Epigenetic Histone Marks of Extended Meta-Polycentric Centromeres of Lathyrus and Pisum Chromosomes
Status PubMed-not-MEDLINE Jazyk angličtina Země Švýcarsko Médium electronic-ecollection
Typ dokumentu časopisecké články
PubMed
26973677
PubMed Central
PMC4771749
DOI
10.3389/fpls.2016.00234
Knihovny.cz E-zdroje
- Klíčová slova
- centromere structure, epigenetic modifications, histone methylation, histone phosphorylation, holocentric, meta-polycentric chromosomes,
- Publikační typ
- časopisecké články MeSH
Species of the legume genera Lathyrus and Pisum possess chromosomes that exhibit a unique structure of their centromeric regions, which is clearly apparent during metaphase by the formation of extended primary constrictions which span up to a third of the length of the chromosome. In addition, these species express two different variants of the CenH3 protein which are co-localized in multiple domains along the poleward surface of the primary constrictions. Here, we show that the constrictions represent a distinct type of chromatin differing from the chromosome arms. In metaphase, histone phosphorylation patterns including H3S10ph, H3S28ph, and H3T3ph were observed along the entire constriction, in a way similar to holocentric chromosomes. On the other hand, distribution of phosphorylated H2AT120 was different from that previously reported from either, holocentric and monocentric chromosomes, occurring at chromatin surrounding but not overlapping CenH3 domains. Since some of these phosphorylations play a role in chromatid cohesion, it can be assumed that they facilitate correct chromosome segregation by ensuring that multiple separate CenH3 domains present on the same chromatid are oriented toward the same pole. The constrictions also displayed distinct patterns of histone methylation marks, being enriched in H3K9me2 and depleted in H3K4me3 and H3K27me2 compared to the chromosome arms. Super-resolution fluorescence microscopy revealed that although both CenH3 protein variants are present in all CenH3 domains detected on metaphase chromosomes, they are only partially co-localized while there are chromatin subdomains which are mostly made of only one CenH3 variant. Taken together, these data revealed specific features of extended primary constrictions of Lathyrus and Pisum and support the idea that they may represent an intermediate stage between monocentric and holocentric chromosomes.
Zobrazit více v PubMed
Ashtiyani R. K., Moghaddam A. M. B., Schubert V., Rutten T., Fuchs J., Demidov D., et al. . (2011). AtHaspin phosphorylates histone H3 at threonine 3 during mitosis and contributes to embryonic patterning in Arabidopsis. Plant J. 68, 443–454. 10.1111/j.1365-313X.2011.04699.x PubMed DOI
Bannister A. J., Zegerman P., Partridge J. F., Miska E. A., Thomas J. O., Allshire R. C., et al. . (2001). Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410, 120–124. 10.1038/35065138 PubMed DOI
Bassett E. A., DeNizio J., Barnhart-Dailey M. C., Panchenko T., Sekulic N., Rogers D. J., et al. . (2012). HJURP uses distinct CENP-A surfaces to recognize and to stabilize CENP-A/histone H4 for centromere assembly. Dev. Cell 22, 749–762. 10.1016/j.devcel.2012.02.001 PubMed DOI PMC
Bernard P., Maure J. F., Partridge J. F., Genier S., Javerzat J. P., Allshire R. C. (2001). Requirement of heterochromatin for cohesion at centromeres. Science 294, 2539–2542. 10.1126/science.1064027 PubMed DOI
Birchler J. A., Gao Z., Sharma A., Presting G. G., Han F. (2011). Epigenetic aspects of centromere function in plants. Curr. Opin. Plant Biol. 14, 217–222. 10.1016/j.pbi.2011.02.004 PubMed DOI
Birchler J. A., Han F. (2013). Centromere epigenetics in plants. J. Genet. Genomics 40, 201–204. 10.1016/j.jgg.2013.03.008 PubMed DOI
Black B. E., Bassett E. A. (2008). The histone variant CENP-A and centromere specification. Curr. Opin. Cell Biol. 20, 91–100. 10.1016/j.ceb.2007.11.007 PubMed DOI
Bolanos-Garcia V. M., Blundell T. L. (2011). BUB1 and BUBR1: multifaceted kinases of the cell cycle. Trends Biochem. Sci. 36, 141–150. 10.1016/j.tibs.2010.08.004 PubMed DOI PMC
Caperta A. D., Rosa M., Delgado M., Karimi R., Demidov D., Viegas W., et al. . (2008). Distribution patterns of phosphorylated Thr 3 and Thr 32 of histone H3 in plant mitosis and meiosis. Cytogenet. Genome Res. 122, 73–79. 10.1159/000151319 PubMed DOI
Cuacos M. H., Franklin F. C., Heckmann S. (2015). Atypical centromeres in plants—what they can tell us. Front. Plant Sci. 6:913. 10.3389/fpls.2015.00913 PubMed DOI PMC
Demidov D., Hesse S., Tewes A., Rutten T., Fuchs J., Karimi Ashtiyani R., et al. . (2009). Aurora1 phosphorylation activity on histone H3 and its cross-talk with other post-translational histone modifications in Arabidopsis. Plant J. 59, 221–230. 10.1111/j.1365-313X.2009.03861.x PubMed DOI
Demidov D., Schubert V., Kumke K., Weiss O., Karimi-Ashtiyani R., Buttlar J., et al. . (2014). Anti-phosphorylated histone H2AThr120: a universal microscopic marker for centromeric chromatin of mono- and holocentric plant species. Cytogenet. Genome Res. 143, 150–156. 10.1159/000360018 PubMed DOI
Dong Q., Han F. (2012). Phosphorylation of histone H2A is associated with centromere function and maintenance in meiosis. Plant J. 71, 800–809. 10.1111/j.1365-313X.2012.05029.x PubMed DOI
Duan Q., Chen H., Costa M., Dai W. (2008). Phosphorylation of H3S10 blocks the access of H3K9 by specific antibodies and histone methyltransferase: implication in regulating chromatin dynamics and epigenetic inheritance during mitosis. J. Biol. Chem. 283, 33585–33590. 10.1074/jbc.M803312200 PubMed DOI PMC
Dunleavy E. M., Zhang W., Karpen G. H. (2013). Solo or doppio: how many CENP-As make a centromeric nucleosome? Nat. Struct. Mol. Biol. 20, 648–650. 10.1038/nsmb.2602 PubMed DOI
Finseth F. R., Dong Y., Saunders A., Fishman L. (2015). Duplication and adaptive evolution of a key centromeric protein in Mimulus, a genus with female meiotic drive. Mol. Biol. Evol. 32, 2694–2706. 10.1093/molbev/msv145 PubMed DOI
Fu S., Gao Z., Birchler J., Han F. (2012). Dicentric chromosome formation and epigenetics of centromere formation in plants. J. Genet. Genomics 39, 125–130. 10.1016/j.jgg.2012.01.006 PubMed DOI
Fuchs J., Demidov D., Houben A., Schubert I. (2006). Chromosomal histone modification patterns—from conservation to diversity. Trends Plant Sci. 11, 199–208. 10.1016/j.tplants.2006.02.008 PubMed DOI
Fuchs J., Jovtchev G., Schubert I. (2008). The chromosomal distribution of histone methylation marks in gymnosperms differs from that of angiosperms. Chromosom. Res. 16, 891–898. 10.1007/s10577-008-1252-4 PubMed DOI
Fuchs J., Schubert I. (2012). Chromosomal distribution and functional interpretation of epigenetic histone marks in plants, in Plant Cytogenetics, eds Bass H. W., Birchler J. A. (New York, NY: Springer; ), 232–246. 10.1007/978-0-387-70869-0 DOI
Funabiki H., Wynne D. J. (2013). Making an effective switch at the kinetochore by phosphorylation and dephosphorylation. Chromosoma 122, 135–158. 10.1007/s00412-013-0401-5 PubMed DOI PMC
Gernand D., Demidov D., Houben A. (2003). The temporal and spatial pattern of histone H3 phosphorylation at serine 28 and serine 10 is similar in plants but differs between mono- and polycentric chromosomes. Cytogenet. Genome Res. 101, 172–176. 10.1159/000074175 PubMed DOI
Gong Z., Wu Y., Koblížková A., Torres G. A., Wang K., Iovene M., et al. . (2012). Repeatless and repeat-based centromeres in potato: implications for centromere evolution. Plant Cell 24, 3559–3574. 10.1105/tpc.112.100511 PubMed DOI PMC
Guerra M., Brasileiro-Vidal A. C., Arana P., Puertas M. J. (2006). Mitotic microtubule development and histone H3 phosphorylation in the holocentric chromosomes of Rhynchospora tenuis (Cyperaceae). Genetica 126, 33–41. 10.1007/s10709-005-1430-7 PubMed DOI
Han F., Lamb J. C., Birchler J. A. (2006). High frequency of centromere inactivation resulting in stable dicentric chromosomes of maize. Proc. Natl. Acad. Sci. U.S.A. 103, 3238–3243. 10.1073/pnas.0509650103 PubMed DOI PMC
Hasson D., Panchenko T., Salimian K. J., Salman M. U., Sekulic N., Alonso A., et al. . (2013). The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat. Struct. Mol. Biol. 20, 687–695. 10.1038/nsmb.2562 PubMed DOI PMC
Heckmann S., Macas J., Kumke K., Fuchs J., Schubert V., Ma L., et al. . (2013). The holocentric species Luzula elegans shows interplay between centromere and large-scale genome organization. Plant J. 73, 555–565. 10.1111/tpj.12054 PubMed DOI
Henikoff S., Dalal Y. (2005). Centromeric chromatin: what makes it unique? Curr. Opin. Genet. Dev. 15, 177–184. 10.1016/j.gde.2005.01.004 PubMed DOI
Higgins J. M. G. (2010). Haspin: a newly discovered regulator of mitotic chromosome behavior. Chromosoma 119, 137–147. 10.1007/s00412-009-0250-4 PubMed DOI PMC
Houben A., Demidov D., Caperta A. D., Karimi R., Agueci F., Vlasenko L. (2007). Phosphorylation of histone H3 in plants–a dynamic affair. Biochim. Biophys. Acta 1769, 308–315. 10.1016/j.bbaexp.2007.01.002 PubMed DOI
Houben A., Demidov D., Gernand D., Meister A., Leach C. R., Schubert I. (2003). Methylation of histone H3 in euchromatin of plant chromosomes depends on basic nuclear DNA content. Plant J. Cell Mol. Biol. 33, 967–973. 10.1046/j.1365-313X.2003.01681.x PubMed DOI
Houben A., Wako T., Furushima-Shimogawara R., Presting G., Künzel G., Schubert I., et al. . (1999). The cell cycle dependent phosphorylation of histone H3 is correlated with the condensation of plant mitotic chromosomes. Plant J. 18, 675–679. 10.1046/j.1365-313X.1999.00496.x PubMed DOI
Ishii T., Karimi-Ashtiyani R., Banaei-Moghaddam A. M., Schubert V., Fuchs J., Houben A. (2015). The differential loading of two barley CENH3 variants into distinct centromeric substructures is cell type- and development-specific. Chromosom. Res. 23, 277–284. 10.1007/s10577-015-9466-8 PubMed DOI
Jacob Y., Feng S., Leblanc C. A., Bernatavichute Y. V., Cokus S., Johnson L. M., et al. (2010). ATXR5 and ATXR6 are novel H3K27 monomethyltransferases required for chromatin structure and gene silencing. Nat. Struct. Mol. Biol. 16, 763–768. 10.1038/nsmb.1611.ATXR5 PubMed DOI PMC
Jasencakova Z., Soppe W. J. J., Meister A., Gernand D., Turner B. M., Schubert I. (2003). Histone modifications in Arabidopsis—high methylation of H3 lysine 9 is dispensable for constitutive heterochromatin. Plant J. 33, 471–480. 10.1046/j.1365-313X.2003.01638.x PubMed DOI
Jeong Y. S., Cho S., Park J. S., Ko Y., Kang Y. K. (2010). Phosphorylation of serine-10 of histone H3 shields modified lysine-9 selectively during mitosis. Genes Cells 15, 181–192. 10.1111/j.1365-2443.2009.01375.x PubMed DOI
Jiang J., Birchler J. A., Parrott W. A., Dawe R. K. (2003). A molecular view of plant centromeres. Trends Plant Sci. 8, 570–575. 10.1016/j.tplants.2003.10.011 PubMed DOI
Kaszás E., Cande W. Z. (2000). Phosphorylation of histone H3 is correlated with changes in the maintenance of sister chromatid cohesion during meiosis in maize, rather than the condensation of the chromatin. J. Cell. Biochem. 113, 3217–3226. PubMed
Kawabe A., Nasuda S., Charlesworth D. (2006). Duplication of centromeric histone H3 (HTR12) gene in Arabidopsis halleri and A. lyrata, plant species with multiple centromeric satellite sequences. Genetics 174, 2021–2032. 10.1534/genetics.106.063628 PubMed DOI PMC
Kelly A. E., Ghenoiu C., Xue J. Z., Zierhut C., Kimura H., Funabiki H. (2010). Survivin reads phosphorylated histone H3 threonine 3 to activate the mitotic kinase Aurora B. Science 330, 235–239. 10.1126/science.1189505 PubMed DOI PMC
Kurihara D., Matsunaga S., Kawabe A., Fujimoto S., Noda M., Uchiyama S., et al. . (2006). Aurora kinase is required for chromosome segregation in tobacco BY-2 cells. Plant J. 48, 572–580. 10.1111/j.1365-313X.2006.02893.x PubMed DOI
Lindroth A. M., Shultis D., Jasencakova Z., Fuchs J., Johnson L., Schubert D., et al. . (2004). Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J. 23, 4286–4296. 10.1038/sj.emboj.7600430 PubMed DOI PMC
Liu H., Qu Q., Warrington R., Rice A., Cheng N., Yu H. (2015). Mitotic transcription installs Sgo1 at centromeres to coordinate chromosome segregation. Mol. Cell 59, 426–436. 10.1016/j.molcel.2015.06.018 PubMed DOI
Manzanero S., Arana P., Puertas M. J., Houben A. (2000). The chromosomal distribution of phosphorylated histone H3 differs between plants and animals at meiosis. Chromosoma 109, 308–317. 10.1007/s004120000087 PubMed DOI
Marques A., Ribeiro T., Neumann P., Macas J., Novák P., Schubert V., et al. . (2015). Holocentromeres in Rhynchospora are associated with genome-wide centromere-specific repeat arrays interspersed among euchromatin. Proc. Natl. Acad. Sci. U.S.A. 112, 13633–13638. 10.1073/pnas.1512255112 PubMed DOI PMC
Marston A. L. (2015). Shugoshins: tension-sensitive pericentromeric adaptors safeguarding chromosome segregation. Mol. Cell. Biol. 35, 634–648. 10.1128/MCB.01176-14 PubMed DOI PMC
Mathieu O., Probst A. V., Paszkowski J. (2005). Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis. EMBO J. 24, 2783–2791. 10.1038/sj.emboj.7600743 PubMed DOI PMC
McManus K. J., Biron V. L., Heit R., Underhill D. A., Hendzel M. J. (2006). Dynamic changes in histone H3 lysine 9 methylations: identification of a mitosis-specific function for dynamic methylation in chromosome congression and segregation. J. Biol. Chem. 281, 8888–8897. 10.1074/jbc.M505323200 PubMed DOI
Monen J., Maddox P. S., Hyndman F., Oegema K., Desai A. (2005). Differential role of CENP-A in the segregation of holocentric C. elegans chromosomes during meiosis and mitosis. Nat. Cell Biol. 7, 1248–1255. 10.1038/ncb1331 PubMed DOI
Moraes I. C. R., Lermontova I., Schubert I. (2011). Recognition of A. thaliana centromeres by heterologous CENH3 requires high similarity to the endogenous protein. Plant Mol. Biol. 75, 253–261. 10.1007/s11103-010-9723-3 PubMed DOI
Nagaki K., Kashihara K., Murata M. (2005). Visualization of diffuse centromeres with centromere-specific histone H3 in the holocentric plant Luzula nivea. Plant Cell 17, 1886–1893. 10.1105/tpc.105.032961 PubMed DOI PMC
Neumann P., Navrátilová A., Schroeder-Reiter E., Koblížková A., Steinbauerová V., Chocholová E., et al. . (2012). Stretching the rules: monocentric chromosomes with multiple centromere domains. PLoS Genet. 8:e1002777. 10.1371/journal.pgen.1002777 PubMed DOI PMC
Neumann P., Pavlíková Z., Koblížková A., Fuková I., Jedličková V., Novák P., et al. . (2015). Centromeres off the hook: massive changes in centromere size and structure following duplication of CenH3 gene in Fabeae species. Mol. Biol. Evol. 32, 1862–1879. 10.1093/molbev/msv070 PubMed DOI PMC
Neumann P., Požárková D., Vrána J., Doležel J., Macas J. (2002). Chromosome sorting and PCR-based physical mapping in pea (Pisum sativum L.). Chromosom. Res. 10, 63–71. 10.1023/A:1014274328269 PubMed DOI
Roudier F., Ahmed I., Bérard C., Sarazin A., Mary-Huard T., Cortijo S., et al. . (2011). Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J. 30, 1928–1938. 10.1038/emboj.2011.103 PubMed DOI PMC
Sanei M., Pickering R., Kumke K., Nasuda S., Houben A. (2011). Loss of centromeric histone H3 (CENH3) from centromeres precedes uniparental chromosome elimination in interspecific barley hybrids. Proc. Natl. Acad. Sci. U.S.A. 108, 498–505. 10.1073/pnas.1103190108 PubMed DOI PMC
Sawicka A., Seiser C. (2012). Histone H3 phosphorylation—A versatile chromatin modification for different occasions. Biochimie 94, 2193–2201. 10.1016/j.biochi.2012.04.018 PubMed DOI PMC
Sekulic N., Bassett E. A., Rogers D. J., Black B. E. (2010). The structure of (CENP-A-H4)2 reveals physical features that mark centromeres. Nature 467, 347–351. 10.1038/nature09323 PubMed DOI PMC
Sekulic N., Black B. E. (2012). Molecular underpinnings of centromere identity and maintenance. Trends Biochem. Sci. 37, 220–229. 10.1016/j.tibs.2012.01.003 PubMed DOI PMC
Shi J., Dawe R. K. (2006). Partitioning of the maize epigenome by the number of methyl groups on histone H3 lysines 9 and 27. Genetics 173, 1571–1583. 10.1534/genetics.106.056853 PubMed DOI PMC
Slee R. B., Steiner C. M., Herbert B.-S., Vance G. H., Hickey R. J., Schwarz T., et al. . (2012). Cancer-associated alteration of pericentromeric heterochromatin may contribute to chromosome instability. Oncogene 31, 3244–3253. 10.1038/onc.2011.502 PubMed DOI
Tachiwana H., Kagawa W., Shiga T., Osakabe A., Miya Y., Saito K., et al. . (2011). Crystal structure of the human centromeric nucleosome containing CENP-A. Nature 476, 232–235. 10.1038/nature10258 PubMed DOI
Vigneron S., Prieto S., Bernis C., Labbé J.-C., Castro A., Lorca T. (2005). Kinetochore localization of spindle checkpoint proteins: who controls whom? Mol. Biol. Cell 15, 4584–4596. 10.1091/mbc.E04-01-0051 PubMed DOI PMC
Wang F., Dai J., Daum J. R., Niedzialkowska E., Banerjee B., Stukenberg P. T., et al. . (2010). Histone H3 Thr-3 phosphorylation by Haspin positions Aurora B at centromeres in mitosis. Science 330, 231–235. 10.1126/science.1189435 PubMed DOI PMC
Wang F., Higgins J. M. G. (2013). Histone modications and mitosis: countermarks, landmarks, and bookmarks. Trends Cell Biol. 23, 175–184. 10.1016/j.tcb.2012.11.005 PubMed DOI
Wang F., Ulyanova N. P., van der Waal M. S., Patnaik D., Lens S. M. A., Higgins J. M. G. (2011). A positive feedback loop involving haspin and aurora B promotes CPC accumulation at centromeres in mitosis. Curr. Biol. 21, 1061–1069. 10.1016/j.cub.2011.05.016 PubMed DOI PMC
Wang M., Tang D., Luo Q., Jin Y., Shen Y., Wang K., et al. . (2012). BRK1, a Bub1-related kinase, is essential for generating proper tension between homologous kinetochores at metaphase I of rice meiosis. Plant Cell 24, 4961–4973. 10.1105/tpc.112.105874 PubMed DOI PMC
Yamagishi Y., Honda T., Tanno Y., Watanabe Y. (2010). Two histone marks establish the inner centromere and chromosome bi-orientation. Science 330, 239–243. 10.1126/science.1194498 PubMed DOI
Zhang W., Colmenares S. U., Karpen G. H. (2012). Assembly of Drosophila centromeric nucleosomes requires CID dimerization. Mol. Cell 45, 263–269. 10.1016/j.molcel.2011.12.010 PubMed DOI PMC
Zhang X., Li X., Marshall J. B., Zhong C. X., Dawe R. K. (2005). Phosphoserines on maize CENTROMERIC HISTONE H3 and histone H3 demarcate the centromere and pericentromere during chromosome segregation. Plant Cell 17, 572–583. 10.1105/tpc.104.028522 PubMed DOI PMC
Zhou Z., Feng H., Zhou B.-R., Ghirlando R., Hu K., Zwolak A., et al. . (2011). Structural basis for recognition of centromere histone variant CenH3 by the chaperone Scm3. Nature 472, 234–237. 10.1038/nature09854 PubMed DOI PMC
A chromosome-scale reference genome of grasspea (Lathyrus sativus)
KNL1 and NDC80 represent new universal markers for the detection of functional centromeres in plants
Super-Resolution Microscopy Reveals Diversity of Plant Centromere Architecture