Distinct effects on gene expression of chemical and genetic manipulation of the cancer epigenome revealed by a multimodality approach.
We tested the hypothesis that the effects on gene expression of altered DNA methylation by 5-aza-2'-deoxycytidine (5-aza-CdR) and genetic (DNMT knockout) manipulation of DNA are similar, and distinct from Trichostatin A (TSA)-induced chromatin decondensation. Surprisingly, the effects of 5-aza-CdR were more similar to those of TSA than to DNMT1, DNMT3B, or double DNMT somatic cell knockout. Furthermore, the effects of 5-aza-CdR were similar at one and five days exposure, suggesting active demethylation or direct influence of both drugs on the stability of methylation and/or chromatin marks. Agents that induce gene activation through hypomethylation may have unintended consequences, since nearly as many genes were downregulated as upregulated after demethylation. In addition, a 75 kb cluster of metallothionein genes was coordinately regulated.
Radiation Oncology Branch, Radiation Oncology Sciences Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
David
D
Gius
Hengmi
H
Cui
C Matthew
CM
Bradbury
John
J
Cook
Deedee K
DK
Smart
Shuping
S
Zhao
Lynn
L
Young
Sheri A
SA
Brandenburg
Yali
Y
Hu
Kheem S
KS
Bisht
Allen S
AS
Ho
David
D
Mattson
Lunching
L
Sun
Peter J
PJ
Munson
Eric Y
EY
Chuang
James B
JB
Mitchell
Andrew P
AP
Feinberg
D000465:Algorithms; D017209:Apoptosis / Q000187:drug effects; D001374:Azacitidine / Q000031:analogs & derivatives* / Q000494:pharmacology; D002455:Cell Division / Q000187:drug effects; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000172:deficiency / Q000235:genetics; D019175:DNA Methylation / Q000187:drug effects*; D000077209:Decitabine; D044127:Epigenesis, Genetic / Q000235:genetics*; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects*; D020868:Gene Silencing / Q000187:drug effects; D016678:Genome; D006801:Humans; D006877:Hydroxamic Acids / Q000494:pharmacology; D008668:Metallothionein / Q000235:genetics; D008780:Methyltransferases / Q000378:metabolism; D009369:Neoplasms / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D015533:Transcriptional Activation; D000097584:DNA Methyltransferase 3B
D001374:Azacitidine; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases; D000077209:Decitabine; D006877:Hydroxamic Acids; D008668:Metallothionein; D008780:Methyltransferases; D012333:RNA, Messenger; D000097584:DNA Methyltransferase 3B; C012589:trichostatin A; C000619380:DNMT1 protein, human