Transcriptionally active heterochromatin in rye B chromosomes

Plant Cell

Volumn 19, Issue 6, 2007, Pages 1738-1749

  Carchilan, Mariana ^a   Delgado, Margarida ^b   Ribeiro, Teresa ^b   Costa Nunes, Pedro ^b   Caperta, Ana ^b   Morais Cecílio, Leonor ^b   Jones, R Neil ^c   Viegas, Wanda ^b   Houbena, Andreas ^a  

^a LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

^b INSTITUTO SUPERIOR DE AGRONOMIA   (Portugal)

^c ABERYSTWYTH UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENES; PLANTS (BOTANY);

HISTONE MODIFICATIONS; INTERPHASE;

GENETIC ENGINEERING;

SECALE CEREALE;

EID: 34547674454     PISSN: 10404651     EISSN: 1532298X     Source Type: Journal    
DOI: 10.1105/tpc.106.046946     Document Type: Article

References (51)

1. Bannister, A.J., Zegerman, P., Partridge, J.F., Miska, E.A., Thomas, J.O., Allshire, R.C., and Kouzarides, T. (2001). Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410: 120-124.
2. Blunden, R., Wilkes, T.J., Forster, J.W., Jiménez, M.M., Sandery, M.J., Karp, A., and Jones, R.N. (1993). Identification of the E3900 family, a 2nd family of rye chromosome B-specific repeated sequences. Genome 36: 706-711.
3. Bouzinba-Segard, H., Guais, A., and Francastel, C. (2006). Accumulation of small murine minor satellite transcripts leads to impaired centromeric architecture and function. Proc. Natl. Acad. Sci. USA 103: 8709-8714.
4. Cao, R., Wang, L.J., Wang, H.B., Xia, L., Erdjument-Bromage, H., Tempst, P., Jones, R.S., and Zhang, Y. (2002). Role of histone H3 lysine 27 methylation in polycomb-group silencing. Science 298: 1039-1043.
5. Castilho, A., Neves, N., Rufini-Castiglione, M., Viegas, W., and Heslop-Harrison, J.S. (1999). 5-Methylcytosine distribution and genome organization in Triticale before and after treatment with 5-azacytidine. J. Cell Sci. 112: 4397-4404.
6. Chomczynski, P., and Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate phenol chloroform extraction. Anal. Biochem. 162: 156-159.
7. Craig, J.M. (2005). Heterochromatin - Many flavours, common themes. Bioessays 27: 17-28.
8. Cunado, N., Barrios, J., and Santos, J.L. (2000). Organization of highly repeated sequences in surface-spread pachytene chromosomes of rye. Genome 43: 945-948.
9. Czermin, B., Melfi, R., McCabe, D., Seitz, V., Imhof, A., and Pirrotta, V. (2002). Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal polycomb sites. Cell 111: 185-196.
10. Dimitri, P., Corradini, N., Rossi, F., and Verni, F. (2005). The paradox of functional heterochromatin. Bioessays 27: 29-41.
11. Francis, N.J., Kingston, R.E., and Woodcock, C.L. (2004). Chromatin compaction by a polycomb group protein complex. Science 306: 1574-1577.
12. Fuchs, J., Demidov, D., Houben, A., and Schubert, I. (2006). Chromosomal histone modification patterns - From conservation to diversity. Trends Plant Sci. 11: 199-208.
13. Heitz, E. (1928). Das Heterochromatin der Moose. Jahrb. Wiss Bot. 69: 762-818.
14. Houben, A., Demidov, D., Gernand, D., Meister, A., Leach, C.R., and Schubert, I. (2003). Methylation of histone H3 in euchromatin of plant chromosomes depends on basic nuclear DNA content. Plant J. 33: 967-973.
15. Houben, A., Kynast, R.G., Heim, U., Hermann, H., Jones, R.N., and Forster, J.W. (1996). Molecular cytogenetic characterisation of the terminal heterochromatic segment of the B-chromosome of rye (Secale cereale). Chromosoma 105: 97-103.
16. Jacobs, S.A., Taverna, S.D., Zhang, Y.N., Briggs, S.D., Li, J.M., Eissenberg, J.C., Allis, C.D., and Khorasanizadeh, S. (2001). Specificity of the HP1 chromo domain for the methylated N-terminus of histone H3. EMBO J. 20: 5232-5241.
17. Jiménez, G., Manzanero, S., and Puertas, M. (2000). Relationship between pachytene synapsis, metaphase I associations, and transmission of 2B and 4B chromosomes in rye. Genome 43: 232-239.
18. Jiménez, M.M., Romera, F., González Sáanchez, M., and Puertas, M.J. (1997). Genetic control of the rate of transmission of rye B chromosomes. 3. Male meiosis and gametogenesis. Heredity 78: 636-644.
19. Jones, N., and Houben, A. (2003). B chromosomes in plants: Escapees from the A chromosome genome? Trends Plant Sci. 8: 417-423.
20. Jones, R.N. (1995). Tansley review no 85 - B chromosomes in plants. New Phytol. 131: 411-434.
21. Jones, R.N., and Puertas, M.J. (1993). The B chromosomes of rye (Secale cereale L.). In Frontiers in Plant Science Research, K.K. Dhir and T.S. Sareen, eds (Delhi, India: Bhagwati Enterprises), pp. 81-112.
22. Kouzarides, T. (2007). Chromatin modifications and their function. Cell 128: 693-705.
23. Langdon, T., Seago, C., Jones, R.N., Ougham, H., Thomas, H., Forster, J.W., and Jenkins, G. (2000). De novo evolution of satellite DNA on the rye B chromosome. Genetics 154: 869-884.
24. Leach, C.R., Houben, A., Field, B., Pistrick, K., Demidov, D., and Timmis, J.N. (2005). Molecular evidence for transcription of B chromosome ribosomal RNA genes in Crepis capillaris. Genetics 171: 269-278.
25. Lima-de-Faria, M., and Jaworska, H. (1972). The relation between the chromosome size gradient and the sequence of DNA replication in rye. Hereditas 70: 39-58.
26. Martin, C., and Zhang, Y. (2005). The diverse functions of histone lysine methylation. Nat. Rev. Mol. Cell Biol. 6: 838-849.
27. May, B.P., Lippman, Z.B., Fang, Y., Spector, D.L., and Martienssen, R.A. (2005). Differential regulation of strand-specific transcripts from Arabidopsis centromeric satellite repeats. PLoS Genet 1: e79.
28. Mette, M.F., Aufsatz, W., Kanno, T., Daxinger, L., Rovina, P., Matzke, M., and Matzke, A.J. (2005). Analysis of double-stranded RNA and small RNAs involved in RNA-mediated transcriptional gene silencing. Methods Mol. Biol. 309: 61-82.
29. Miao, F., and Natarajan, R. (2005). Mapping global histone methylation patterns in the coding regions of human genes. Mol. Cell. Biol. 25: 4650-4661.
30. Morais-Cecílio, L., Delgado, M., Jones, R.N., and Viegas, W. (1996). Painting rye B chromosomes in wheat: Interphase chromatin organization, nuclear disposition and association in plants with two, three or four Bs. Chromosome Res. 4: 195-200.
31. Noma, K., Allis, C.D., and Grewal, S.I.S. (2001). Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 293: 1150-1155.
32. Ribeiro, T., Pires, B., Delgado, M., Viegas, W., Jones, N., and Morais-Cecílio, L. (2004). Evidence for 'cross-talk' between A and B chromosomes of rye. Proc. R. Soc. Lond. B Biol. Sci. 271: S482-S484.
33. Rice, J.C., Briggs, S.D., Ueberheide, B., Barber, C.M., Shabanowitz, J., Hunt, D.F., Shinkai, Y., and Allis, C.D. (2003). Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol. Cell 12: 1591-1598.
34. Richards, E.J., and Elgin, S.C.R. (2002). Epigenetic codes for heterochromatin formation and silencing: Rounding up the usual suspects. Cell 108: 489-500.
35. Rimpau, J., and Flavell, R.B. (1975). Characterization of rye B chromosome DNA by DNA-DNA hybridization. Chromosoma 52: 207-217.
36. Rizzi, N., Denegri, M., Chiodi, I., Corioni, M., Valgardsdottir, R., Cobianchi, F., Riva, S., and Biamonti, G. (2004). Transcriptional activation of a constitutive heterochromatic domain of the human genome in response to heat shock. Mol. Biol. Cell 15: 543-551.
37. Sandery, M.J., Forster, J.W., Blunden, R., and Jones, R.N. (1990). Identification of a family of repeated sequences on the rye B-chromosome. Genome 33: 908-913.
38. Santos, A.P., Abranches, R., Stoger, E., Beven, A., Viegas, W., and Shaw, P.J. (2002). The architecture of interphase chromosomes and gene positioning are altered by changes in DNA methylation and histone acetylation. J. Cell Sci. 115: 4597-4605.
39. Santos-Rosa, H., Schneider, R., Bannister, A.J., Sherriff, J., Bernstein, B.E., Emre, N.C.T., Schreiber, S.L., Mellor, J., and Kouzarides, T. (2002). Active genes are tri-methylated at K4 of histone H3. Nature 419: 407-411.
40. Schlegel, R., and Gill, B.S. (1984). N-banding analysis of rye chromosomes and the relationship between N-banded and C-banded heterochromatin. Can. J. Genet. Cytol. 26: 765-769.
41. Schwarzacher, T. (2003). DNA, chromosomes, and in situ hybridization. Genome 46: 953-962.
42. Schwarzacher, T., and Heslop-Harrison, J.S. (2000). Practical in Situ Hybridisation. (Oxford, UK: Bios).
43. Shi, Y.J., Lan, F., Matson, C., Mulligan, P., Whetstine, J.R., Cole, P.A., Casero, R.A., and Shi, Y. (2004). Histone demethylation mediated by the nuclear arnine oxidase homolog LSD1. Cell 119: 941-953.
44. Spada, F., Vincent, M., and Thompson, E.M. (2005). Plasticity of histone modifications across the invertebrate to vertebrate transition: Histone H3 lysine 4 trimethylation in heterochromatin. Chromosome Res. 13: 57-72.
45. Timmis, J.N., Ingle, J., Sinclair, J., and Jones, R.N. (1975). Genomic quality of rye B chromosomes. J. Exp. Bot. 26: 367-378.
46. Tsujimoto, H., and Niwa, K. (1992). DNA-structure of the B-chromosome of rye revealed by in situ hybridization using repetitive sequences. Jpn. J. Genet. 67: 233-241.
47. Ugarkovic, D. (2005). Functional elements residing within satellite DNAs. EMBO Rep. 6: 1035-1039.
48. Wilkes, T.M., Francki, M.G., Langridge, P., Karp, A., Jones, R.N., and Forster, J.W. (1995). Analysis of rye B-chromosome structure using fluorescence insitu hybridization (FISH). Chromosome Res. 3: 466-472.
49. Zegerman, P., Canas, B., Pappin, D., and Kouzarides, T. (2002). Histone H3 lysine 4 methylation disrupts binding of nucleosome remodeling and deacetylase (NuRD) repressor complex. J. Biol. Chem. 277: 11621-11624.
50. Zhang, H., et al. (2004). Large-scale analysis of the barley transcriptome based on expressed sequence tags. Plant J. 40: 276-290.
51. Zhang, W., Yi, C., Bao, W., Liu, B., Cui, J., Yu, H., Cao, X., Gu, M., Liu, M., and Cheng, Z. (2005). The transcribed 165-bp CentO satellite is the major functional centromeric element in the wild rice species Oryza punctata. Plant Physiol. 139: 306-315.