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Arabidopsis thaliana

ABSTRACT: Chromosomal Architecture of Arabidopsis and its Implication in Transposon Intergration

PROVIDER: PRJNA241437 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1197490_1.fastq.gz	Fastqsanger.gz
	SRR1197490_2.fastq.gz	Fastqsanger.gz
	SRR1197491_1.fastq.gz	Fastqsanger.gz
	SRR1197491_2.fastq.gz	Fastqsanger.gz
	SRR1197492_1.fastq.gz	Fastqsanger.gz

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Arabidopsis thaliana

Project description:Characterization of chromosomal architecture in Arabidopsis thaliana by Chromosome Conformation Capture

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Chromosomal Architecture of Arabidopsis and its Implication in Transposon Intergration

Project description:Efficient storing and readout of genetic information is not only dependent on tight epigenetic regulation but also on the spatial organization and folding of chromosomes. Although the epigenome of the model plant Arabidopsis has been extensively studied, its interplay with chromosomal architecture is less well understood. We show that chromosomal architecture is tightly linked to the epigenetic state and furthermore how physical constraints such as nuclear size influence folding principles of chromatin. In addition to global principles of chromatin organisation, we describe a novel nuclear structure, termed KNOT, in which genomic regions of all five Arabidopsis chromosomes highly interact. These regions are characterized as heterochromatic islands within the euchromatin and likely represent preferred landing sites for transposons, suggesting a novel transposon defence mechanism in the Arabidopsis nucleus.

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Project description:Background: The packaging of long chromatin fibres in the nucleus poses a major challenge, as it must fulfil both physical and functional requirements. Until recently, insight into the chromosomal architecture of plants was mainly provided by cytogenetic studies. Complementary to these analyses, chromosome conformation technologies promise to refine and improve our view on chromosomal architecture and to provide a more generalised description of nuclear organization. Results: Employing circular chromosome conformation capture (4C), this study describes chromosomal architecture in Arabidopsis nuclei from a genome-wide perspective. Surprisingly, the linear organisation of chromosomes is reflected in the genome-wide interactome. In addition, we studied the interplay of the interactome and epigenetic marks and report that the heterochromatic knob on the short arm of chromosome 4 (hk4s) maintained a pericentromere-like interaction profile and interactome despite its euchromatic surrounding. Conclusion: Despite the extreme condensation that is necessary to pack the chromosomes into the nucleus, the Arabidopsis genome appears to be packed in a predictive manner, according to the following criteria: (i) heterochromatin and euchromatin represent two distinct interactomes, (ii) interactions between chromosomes correlates with the linear position on the chromosome arm, and (iii) distal chromosome regions have a higher potential to interact with other chromosomes.

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Project description:Genomic architecture of biomass heterosis in Arabidopsis

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