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  • Cold Spring Harbor Laboratory  (7)
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  • Cold Spring Harbor Laboratory  (7)
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  • 1
    Online-Ressource
    Online-Ressource
    Maize centromeres expand and adopt a uniform size in the genetic background of oat
    Cold Spring Harbor Laboratory ; 2014
    In:  Genome Research Vol. 24, No. 1 ( 2014-01), p. 107-116
    Details
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 24, No. 1 ( 2014-01), p. 107-116
    Kurzfassung: Most existing centromeres may have originated as neocentromeres that activated de novo from noncentromeric regions. However, the evolutionary path from a neocentromere to a mature centromere has been elusive. Here we analyzed the centromeres of nine chromosomes that were transferred from maize into oat as the result of an inter-species cross. Centromere size and location were assayed by chromatin immunoprecipitation for the histone variant CENH3, which is a defining feature of functional centromeres. Two isolates of maize chromosome 3 proved to contain neocentromeres in the sense that they had moved from the original site, whereas the remaining seven centromeres (1, 2, 5, 6, 8, 9, and 10) were retained in the same area in both species. In all cases, the CENH3-binding domains were dramatically expanded to encompass a larger area in the oat background (∼3.6 Mb) than the average centromere size in maize (∼1.8 Mb). The expansion of maize centromeres appeared to be restricted by the transcription of genes located in regions flanking the original centromeres. These results provide evidence that (1) centromere size is regulated; (2) centromere sizes tend to be uniform within a species regardless of chromosome size or origin of the centromere; and (3) neocentromeres emerge and expand preferentially in gene-poor regions. Our results suggest that centromere size expansion may be a key factor in the survival of neocentric chromosomes in natural populations.
    Materialart: Online-Ressource
    ISSN: 1088-9051
    URL: Article
    DOI: 10.1101/gr.160887.113
    RVK:
    XA 10000
    Sprache: Englisch
    Verlag: Cold Spring Harbor Laboratory
    Publikationsdatum: 2014
    ZDB Id: 1483456-X
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
  • 2
    Online-Ressource
    Online-Ressource
    Distinct DNA methylation patterns associated with active and inactive centromeres of the maize B chromosome
    Cold Spring Harbor Laboratory ; 2011
    In:  Genome Research Vol. 21, No. 6 ( 2011-06), p. 908-914
    Details
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 21, No. 6 ( 2011-06), p. 908-914
    Kurzfassung: Centromeres are determined by poorly understood epigenetic mechanisms. Centromeres can be activated or inactivated without changing the underlying DNA sequences. However, virtually nothing is known about the epigenetic transition of a centromere from an active to an inactive state because of the lack of examples of the same centromere exhibiting alternative forms and being distinguishable from other centromeres. The centromere of the supernumerary B chromosome of maize provides such an opportunity because its functional core can be cytologically tracked, and an inactive version of the centromere is available. We developed a DNA fiber-based technique that can be used to assess the levels of cytosine methylation associated with repetitive DNA sequences. We report that DNA sequences in the normal B centromere exhibit hypomethylation. This methylation pattern is not affected by the genetic background or structural rearrangement of the B chromosome, but is slightly changed when the B chromosome is transferred to oat as an addition chromosome. In contrast, an inactive version of this same centromere exhibits hypermethylation, indicating that the inactive centromere was modified into a different epigenetic state at the DNA level.
    Materialart: Online-Ressource
    ISSN: 1088-9051
    URL: Article
    DOI: 10.1101/gr.116202.110
    RVK:
    XA 10000
    Sprache: Englisch
    Verlag: Cold Spring Harbor Laboratory
    Publikationsdatum: 2011
    ZDB Id: 1483456-X
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
  • 3
    Online-Ressource
    Online-Ressource
    DNA methylation and heterochromatinization in the male-specific region of the primitive Y chromosome of papaya
    Cold Spring Harbor Laboratory ; 2008
    In:  Genome Research Vol. 18, No. 12 ( 2008-12), p. 1938-1943
    Details
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 18, No. 12 ( 2008-12), p. 1938-1943
    Kurzfassung: Sex chromosomes evolved from autosomes. Recombination suppression in the sex-determining region and accumulation of deleterious mutations lead to degeneration of the Y chromosomes in many species with heteromorphic X/Y chromosomes. However, how the recombination suppressed domain expands from the sex-determining locus to the entire Y chromosome remains elusive. The Y chromosome of papaya ( Carica papaya ) diverged from the X chromosome approximately 2–3 million years ago and represents one of the most recently emerged Y chromosomes. Here, we report that the male-specific region of the Y chromosome (MSY) spans ∼13% of the papaya Y chromosome. Interestingly, the centromere of the Y chromosome is embedded in the MSY. The centromeric domain within the MSY has accumulated significantly more DNA than the corresponding X chromosomal domain, which leads to abnormal chromosome pairing. We observed four knob-like heterochromatin structures specific to the MSY. Fluorescence in situ hybridization and immunofluorescence assay revealed that the DNA sequences associated with the heterochromatic knobs are highly divergent and heavily methylated compared with the sequences in the corresponding X chromosomal domains. These results suggest that DNA methylation and heterochromatinization play an important role in the early stage of sex chromosome evolution.
    Materialart: Online-Ressource
    ISSN: 1088-9051
    URL: Article
    DOI: 10.1101/gr.078808.108
    RVK:
    XA 10000
    Sprache: Englisch
    Verlag: Cold Spring Harbor Laboratory
    Publikationsdatum: 2008
    ZDB Id: 1483456-X
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
  • 4
    Online-Ressource
    Online-Ressource
    Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs
    Cold Spring Harbor Laboratory ; 2009
    In:  Genome Research Vol. 19, No. 1 ( 2009-01), p. 42-56
    Details
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 19, No. 1 ( 2009-01), p. 42-56
    Kurzfassung: Small RNAs regulate the genome by guiding transcriptional and post-transcriptional silencing machinery to specific target sequences, including genes and transposable elements (TEs). Although miniature inverted-repeat transposable elements (MITEs) are closely associated with euchromatic genes, the broader functional impact of these short TE insertions in genes is largely unknown. We identified 22 families of MITEs in the Solanaceae ( MiS1 – MiS22 ) and found abundant MiS insertions in Solanaceae genomic DNA and expressed sequence tags (EST). Several Solanaceae MITEs generate genome changes that potentially affect gene function and regulation, most notably, a MiS insertion that provides a functionally indispensable alternative exon in the tobacco mosaic virus N resistance gene. We show that MITEs generate small RNAs that are primarily 24 nt in length, as detected by Northern blot hybridization and by sequencing small RNAs of Solanum demissum, Nicotiana glutinosa , and Nicotiana benthamiana . Additionally, we show that stable RNAi lines silencing DICER-LIKE3 ( DCL3 ) in tobacco and RNA-dependent RNA polymerase 2 ( RDR2 ) in potato cause a reduction in 24-nt MITE siRNAs, suggesting that, as in Arabidopsis , TE-derived siRNA biogenesis is DCL3 and RDR2 dependent. We provide evidence that DICER-LIKE4 (DCL4) may also play a role in MITE siRNA generation in the Solanaceae.
    Materialart: Online-Ressource
    ISSN: 1088-9051
    URL: Article
    DOI: 10.1101/gr.078196.108
    RVK:
    XA 10000
    Sprache: Englisch
    Verlag: Cold Spring Harbor Laboratory
    Publikationsdatum: 2009
    ZDB Id: 1483456-X
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
  • 5
    Online-Ressource
    Online-Ressource
    Toward a Cytological Characterization of the Rice Genome
    Cold Spring Harbor Laboratory ; 2001
    In:  Genome Research Vol. 11, No. 12 ( 2001-12-01), p. 2133-2141
    Details
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 11, No. 12 ( 2001-12-01), p. 2133-2141
    Kurzfassung: Rice ( Oryza sativa L.) will be the first major crop, as well as the first monocot plant species, to be completely sequenced. Integration of DNA sequence-based maps with cytological maps will be essential to fully characterize the rice genome. We have isolated a set of 24 chromosomal arm-specific bacterial artificial chromosomes to facilitate rice chromosome identification. A standardized rice karyotype was constructed using meiotic pachytene chromosomes of O. sativa spp. japonica rice var. Nipponbare. This karyotype is anchored by centromere-specific and chromosomal arm-specific cytological landmarks and is fully integrated with the most saturated rice genetic linkage maps in which Nipponbare was used as one of the mapping parents. An ideogram depicting the distribution of heterochromatin in the rice genome was developed based on the patterns of 4',6-diamidino-2-phenylindole staining of the Nipponbare pachytene chromosomes. The majority of the heterochromatin is distributed in the pericentric regions with some rice chromosomes containing a significantly higher proportion of heterochromatin than other chromosomes. We showed that pachytene chromosome-based fluorescence in situ hybridization analysis is the most effective approach to integrate DNA sequences with euchromatic and heterochromatic features.
    Materialart: Online-Ressource
    ISSN: 1088-9051 , 1549-5469
    URL: Article
    DOI: 10.1101/gr.194601
    RVK:
    XA 10000
    Sprache: Englisch
    Verlag: Cold Spring Harbor Laboratory
    Publikationsdatum: 2001
    ZDB Id: 1483456-X
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
  • 6
    Online-Ressource
    Online-Ressource
    A Fine Physical Map of the Rice Chromosome 4
    Cold Spring Harbor Laboratory ; 2002
    In:  Genome Research Vol. 12, No. 5 ( 2002-05-01), p. 817-823
    Details
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 12, No. 5 ( 2002-05-01), p. 817-823
    Kurzfassung: As part of an international effort to completely sequence the rice genome, we have produced a fine bacterial artificial chromosome (BAC)-based physical map of the Oryza sativa japonica Nipponbare chromosome 4 through an integration of 114 sequenced BAC clones from a taxonomically related subspecies O. sativa indica Guangluai 4 and 182 RFLP and 407 expressed sequence tag (EST) markers with the fingerprinted data of the Nipponbare genome. The map consists of 11 contigs with a total length of 34.5 Mb covering 94% of the estimated chromosome size (36.8 Mb). BAC clones corresponding to telomeres, as well as to the centromere position, were determined by BAC-pachytene chromosome fluorescence in situ hybridization (FISH). This gave rise to an estimated length ratio of 5.13 for the long arm and 2.9 for the short arm (on the basis of the physical map), which indicates that the short arm is a highly condensed one. The FISH analysis and physical mapping also showed that the short arm and the pericentromeric region of the long arm are rich in heterochromatin, which occupied 45% of the chromosome, indicating that this chromosome is likely very difficult to sequence. To our knowledge, this map provides the first example of a rapid and reliable physical mapping on the basis of the integration of the data from two taxonomically related subspecies. [The following individuals and institutions kindly provided reagents, samples, or unpublished information as indicated in the paper: S. McCouch, T. Sasaki, and Monsanto.]
    Materialart: Online-Ressource
    ISSN: 1088-9051 , 1549-5469
    URL: Article
    DOI: 10.1101/gr.48902
    RVK:
    XA 10000
    Sprache: Englisch
    Verlag: Cold Spring Harbor Laboratory
    Publikationsdatum: 2002
    ZDB Id: 1483456-X
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
  • 7
    Online-Ressource
    Online-Ressource
    High-resolution mapping of open chromatin in the rice genome
    Cold Spring Harbor Laboratory ; 2012
    In:  Genome Research Vol. 22, No. 1 ( 2012-01), p. 151-162
    Details
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 22, No. 1 ( 2012-01), p. 151-162
    Kurzfassung: Gene expression is controlled by the complex interaction of transcription factors binding to promoters and other regulatory DNA elements. One common characteristic of the genomic regions associated with regulatory proteins is a pronounced sensitivity to DNase I digestion. We generated genome-wide high-resolution maps of DNase I hypersensitive (DH) sites from both seedling and callus tissues of rice ( Oryza sativa ). Approximately 25% of the DH sites from both tissues were found in putative promoters, indicating that the vast majority of the gene regulatory elements in rice are not located in promoter regions. We found 58% more DH sites in the callus than in the seedling. For DH sites detected in both the seedling and callus, 31% displayed significantly different levels of DNase I sensitivity within the two tissues. Genes that are differentially expressed in the seedling and callus were frequently associated with DH sites in both tissues. The DNA sequences contained within the DH sites were hypomethylated, consistent with what is known about active gene regulatory elements. Interestingly, tissue-specific DH sites located in the promoters showed a higher level of DNA methylation than the average DNA methylation level of all the DH sites located in the promoters. A distinct elevation of H3K27me3 was associated with intergenic DH sites. These results suggest that epigenetic modifications play a role in the dynamic changes of the numbers and DNase I sensitivity of DH sites during development.
    Materialart: Online-Ressource
    ISSN: 1088-9051
    URL: Article
    DOI: 10.1101/gr.131342.111
    RVK:
    XA 10000
    Sprache: Englisch
    Verlag: Cold Spring Harbor Laboratory
    Publikationsdatum: 2012
    ZDB Id: 1483456-X
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
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