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E-GEOD-28170 - The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset

Status
Released on 25 March 2011, last updated on 11 August 2015
Organism
Homo sapiens
Samples (5)
Protocols (3)
Description
The most common mutation in human melanoma, BRAF(V600E), activates the serine/threonine kinase BRAF and causes excessive activity in the mitogen-activated protein kinase pathway. BRAF(V600E) mutations are also present in benign melanocytic naevi, highlighting the importance of additional genetic alterations in the genesis of malignant tumours. Such changes include recurrent copy number variations that result in the amplification of oncogenes. For certain amplifications, the large number of genes in the interval has precluded an understanding of the cooperating oncogenic events. Here we have used a zebrafish melanoma model to test genes in a recurrently amplified region of chromosome 1 for the ability to cooperate with BRAF(V600E) and accelerate melanoma. SETDB1, an enzyme that methylates histone H3 on lysine 9 (H3K9), was found to accelerate melanoma formation significantly in zebrafish. Chromatin immunoprecipitation coupled with massively parallel DNA sequencing and gene expression analyses uncovered genes, including HOX genes, that are transcriptionally dysregulated in response to increased levels of SETDB1. Our studies establish SETDB1 as an oncogene in melanoma and underscore the role of chromatin factors in regulating tumorigenesis. ChIP was performed from short-term cultures of WM262 and WM451Lu cells.
Experiment type
ChIP-seq 
Contacts
Richard A Young, Steve Bilodeau
Citation
The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset. Ceol CJ, Houvras Y, Jane-Valbuena J, Bilodeau S, Orlando DA, Battisti V, Fritsch L, Lin WM, Hollmann TJ, Ferré F, Bourque C, Burke CJ, Turner L, Uong A, Johnson LA, Beroukhim R, Mermel CH, Loda M, Ait-Si-Ali S, Garraway LA, Young RA, Zon LI. , PMID:21430779
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-28170.idf.txt
Sample and data relationshipE-GEOD-28170.sdrf.txt
Processed data (1)E-GEOD-28170.processed.1.zip
Links