CBX5 (gene) explained

Chromobox protein homolog 5 is a protein that in humans is encoded by the CBX5 gene.^{[1] [2]} It is a highly conserved, non-histone protein part of the heterochromatin family. The protein itself is more commonly called (in humans) HP1α. Heterochromatin protein-1 (HP1) has an N-terminal domain that acts on methylated lysines residues leading to epigenetic repression. The C-terminal of this protein has a chromo shadow-domain (CSD) that is responsible for homodimerizing, as well as interacting with a variety of chromatin-associated, non-histone proteins.

Structure

HP1α is 191 amino acids in length containing 6 exons.^{[3] [4]} As mentioned above, this protein contains two domains, an N-terminal chromodomain (CD) and a C- terminal chromoshadow domain (CSD). The CD binds with histone 3 through a methylated lysine residue at position 9 (H3K9) while the C-terminal CSD homodimerizes and interacts with a variety of other chromatin-associated, non-histone related proteins. Connecting these two domains is the hinge region.^[5]

Chromodomain

Once translated, the chromodomain will take on a globular conformation consisting of three β-sheets and one α-helix. The β-sheets are packed up against the helix at the carboxy terminal segment. The charges on the β sheets are negative thus making it difficult for it to bind to the DNA as a DNA-binding motif. Instead, HP1α binds to the histones as a protein interaction motif. Specific binding to CD to the methylated H3K9 is mediated by three hydrophobic side chains called the "hydrophobic box". Other sites on HP1 will interact with the H3 tails from neighbouring histones which will give structure to the flexible N-terminal tail of the histones. Neighbouring H3 histones can affect HP1 binding by post-translationally modifying the tails.

Chromoshadow domain

The CSD much resembles that of the CD. It too has a globular conformation containing three β-sheets, however it possesses two α-helices as opposed to just the one in the CD. The CSD readily homodimerizes in vitro and as a result forms a groove which can accommodate HP1 associated proteins that have a specific consensus sequence: PxVxL, where P is Proline, V is Valine, L is Leucine and x is any amino acid.

Mechanism of action

HP1α primarily functions as a gene silencer, which is dependent on the interactions between the CD and the methyl H3K9 mark.^[6] The hydrophobic box on the CD provides the appropriate environment for the methylated lysine residue. While the exact mechanism of how gene silencing is done is unknown, experimental data concluded the rapid exchange of biological macromolecules in and out of the heterochromatin region. This suggests HP1 isn't acting as a glue holding the heterochromatin together, but rather there are competing molecules within that interact in various ways to create a closed complex leading to gene repression or an open, euchromatin structure with gene activation. HP1 concentration is higher and more static in areas of the chromosome where methylated H3K9 residues reside, giving the chromosome its closed, gene-repressed heterochromatin structure. It has also been shown that the more methylated the H3 lysine is, the higher the affinity HP1 has for it. That is, trimethylated lysine residues bind tighter to HP1 than dimethylated residues, which bind better than monomethylated residues.

The localisation driving factor is currently unknown.

Evolutionary conservation

HP1α is a highly evolutionarily conserved protein, existing in species such as Schizosaccharomyces pombe, a type of yeast, all the way to humans. The N-terminal chromodomain and C-terminal chromoshadow domain appear to be much more conserved (approximately 50-70% amino acid similarity) than the hinge region (approximately 25-30% similarity with the Drosophila HP1 homolog).

Interactions

CBX5 (gene) has been shown to interact with:

• CBX1,
• CBX3,
• CHAF1A,
• DNMT3B,^[7]
• HDAC4,
• HDAC9,^[8]
• Histone deacetylase 5,^[8]
• Ku70,^[9]
• Lamin B receptor,^[10]
• MBD1,^{[11] [12]}
• MIS12,^[13]
• SMARCA4,
• SUV39H1,^{[8] [12] [14]}
• TAF4,^[15] and
• TRIM28.^{[16] [17] [18] [19]}
• STAT5A,^[20]

See also

• Heterochromatin protein 1

Further reading

• Saunders WS, Chue C, Goebl M, Craig C, Clark RF, Powers JA, Eissenberg JC, Elgin SC, Rothfield NF, Earnshaw WC . Molecular cloning of a human homologue of Drosophila heterochromatin protein HP1 using anti-centromere autoantibodies with anti-chromo specificity . Journal of Cell Science . 104 . 2 . 573–82 . Feb 1993 . 10.1242/jcs.104.2.573 . 8505380 .
• Sugimoto K, Yamada T, Muro Y, Himeno M . Human homolog of Drosophila heterochromatin-associated protein 1 (HP1) is a DNA-binding protein which possesses a DNA-binding motif with weak similarity to that of human centromere protein C (CENP-C) . Journal of Biochemistry . 120 . 1 . 153–9 . Jul 1996 . 8864858 . 10.1093/oxfordjournals.jbchem.a021378 .
• Ye Q, Callebaut I, Pezhman A, Courvalin JC, Worman HJ . Domain-specific interactions of human HP1-type chromodomain proteins and inner nuclear membrane protein LBR . The Journal of Biological Chemistry . 272 . 23 . 14983–9 . Jun 1997 . 9169472 . 10.1074/jbc.272.23.14983 . 39872511 . free .
• Lessard J, Baban S, Sauvageau G . Stage-specific expression of polycomb group genes in human bone marrow cells . Blood . 91 . 4 . 1216–24 . Feb 1998 . 9454751 . 10.1182/blood.V91.4.1216. free .
• Ainsztein AM, Kandels-Lewis SE, Mackay AM, Earnshaw WC . INCENP centromere and spindle targeting: identification of essential conserved motifs and involvement of heterochromatin protein HP1 . The Journal of Cell Biology . 143 . 7 . 1763–74 . Dec 1998 . 9864353 . 2175214 . 10.1083/jcb.143.7.1763 .
• Minc E, Allory Y, Worman HJ, Courvalin JC, Buendia B . Localization and phosphorylation of HP1 proteins during the cell cycle in mammalian cells . Chromosoma . 108 . 4 . 220–34 . Aug 1999 . 10460410 . 10.1007/s004120050372 . 12381860 .
• Murzina N, Verreault A, Laue E, Stillman B . Heterochromatin dynamics in mouse cells: interaction between chromatin assembly factor 1 and HP1 proteins . Molecular Cell . 4 . 4 . 529–40 . Oct 1999 . 10549285 . 10.1016/S1097-2765(00)80204-X . free .
• Nielsen AL, Ortiz JA, You J, Oulad-Abdelghani M, Khechumian R, Gansmuller A, Chambon P, Losson R . Interaction with members of the heterochromatin protein 1 (HP1) family and histone deacetylation are differentially involved in transcriptional silencing by members of the TIF1 family . The EMBO Journal . 18 . 22 . 6385–95 . Nov 1999 . 10562550 . 1171701 . 10.1093/emboj/18.22.6385 .
• Zhao T, Heyduk T, Allis CD, Eissenberg JC . Heterochromatin protein 1 binds to nucleosomes and DNA in vitro . The Journal of Biological Chemistry . 275 . 36 . 28332–8 . Sep 2000 . 10882726 . 10.1074/jbc.M003493200 . free .
• Lechner MS, Begg GE, Speicher DW, Rauscher FJ . Molecular determinants for targeting heterochromatin protein 1-mediated gene silencing: direct chromoshadow domain-KAP-1 corepressor interaction is essential . Molecular and Cellular Biology . 20 . 17 . 6449–65 . Sep 2000 . 10938122 . 86120 . 10.1128/MCB.20.17.6449-6465.2000 .
• Song K, Jung Y, Jung D, Lee I . Human Ku70 interacts with heterochromatin protein 1alpha . The Journal of Biological Chemistry . 276 . 11 . 8321–7 . Mar 2001 . 11112778 . 10.1074/jbc.M008779200 . 84712852 . free .
• Lachner M, O'Carroll D, Rea S, Mechtler K, Jenuwein T . Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins . Nature . 410 . 6824 . 116–20 . Mar 2001 . 11242053 . 10.1038/35065132 . 4331863 .
• Bannister AJ, Zegerman P, Partridge JF, Miska EA, Thomas JO, Allshire RC, Kouzarides T . Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain . Nature . 410 . 6824 . 120–4 . Mar 2001 . 11242054 . 10.1038/35065138 . 4334447 .
• Nielsen AL, Oulad-Abdelghani M, Ortiz JA, Remboutsika E, Chambon P, Losson R . Heterochromatin formation in mammalian cells: interaction between histones and HP1 proteins . Molecular Cell . 7 . 4 . 729–39 . Apr 2001 . 11336697 . 10.1016/S1097-2765(01)00218-0 . free . 10261/308369 . free .
• Wheatley SP, Carvalho A, Vagnarelli P, Earnshaw WC . INCENP is required for proper targeting of Survivin to the centromeres and the anaphase spindle during mitosis . Current Biology . 11 . 11 . 886–90 . Jun 2001 . 11516652 . 10.1016/S0960-9822(01)00238-X . 381637 . free . 2001CBio...11..886W .
• Scholzen T, Endl E, Wohlenberg C, van der Sar S, Cowell IG, Gerdes J, Singh PB . The Ki-67 protein interacts with members of the heterochromatin protein 1 (HP1) family: a potential role in the regulation of higher-order chromatin structure . The Journal of Pathology . 196 . 2 . 135–44 . Feb 2002 . 11793364 . 10.1002/path.1016 . 36130549 .
• Weinmann AS, Yan PS, Oberley MJ, Huang TH, Farnham PJ . Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis . Genes & Development . 16 . 2 . 235–44 . Jan 2002 . 11799066 . 155318 . 10.1101/gad.943102 .
• Sugimoto K, Tasaka H, Dotsu M . Molecular behavior in living mitotic cells of human centromere heterochromatin protein HPLalpha ectopically expressed as a fusion to red fluorescent protein . Cell Structure and Function . 26 . 6 . 705–18 . Dec 2001 . 11942629 . 10.1247/csf.26.705 . free .
• Vassallo MF, Tanese N . Isoform-specific interaction of HP1 with human TAFII130 . Proceedings of the National Academy of Sciences of the United States of America . 99 . 9 . 5919–24 . Apr 2002 . 11959914 . 122877 . 10.1073/pnas.092025499 . 2002PNAS...99.5919V . free .

Notes and References

1. Ye Q, Worman HJ . Interaction between an integral protein of the nuclear envelope inner membrane and human chromodomain proteins homologous to Drosophila HP1 . The Journal of Biological Chemistry . 271 . 25 . 14653–6 . Jun 1996 . 8663349 . 10.1074/jbc.271.25.14653 . 23643628 . free .
2. Web site: Entrez Gene: CBX5 chromobox homolog 5 (HP1 alpha homolog, Drosophila).
3. Web site: OMIM Entry- * 604478 - CHROMOBOX HOMOLOG 5; CBX5. omim.org. 2015-11-02.
4. Lomberk G, Wallrath L, Urrutia R . 2006 . The heterochromatin protein 1 family . Genome Biol . 7 . 7. 228 . 10.1186/gb-2006-7-7-228 . 17224041 . 1779566 . free .
5. Heterochromatin Protein 1: a pervasive controlling influence. Hiragami. K. 15 August 2005. Cellular and Molecular Life Sciences. 10.1007/s00018-005-5287-9. 16261261. 62. 23. 2711–2726. 31117054. 11139183.
6. Web site: CBX5 chromobox homolog 5 [Homo sapiens (human)] - Gene - NCBI]. www.ncbi.nlm.nih.gov. 2015-10-16.
7. Lehnertz B, Ueda Y, Derijck AA, Braunschweig U, Perez-Burgos L, Kubicek S, Chen T, Li E, Jenuwein T, Peters AH . Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin . Current Biology . 13 . 14 . 1192–200 . Jul 2003 . 12867029 . 10.1016/s0960-9822(03)00432-9. 2320997 . free . 2003CBio...13.1192L .
8. Zhang CL, McKinsey TA, Olson EN . Association of class II histone deacetylases with heterochromatin protein 1: potential role for histone methylation in control of muscle differentiation . Molecular and Cellular Biology . 22 . 20 . 7302–12 . Oct 2002 . 12242305 . 139799 . 10.1128/mcb.22.20.7302-7312.2002.
9. Song K, Jung Y, Jung D, Lee I . Human Ku70 interacts with heterochromatin protein 1alpha . The Journal of Biological Chemistry . 276 . 11 . 8321–7 . Mar 2001 . 11112778 . 10.1074/jbc.M008779200 . 84712852 . free .
10. Ye Q, Worman HJ . Interaction between an integral protein of the nuclear envelope inner membrane and human chromodomain proteins homologous to Drosophila HP1 . The Journal of Biological Chemistry . 271 . 25 . 14653–6 . Jun 1996 . 8663349 . 10.1074/jbc.271.25.14653. 23643628 . free .
11. Reese BE, Bachman KE, Baylin SB, Rountree MR . The methyl-CpG binding protein MBD1 interacts with the p150 subunit of chromatin assembly factor 1 . Molecular and Cellular Biology . 23 . 9 . 3226–36 . May 2003 . 12697822 . 153189 . 10.1128/mcb.23.9.3226-3236.2003.
12. Fujita N, Watanabe S, Ichimura T, Tsuruzoe S, Shinkai Y, Tachibana M, Chiba T, Nakao M . Methyl-CpG binding domain 1 (MBD1) interacts with the Suv39h1-HP1 heterochromatic complex for DNA methylation-based transcriptional repression . The Journal of Biological Chemistry . 278 . 26 . 24132–8 . Jun 2003 . 12711603 . 10.1074/jbc.M302283200 . 24340120 . free .
13. Obuse C, Iwasaki O, Kiyomitsu T, Goshima G, Toyoda Y, Yanagida M . A conserved Mis12 centromere complex is linked to heterochromatic HP1 and outer kinetochore protein Zwint-1 . Nature Cell Biology . 6 . 11 . 1135–41 . Nov 2004 . 15502821 . 10.1038/ncb1187 . 39408000 .
14. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M . Towards a proteome-scale map of the human protein-protein interaction network . Nature . 437 . 7062 . 1173–8 . Oct 2005 . 16189514 . 10.1038/nature04209 . 2005Natur.437.1173R . 4427026 .
15. Vassallo MF, Tanese N . Isoform-specific interaction of HP1 with human TAFII130 . Proceedings of the National Academy of Sciences of the United States of America . 99 . 9 . 5919–24 . Apr 2002 . 11959914 . 122877 . 10.1073/pnas.092025499 . 2002PNAS...99.5919V . free .
16. Nielsen AL, Oulad-Abdelghani M, Ortiz JA, Remboutsika E, Chambon P, Losson R . Heterochromatin formation in mammalian cells: interaction between histones and HP1 proteins . Molecular Cell . 7 . 4 . 729–39 . Apr 2001 . 11336697 . 10.1016/S1097-2765(01)00218-0. free . 10261/308369 . free .
17. Lechner MS, Begg GE, Speicher DW, Rauscher FJ . Molecular determinants for targeting heterochromatin protein 1-mediated gene silencing: direct chromoshadow domain-KAP-1 corepressor interaction is essential . Molecular and Cellular Biology . 20 . 17 . 6449–65 . Sep 2000 . 10938122 . 86120 . 10.1128/mcb.20.17.6449-6465.2000.
18. Nielsen AL, Sanchez C, Ichinose H, Cerviño M, Lerouge T, Chambon P, Losson R . Selective interaction between the chromatin-remodeling factor BRG1 and the heterochromatin-associated protein HP1alpha . The EMBO Journal . 21 . 21 . 5797–806 . Nov 2002 . 12411497 . 131057 . 10.1093/emboj/cdf560.
19. Cammas F, Oulad-Abdelghani M, Vonesch JL, Huss-Garcia Y, Chambon P, Losson R . Cell differentiation induces TIF1beta association with centromeric heterochromatin via an HP1 interaction . Journal of Cell Science . 115 . Pt 17 . 3439–48 . Sep 2002 . 10.1242/jcs.115.17.3439 . 12154074 . free .
20. Hu X, Dutta P, Tsurumi A, Li J, Wang J, Land H, Li WX . Unphosphorylated STAT5A stabilizes heterochromatin and suppresses tumor growth . Proc Natl Acad Sci U S A . 110 . 25 . 10213–10218 . Jun 2013 . 23733954 . 10.1073/pnas.1221243110 . 3690839. 2013PNAS..11010213H . free .