Human Molecular Genetics, 2001, Vol. 10, No. 6 645-652
© 2001 Oxford University Press
Association of acetylated histones with paternally expressed genes in the Prader–Willi deletion region
1Howard Hughes Medical Institute and 2Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
Received 5 January 2001; Revised and Accepted 5 February 2001.
 |
ABSTRACT |
|---|
 TOP ABSTRACT INTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
|---|
Imprinted genes within the Prader–Willi/Angelman syndrome region of human chromosome 15q11–q13 are regulated by a mechanism involving allele-specific DNA methylation. Since transcriptional regulation by DNA methylation involves histone deacetylation, we explored whether differences in histone acetylation exist between the two parental alleles of SNRPN and other paternally expressed genes in the region by using a chromatin immunoprecipitation assay with antibodies against acetylated histones H3 and H4. SNRPN exon 1, which is methylated on the silent maternal allele, was associated with acetylated histones on the expressed paternal allele only. SNRPN intron 7, which is methylated on the paternal allele, was not associated with acetylated histones on either allele. The paternally expressed genes NDN, IPW, PWCR1 and MAGEL2 were not associated with acetylated histones on either allele. Treatment of the lymphoblastoid cells with trichostatin A, a histone deacetylase inhibitor, did not result in any changes to SNRPN expression or association of acetylated histones with exon 1. Treatment with 5-aza-deoxycytidine (5-aza-dC), which inhibits DNA methylation, resulted in activation of SNRPN expression from the maternal allele, but was not accompanied by acetylation of histones. Our finding of allele-specific association of acetylated histones with the SNRPN exon 1 region, which encompasses the imprinting center, suggests that histone acetylation at this site may be important for regulation of SNRPN and of other paternally expressed genes in the region. On the silent allele, 5-aza-dC treatment altered SNRPN expression, but not association with acetylated histones, suggesting that histone acetylation is a secondary event in the process of gene reactivation by CpG demethylation.
|
INTRODUCTION |
|---|
|
TOPABSTRACTINTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
|---|
Genomic imprinting refers to the phenomenon in mammalian somatic cells where a subset of genes is expressed from only one parental allele. The imprint is established during gametogenesis and maintained by allele-specific DNA methylation patterns (1–4). Imprinted genes are often clustered in the genome, as in human chromosome region 15q11–q13 and in the conserved syntenic region on mouse chromosome 7C-D1. The study of spontaneous (in human) or induced (in mice) microdeletions has provided evidence for regional control of the imprinted status of genes that are widely scattered over this region (5–7).
Prader–Willi syndrome (PWS) is caused by lack of expression of genes, distributed throughout a 4.5 Mb deletion region, that are normally expressed only from the paternal chromosome 15. These genes include SNRPN (8), IPW (9), NDN (10,11), ZNF127 (12), MAGEL2 (13) and PWCR1 that encodes novel C/D box snoRNAs (14,15). PWS is characterized by neonatal hypotonia, hypogonadism, short stature associated with abnormal growth hormone secretion, facial dysmorphia, small hands and feet and hyperphagia leading to obesity if untreated. Brain function is affected by mild to moderate mental retardation, learning difficulties and obsessive-compulsive behavior (16). Approximately 70% of PWS cases are caused by de novo deletions occurring through inter- or intrachromosomal rearrangements between flanking regions of high sequence similarity (17,18). Whereas deletions that occur on the paternal allele give rise to PWS, Angelman Syndrome (AS), a disorder clinically distinct from PWS, is caused by a deletion of the same region on the maternal allele in ~70% of cases (19). Most of the remaining PWS cases have maternal uniparental disomy (UPD) representing a rescue from lethal trisomy 15. A small number of mostly familial cases have microdeletions the 5' region of SNRPN that lead to loss of expression of the paternally expressed genes in the region (5,20). These microdeletions define the location of cis-acting regulatory elements (the so-called ‘imprinting center’, IC) which has recently been delimited to a <4.3 kb region spanning the differentially methylated SNRPN CpG island and exon 1 (21). AS is believed to be due to the loss of UBE3A, which is expressed only from the maternal allele in the brain (19). Mutations in UBE3A have been reported in non-deletion, non-UPD AS cases (22,23).
Differential gene expression patterns can be associated with differences in higher order chromatin organization. When the chromatin structure throughout the SNRPN transcription unit was systematically evaluated for sensitivity to nucleases, the region surrounding exon 1 was found to contain two distinct strong nuclease hypersensitive sites exclusively on the paternal allele (24). The same region is heavily methylated and nuclease-resistant on the maternal allele (25). Several weaker, maternal allele-specific hypersensitive sites were also identified within the SNRPN locus. One of these is localized in intron 7, which contains CpG sites that are consistently methylated on the expressed paternal allele (24).
Transcriptional repression by DNA methylation has been linked to the deacetylation of core histones H3 and H4 at the level of individual genes or of whole chromosomes (26–29). In mammals, the inactive X-chromosome, which is heavily methylated, is associated with hypoacetylated histones (30). A recent study of genes that have been silenced by DNA methylation in a variety of cancer cell lines demonstrated that these genes could be reactivated by drugs that either demethylate the DNA (5-aza-deoxycytidine, 5-aza-dC) or that act to inhibit a histone deacetylase (trichostatin A, TSA). Addition of both drugs together had a synergistic effect on expression (31). Likewise, histones H3 and H4 associated with the normal unmethylated FMR1 gene are acetylated, whereas those associated with FMR1 bearing an expanded highly methylated CGG repeat are not acetylated (32). We therefore hypothesized that differential histone acetylation might be involved in regulating the allele-specific expression of genes within the 15q11–q13 region. Here we investigated if differences in histone H3 and H4 acetylation exist between the two parental alleles of SNRPN and of other paternally expressed genes in the region, and if treatments with 5-aza-dC and HDAC inhibitors could alter the patterns of expression and histone acetylation of SNRPN.
|
RESULTS |
|---|
|
TOPABSTRACTINTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
|---|
To study the effect of histone acetylation on imprinted expression of genes within the PWS/AS deletion region, we set out to determine whether paternally expressed genes from the region are associated with acetylated histones in an allele-specific manner. The model systems used for these experiments were lymphoblastoid cell lines (LCLs) from individuals with PWS or AS, and from normal controls. The mutant cell lines allow for the analysis of either the maternal (for PWS) or paternal (for AS) allele due to a loss of the opposite allele by deletion or UPD. In PWS cells with an imprinting defect, the maternal allele is still present but has assumed a paternal imprinting pattern. Immortalized cell lines, such as LCLs, maintain their allele-specific methylation and expression patterns at imprinted loci within the PWS/AS deletion region (9). To assess the association of acetylated histones with imprinted genes, we used the chromatin immunoprecipitation (ChIP) assay (31,32). The ChIP assay relies on the ability of specific antibodies to immunoprecipitate acetylated histones and the genomic DNA that is closely associated with them. Following steps of histone–DNA crosslinking, chromatin shearing, immunoprecipitation and release of the precipitated DNA fragments, the presence of a gene of interest is detected by PCR using gene-specific primers. A multiplex PCR with primers for a positive control gene, in this case GAPDH, allows for a semi-quantitative assay of association of a particular DNA sequence with acetylated histones.
Allele-specific association of acetylated histones with SNRPN
First, we addressed the association of acetylated histones H3 and H4 with the region surrounding exon 1 of SNRPN. In addition to being part of the SNRPN promoter, this region is also part of the IC, which is defined by microdeletions that result in changes to the expression and methylation status of the entire region (6,21). This CpG-rich region is highly methylated on the silent, maternal allele and is unmethylated, as well as hypersensitive to nucleases, on the expressed paternal allele (24,25). Two primer pairs were chosen around SNRPN exon 1 to amplify regions a and b (Fig. 1A). These primer sets were used individually in multiplex PCR along with primers that amplify the 5' end of the ubiquitously expressed GAPDH gene. The results of the multiplex PCR following immunoprecipitation with antibodies specific for the acetylated form of histone H3 (upper panel) or histone H4 (lower panel) are shown in Figure 1B. These data were obtained with primers that amplify region b; very similar results were obtained for region a. For all four PWS cell lines, the SNRPN exon 1 region was not amplified in the immunoprecipitated sample, although it was amplified from the input control. In contrast, SNRPN exon 1 was detected in the immunoprecipitated samples from AS and control cell lines. Since the PWS cell lines contain only the maternal allele and AS cells contain only the paternal allele, these results demonstrate that acetylated histones are present only on the paternal allele in LCL cells.
|
Allele-specific expression of SNRPN was confirmed in the same batch of cells used for the ChIP assay (Fig. 1D). Thus, expression of SNRPN is correlated with acetylation of histones H3 and H4 that are associated with the exon 1 region. These results were reproducible in several experiments with two different primer pairs that amplify adjacent parts of the SNRPN exon 1 region (Fig. 1A).
Quantitation of the results of six independent ChIP assays with antibodies against acetylated histone H3 or H4 is shown in Figure 2. With either primer pair, little SNRPN signal was detected following immunoprecipitation from PWS cells, as compared to the signal from the input control. As expected, the SNRPN signal detected following immunoprecipitation from AS cells was comparable to that detected in the input controls. For the normal cell lines, a SNRPN signal was detected in the immunoprecipitated samples, but it was much lower than that for the input control, suggesting that only one of the two alleles was detected following immunoprecipitation with antibodies against acetylated histones. From the results obtained with the PWS and AS cell lines, we infer that only the paternal allele is detected from the control cell lines. For both the AS and normal cell lines, amplification following immunoprecipitation was more efficient for region b, possibly indicating that more acetylated histones H3 and H4 are associated with this region than with region a. In contrast to the exon 1 region of SNRPN, intron 7 of SNRPN is methylated on the expressed paternal allele and is more sensitive to nucleases on the silent, maternal allele (24,33). Analysis of this region with the ChIP assay revealed no association with acetylated histones on either allele (Fig. 1C).
|
Acetylated histones are not associated with other genes in the PWS deletion region
The ChIP assay was used to determine whether other imprinted genes from within the region were also associated with acetylated histones H3 and H4 in an allele-specific manner. For these experiments, primers were designed for each gene and PCR conditions were established to allow for multiplex amplification with the GAPDH primers (Table 1). Following immunoprecipitation with antibodies for acetylated histone H3 or H4, NDN DNA was not detected from PWS, AS or normal control cell lines, although it was detected in the input fraction from all cell lines (Fig. 3A). RT–PCR analysis of the same cells used for the ChIP assay confirms allele-specific expression of NDN (Fig. 3A). Analysis of IPW and PWCR1 (Fig. 3B and C) revealed results similar to those of NDN, although for PWCR1, a low level of signal was detected in all cell lines following immunoprecipitation (Fig. 3C). Although allele-specific expression was maintained in these cell lines, it was not correlated with allele-specific histone acetylation in the regions of the IPW and PWCR1 genes that were amplified in the ChIP assay. Similar to NDN, IPW and PWCR1, MAGEL2 was not associated with acetylated histones in any of the cell lines (data not shown). Consistent with its known brain-specific expression pattern (13), MAGEL2 expression was not detected in any of the LCLs studied (data not shown).
|
|
Activation of the maternal allele of SNRPN was not coupled to acetylation of histones in the region
To further investigate the role of DNA methylation and histone acetylation in the allele-specific expression of SNRPN, we treated the LCLs from PWS, AS and control individuals with 5-aza-dC, a DNA methyltransferase inhibitor, TSA, a histone deacetylase inhibitor (34) or a combination of both drugs. Treatment with TSA alone did not result in any alteration of expression of SNRPN nor in any change in the patterns of association with acetylated histones (data not shown). Following treatment with 5-aza-dC, however, expression of SNRPN was activated in PWS cell lines (Fig. 4A). Treatment with both drugs did not lead to further increases in expression over that achieved with 5-aza-dC alone. Interestingly, treatment with 5-aza-dC or with both 5-aza-dC and TSA did not lead to changes in the association of acetylated histones with SNRPN exon 1 in any of the cell lines tested (Fig. 4B). These results were reproducible in independent experiments and with both SNRPN primer pairs (data not shown).
|
|
DISCUSSION |
|---|
|
TOPABSTRACTINTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
|---|
Numerous studies have identified a role for histone deacetylation in the transcriptional repression of genes with methylated promoters. The effect is mediated by methyl-CpG binding proteins that form a complex with histone deacetylases (26–29). While most studies were performed with transfected cell lines or Xenopus oocytes, a few recent reports have focused on endogenous mutations in mammalian cells. Coffee et al. (32) demonstrated that acetylated core histones were associated with the promoter region of the FMR1 gene in normal individuals, but not in patients with fragile X syndrome who carry an expanded 5'-(CGG)n repeat that leads to heavy methylation of the FMR1 promoter and transcriptional silencing. Since allele-specific differential CpG methylation plays a central role in the regulation of imprinted genes, including those in the PWS/AS region, we sought to determine whether acetylated histones might be associated with the monoallelic expression of SNRPN and other paternally expressed genes in the region. In established LCLs from PWS and AS individuals, the SNRPN exon 1 region of the expressed paternal allele, but not of the methylated silent maternal allele, was associated with acetylated histones. Treatment of these cells with an HDAC inhibitor (TSA) did not result in activation of the maternal SNRPN gene, nor in acetylation of the associated core histones. Treatment with the DNA demethylating agent 5-aza-dC did lead to expression of the normally silent maternal SNRPN allele; however, this activation of transcription was not accompanied by an increase in association with acetylated histones. Analysis of several other paternally expressed genes within the region revealed no allele-specific association with acetylated histones.
While this manuscript was in preparation, Saitoh and Wada () reported allele-specific association of acetylated histones H3 and H4 with exon 1 of SNRPN, as revealed by ChIP assays. Although our results confirm this observation, the current study differs in several respects. First, Saitoh and Wada’s data (35) suggest that the body of the SNRPN gene is associated with acetylated histones H3 and H4 on both alleles. Our study demonstrates that, although exon 1 of SNRPN is associated with acetylated histones H3 and H4 in an allele-specific manner, intron 7 is not associated with acetylated histones on either allele. We investigated intron 7 because of its known allele-specific methylation and nuclease hypersensitivity patterns. In contrast, Saitoh and Wada (35) ocused on exons 2–10 of the SNRPN gene. Second, while treatment of PWS LCLs with 5-aza-dC led to activation of the silent maternal SNRPN allele in both studies, we did not detect an association with acetylated histone H4 as reported by Saitoh and Wada (35). The concentration of 5-aza-dC was lower in our experiments, 500 nM versus 1 µM, and the duration of treatment was 6 instead of 7 days. Higher drug concentrations were lethal to our cells and could not be tested. Therefore, we cannot exclude that lower doses might be sufficient for activation of SNRPN, while higher doses may be necessary to achieve detectable acetylation of histones associated with the region. Third, Saitoh and Wada (35) limited their study to SNRPN, but we chose to investigate other paternally expressed genes within the 2 Mb imprinted domain as well.
Unlike SNRPN, the paternally expressed genes NDN, IPW, PWCR1 and MAGEL2 demonstrated no significant association of acetylated histones with either allele. In the LCLs studied, all genes except MAGEL2 were expressed in an allele-specific fashion, but there was no correlation between expression and association of acetylated histones. These results suggest that allele-specific histone acetylation is not directly involved in the transcriptional regulation of other paternally expressed genes in the region. For NDN, the primers used for the ChIP analysis were directed to the coding region of the gene; therefore, acetylated histones associated only with the promoter could have been missed. This possibility is unlikely, however, because the region amplified by the primers is located <1 kb from the 5' end of the gene, and the average size of DNA fragments generated by the sonication procedure was ~2 kb (data not shown). Efforts to generate suitable PCR primers within the NDN promoter region were unsuccessful because of the high GC content. Similarly, primers to both IPW and PWCR1 were located downstream of the transcription start site, although they were much closer to it than those for NDN. Although unlikely, the possibility remains that acetylated histones are associated with the promoter region of one or more of these genes and the association was not detected in these studies.
Histone acetylation levels and their relationship to DNA methylation and reactivation of transcription have been studied for other imprinted genes with quite variable results. In primary mouse fibroblasts, the H19 gene was associated with acetylated histone H3 and H4 on the expressed maternal allele only (36). In contrast, Igf2, which is linked to H19 and expressed from the paternal allele, was found to be associated with acetylated histones on both alleles at two different regions, within the 3' untranslated region and upstream of the P2 promoter (36). In that study, treatment of mouse fibroblasts with either 5-aza-dC or TSA alone resulted in the activation of Igf2, but not H19. The silent H19 allele was reactivated only by the addition of both drugs (36). In mouse fibroblasts from interspecies hybrids, the sense transcript of the insulin-like growth factor-II receptor (Igf2r) is maternally expressed and an antisense transcript is paternally expressed. The promoters of both transcripts are hypermethylated on the silent allele and associated with acetylated histones on the expressed allele (37). After treatment with TSA, sense transcripts were activated, but to a lesser degree than antisense transcripts. Interestingly, HpaII digestion revealed a decrease in DNA methylation of the promoter regions in response to TSA treatment in a dose-dependent fashion (37).
In addition to these imprinted loci, the mutant FMR1 gene, which is silenced by expansions of the CGG repeat, can be activated by drugs that alter DNA methylation and histone acetylation (38,39). Treatment of LCLs from males with the fragile X mental retardation syndrome with either 5-aza-dC or HDAC inhibitors caused FMR1 reactivation, but both drugs together acted synergistically, increasing expression levels 2–5-fold as compared to treatment with 5-aza-dC alone (39). A similar synergistic effect has been reported for the reactivation of silenced and hypermethylated tumor suppressor genes in a human colon carcinoma cell line (31). In an independent study, Coffee et al. (32) found reactivation of the silent FMR1 gene with 5-aza-dC but saw no effect of TSA on expression. Treatment with 5-aza-dC led to reassociation of acetylated histones H3 and H4 with the FMR1 promoter, but treatment with TSA caused reassociation only with acetylated histone H4, not H3. The effect of treatment with both drugs was not assessed (32).
In the current study, activation of SNRPN could be accomplished by treatment of the cells with 5-aza-dC alone. We saw no effect of TSA treatment on expression of SNRPN or on association of acetylated histones with SNRPN exon 1, either in the presence or absence of 5-aza-dC. These results suggest that DNA methylation is the primary mechanism of transcriptional repression at this site. The results could also indicate that a histone deacetylase that is not inhibited by TSA is involved in the regulation of SNRPN. As illustrated by the examples discussed above, the mechanistic relationships between DNA methylation and histone acetylation may be variable and complex. Silencing mechanisms that act on densely methylated DNA may function independently of histone deacetylase activity, as has been shown for a proviral induction system (40).
The region surrounding SNRPN exon 1 is critically important for establishing and maintaining paternal expression of genes within the entire 2 Mb imprinted domain in human and mouse (6,7,41,42). Although LCLs do not necessarily reflect what happens in the brain, they have been widely used for studies of methylation and chromatin organization. Studies of LCLs have shown that this region is hypersensitive to nucleases on the expressed paternal allele and hypermethylated on the silent maternal allele (24,25). Differentially methylated regions (DMRs) such as this one are important for the maintenance of imprinted expression patterns. The finding of allele-specific association of acetylated histones with the DMR at SNRPN exon 1 suggests that allele-specific regulation of SNRPN expression involves histone acetylation and deacetylation. In contrast, the DMR in intron 7 was not associated with acetylated histones on either allele, indicating that the role this internal DMR may play for imprinting, if any, is not mediated by differential chromatin conformation. The results of this and other studies indicate that the allele-specific regulation of imprinted genes involves both DNA methylation and histone acetylation and that mechanisms for such regulation are likely to be locus or region specific.
|
MATERIALS AND METHODS |
|---|
|
TOPABSTRACTINTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
|---|
Cell lines and cell culture
Epstein–Barr Virus (EBV)-transformed LCLs were obtained from a variety of sources. LCL 1425 (NL), LCL 1491 (NL) and LCL 1101 [AS: del (15) (q11q13) mat] were previously transformed in our laboratory. LCL 863 and LCL 865 [PWS: del (15) (q11.2q13.1) pat, GM09133 and GM10184] and LCL 1201 [AS: del (15) (q11q13) mat, GM11404] were obtained from the Human Mutant Cell Repository at the Coriell Institute (Camden, NJ). LCL 1309 (PWS: O family microdeletion) was obtained from A. Beaudet (Baylor College of Medicine, Houston, TX), and LCL 1514 (PWS: maternal UPD15) was obtained from V. Lindgren (University of Chicago, Chicago, IL). All cell lines were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (Life Technologies), glutamine and antibiotics.
Drug treatments
For all drug treatments, cells were counted and seeded at a concentration of 5 x 105 cells/ml TSA (1 mM stock; Sigma) or an equal volume of ethanol (for untreated samples) was added to the culture medium to a final concentration of 300 nM. Cells were cultured for 48 h before harvesting. For treatment with 5-aza-dC (Sigma), cells were synchronized with thymidine (32) (1 mM, Sigma) for two 8 h blocks separated by one 10 h release. Following the first thymidine block, 5-aza-dC was added to a concentration of 500 nM. Cells were cultured for 6 days with fresh 5-aza-dC added to 500 nM each day, and the media was changed every 48 h. For cells treated with both 5-aza-dC and TSA, TSA was added to a concentration of 300 nM for the final 24 h of incubation. After incubation with the drugs, cells were harvested for chromatin immunoprecipitation ChIP and RNA extraction.
ChIP
Antibodies against acetylated histones H3 and H4 were obtained from Upstate Biotech. ChIP was carried out as recommended by the manufacturer with modifications. Approximately 3 x 106 cells were lysed in 0.5 ml SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris–HCl pH 8.1). Following sonication and centrifugation, the diluted, pre-cleared lysate was divided between four tubes, 1 ml for each antibody tested and for a control without antibody, and 0.5 ml for input control. Input samples were frozen at –20°C overnight and then thawed and purified with the immunoprecipitated samples. DNA from the immunoprecipitated and input samples was purified as recommended by Upstate Biotech, and DNA pellets were resuspended in either 50 µl (test) or 150 µl (input) 10 mM Tris pH 8.0. Five microliters of each sample were used as a template for multiplex PCR.
Multiplex PCR
All amplification reactions were carried out with both gene- and GAPDH-specific primers included. Primers to amplify GAPDH were designed from the published sequence (Table 1). Amplification conditions for multiplex PCR were empirically derived for each gene-specific primer pair to maximize specificity of amplification and product dependence on target quantity. All amplifications consisted of 30 cycles of 95°C for 45 s, primer-specific annealing temperature for 45 s and 72°C for 45 s, except for some NDN amplifications, which consisted of 32 cycles. The primers and conditions for PCR of paternally expressed genes are shown in Table 1. Multiplex PCR products were separated on 2% agarose gels (for SNRPN intron 7) or 3% Nusieve GTC agarose gels (for all other products, FMC BioProducts). After electrophoresis, the gels were stained with ethidium bromide and imaged. Quantitation of signal intensities was carried out by using the Alpha Imager 2200 Documentation and Analysis System (Alpha Innotech).
RT–PCR
RNA was extracted from lymphoblastoid cells using RNA-STAT 60 (TelTest ‘B’), as recommended by the manufacturer, and an aliquot (3 µg) of RNA was treated with DNase (RNase-free; Roche) for 30 min at 37°C. After incubation at 70°C for 15 min, cDNA synthesis was carried out using random hexamers as primers (Amersham Pharmacia Biotech) and Superscript II Reverse Transcriptase (Life Technologies). One-tenth of a cDNA synthesis reaction was used as a template for PCR amplification. All PCR conditions were 95°C for 5 min, 35 cycles of 95°C for 30 s, primer-specific annealing temperature for 30 s, and 72°C for 45 s, and 72°C for 10 min. The primers and conditions for amplification are shown in Table 1.
|
ACKNOWLEDGEMENTS |
|---|
We gratefully acknowledge A. Beaudet and V. Lindgren for PWS cell lines, T. Kolesnikov for technical assistance, K. Redman for administrative assistance and T. de los Santos, J. Schweizer and M. Wan for helpful discussions. This work was supported by the Howard Hughes Medical Institute.
|
FOOTNOTES |
|---|
+ Present address: Bio-Research Solutions Unit, Agilent Technologies, Palo Alto, CA, USA
§ To whom correspondence should be addressed at: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5323, USA. Tel: +1 650 725 8089; Fax: +1 650 725 8112; Email: francke@cmgm.stanford.edu
|
REFERENCES |
|---|
|
TOPABSTRACTINTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
|---|
1 Li, E., Beard, C. and Jaenisch, R. (1993) Role for DNA methylation in genomic imprinting. Nature, 366, 362–365.[Medline]
2 Barlow, D.P. (1995) Gametic imprinting in mammals. Science, 270, 1610–1613.
3 Tucker, K.L., Beard, C., Dausmann, J., Jackson-Grusby, L., Laird, P.W., Lei, H., Li, E. and Jaenisch, R. (1996) Germ-line passage is required for establishment of methylation and expression patterns of imprinted but not of nonimprinted genes. Genes Dev., 10, 1008–1020.
4 Bartolomei, M.S. and Tilghman, S.M. (1997) Genomic imprinting in mammals. Annu. Rev. Genet., 31, 493–525.[Web of Science][Medline]
5 Sutcliffe, J.S., Nakao, M., Christian, S., Orstavik, K.H., Tommerup, N., Ledbetter, D.H. and Beaudet, A.L. (1994) Deletions of a differentially methylated CpG island at the SNRPN gene define a putative imprinting control region. Nature Genet., 8, 52–58.[Web of Science][Medline]
6 Saitoh, S., Buiting, K., Rogan, P.K., Buxton, J.L., Driscoll, D.J., Arnemann, J., Konig, R., Malcolm, S., Horsthemke, B. and Nicholls, R.D. (1996) Minimal definition of the imprinting center and fixation of chromosome 15q11-q13 epigenotype by imprinting mutations. Proc. Natl Acad. Sci. USA, 93, 7811–7815.
7 Yang, T., Adamson, T.E., Resnick, J.L., Leff, S., Wevrick, R., Francke, U., Jenkins, N.A., Copeland, N.G. and Brannan, C.I. (1998) A mouse model for Prader–Willi syndrome imprinting-centre mutations. Nature Genet., 19, 25–31.[Web of Science][Medline]
8 Özçelik, T., Leff, S.E., Robinson, W.P., Donlon, T., Lalande, M., Sanjines, E., Schinzel, A. and Francke, U. (1992) Small nuclear ribonucleoprotein polypeptide N (SNRPN), an expressed gene in the Prader–Willi syndrome critical region. Nature Genet., 2, 265–269.[Web of Science][Medline]
9 Wevrick, R., Kerns, J.A. and Francke, U. (1994) Identification of a novel paternally expressed gene in the Prader–Willi syndrome region. Hum. Mol. Genet., 3, 1877–1882.
10 Jay, P., Rougeulle, C., Massacrier, A., Moncla, A., Mattei, M.G., Malzac, P., Roeckel, N., Taviaux, S., Lefranc, J.L., Cau, P. et al. (1997) The human necdin gene, NDN, is maternally imprinted and located in the Prader–Willi syndrome chromosomal region. Nature Genet., 17, 357–361.[Web of Science][Medline]
11 MacDonald, H.R. and Wevrick, R. (1997) The necdin gene is deleted in Prader–Willi syndrome and is imprinted in human and mouse. Hum. Mol. Genet., 6, 1873–1878.
12 Jong, M.T., Gray, T.A., Ji, Y., Glenn, C.C., Saitoh, S., Driscoll, D.J. and Nicholls, R.D. (1999) A novel imprinted gene, encoding a RING zinc-finger protein and overlapping antisense transcript in the Prader–Willi syndrome critical region. Hum. Mol. Genet., 8, 783–793.
13 Boccaccio, I., Glatt-Deeley, H., Watrin, F., Roeckel, N., Lalande, M. and Muscatelli, F. (1999) The human MAGEL2 gene and its mouse homologue are paternally expressed and mapped to the Prader–Willi region. Hum. Mol. Genet., 8, 2497–2505.
14 de Los Santos, T., Schweizer, J., Rees, C.A. and Francke, U. (2000) Small evolutionarily conserved RNA, resembling C/D box small nucleolar RNA, is transcribed from PWCR1, a novel imprinted gene in the Prader–Willi deletion region, which is highly expressed in brain. Am. J. Hum. Genet., 67, 1067–1082.[Web of Science][Medline]
15 Cavaille, J., Buiting, K., Kiefmann, M., Lalande, M., Brannan, C.I., Horsthemke, B., Bachellerie, J.P., Brosius, J. and Huttenhofer, A. (2000) Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. Proc. Natl Acad. Sci. USA, 97, 14311–14316.
16 Cassidy, S.B. and Schwartz, S. (1998) Prader–Willi and Angelman syndromes, disorders of genomic imprinting. Medicine (Baltimore), 77, 140–151.[Medline]
17 Carrozzo, R., Rossi, E., Christian, S.L., Kittikamron, K., Livieri, C., Corrias, A., Pucci, L., Fois, A., Simi, P., Bosio, L. et al. (1997) Inter- and intrachromosomal rearrangements are both involved in the origin of 15q11-q13 deletions in Prader–Willi syndrome. Am. J. Hum. Genet., 61, 228–231.[Web of Science][Medline]
18 Amos-Landgraf, J.M., Ji, Y., Gottlieb, W., Depinet, T., Wandstrat, A.E., Cassidy, S.B., Driscoll, D.J., Rogan, P.K., Schwartz, S. and Nicholls, R.D. (1999) Chromosome breakage in the Prader–Willi and Angelman syndromes involves recombination between large, transcribed repeats at proximal and distal breakpoints. Am. J. Hum. Genet., 65, 370–386.[Web of Science][Medline]
19 Jiang, Y., Lev-Lehman, E., Bressler, J., Tsai, T.F. and Beaudet, A.L. (1999) Genetics of Angelman syndrome. Am. J. Hum. Genet., 65, 1–6.[Web of Science][Medline]
20 Buiting, K., Saitoh, S., Gross, S., Dittrich, B., Schwartz, S., Nicholls, R.D. and Horsthemke, B. (1995) Inherited microdeletions in the Angelman and Prader–Willi syndromes define an imprinting centre on human chromosome 15. [Published erratum appears in Nature Genet. (1995) 10, 249.] Nature Genet., 9, 395–400.
21 Ohta, T., Gray, T.A., Rogan, P.K., Buiting, K., Gabriel, J.M., Saitoh, S., Muralidhar, B., Bilienska, B., Krajewska-Walasek, M., Driscoll, D.J. et al. (1999) Imprinting-mutation mechanisms in Prader–Willi syndrome. Am. J. Hum. Genet., 64, 397–413.[Web of Science][Medline]
22 Matsuura, T., Sutcliffe, J.S., Fang, P., Galjaard, R.J., Jiang, Y.H., Benton, C.S., Rommens, J.M. and Beaudet, A.L. (1997) De novo truncating mutations in E6-AP ubiquitin-protein ligase gene (UBE3A) in Angelman syndrome. Nature Genet., 15, 74–77.[Web of Science][Medline]
23 Kishino, T., Lalande, M. and Wagstaff, J. (1997) UBE3A/E6-AP mutations cause Angelman syndrome. [Published erratum appears in Nature Genet. (1997) 15, 411.] Nature Genet., 15, 70–73.[Web of Science][Medline]
24 Schweizer, J., Zynger, D. and Francke, U. (1999) In vivo nuclease hypersensitivity studies reveal multiple sites of parental origin-dependent differential chromatin conformation in the 150 kb SNRPN transcription unit. Hum. Mol. Genet., 8, 555–566.
25 Glenn, C.C., Saitoh, S., Jong, M.T., Filbrandt, M.M., Surti, U., Driscoll, D.J. and Nicholls, R.D. (1996) Gene structure, DNA methylation and imprinted expression of the human SNRPN gene. Am. J. Hum. Genet., 58, 335–346.[Web of Science][Medline]
26 Jones, P.L., Veenstra, G.J., Wade, P.A., Vermaak, D., Kass, S.U., Landsberger, N., Strouboulis, J. and Wolffe, A.P. (1998) Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nature Genet., 19, 187–191.[Web of Science][Medline]
27 Nan, X., Ng, H.H., Johnson, C.A., Laherty, C.D., Turner, B.M., Eisenman, R.N. and Bird, A. (1998) Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature, 393, 386–389.[Medline]
28 Ng, H.H. and Bird, A. (1999) DNA methylation and chromatin modification. Curr. Opin. Genet. Dev., 9, 158–163.[Web of Science][Medline]
29 Wade, P.A., Gegonne, A., Jones, P.L., Ballestar, E., Aubry, F. and Wolffe, A.P. (1999) Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Nature Genet., 23, 62–66.[Web of Science][Medline]
30 Jeppesen, P. and Turner, B.M. (1993) The inactive X chromosome in female mammals is distinguished by a lack of histone H4 acetylation, a cytogenetic marker for gene expression. Cell, 74, 281–289.[Web of Science][Medline]
31 Cameron, E.E., Bachman, K.E., Myohanen, S., Herman, J.G. and Baylin, S.B. (1999) Synergy of demethylation and histone deacetylase inhibition in the re-expression of genes silenced in cancer. Nature Genet., 21, 103–107.[Web of Science][Medline]
32 Coffee, B., Zhang, F., Warren, S.T. and Reines, D. (1999) Acetylated histones are associated with FMR1 in normal but not fragile X-syndrome cells. [Published erratum appears in Nature Genet. (1999) 22, 209.] Nature Genet., 22, 98–101.[Web of Science][Medline]
33 Glenn, C.C., Porter, K.A., Jong, M.T., Nicholls, R.D. and Driscoll, D.J. (1993) Functional imprinting and epigenetic modification of the human SNRPN gene. Hum. Mol. Genet., 2, 2001–2005.
34 Arts, J., Lansink, M., Grimbergen, J., Toet, K.H. and Kooistra, T. (1995) Stimulation of tissue-type plasminogen activator gene expression by sodium butyrate and trichostatin A in human endothelial cells involves histone acetylation. Biochem. J., 310, 171–176.
35 Saitoh, S. and Wada, T. (2000) Parent-of-origin specific histone acetylation and reactivation of a key imprinted gene locus in Prader–Willi Syndrome. Am. J. Hum. Genet., 66, 1958–1962.[Web of Science][Medline]
36 Pedone, P.V., Pikaart, M.J., Cerrato, F., Vernucci, M., Ungaro, P., Bruni, C.B. and Riccio, A. (1999) Role of histone acetylation and DNA methylation in the maintenance of the imprinted expression of the H19 and Igf2 genes. FEBS Lett., 458, 45–50.[Web of Science][Medline]
37 Hu, J.F., Pham, J., Dey, I., Li, T., Vu, T.H. and Hoffman, A.R. (2000) Allele-specific histone acetylation accompanies genomic imprinting of the insulin-like growth factor II receptor gene. Endocrinology, 141, 4428–4435.
38 Chiurazzi, P., Pomponi, M.G., Willemsen, R., Oostra, B.A. and Neri, G. (1998) In vitro reactivation of the FMR1 gene involved in fragile X syndrome. Hum. Mol. Genet., 7, 109–113.
39 Chiurazzi, P., Pomponi, M.G., Pietrobono, R., Bakker, C.E., Neri, G. and Oostra, B.A. (1999) Synergistic effect of histone hyperacetylation and DNA demethylation in the reactivation of the FMR1 gene. Hum. Mol. Genet., 8, 2317–2323.
40 Lorincz, M.C., Schubeler, D., Goeke, S.C., Walters, M., Groudine, M. and Martin, D.I. (2000) Dynamic analysis of proviral induction and de novo methylation: implications for a histone deacetylase-independent, methylation density-dependent mechanism of transcriptional repression. Mol. Cell. Biol., 20, 842–850.
41 Bielinska, B., Blaydes, S.M., Buiting, K., Yang, T., Krajewska-Walasek, M., Horsthemke, B. and Brannan, C.I. (2000) De novo deletions of SNRPN exon 1 in early human and mouse embryos result in a paternal to maternal imprint switch. [Published erratum appears in Nature Genet. (2000) 25, 241.] Nature Genet., 25, 74–78.[Web of Science][Medline]
42 Shemer, R., Hershko, A.Y., Perk, J., Mostoslavsky, R., Tsuberi, B., Cedar, H., Buiting, K. and Razin, A. (2000) The imprinting box of the Prader–Willi/Angelman syndrome domain. Nature Genet., 26, 440–443.[Web of Science][Medline]
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  B. Lubyova, M. J. Kellum, J. A. Frisancho, and P. M. Pitha Stimulation of c-Myc Transcriptional Activity by vIRF-3 of Kaposi Sarcoma-associated Herpesvirus J. Biol. Chem., November 2, 2007; 282(44): 31944 - 31953. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M.-Y. Wu, T.-F. Tsai, and A. L. Beaudet Deficiency of Rbbp1/Arid4a and Rbbp1l1/Arid4b alters epigenetic modifications and suppresses an imprinting defect in the PWS/AS domain. Genes & Dev., October 15, 2006; 20(20): 2859 - 2870. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. M. Valley, L. M. Pertz, B. S. Balakumaran, and H. F. Willard Chromosome-wide, allele-specific analysis of the histone code on the human X chromosome Hum. Mol. Genet., August 1, 2006; 15(15): 2335 - 2347. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Makedonski, L. Abuhatzira, Y. Kaufman, A. Razin, and R. Shemer MeCP2 deficiency in Rett syndrome causes epigenetic aberrations at the PWS/AS imprinting center that affects UBE3A expression Hum. Mol. Genet., April 15, 2005; 14(8): 1049 - 1058. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. H. Vu, T. Li, and A. R. Hoffman Promoter-restricted histone code, not the differentially methylated DNA regions or antisense transcripts, marks the imprinting status of IGF2R in human and mouse Hum. Mol. Genet., October 1, 2004; 13(19): 2233 - 2245. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. C. Y. Lau, M. L. Hanel, and R. Wevrick Tissue-specific and imprinted epigenetic modifications of the human NDN gene Nucleic Acids Res., June 24, 2004; 32(11): 3376 - 3382. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Sakamoto, J. Liu, A. Greene, M. Chen, and L. S. Weinstein Tissue-specific imprinting of the G protein Gs{alpha} is associated with tissue-specific differences in histone methylation Hum. Mol. Genet., April 15, 2004; 13(8): 819 - 828. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Yang, T. Li, T. H. Vu, G. A. Ulaner, J.-F. Hu, and A. R. Hoffman The Histone Code Regulating Expression of the Imprinted Mouse Igf2r Gene Endocrinology, December 1, 2003; 144(12): 5658 - 5670. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Jiang, F. Yang, P. G. M. van Overveld, V. Vedanarayanan, S. van der Maarel, and M. Ehrlich Testing the position-effect variegation hypothesis for facioscapulohumeral muscular dystrophy by analysis of histone modification and gene expression in subtelomeric 4q Hum. Mol. Genet., November 15, 2003; 12(22): 2909 - 2921. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||