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| Status |
Public on Nov 16, 2013 |
| Title |
Genome-wide maps of chromatin state in Williams-Beuren (WBS), Williams-Beuren Region duplication (WBRdupS), Smith-Magenis (DGS), DiGeorge (DGS) lymphoblastoid cell lines |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Copy number variants (CNV) influence the expression of genes that map not only within, but also on their flanks. To assess the possible mechanism(s) underlying this “neighboring effect”, we compared intrachromosomal interactions and histone modifications in cell lines of patients affected by genomic disorders and control individuals. We detected alteration of intrachromosomal interactions (chromosomal looping) between the loci of affected genes and the rearranged interval using chromosome conformation capture (4C-seq). These results are consistent with the observed gene expression alterations. We also pinpointed concomitant changes in histone modifications between samples. Modified genes were often looping together, possibly forming an interacting cluster. We conclude that large genomic rearrangements can lead to chromatin conformation changes that extend far away from the structural variant, thus possibly modulating expression globally and modifying the phenotype. For example, we observe that the chromatin conformation, histone marks and relative expression levels of the AUTS2 gene, mutations of which are associated with autism and intellectual disabilities, are modified in Williams-Beuren syndrome patients cell lines.
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| Overall design |
Examination of 2 different histone modifications in genomic disorders patients' cell lines.
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| Contributor(s) |
Witwicki RM, Migliavacca E, Gheldof N, Reymond A |
| Citation(s) |
24265791 |
| Submission date |
Nov 17, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexandre Reymond |
| E-mail(s) |
alexandre.reymond@unil.ch
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| Organization name |
UNIL
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| Department |
CIG
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| Lab |
Reymond
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| Street address |
Dorigny
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| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
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| Samples (10)
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| Relations |
| SRA |
SRP009390 |
| BioProject |
PRJNA148607 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE33784_ChIP_protocol.txt.gz |
592 b |
(ftp)(http) |
TXT |
| GSE33784_RAW.tar |
2.2 Gb |
(http)(custom) |
TAR (of BED, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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