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Series GSE5891 Query DataSets for GSE5891
Status Public on Sep 22, 2006
Title Nuclear organization of active and inactive chromatin domains revealed by 4C technology
Organism Mus musculus
Experiment type Expression profiling by array
Summary The spatial organization of DNA in the cell nucleus is an emerging key contributor to genomic function. We have developed 4C technology, or 3C-on-chip, which allows for an unbiased genome-wide search for DNA loci that contact a given locus in the nuclear space. We demonstrate here that active and inactive genes are engaged in many long-range intrachromosomal interactions and can also form interchromosomal contacts. The active b-globin locus in fetal liver contacts mostly transcribed, but not necessarily tissue-specific, loci elsewhere on chromosome 7, while the inactive locus in fetal brain contacts different, transcriptionally silent, loci. A housekeeping gene in a gene dense region on chromosome 8 forms long-range contacts predominantly with other active gene clusters, both in cis and in trans, and many of these intra- and interchromosomal interactions are conserved between the tissues analyzed. Our data demonstrate that chromosomes fold into areas of active chromatin and areas of inactive chromatin and establish 4C technology as a powerful tool to study nuclear architecture.
Keywords: 4C technology
Overall design Gene expression arrays were performed in triplicate, according to standard procedures (Affymetrix). 4C experiments were performed in duplo (biologically independent samples), dye swap was included. Hybriisation was performed on dedicated micro-arrays. Probes (60-mers) were selected from the sequences 100 bp up –and downstream of HindIII sites. To prevent cross-hybridization, probes that had any similarity with highly abundant repeats (RepBase 10.09) were removed from the probeset. In addition, probes that gave more than two BLAST hits in the genome were also removed from the probeset. Sequence alignments were performed using MegaBLAST using the standard settings. A hit was defined as an alignment of 30 nt or longer.
Contributor(s) Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, van Steensel B, de Laat W
Citation(s) 17033623
Submission date Sep 21, 2006
Last update date Feb 11, 2019
Contact name Wouter de Laat
Phone 31-10-4087164
Fax 31-10-4089468
Organization name Erasmus MC
Department Cell Biology
Street address Dr. Molewaterplein 50
City Rotterdam
ZIP/Postal code 3015 GE
Country Netherlands
Platforms (3)
GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
GPL4344 deLaat_4C_2005_11
GPL4345 deLaat_4C_2005_06
Samples (18)
GSM136889 4C_HS2-fetal_brain-B
GSM136890 4C_HS2-fetal_liver-B
GSM136891 4C_HS2-fetal_liver-A
BioProject PRJNA97317

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