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| Status |
Public on Nov 01, 2013 |
| Title |
Characterization of chromosomal architecture in Arabidopsis thaliana by Chromosome Conformation Capture |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Other
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| Summary |
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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| Overall design |
This study includes circular chromosome conformation capture (4C) sequencing information of 13 samples, present in two batches, each present in duplicates (A and B). The individual 4C sequencing information can be retrieved by the 4C primer sequence, given in the 4C primer information file.
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| Contributor(s) |
Grob S |
| Citation(s) |
24267747 |
| Submission date |
Aug 26, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Stefan Grob |
| E-mail(s) |
sgrob@botinst.uzh.ch
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| Organization name |
University of Zurich
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| Department |
Institute of Plant Biology
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| Lab |
Grossniklaus Lab
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| Street address |
Zollikerstrasse 107
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| City |
Zurich |
| ZIP/Postal code |
8008 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
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| Samples (26)
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| Relations |
| BioProject |
PRJNA216987 |
| SRA |
SRP029215 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE50181_RAW.tar |
241.3 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE50181_primer_information_file.xlsx.gz |
44.1 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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