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Series GSE41356 Query DataSets for GSE41356
Status Public on Jul 01, 2014
Title Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by genome tiling array
Genome variation profiling by genome tiling array
Summary Background
Segmental duplications (SDs) are not evenly distributed along chromosomes. The reasons for this biased susceptibility to SD insertion are poorly understood. Accumulation of SDs is associated with increased genomic instability, which can lead to structural variants and genomic disorders such as the Williams-Beuren syndrome. Despite these adverse effects, SDs have become fixed in the human genome. Focusing on chromosome 7, which is particularly rich in interstitial SDs, we have investigated the distribution of SDs in the context of evolution and the three dimensional organisation of the chromosome in order to gain insights into the mutual relationship of SDs and chromatin topology.

Intrachromosomal SDs preferentially accumulate in those segments of chromosome 7 that are homologous to marmoset chromosome 2. Although this formerly compact segment has been re-distributed to three different sites during primate evolution, we can show by means of public data on long distance chromatin interactions that these three intervals, and consequently the paralogous SDs mapping to them, have retained their spatial proximity in the nucleus. Focusing on SD clusters implicated in the aetiology of the Williams-Beuren syndrome locus we demonstrate by cross-species comparison that these SDs have inserted at the borders of a topological domain and that they flank regions with distinct DNA conformation.

Our study suggests a link of nuclear architecture and the propagation of SDs across chromosome 7, either by promoting regional SD insertion or by contributing to the establishment of higher order chromatin organisation themselves. The latter could compensate for the high risk of structural rearrangements and thus may have contributed to their evolutionary fixation in the human genome.

Overall design 2 cell lines-5 samples: 2x DNA fragmentation during apoptosis; 3x ChIP (2x H4K8ac, 1x H3)
IMR90: 1x DNA fragmentation during apoptosis; 1x H4K8ac ChIP. Both hybridized on a custom designed 4x 180k oligonucleotide microarray
Contributor(s) Ullmann R
Citation(s) 24973960
Submission date Oct 04, 2012
Last update date Mar 21, 2017
Contact name Reinhard Ullmann
Phone 00493084131251
Organization name MPIMG
Department Human Molecular Genetics
Lab Molecular Cytogenetics
Street address Ihnestr.73
City Berlin
ZIP/Postal code 14195
Country Germany
Platforms (2)
GPL9777 Agilent-021850 SurePrint G3 Human CGH Microarray (Feature Number version)
GPL17964 Agilent-037305 SurePrint G3 Human Custom CGH Microarray 4x180K
Samples (7)
GSM1015443 IMR90 H3
GSM1015444 IMR90 H4K8ac (GPL9777)
GSM1015445 IMR90 Apoptosis (GPL9777)
BioProject PRJNA176661

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE41356_RAW.tar 705.3 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
Processed data provided as supplementary file

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