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PMID: 17295128 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S. Review

Rice as a model for centromere and heterochromatin research.

Yan H, Jiang J

Abstract

Rice (Oryza sativa) has become an important model plant species in numerous research projects involving genome, molecular and evolutionary biology. In this review we describe the reasons why rice provides an excellent model system for centromere and heterochromatin research. In most multicellular eukaryotes, centromeres and heterochromatic domains contain long arrays of repetitive DNA elements that are recalcitrant to DNA sequencing. In contrast, three rice centromeres and the majority of the cytologically defined heterochromatin in the rice genome have been sequenced to high quality, providing an unparalleled resource compared to other model multicellular eukaryotes. Most importantly, active genes have been discovered in the functional domains of several rice centromeres. The centromeric genes and sequence resources provide an unprecedented opportunity to study function and evolution of centromeres and centromere-associated genes.

MeSH Terms
Centromere/genetics Epigenesis, Genetic Evolution, Molecular Gene Expression Regulation, Plant Heterochromatin/metabolism,ultrastructure Histones/metabolism Models, Genetic Oryza/genetics,metabolism Transcription, Genetic
Chemicals
Heterochromatin Histones
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Yan Huihuang
Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA.
Jiang Jiming
References (62)
62 references, click to expand
  1. A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription.
    Plant Cell. 2005 Jun;17(6):1641-57 PMID: 15863518
  2. Conflict begets complexity: the evolution of centromeres.
    Curr Opin Genet Dev. 2002 Dec;12(6):711-8 PMID: 12433586
  3. Transmission of a fully functional human neocentromere through three generations.
    Am J Hum Genet. 1999 May;64(5):1440-4 PMID: 10205277
  4. High throughput T-DNA insertion mutagenesis in rice: a first step towards in silico reverse genetics.
    Plant J. 2004 Aug;39(3):450-64 PMID: 15255873
  5. High-resolution single-copy gene fluorescence in situ hybridization and its use in the construction of a cytogenetic map of maize chromosome 9.
    Plant Cell. 2006 Mar;18(3):529-44 PMID: 16461583
  6. High frequency of centromere inactivation resulting in stable dicentric chromosomes of maize.
    Proc Natl Acad Sci U S A. 2006 Feb 28;103(9):3238-43 PMID: 16492777
  7. The transcribed 165-bp CentO satellite is the major functional centromeric element in the wild rice species Oryza punctata.
    Plant Physiol. 2005 Sep;139(1):306-15 PMID: 16113220
  8. Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species.
    Proc Natl Acad Sci U S A. 2005 Aug 16;102(33):11793-8 PMID: 16040802
  9. Oxymoron no more: the expanding world of heterochromatic genes.
    Trends Genet. 2006 Jun;22(6):330-8 PMID: 16690158
  10. A molecular view of plant centromeres.
    Trends Plant Sci. 2003 Dec;8(12):570-5 PMID: 14659705
  11. Evolution of heterochromatic genes of Drosophila.
    Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):10958-63 PMID: 16033869
  12. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica).
    Science. 2002 Apr 5;296(5565):92-100 PMID: 11935018
  13. Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere.
    Plant Cell. 2006 Sep;18(9):2123-33 PMID: 16877494
  14. Evolutionary movement of centromeres in horse, donkey, and zebra.
    Genomics. 2006 Jun;87(6):777-82 PMID: 16413164
  15. The complete sequence of a heterochromatic island from a higher eukaryote. The Cold Spring Harbor Laboratory, Washington University Genome Sequencing Center, and PE Biosystems Arabidopsis Sequencing Consortium.
    Cell. 2000 Feb 4;100(3):377-86 PMID: 10676819
  16. Centromeric chromatin exhibits a histone modification pattern that is distinct from both euchromatin and heterochromatin.
    Nat Struct Mol Biol. 2004 Nov;11(11):1076-83 PMID: 15475964
  17. Sequence and analysis of rice chromosome 4.
    Nature. 2002 Nov 21;420(6913):316-20 PMID: 12447439
  18. A draft sequence of the rice genome (Oryza sativa L. ssp. indica).
    Science. 2002 Apr 5;296(5565):79-92 PMID: 11935017
  19. Transcription within a functional human centromere.
    Mol Cell. 2003 Aug;12(2):509-16 PMID: 14536089
  20. Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome.
    Nat Genet. 2005 Aug;37(8):809-19 PMID: 15976807
  21. The paradox of functional heterochromatin.
    Bioessays. 2005 Jan;27(1):29-41 PMID: 15612038
  22. The centromere composition of multiple repetitive sequences on rice chromosome 5.
    Chromosoma. 2001 Aug;110(4):284-91 PMID: 11534820
  23. Retrotransposon-related DNA sequences in the centromeres of grass chromosomes.
    Genetics. 1998 Dec;150(4):1615-23 PMID: 9832537
  24. A fine physical map of the rice chromosome 4.
    Genome Res. 2002 May;12(5):817-23 PMID: 11997348
  25. Rice (Oryza sativa) centromeric regions consist of complex DNA.
    Proc Natl Acad Sci U S A. 1998 Jul 7;95(14):8135-40 PMID: 9653153
  26. Permissive transcriptional activity at the centromere through pockets of DNA hypomethylation.
    PLoS Genet. 2006 Feb;2(2):e17 PMID: 16477312
  27. Molecular phylogeny of Oryzeae (Poaceae) based on DNA sequences from chloroplast, mitochondrial, and nuclear genomes.
    Am J Bot. 2005 Sep;92(9):1548-58 PMID: 21646172
  28. Assembly and characterization of heterochromatin and euchromatin on human artificial chromosomes.
    Genome Biol. 2004;5(11):R89 PMID: 15535865
  29. Comparative genetics at the gene and chromosome levels between rice ( Oryza sativa) and wildrice ( Zizania palustris).
    Theor Appl Genet. 2003 Sep;107(5):773-82 PMID: 12904864
  30. Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture.
    Genome Biol. 2005;6(6):R52 PMID: 15960804
  31. A high-density rice genetic linkage map with 2275 markers using a single F2 population.
    Genetics. 1998 Jan;148(1):479-94 PMID: 9475757
  32. Composition and structure of the centromeric region of rice chromosome 8.
    Plant Cell. 2004 Apr;16(4):967-76 PMID: 15037733
  33. Heterochromatic sequences in a Drosophila whole-genome shotgun assembly.
    Genome Biol. 2002;3(12):RESEARCH0085 PMID: 12537574
  34. Centromere mapping and orientation of the molecular linkage map of rice (Oryza sativa L.).
    Proc Natl Acad Sci U S A. 1996 Jun 11;93(12):6163-8 PMID: 8650237
  35. CHROMOSOME MORPHOLOGY IN ZEA MAYS.
    Science. 1929 Jun 14;69(1798):629 PMID: 17760028
  36. Stable barley chromosomes without centromeric repeats.
    Proc Natl Acad Sci U S A. 2005 Jul 12;102(28):9842-7 PMID: 15998740
  37. Centromere emergence in evolution.
    Genome Res. 2001 Apr;11(4):595-9 PMID: 11282974
  38. Cytogenetics for the model system Arabidopsis thaliana.
    Plant J. 1998 Mar;13(6):867-76 PMID: 9681023
  39. The evolution of restricted recombination and the accumulation of repeated DNA sequences.
    Genetics. 1986 Apr;112(4):947-62 PMID: 3957013
  40. The map-based sequence of the rice genome.
    Nature. 2005 Aug 11;436(7052):793-800 PMID: 16100779
  41. Transcription and histone modifications in the recombination-free region spanning a rice centromere.
    Plant Cell. 2005 Dec;17(12):3227-38 PMID: 16272428
  42. Partitioning of the maize epigenome by the number of methyl groups on histone H3 lysines 9 and 27.
    Genetics. 2006 Jul;173(3):1571-83 PMID: 16624902
  43. T-DNA insertional mutagenesis for activation tagging in rice.
    Plant Physiol. 2002 Dec;130(4):1636-44 PMID: 12481047
  44. Human centromere repositioning "in progress".
    Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6542-7 PMID: 15084747
  45. Contribution of the Tos17 retrotransposon to rice functional genomics.
    Curr Opin Plant Biol. 2001 Apr;4(2):118-22 PMID: 11228433
  46. Role of transposable elements in heterochromatin and epigenetic control.
    Nature. 2004 Jul 22;430(6998):471-6 PMID: 15269773
  47. The centromere paradox: stable inheritance with rapidly evolving DNA.
    Science. 2001 Aug 10;293(5532):1098-102 PMID: 11498581
  48. Genetic conflicts during meiosis and the evolutionary origins of centromere complexity.
    Biochem Soc Trans. 2006 Aug;34(Pt 4):569-73 PMID: 16856863
  49. Numbers and Distribution of Chromosome Knobs in United States Maize.
    Genetics. 1949 Sep;34(5):524-36 PMID: 17247331
  50. Primary trisomics of rice: origin, morphology, cytology and use in linkage mapping.
    Genetics. 1984 May;107(1):141-63 PMID: 17246212
  51. Chromosome 6 phylogeny in primates and centromere repositioning.
    Mol Biol Evol. 2003 Sep;20(9):1506-12 PMID: 12832646
  52. Structural features of the rice chromosome 4 centromere.
    Nucleic Acids Res. 2004 Apr 02;32(6):2023-30 PMID: 15064362
  53. Toward a cytological characterization of the rice genome.
    Genome Res. 2001 Dec;11(12):2133-41 PMID: 11731505
  54. Genome-wide transcription analyses in rice using tiling microarrays.
    Nat Genet. 2006 Jan;38(1):124-9 PMID: 16369532
  55. Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon.
    Plant Cell. 2002 Aug;14(8):1691-704 PMID: 12172016
  56. Human centromeric chromatin is a dynamic chromosomal domain that can spread over noncentromeric DNA.
    Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4186-91 PMID: 16537506
  57. Recurrent sites for new centromere seeding.
    Genome Res. 2004 Sep;14(9):1696-703 PMID: 15342555
  58. Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice.
    Mol Biol Evol. 2005 Apr;22(4):845-55 PMID: 15616142
  59. Sequencing of a rice centromere uncovers active genes.
    Nat Genet. 2004 Feb;36(2):138-45 PMID: 14716315
  60. Origin, dispersal, cultivation and variation of rice.
    Plant Mol Biol. 1997 Sep;35(1-2):25-34 PMID: 9291957
  61. Comprehensive molecular cytogenetic analysis of sorghum genome architecture: distribution of euchromatin, heterochromatin, genes and recombination in comparison to rice.
    Genetics. 2005 Dec;171(4):1963-76 PMID: 16143604
  62. Integrated cytogenetic map of chromosome arm 4S of A. thaliana: structural organization of heterochromatic knob and centromere region.
    Cell. 2000 Feb 4;100(3):367-76 PMID: 10676818
Article Info
Journal
Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology
Abbr.
Chromosome Res
ISSN
0967-3849
Published
2007-00-00
Pages
77-84
Language
English
Region
Netherlands
NLM ID
9313452
Subset
IM
Analysis Services
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