unlike core histones featuring a so-called histone fold, H1s typically have a short basic N-terminal domain, a globular domain and a lysine-rich C-terminal domain (the N- and C-termini are also referred to as tails).[7] H1s are also less conserved than the core histones. The mammalian H1 isoforms are paralogs, which means their encoding genes originated from gene duplication events. The corresponding H1 variants in two different species, such as human and mouse H1.4 are orthologs – they had a common ancestor gene and were separated by speciation. Within one species, the paralogous H1 variants show a high conservation of the globular core domain, while the N- and C-termini are more divergent. At the same time H1 orthologs among mammals are highly conserved across the whole protein sequence, for example human and mouse H1.4 share 93.6% sequence identity.[2]

Function

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The extent to which individual H1 variants can be redundant and what their distinct functions are isn't yet clear. The fact that many individual H1 variant knockouts in mice are viable and show compensation by other H1 variants seems to support the hypothesis of redundancy.[8][9][10][11] However, many lines of evidence suggest specific functions exist for H1 variants. For example, individual H1 variant knockout mice reveal specific phenotypes and distinct effects on gene expression and chromatin structure.[9][10][12][13][14][15] Also, different isotypes show different localization and bind to chromatin with different affinities.[16][17][18][19][20][21]

Therefore, a model has been proposed according to which H1 variants have two distinct roles, a common and a specific one:[2] Individual H1 proteins are redundant in their ability to compact chromatin globally and to stabilize overall higher order chromatin structures. Such a common role can therefore be compensated in mutant cells by increasing the amount of other H1 variants. However, at the level of local chromatin organization, individual variants can regulate a subset of specific genes both in a negative and positive way.[2]

Nomenclature

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Multiple nomenclatures (around 12) for linker histone variants have been proposed and used in publications previously, greatly complicating comparison across studies. In 1994 Parseghian et al. have attempted to create a system in which variant designations were applied uniformly to orthologs across mammalian species,[22] however this nomenclature hasn't been taken up by other laboratories. In 2012, a diverse group of scientists from multiple institutions across the world working on different aspects of histone biology proposed a unified phylogeny-based nomenclature for histone variants, including H1 histones, with the aim of producing informative and easily searchable histone variant names.[5]

See also

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References

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  1. ^ Jordan, Albert (2016-03-01). "Histone H1 in gene expression and development". Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 1859 (3): 429–430. doi:10.1016/j.bbagrm.2016.01.001. hdl:10261/133904. ISSN 0006-3002. PMID 26772994.
  2. ^ a b c d e Izzo, Annalisa; Kamieniarz, Kinga; Schneider, Robert (2008-04-01). "The histone H1 family: specific members, specific functions?". Biological Chemistry. 389 (4): 333–343. doi:10.1515/BC.2008.037. ISSN 1431-6730. PMID 18208346. S2CID 1516241.
  3. ^ Kinkade, JM; Cole, RD (Dec 25, 1966). "The resolution of four lysine-rich histones derived from calf thymus". J Biol Chem. 241 (24): 5790–7. doi:10.1016/S0021-9258(18)96342-8. PMID 5954358.
  4. ^ Kinkade, JM; Cole, RD (Dec 25, 1966). "A structural comparison of different lysine-rich histones of calf thymus". J Biol Chem. 241 (24): 5798–805. doi:10.1016/S0021-9258(18)96343-X. PMID 5954359.
  5. ^ a b Talbert, Paul B.; Ahmad, Kami; Almouzni, Geneviève; Ausió, Juan; Berger, Frederic; Bhalla, Prem L.; Bonner, William M.; Cande, W. Zacheus; Chadwick, Brian P. (2012-01-01). "A unified phylogeny-based nomenclature for histone variants". Epigenetics & Chromatin. 5: 7. doi:10.1186/1756-8935-5-7. ISSN 1756-8935. PMC 3380720. PMID 22650316.
  6. ^ Kasinsky, H. E.; Lewis, J. D.; Dacks, J. B.; Ausió, J. (2001-01-01). "Origin of H1 linker histones". FASEB Journal. 15 (1): 34–42. doi:10.1096/fj.00-0237rev. ISSN 0892-6638. PMID 11149891. S2CID 10089116.
  7. ^ Crane-Robinson, C. (2016-03-01). "Linker histones: History and current perspectives". Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 1859 (3): 431–435. doi:10.1016/j.bbagrm.2015.10.008. ISSN 0006-3002. PMID 26459501.
  8. ^ Fan, Y.; Sirotkin, A.; Russell, R. G.; Ayala, J.; Skoultchi, A. I. (2001-12-01). "Individual somatic H1 subtypes are dispensable for mouse development even in mice lacking the H1(0) replacement subtype". Molecular and Cellular Biology. 21 (23): 7933–7943. doi:10.1128/MCB.21.23.7933-7943.2001. ISSN 0270-7306. PMC 99962. PMID 11689686.
  9. ^ a b Fan, Yuhong; Nikitina, Tatiana; Morin-Kensicki, Elizabeth M.; Zhao, Jie; Magnuson, Terry R.; Woodcock, Christopher L.; Skoultchi, Arthur I. (2003-07-01). "H1 linker histones are essential for mouse development and affect nucleosome spacing in vivo". Molecular and Cellular Biology. 23 (13): 4559–4572. doi:10.1128/mcb.23.13.4559-4572.2003. ISSN 0270-7306. PMC 164858. PMID 12808097.
  10. ^ a b Alami, Raouf; Fan, Yuhong; Pack, Stephanie; Sonbuchner, Timothy M.; Besse, Arnaud; Lin, Qingcong; Greally, John M.; Skoultchi, Arthur I.; Bouhassira, Eric E. (2003-05-13). "Mammalian linker-histone subtypes differentially affect gene expression in vivo". Proceedings of the National Academy of Sciences of the United States of America. 100 (10): 5920–5925. Bibcode:2003PNAS..100.5920A. doi:10.1073/pnas.0736105100. ISSN 0027-8424. PMC 156302. PMID 12719535.
  11. ^ Sirotkin, AM; Edelmann, W; Cheng, G; Klein-Szanto, A; Kucherlapati, R; Skoultchi, AI (3 July 1995). "Mice develop normally without the H1(0) linker histone". Proc Natl Acad Sci U S A. 92 (14): 6434–8. Bibcode:1995PNAS...92.6434S. doi:10.1073/pnas.92.14.6434. PMC 41532. PMID 7604008.
  12. ^ Fan, Yuhong; Nikitina, Tatiana; Zhao, Jie; Fleury, Tomara J.; Bhattacharyya, Riddhi; Bouhassira, Eric E.; Stein, Arnold; Woodcock, Christopher L.; Skoultchi, Arthur I. (2005-12-29). "Histone H1 depletion in mammals alters global chromatin structure but causes specific changes in gene regulation". Cell. 123 (7): 1199–1212. doi:10.1016/j.cell.2005.10.028. ISSN 0092-8674. PMID 16377562. S2CID 8378657.
  13. ^ Gabrilovich, Dmitry I.; Cheng, Pingyan; Fan, Yuhong; Yu, Bin; Nikitina, Ekaterina; Sirotkin, Allen; Shurin, Michael; Oyama, Tsunehiro; Adachi, Yasushi (2002-08-01). "H1(0) histone and differentiation of dendritic cells. A molecular target for tumor-derived factors". Journal of Leukocyte Biology. 72 (2): 285–296. doi:10.1189/jlb.72.2.285. ISSN 0741-5400. PMID 12149419. S2CID 40524167.
  14. ^ Martianov, Igor; Brancorsini, Stefano; Catena, Raffaella; Gansmuller, Anne; Kotaja, Noora; Parvinen, Martti; Sassone-Corsi, Paolo; Davidson, Irwin (2005-02-22). "Polar nuclear localization of H1T2, a histone H1 variant, required for spermatid elongation and DNA condensation during spermiogenesis". Proceedings of the National Academy of Sciences of the United States of America. 102 (8): 2808–2813. Bibcode:2005PNAS..102.2808M. doi:10.1073/pnas.0406060102. ISSN 0027-8424. PMC 549447. PMID 15710904.
  15. ^ Tanaka, Hiromitsu; Iguchi, Naoko; Isotani, Ayako; Kitamura, Kouichi; Toyama, Yoshiro; Matsuoka, Yasuhiro; Onishi, Masayoshi; Masai, Kumiko; Maekawa, Mamiko (2005-08-01). "HANP1/H1T2, a novel histone H1-like protein involved in nuclear formation and sperm fertility". Molecular and Cellular Biology. 25 (16): 7107–7119. doi:10.1128/MCB.25.16.7107-7119.2005. ISSN 0270-7306. PMC 1190238. PMID 16055721.
  16. ^ Parseghian, M. H.; Newcomb, R. L.; Winokur, S. T.; Hamkalo, B. A. (2000-01-01). "The distribution of somatic H1 subtypes is non-random on active vs. inactive chromatin: distribution in human fetal fibroblasts". Chromosome Research. 8 (5): 405–424. doi:10.1023/A:1009262819961. ISSN 0967-3849. PMID 10997781. S2CID 28425496.
  17. ^ Th'ng, John P. H.; Sung, Rohyun; Ye, Ming; Hendzel, Michael J. (2005-07-29). "H1 family histones in the nucleus. Control of binding and localization by the C-terminal domain". The Journal of Biological Chemistry. 280 (30): 27809–27814. doi:10.1074/jbc.M501627200. ISSN 0021-9258. PMID 15911621.
  18. ^ Orrego, Mary; Ponte, Imma; Roque, Alicia; Buschati, Natascha; Mora, Xavier; Suau, Pedro (2007-01-01). "Differential affinity of mammalian histone H1 somatic subtypes for DNA and chromatin". BMC Biology. 5: 22. doi:10.1186/1741-7007-5-22. ISSN 1741-7007. PMC 1890542. PMID 17498293.
  19. ^ Izzo, Annalisa; Kamieniarz-Gdula, Kinga; Ramírez, Fidel; Noureen, Nighat; Kind, Jop; Manke, Thomas; van Steensel, Bas; Schneider, Robert (2013-06-27). "The genomic landscape of the somatic linker histone subtypes H1.1 to H1.5 in human cells". Cell Reports. 3 (6): 2142–2154. doi:10.1016/j.celrep.2013.05.003. ISSN 2211-1247. PMID 23746450.
  20. ^ Millán-Ariño, Lluís; Islam, Abul B. M. M. K.; Izquierdo-Bouldstridge, Andrea; Mayor, Regina; Terme, Jean-Michel; Luque, Neus; Sancho, Mónica; López-Bigas, Núria; Jordan, Albert (2014-04-01). "Mapping of six somatic linker histone H1 variants in human breast cancer cells uncovers specific features of H1.2". Nucleic Acids Research. 42 (7): 4474–4493. doi:10.1093/nar/gku079. ISSN 1362-4962. PMC 3985652. PMID 24476918.
  21. ^ Millán-Ariño, Lluís; Izquierdo-Bouldstridge, Andrea; Jordan, Albert (2016-03-01). "Specificities and genomic distribution of somatic mammalian histone H1 subtypes". Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 1859 (3): 510–519. doi:10.1016/j.bbagrm.2015.10.013. ISSN 0006-3002. PMID 26477490.
  22. ^ Parseghian, MH; Henschen, AH; Krieglstein, KG; Hamkalo, BA (April 1994). "A proposal for a coherent mammalian histone H1 nomenclature correlated with amino acid sequences". Protein Sci. 3 (4): 575–87. doi:10.1002/pro.5560030406. PMC 2142865. PMID 8003976.
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