| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
Priority Reports |
1 Genomic Medicine Institute, Lerner Research Institute, Cleveland, Ohio; 2 First Department of Internal Medicine, and 3 Department of Molecular Biology, Cancer Research Institute, Sapporo Medical University, Chuo-ku, Japan; and 4 Biometry and Clinical Trials Division, 5 Cancer Biology Division, and 6 The Johns Hopkins Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
Requests for reprints: Angela H. Ting, Cleveland Clinic Foundation. E-mail: tinga{at}ccf.org or Hiromu Suzuki, Sapporo Medical University. E-mail: hsuzuki{at}sapmed.ac.jp or Stephen B. Baylin, Bunting Blaustein Cancer Center, The Johns Hopkins University, 1650 Orleans Street, Suite 541, Baltimore, MD 21231. Phone: 410-955-8506; Fax: 410-614-9984; E-mail: sbaylin{at}jhmi.edu.
| Abstract |
|---|
|
|
|---|
| Introduction |
|---|
|
|
|---|
Recently, several groups have shown that synthetic small double-stranded RNAs homologous to gene promoter regions are able to induce transcriptional gene silencing at the targeted loci in human cells (3–6). This dsRNA-dependent Transcriptional Silencing (RdTS) was reproducibly found to associate with an enrichment of the silencing histone modification, H3 lysine 9 dimethylation (H3K9me2) but not DNA methylation in acute silencing events. However, H3K9me2 have been shown to precede DNA hypermethylation in the resilencing and remethylation of the tumor suppressor gene, p16ink4a, in HCT116 colon cancer cells (7), and therefore, it remains possible that RdTS may be a mechanism to initiate abnormal epigenetic silencing. Because other known RNA-mediated epigenetic silencing mechanisms in yeast (8, 9) and plants (10–12) all require the processing of RNA precursors by DICER, we investigated the possibility that DICER, an essential component of the RNAi pathway, is also required for the proper maintenance of epigenetic silencing in human cancer cells.
| Materials and Methods |
|---|
|
|
|---|
Microarray analysis. Total RNA was harvested from log phase cells using Trizol (Invitrogen) and the RNeasy kit (Qiagen) according to manufacturer's instructions, including a DNase digestion step. RNA was quantified using NanoDrop ND-100 followed by quality assessment with 2100 Bioanalyzer (Agilent Technologies). RNA concentrations for individual samples were >200 ng/µL, with 28 s/18 s ratios >2.2 and RNA integrity of 10 (10 scored as the highest). Sample amplification and labeling were performed using the Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies) according to manufacturer's instructions. The labeled cRNA was purified using the RNeasy mini kit (Qiagen). RNA spike-in controls were added to RNA samples before amplification. Samples (0.75 µg) labeled with Cy3 or Cy5 were mixed with control targets, assembled on Oligo Microarray, hybridized, and processed according to the Agilent microarray protocol. Scanning was performed with the Agilent G2565BA microarray scanner using settings recommended by Agilent Technologies. Microarray data Gene Expression Omnibus accession numbers are GSM147895 and GSM147932 (dye swap). An identical experiment was performed using the Affymetrix platform according to the Affymetrix microarray protocol. The results for the Agilent microarray experiments are shown in Fig. 1 .
|
Reverse transcription-PCR. Total RNA were extracted from cell pellets with RNeasy Mini kit (Qiagen) and treated with DNase (Qiagen). Two micrograms of total RNA per sample were used in first-strand cDNA synthesis using Superscript 1st Strand Synthesis System (Invitrogen) with random hexamer primers. One microliter of cDNA were used for subsequent PCR reactions. PCR products were resolved on 2% agarose gels containing GelStar nucleic acid stain (Cambex) and visualized with Kodak Gel Logic 200 Imaging System. Real-time reverse transcription-PCR (RT-PCR) was carried out using Taq Man Gene Expression Assays (Applied Biosystems) and a 7900HT Fast Real-Time PCR System (Applied Biosystems) according to manufacturer's instructions. SDS2.2.2 software (Applied Biosystems) was used to perform comparative
cycle threshold analysis. GAPDH served as endogenous control. PCR conditions and primers used are available upon request.
DNA methylation analysis. Genomic DNA were extracted and treated with sodium bisulfite as previously described (13). Bisulite converted DNA was used in PCR reactions with nondiscriminatory bisulfite sequencing PCR primers. Bisulfite sequencing PCR primers and conditions are available upon request. The PCR products were subsequently cloned into the TOPO TA vector (Invitrogen) and sequenced with the M13R primer.
Chromatin immunoprecipitation assay. Cells were crosslinked and processed after the UpState Chromatin Immunoprecipitation (ChIP) Assay kit protocol (UpState). One hundred fifty micrograms of sonicated DNA were used for each immunoprecipiration (IP) reaction. Rabbit anti-H3 dimethyl-K4 (5 µg/IP; Upstate), rabbit anti-H3 dimethyl-K9, rabbit anti-H3 trimethyl-K9, rabbit anti-H3 dimethyl-K27, and rabbit anti-H3 trimethyl-K27 (10 µg/IP; gifts from T. Jenuwein of Research Institute of Molecular Pathology, Vienna, Austria) antibodies were used for the specific IP of the respective histone residues. No antibody and rabbit anti-HA antibody (10 µg/IP; Santa Cruz; SC805) were performed as controls. Fifty microliters of sonicated, pre-IP DNA from each sample were used as input controls. The final results for each sample were normalized to respective inputs. PCR conditions and primers used are available upon request.
McrBC digestion. Five micrograms of genomic DNA and 50 units of McrBC (New England Biolabs) enzyme were incubated with 1x NEBuffer, 100 µg/mL bovine serum albumin, and 1 mmol/L GTP for 12 h at 37°C. One third of each reaction was electrophoresed on 0.8% agarose gels containing GelStar nucleic acid stain (Cambex) and visualized with Kodak Gel Logic 200 Imaging System.
Western blotting. Twenty micrograms of whole cell lysates from each sample were resolved on 4% to 2% Bis-Tris gel and transferred onto a nitrocellulose membrane. The membrane was blocked in 10% milk in TTBS overnight at 4°C and incubated with 1:1,000 mouse anti-DICER1 (Imgenx), 1:500 rabbit anti-DNMT1 (Santa Cruz), and 1:10,000 mouse anti-βactin (Sigma) for 2 h at room temperature. The secondary antibodies are used at 1:1,000 for DICER1, 1:500 for DNMT1, and 1:10,000 for βactin.
Methyltransferase activity assay. DNA methyltransferase activity assays were performed as described previously (14). Briefly, 15 µg whole cell lysates were incubated with hemimethylated DNA oligos, S-adenosyl-L-[methyl-3H]methionine (3H-AdoMet; Amersham Biosciences), in reaction buffer [20 mmol/L Tris-HCl (pH 7.4), 1 mmol/L EDTA, 5% glycerol, and 1 mmol/L DTT]. After incubation at 37°C, reactions were stopped at various time points by adding one volume of 10 mmol/L nonradioactive S-adenosyl-L-methionine (Sigma). The reactions were bound to a SAM2 96 Biotin Capture plate (Promega). The plate was washed five times with PBS containing 2 mol/L NaCl and twice with dH2O to remove His6-DNMT and unreacted 3H-AdoMet. After drying the plate, 80 µL of Microscint-PS scintillation fluid (PerkinElmer) was added to each well, and tritium incorporation was quantified using the TopCount NXT liquid scintillation counter (PerkinElmer). All reactions were performed in sextuplicate. Data obtained were analyzed using the Enzyme Kinetics module of SigmaPlot (Systat Software).
| Results and Discussion |
|---|
|
|
|---|
|
|
|
DICER-mediated epigenetic gene silencing has been described in both plants and yeast. In plants, a RNA-directed DNA Methylation pathway uses RNA species to direct DNA cytosine methylation and repressive histone modifications to homologous DNA sequences to initiate transcriptional silencing (11, 12). Furthermore, RNA-dependent heterochromatin assembly has also been described in yeast for normal silencing of centromeric repeats (8, 9). Although DNA methylation is absent from the yeast system, histone tail modifications usually associated with DNA methylation, such as histone H3 lysine 9 and lysine 27 methylation, are recruited to the silenced yeast loci by double-stranded RNA molecules with sequence homology (21). Both of the above processes lead to the epigenetically silenced state, which resembles that observed for epigenetically silenced genes in cancer.
Given the above, we thus examined SFRP4 and ICAM-1 promoters by ChIP analyses for chromatin modifications that might provide insight into mechanisms that define the DICER-targeted genes. We observed some changes in chromatin modifications at DICER regulated loci that seem to be distinctive from other hypermethylated genes studied thus far (Supplementary Fig. S5; ref. 22). The demethylated and transcriptionally active SFRP4 and ICAM-1 promoters in the DICERex5 cells exhibited an increase in the enrichment of histone H3 lysine 4 dimethylation (H3K4me2) and general decreases in the enrichment of histone H3K9me2 (Supplementary Fig. S5A). These changes are identical to those seen in multiple other DNA hypermethylated genes when induced to demethylate by DAC, or in DKO cells (summary for these other genes in Supplementary Fig. S5B; ref. 22). However, unlike these previously characterized DNA hypermethylated promoters, histone H3 lysine 27 tri-methylation (H3K27me3) showed a small but consistent decrease across the entire promoter regions at the DICER-regulated SFRP4 and ICAM-1 promoters. All other DNA demethylated promoters evaluated to date seemed to retain or augment H3K27me3 (Supplementary Fig. S5B; ref. 22). This pattern of increase in H3K4me2 and decrease in H3K27me3 was not observed for the unresponsive loci, SFRP1, SFRP2, GATA4, and GATA5, in the DICERex5 cells. This suggested that the observed changes in chromatin modifications could be characteristic of the DICER-target genes.
The high degree of similarity between the RNA-mediated epigenetic gene silencing mechanisms in diverse systems, including what has been observed in human cancer with synthetic RNA oligonucleotides, suggest an evolutionarily conserved mechanism. In the present study, we established that DICER, an essential protein of the RNAi pathway in all organisms studied thus far, was indispensable for the full maintenance of promoter DNA hypermenthylation and transcriptional repression of select endogenous loci in cancer cells. We attempted to verify whether DICER is also responsible for the initiation of epigenetic silencing at these target loci by ectopically expressing functional DICER in the DICERex5 cells. However, the re-expression of DICER seemed to be lethal, and therefore, this point requires further investigation (data not shown). To our knowledge, this is the first observation directly linking DICER and mammalian epigenetic silencing of endogenous protein coding loci. It is suggestive of RdTS being a mechanism involved in aberrant hypermethylation in human cancer cells. Alternatively, the derepression of these genes could be a secondary effect due to the loss of miRNA repression of upstream common transcription factors/repressors as a result of dysregulation of the miRNA pathway.
We only observed such loss of epigenetic silencing at a subset of the many genes known to be hypermethylated and silenced in colon cancer cells. We may have missed other target genes in our initial microarray screening because SFRP4 is clearly a target locus that lacked change of expression detectable by the microarray. Also, because the DICERex5 allele is only hypomorphic, we might not have observed the fullest effects of loss of DICER function relating to epigenetic silencing. Alternatively, our more favored hypothesis is that this pathway is only responsible for select epigenetically controlled genes. DICER processes only a subset of noncoding RNA, such as miRNA, but not all noncoding RNA that could influence epigenetic silencing. For instance, the antisense RNA involved in the epigenetic silencing of the p15 locus does not require DICER (23). What differentiates DICER-regulated genes from the rest of the epigenetically controlled loci remains to be determined. The histone modification changes we observed for these loci may be the first step toward characterizing these genes. Because H3K27me3 is thought to be specifically mediated by Polycomb group (PcG) proteins, the observed changes in H3K27me3 modification unique to SFRP4 and ICAM-1 could indicate that DICER-mediated epigenetic silencing requires PcG proteins to maintain DNA methylation. This hypothesis is in line with observations in Drosophila, where full PcG-mediated long-range gene silencing required RITS components, including dcr-2 (24). Exactly which and how PcG proteins may participate in this DICER-mediated epigenetic silencing in human cancer cells should be further examined.
In summary, we have shown that at least some genes that become DNA hypermethylated and silenced in cancer cells require DICER to maintain this epigenetic status. The only well-defined role for DICER is to process dsRNAs, and therefore, RNA molecules may be involved in the initiation and/or maintenance in this novel silencing pathway. Therefore, it is imperative that we continue working on identifying the specific mechanism of this DICER-dependent epigenetic silencing, its relationship to the RdTS phenomenon, and ultimately, its role in cancer progression and normal development. Current therapies aimed at reversing epigenetic defects focus heavily on DNMT and histone-modifying enzyme inhibitors. The study of this DICER-mediated gene silencing will help enrich our understanding of the nature of aberrant epigenetic silencing in cancers and may prove useful in revealing new targets for cancer therapies aimed at circumventing epigenetic defects.
| Acknowledgments |
|---|
The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
We thank Drs. Bert Vogelstein and Judith Bender for helpful discussions and critical reading of the manuscript, Dr. Wayne Yu for technical assistance with the microarray studies, and Dr. Thomas Jenuwein (Research Institute of Molecular Pathology, Vienna, Austria) for the generous gifts of antibodies against the various histone modifications.
| Footnotes |
|---|
A.H. Ting and H. Suzuki contributed equally to this work.
Received 11/28/07. Revised 2/14/08. Accepted 3/ 7/08.
| References |
|---|
|
|
|---|
This article has been cited by other articles:
![]() |
M. T. McCabe, J. C. Brandes, and P. M. Vertino Cancer DNA Methylation: Molecular Mechanisms and Clinical Implications Clin. Cancer Res., June 15, 2009; 15(12): 3927 - 3937. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. Muhonen and H. Holthofer Epigenetic and microRNA-mediated regulation in diabetes Nephrol. Dial. Transplant., April 1, 2009; 24(4): 1088 - 1096. [Full Text] [PDF] |
||||
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| Cancer Research | Clinical Cancer Research |
| Cancer Epidemiology Biomarkers & Prevention | Molecular Cancer Therapeutics |
| Molecular Cancer Research | Cancer Prevention Research |
| Cancer Prevention Journals Portal | Cancer Reviews Online |
| Annual Meeting Education Book | Meeting Abstracts Online |