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Series GSE24632 Query DataSets for GSE24632
Status Public on Nov 15, 2010
Title ZNF274 colocalizes with the histone methyltransferase SETDB1 at ZNF 3' ends.
Project ENCODE
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Only a small percentage of human transcription factors (e.g. those associated with a specific differentiation program) are expressed in a given cell type. Thus, cell fate is mainly determined by cell type-specific silencing of transcription factors that drive different cellular lineages. Several histone modifications have been associated with gene silencing, including H3K27me3 and H3K9me3. We have previously shown that the two largest classes of mammalian transcription factors are marked by distinct histone modifications; homeobox genes are marked by H3K27me3 and zinc finger genes are marked by H3K9me3. Several histone methyltransferases (e.g. G9a and SETDB1) may be involved in mediating the H3K9me3 silencing mark. We have used ChIP-chip (GSE24480) and ChIP-seq to demonstrate that SETDB1, but not G9a, is associated with regions of the genome enriched for H3K9me3. A current model is that SETDB1 is recruited to specific genomic locations via interaction with the corepressor TRIM28 (KAP1), which is in turn recruited to the genome via interaction with zinc finger transcription factors that contain a Kruppel-associated box (KRAB) domain. However, specific KRAB-ZNFs that recruit TRIM28 (KAP1) and SETDB1 to the genome have not been identified. We now show that ZNF274 (a KRAB-ZNF that contains 5 C2H2 zinc finger domains), can interact with KAP1 in vitro and, using ChIP-seq, we show that ZNF274 binding sites co-localize with SETDB1, KAP1, and H3K9me3 at the 3’ ends of zinc finger genes. Knockdown of ZNF274 with siRNAs reduced the levels of KAP1 and SETDB1 recruitment to the binding sites. These studies provide the first identification of a KRAB domain-containing ZNFs that is involved in recruitment of the KAP1 and SETDB1 to the human genome.

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Overall design 7 total ChIP-seq datasets; 4 ZNF274 datasets done in duplicate from 4 different cell lines; 1 KAP1 duplicate dataset done in duplicate from K562 cells; 1 SetDB1 duplicate dataset from K562 cells; 1 H3K9me3 duplicate dataset from K562 cells
Web link
Contributor(s) Frietze S, Farnham PJ
Citation(s) 21170338
BioProject PRJNA63447
Submission date Oct 12, 2010
Last update date May 15, 2019
Contact name Philip Cayting
Organization name Stanford University
Department Genetics
Lab Snyder
Street address 1501 S California Ave
City Palo Alto
State/province CA
ZIP/Postal code 94304
Country USA
Platforms (1)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (14)
GSM607481 ZNF274_K562_ChIP-seq_rep1
GSM607482 ZNF274_K562_ChIP-seq_rep2
GSM607483 ZNF274_HepG2_ChIP-seq_rep1
SRA SRP003803

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Supplementary file Size Download File type/resource
GSE24632_RAW.tar 8.2 Gb (http)(custom) TAR (of BAM, BED, BEDGRAPH, BIGWIG, TAGALIGN)
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Processed data provided as supplementary file
Raw data are available in SRA

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