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Series GSE8854 Query DataSets for GSE8854
Status Public on May 07, 2008
Title Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by genome tiling array
Summary Proper genome functionality is underpinned by the non-random, spatial or ganisation of chromatin. At the periphery of the nucleus, the association of chr omatin with the nuclear lamina is thought to facilitate both structural organisa tion and regulation of gene expression. Except for a small number of individual loci, the regions of the human genome that locate at the nuclear lamina have not been identified. Here we used DamID to map the interaction sites of lamin B1 at high resolution in human fibroblasts. We show that almost half of the human gen ome preferentially associates with the nuclear lamina. Chromatin-lamina interact ions occur via sharply demarcated domains of up to several megabases in size, wh ich are bordered by similar sized domains that do not associate with the lamina. Lamina associated domains (LADs) are typified by low gene density and low gene expression levels. This is reflected by low levels of PolII binding and histone modification H3K4me2, in combination with enrichment of H3K27me3 (and H3K9?). A considerable subset of LADs is flanked by active promoters pointing outwards, or by the insulator protein CTCF, suggesting possible mechanisms of LAD confinemen t. Finally, we found that chromosome re-arrangements occur more frequently betwe en loci located either within or outside LADs. The identification of enormous, s harply defined stretches of the human genome that associate with the nuclear lam ina provides unprecedented insights into the 3D organisation of chromatin within the nucleus. Our results reveal the division of the human genome into periphera l and internal domains, which is echoed in genome functionality.
Keywords: DamID
Overall design DamID profiling of LaminB1 and Emerin in human fibroblasts. Two biological replicate samples of LaminB1 and of Emerin were hybridized in dye swap orientation on high density array covering human chromosome HSA4. Two biological replicate samples of LaminB1 were hybridized in dye swap orientation on a series of 8 high density arrays covering the whole human genome.
Contributor(s) Guelen L, Pagie L, van Steensel B
Citation(s) 18463634
Submission date Aug 22, 2007
Last update date Mar 17, 2012
Contact name Bas van Steensel
Phone + 31 20 512 2040
Fax +31 20 669 1383
Organization name Netherlands Cancer Institute
Department division of Molecular Biology
Lab van Steensel group
Street address Plesmanlaan 121
City Amsterdam
ZIP/Postal code 1066 CX
Country Netherlands
Platforms (9)
GPL5644 NKI/VanSteensel_HSA_390k_1/8_v070724
GPL5646 NKI/VanSteensel_HSA_390k_2/8_v070724
GPL5648 NKI/VanSteensel_HSA_390k_3/8_v070724
Samples (10)
GSM220158 Tig3 human fibroblast cells, LaminB1 DamID, platform 1/8
GSM220159 Tig3 human fibroblast cells, LaminB1 DamID, platform 2/8
GSM220160 Tig3 human fibroblast cells, LaminB1 DamID, platform 3/8
BioProject PRJNA102207

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
GSE8854_RAW.tar 64.5 Mb (http)(custom) TAR (of TSV)
GSE8854_README.txt 1.5 Kb (ftp)(http) TXT
Processed data included within Sample table

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