Pairing of lacO tandem repeats in Arabidopsis thaliana nuclei requires the presence of hypermethylated, large arrays at two chromosomal positions, but does not depend on H3-lysine-9-dimethylation

Jovtchev, Gabriele; Borisova, Branimira E.; Kuhlmann, Markus; Fuchs, Jörg; Watanabe, Koichi; Schubert, Ingo; Mette, Michael Florian

doi:10.1007/s00412-011-0335-8

Cited by 17 publications

(9 citation statements)

References 48 publications

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“…These results are consistent with the focused analysis of 13 A. thaliana genomic regions by 4C (Grob et al 2013). Experiments with lacO repeat arrays integrated in the A. thaliana genome have suggested that the clustering of lacO sequences at distant loci depended on heterochromatic marks (Jovtchev et al 2011). The clustering of heterochromatin is in line with the observation of ''AB compartments'' from animal Hi-C data sets, where euchromatin and heterochromatin are spatially segregated (Lieberman-Aiden et al 2009).…”

Section: Discussionsupporting

confidence: 76%

Genome-wide analysis of local chromatin packing in Arabidopsis thaliana

et al. 2014

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The spatial arrangement of interphase chromosomes in the nucleus is important for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional genome organization of the plant Arabidopsis thaliana. We find that local chromatin packing differs from the patterns seen in animals, with kilobasepair-sized segments that have much higher intrachromosome interaction rates than neighboring regions, representing a dominant local structural feature of genome conformation in A. thaliana. These regions, which appear as positive strips on two-dimensional representations of chromatin interaction, are enriched in epigenetic marks H3K27me3, H3.1, and H3.3. We also identify more than 400 insulator-like regions. Furthermore, although topologically associating domains (TADs), which are prominent in animals, are not an obvious feature of A. thaliana genome packing, we found more than 1000 regions that have properties of TAD boundaries, and a similar number of regions analogous to the interior of TADs. The insulator-like, TAD-boundary-like, and TAD-interior-like regions are each enriched for distinct epigenetic marks and are each correlated with different gene expression levels. We conclude that epigenetic modifications, gene density, and transcriptional activity combine to shape the local packing of the A. thaliana nuclear genome.

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Section: Discussionsupporting

confidence: 76%

Genome-wide analysis of local chromatin packing in Arabidopsis thaliana

et al. 2014

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“…Homologous transgenic tandem repetitive sequences pair more often with each other and associate with chromocenters in A. thaliana nuclei than flanking euchromatin (Jovtchev et al 2008(Jovtchev et al , 2011Pecinka et al 2005). Similarly, sister chromatid cohesion at endogenous centromeric repetitive sequences is increased compared with euchromatic sequences in Arabidopsis.…”

Section: Discussionmentioning

confidence: 87%

Interphase chromatin organisation in Arabidopsis nuclei: constraints versus randomness

2012

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The spatial chromatin organisation and molecular interactions within and between chromatin domains and chromosome territories (CTs) are essential for fundamental processes such as replication, transcription and DNA repair via homologous recombination. To analyse the distribution and interaction of whole CTs, centromeres, (sub)telomeres and ~100-kb interstitial chromatin segments in endopolyploid nuclei, specific FISH probes from Arabidopsis thaliana were applied to 2-64C differentiated leaf nuclei. Whereas CTs occupy a distinct and defined volume of the nucleus and do not obviously intermingle with each other in 2-64C nuclei, ~100-kb sister chromatin segments within these CTs become more non-cohesive with increasing endopolyploidy. Centromeres, preferentially located at the nuclear periphery, may show ring- or half-moon like shapes in 2C and 4C nuclei. Sister centromeres tend to associate up to the 8C level. From 16C nuclei on, they become progressively separated. The higher the polyploidy level gets, the more separate chromatids are present. Due to sister chromatid separation in highly endopolyploid nuclei, the centromeric histone variant CENH3, the 180-bp centromeric repeats and pericentromeric heterochromatin form distinct subdomains at adjacent but not intermingling positions. The (sub)telomeres are frequently associated with each other and with the nucleolus and less often with centromeres. The extent of chromatid separation and of chromatin decondensation at subtelomeric chromatin segments varies between chromosome arms. A mainly random distribution and similar shapes of CTs even at higher ploidy levels indicate that in general no substantial CT reorganisation occurs during endopolyploidisation. Non-cohesive sister chromatid regions at chromosome arms and at the (peri)centromere are accompanied by a less dense chromatin conformation in highly endopolyploid nuclei. We discuss the possible function of this conformation in comparison to transcriptionally active regions at insect polytene chromosomes.

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“…Successful application of the LacO/LacI system for GFP tagging of distinct chromosomal loci in living A. thaliana has already been described (Kato and Lam, 2001;Pecinka et al, 2005;Watanabe et al, 2005;Jovtchev et al, 2008Jovtchev et al, , 2011. Indeed, preliminary data suggest that the LacO/LacI system can be exploited also for ectopic plant kinetochore assembly, providing dicentric chromosomes for subsequent splitting into artificial minichromosomes (Teo et al, 2013).…”

Section: De Novo Generation Of Centromeres At Tandem Repeatsmentioning

confidence: 99%

Engineered plant minichromosomes

Houben¹,

Mette²,

Teo³

et al. 2013

Int. J. Dev. Biol.

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Minichromosomes offer an enormous potential for plant breeding and biotechnology, because they may simultaneously transfer and stably express multiple genes. Segregating independently of their host chromosomes, they provide a platform for accelerating plant breeding. Minichromosomes can be established from cloned components in vivo (bottom up) or via engineering of natural chromosomes (top down). When they possess functional centromeres and telomeres, they should be stably inherited, but their meiotic transmission rate is below that of endogenous chromosomes. To achieve the customized generation and control the regular transmission of minichromosomes are important challenges for applied research in chromosome biology. Here, construction and biology of plant minichromosomes are compared with data available for yeast and animal systems.

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Pairing of lacO tandem repeats in Arabidopsis thaliana nuclei requires the presence of hypermethylated, large arrays at two chromosomal positions, but does not depend on H3-lysine-9-dimethylation

Cited by 17 publications

References 48 publications

Genome-wide analysis of local chromatin packing in Arabidopsis thaliana

Genome-wide analysis of local chromatin packing in Arabidopsis thaliana

Interphase chromatin organisation in Arabidopsis nuclei: constraints versus randomness

Engineered plant minichromosomes

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