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Series GSE5445 Query DataSets for GSE5445
Status Public on Oct 16, 2006
Title Human Heterochromatin Proteins form Large Domains Containing KRAB-ZNF Genes
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by genome tiling array
Summary Heterochromatin is important for gene regulation and chromosome structure, but the genes that are occupied by heterochromatin proteins in the mammalian genome are largely unknown. We have adapted the DamID method to systematically identify target genes of the heterochromatin proteins HP1 and SUV39H1 in human and mouse cells. Unexpectedly, we found that HP1beta (CBX1) and SUV39H1 bind to genes encoding KRAB domain containing zinc finger (KRAB-ZNF) transcriptional repressors. These genes constitute one of the largest gene families and are organized in clusters in the human genome. Preference of CBX1 for this gene family was observed in both human and mouse cells. High-resolution mapping on human Chromosome 19 revealed that CBX1 coats large domains 0.1 - 4Mb in size, which coincide with the position of KRAB-ZNF gene clusters. These domains show an intricate CBX1 binding pattern: while CBX1 is globally elevated throughout the domains, it is absent from the promoters and binds more strongly to the 3’ ends of KRAB-ZNF genes. KRAB-ZNF domains contain large numbers of LINE elements, which may contribute to CBX1 recruitment. These results uncover a surprising link between heterochromatin and a large family of regulatory genes in mammals. We suggest a role for heterochromatin in the evolution of the KRAB-ZNF gene family.
Keywords: DamID, chromatin profiling, DNA microarray, expression profiling.
Overall design In this study we mapped the genomic binding sites of heterochromatin proteins CBX1, CBX3, CBX5 and SUV39H1 in different cell types using the DamID method.
DamID involves the low level expression of a fusion protein consisting of DNA adenine methyltransferase (Dam) and a chromatin protein of interest. This fusion protein is targeted to the native binding sites of the chromatin protein, where Dam methylates adenines in the surrounding DNA. The methylated DNA fragments were isolated and amplified by selective PCR, labeled with a fluorescent dye and hybridized to microarrays.
In this study we used 3 different array platforms for detection of amplified methylated DNA fragments. All experiments were done with samples obtained from independent experiments and include dye swaps.
In addition, we made an mRNA expression profile of MCF7 cells (4 arrays)
Web link
Contributor(s) Vogel MJ, Guelen L, de Wit E, Peric Hupkes D, Loden M, Talhout W, Feenstra M, Abbas B, Classen A, van Steensel B
Citation(s) 17038565
Submission date Aug 03, 2006
Last update date Apr 24, 2013
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 (5)
GPL3676 NKI-CMF Homo sapiens 35k oligo array
GPL3698 NKI-CMF Homo sapiens 19k cDNA array
GPL3701 NKI/VanSteensel_HSAP_390k_2005-08-15_Vogel_human
Samples (34)
GSM124306 MCF7_DamID_CBX1V5EcoDam(Cy5)-EcoDam(Cy3)_HO44-38_SeriesB
GSM124307 MCF7_DamID_CBX1V5EcoDam(Cy3)-EcoDam(Cy5)_HO44-42_SeriesC
GSM124319 MCF7_DamID_CBX1V5EcoDam(Cy5)-EcoDam(Cy3)_HO44-44_SeriesD
BioProject PRJNA96117

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
GSE5445_CBX1-T4Dam_GPL3698.txt 738.9 Kb (ftp)(http) TXT
GSE5445_CBX1_GPL3698.txt 738.1 Kb (ftp)(http) TXT
GSE5445_CBX1_GPL4035.txt 1.5 Mb (ftp)(http) TXT
GSE5445_CBX1_MEFs_GPL4036.txt 1.3 Mb (ftp)(http) TXT
GSE5445_CBX1_NimbleGen_GPL3701.txt 48.6 Mb (ftp)(http) TXT
GSE5445_CBX3-T4Dam_GPL3698.txt 739.7 Kb (ftp)(http) TXT
GSE5445_CBX5-T4Dam_GPL3698.txt 737.2 Kb (ftp)(http) TXT
GSE5445_EcoDam_cbx_GPL4035.txt 1.5 Mb (ftp)(http) TXT
GSE5445_EcoDam_suv_GPL4035.txt 1.5 Mb (ftp)(http) TXT
GSE5445_MCF7_Expression_GPL3676.txt 954.7 Kb (ftp)(http) TXT
GSE5445_RAW.tar 462.4 Mb (http)(custom) TAR (of TIFF)
GSE5445_README_GSE5445.txt 3.6 Kb (ftp)(http) TXT
GSE5445_SUV39H1_GPL4035.txt 1.5 Mb (ftp)(http) TXT

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