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Endocrinology Vol. 144, No. 12 5658-5670
Copyright © 2003 by The Endocrine Society

The Histone Code Regulating Expression of the Imprinted Mouse Igf2r Gene

Youwen Yang, Tao Li, Thanh H. Vu, Gary A. Ulaner, Ji-Fan Hu and Andrew R. Hoffman

Medical Service, Veterans Affairs Palo Alto Health Care System, and Department of Medicine, Stanford University, Palo Alto, California 94304

Address all correspondence and requests for reprints to: Andrew Hoffman, Medical Service, Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, California 94304. E-mail: arhoffman{at}stanford.edu; or Thanh H. Vu, Stanford Medical School, 3801 Miranda Avenue, Palo Alto, California 94304. E-mail: thanhvu{at}stanford.edu.


   Abstract
Top
 Abstract
Introduction
 Materials and Methods
 Results
 Discussion
 References
 
The mouse IGF-II receptor (Igf2r) and its antisense transcript Air are reciprocally imprinted in most normal tissues. Several mechanisms have been hypothesized to explain Igf2r-Air imprinting, including Igf2r silencing by Air, and transcriptional repression of Igf2r-Air by two differentially methylated regions (DMR1 and DMR2). We employed Mus musculus x Mus spretus interspecific mice and chromatin immunoprecipitation (ChIP) to investigate allele-specific histone modifications in the two DMRs. We show that, in both DMRs, the active alleles of both Igf2r, and Air are associated with acetylated histones (H3, and H4), acetyl lysine 9 of histone H3 (H3 K9-Ac), and methyl lysine 4 of histone H3 (H3 K4-Me). The silenced alleles are associated with methylated DNA, deacetylated H3 K9, and unmethylated H3 K4. Allele-specific histone modifications are present in the DMR2 that is established in the gametes and represents the DNA gametic-imprint of the Igf2r. In the DMR2 from liver, kidney, and central nervous system tissues, H3 K9 methylation is associated exclusively with the silenced allele, and H3 S10 phosphorylation with the active alleles. Treatment of fibroblast cells with 5-aza-deoxycytidine and/or Trichostatin A led to partial reactivation of the silenced allele, which correlates with biallelic histone acetylation. In central nervous system, despite the presence of imprinted Air transcripts, biallelic expression of Igf2r occurs. The tissue-specific relaxation of Igf2r imprinting correlates with biallelic histone acetylation, and biallelic H3 K4 methylation in the promoter region of Igf2r (DMR1). We propose a model of the histone code for Igf2r, and Air imprinting that defines histone modifications specific for the putative gametic imprint DMR2, and explains the tissue-specific imprinting of Igf2r in the mouse and the absence of IGF2R imprinting in human.


   Introduction
Top
 Abstract
 Introduction
Materials and Methods
 Results
 Discussion
 References
 
GENOMIC IMPRINTING REFERS to a mechanism whereby only one of the two parental alleles is normally expressed while the other parental allele is not transcribed. The epigenetic marks associated with imprinted genes have recently been examined, and it is clear that DNA methylation, histone acetylation, and histone methylation are differentially present on the expressed and silenced alleles (1, 2, 3, 4, 5, 6, 7, 8, 9, 10).

One of the most intensively studied imprinted genes is the gene that encodes the IGF-II receptor/mannose-6-phosphate receptor (IGF2R). The gene is maternally expressed in marsupials, rodents, and artiodactyls (including cows and pigs), but it is biallelically expressed in primates, including humans (11, 12, 13). The IGF-II receptor binds IGF-II, a potent mitogen, and then internalizes it and transports it to the lysosome for degradation. In the absence of the receptor, IGF-II levels increase, leading to increased growth in the fetus (14) and, potentially, increased cell growth after birth. Numerous malignancies have been associated with loss of heterozygosity of IGF2R (15). Thus, it has been suggested that IGF2R is a tumor suppressor gene (16), especially in liver (17), where IGF-II may play an important role in carcinogenesis (18).

The mouse Igf2r gene is an imprinted gene that encodes two reciprocally imprinted transcripts, each of which is associated with a differentially methylated region (DMR) (19). The first region (DMR1) includes the promoter for the sense Igf2r transcript, whereas DMR2, which includes the promoter for Igf2r antisense (also known as Air), is located within the second intron of the gene. DMR2 is the putative methylated CpG gametic-imprint, because it is inherited from the female gamete, whereas allele-specific region 1 methylation is not completed until postnatal d 4 (20). Dynamic changes in epigenetic modifications in region 2 may function as signals to guide the establishment of genomic imprinting during development. The very large (108 kb) noncoding RNA Air has been shown to suppress the expression of the sense Igf2r as well as the expression of two other nearby paternally imprinted genes, Slc22a2 and Slc22a3 (21). Deletion of Air leads to loss of Igf2r imprinting in peripheral tissues (22). However, regulation of Igf2r expression in the central nervous system (CNS) does not seem to be determined by Air. Although Air is maternally imprinted in the CNS as well as in peripheral tissues, Igf2r sense transcripts are biallelically expressed in brain (23).

The human IGF2R gene also contains a DMR in intron 2 (24), but no antisense transcripts have been detected, and the gene is always biallelically expressed (25, 26). Thus, it seems that, though the DNA is "marked" for imprinting, the putative imprint is never read, and both alleles are transcribed. To understand this lack of epigenetic readout, we were interested in examining the histone code for the mouse Igf2r gene to learn if histone modifications represented the determining epigenetic feature.

The role of histones as active participants in gene regulation has only recently been appreciated. Previously, these proteins, which are assembled into nucleosomes, forming beads around which the DNA is wrapped, were considered to be relatively inert scaffolding for packaging the genetic material. However, the histone amino-terminal tails extend away from the central core and are thus available for posttranslational, reversible acetylation; methylation; phosphorylation; and ubiquitination (27). The array and combination of these specific attachments to the various histones constitute a distinct code that may entail thousands of histone isoforms and which may make it possible to determine how these proteins will interact with their nearby DNA sequences (28). By reading the histone code, it may be possible to predict which gene products will be transcribed, and thus determine a cell’s RNA repertoire and ultimately its proteome. The task of interpreting the histone code is still in its very early stages, because it is not yet clear that we have identified the full gamut of covalent modifications and attachments, or how the various combinations of such changes (e.g. H4 acetylation and H3 K9 methylation) on a single nucleosome or on adjacent nucleosomes interact with one another to modify gene expression (29). We hypothesize that there may be unique histone codes for imprinted (silenced) alleles in primary and secondary imprints, and that various DMRs may attract a set of unique or characteristic histone modifiers. To investigate these hypotheses, we have studied the histone code of Igf2r and Air in CNS, and peripheral tissues in detail, and we have examined how pharmacologic modulators of histone acetylation and DNA methylation alter the histone code and gene expression.


   Materials and Methods
Top
 Abstract
 Introduction
 Materials and Methods
Results
 Discussion
 References
 
Interspecific mice and skin fibroblast cells
We used interspecific mice to distinguish the two parental alleles. Housing and all procedures were performed according to protocols approved by the Institutional Care and Use Committee at the Veterans Affairs Palo Alto Health Care System. Mus spretus male mice were mated with Mus musculus female mice, and the heterozygous F1 mice were killed at ages 1 d, 1 month, and 12 months. Liver, kidney, and CNS tissues were dissected, snap-frozen in liquid nitrogen, and stored at -70 C. Fresh skin of newborn F1 mice was removed under sterile conditions, and the tissue was minced into small pieces in PBS. After a brief centrifugation (5 min at 150 g), the minced tissues were suspended and cultured in DMEM (Invitrogen, Carlsbad, CA), supplemented with 15% fetal bovine serum and 100 U/ml penicillin and 100 µg/ml of streptomycin and grown at 37 C with 5% CO2. The medium was replaced with fresh medium, 24 h after plating. When confluent, the cells were trypsinized and subcultured into fresh plates. Confluent cells were collected and were preserved in liquid nitrogen for further study (30, 31).

Treatment of cells with 5-aza-deoxycytidine (AzaC) and Trichostatin A (TSA)
We and others have reported that treatment of fibroblast cells with AzaC (a DNA demethylating agent) and TSA (a histone deacetylation-blocking reagent) led to reactivation of the silenced alleles of imprinted genes (1, 32, 33, 34, 35). The reactivation has been linked to a change of DNA methylation, i.e. partial demethylation of a CpG island of the normally silenced allele. F1 fibroblasts at passages three to six were seeded in six-well plates at a density of approximately 2 x 105 cells/well. After 24-h seeding, the culture medium was replaced with media containing AzaC (0.2 µM) and/or TSA (0.33 µM). The cells were treated with AzaC for 7 d (three media replacements) or with TSA for 20 h (or the last 20 h of AzaC+TSA treatment). Similar TSA results were obtained using treatment for 16–24 h. We avoided prolonged treatment with TSA (more than 24 h), because this may lead to cell cycle arrest. After treatment, cells were washed twice with PBS and were analyzed by chromatin immunoprecipitation (ChIP) assay or were used for DNA and RNA preparations.

Nucleic acid preparation
Total nucleic acid (TNA) was prepared using a solution of 4 M guanidinium thiocyanate, 1% 2-mercaptoethanol, and 0.5% Sarkosyl as described previously (36). The homogenate was extracted with phenol/chloroform and then precipitated with 2-propanol. The TNA pellet was dissolved in water and precipitated with ammonium acetate and ethanol. The pellet was washed with 75% ethanol and dissolved in distilled water. RNA was prepared using Tri-reagent and followed the recommended protocol (Sigma, St. Louis, MO).

Mouse Igf2r polymorphisms and DNA sequencing
We sequenced the M. spretus Igf2r by conventional PCR cloning sequencing. We amplified M. spretus genomic DNA by using oligonucleotide primers designed from M. musculus database (GenBank, National Center for Biotechnology Information). The amplified products were verified by agarose gel electrophoresis, and cloned by TOPO-TA cloning kit (Invitrogen). DNA sequencing was performed on an ABI 377 sequencer using Big-Dye terminator chemistry (Perkin-Elmer, Wellesley, MA). Sequences were read on both strands of DNA. Polymorphic sites that were small insertion/deletion or restriction polymorphisms were selected for this study. All polymorphic sites were confirmed by restriction fragment length polymorphism (RFLP)-PCR. Primer sequences for the RFLP-PCR, PCR products, polymorphic sites, and the allelic identification are summarized in Table 1Go.


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  		TABLE 1. PCR primer, PCR products, and allelic differentiation

 
Reverse transcription (RT)
RT was performed with Maloney murine leukemia virus reverse transcriptase (Invitrogen) using both random hexamers and oligo d(T)17 primers as described previously (36). To eliminate any residual genomic DNA, total RNAs were treated with DNaseI (Takara, Shiga, Japan) for 45 min (2 U/µg RNA) and then extracted with phenolchloroform before RT.

Standard PCR and restriction enzyme digestion
Each PCR (3-µl vol under liquid wax) contained approximately 20 ng DNA (or cDNA), 0.1 µM appropriate primers, 50 µM deoxynucleotide triphosphate, 0.2 U KlenTaq I (Ab Peptides, St. Louis, MO), and 0.3 µCi 32P deoxy-CTP (Amersham). PCR conditions were: 95 C for 60 sec, followed by 30–35 cycles of 95 C for 10 sec, and optimal annealing temperature (60–65 C, determined by a gradient-temperature Eppendorff thermal cycler) for 90 sec, and finally 72 C for 10 min. We designed a simple protocol by adding an equal volume (1 µl) of template DNA, equal volume of primers, and equal volume of 3 x master PCR mixture under 15 µl of liquid wax. The master PCR mix, containing KlenTaq I, was added at the annealing step of the first PCR cycle (hot start). To avoid the complication of heteroduplex formation, labeled nucleotide (32P dCTP) or end-labeled primers were added in 1x PCR mixture at the last cycle of amplification. PCR products were digested with appropriate enzymes (New England Biolabs, Beverly, MA; 1 U) in a total vol of 10 µl at 37 C for 12 h under liquid wax. The digested products were separated on 5% polyacrylamide-urea gel, and visualized by a PhosphorImager (Molecular Dynamics, Sunnyvale, CA).

Allelic expression of Igf2r and Air by RT-PCR
Igf2r and Air transcripts from AzaC-and/or TSA-treated cells were amplified by RT-PCR (35 cycles of 95 C, and 65 C). In the case of the Igf2r transcript, we used primers p#6105 in exon 47 and p#971 in exon 48 (Fig. 1Go) to amplify 164 b cDNA-specific product (Table 1Go). A Hae III site common for both parental alleles serves as an internal digestion control, whereas the unique polymorphic Hae III is present only in the paternal Spretus allele. In the case of the Air transcript that extends beyond exon 1 of Igf2r, a 16-bp deletion in M. Spretus (primers p#6458 and p#8–04) was used to identify the two parental alleles (23). Relative levels of the two parental alleles were based on PhosphorImager scanning density.



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  		FIG. 1. Histone acetylation is enriched in the mouse Igf2r and Air DMRs. A, Map of mouse Igf2r and Air showing location of primers used for the ChIP assay. Amplicons a1, b1, b2, and c1 are used for ChIP scanning. Amplicons a and b (DMR1), c and d (DMR2), and e (exon 48) are used for allelic differentiation (maternal C57BL vs. paternal Spretus). Amplicon b (105 bp) and amplicon e (138 bp, Table 1Go) are also used for RT-PCR to assess the allelic expression of Air and Igf2r, respectively. Expected PCR products are in base pairs (b). B, ChIP assay on primary F1 fibroblast cells across Igf2r and Air region using anti-acetylated-histone 3 antibody (H3-Ac). Top panel, ChIP-PCR of the input DNA before immunoprecipitation. Bottom panel, ChIP-PCR after immunoprecipitation using anti-H3-Ac antibodies. PCR was performed in duplicate. Target products are identified by size (b). Note the absence of PCR products in the bottom panel (107 b in a1, 127 b in e), marked by asterisks, despite the presence of internal controls, Ig-k, and ß-actin. Mat, Maternal; Pat, paternal.

 
Preparation of di- and mononucleosomes by formaldehyde cross-linking and sonication.
We used the ChIP assay kit from Upstate Biotechnology (Santa Cruz, CA) About 1–5 million cells (or 0.1 g) of fresh or frozen tissues were fixed with 1% formaldehyde for 10 min at 37 C in cell culture media. The formaldehyde cross-linked cells in 0.6 ml sodium dodecyl sulfate lysis buffer were sonicated for 180 sec (10 sec on, and 5 sec off) on ice. Cells from minced tissues (10 mg liver, 15 mg kidney, or 30 mg brain tissues) were sonicated for 270 sec. We used a Branson sonicator with a 2-mm microtip, and setting of 40% for output control, and 90% for duty cycle. The sonicated chromatin was centrifuged for 14,000 rpm for 10 min at 4 C, aliquoted, and snap-frozen in liquid nitrogen, and stored at -70 C.

ChIP.
Antibodies obtained from Upstate Biotechnology (Waltham, MA) include: H4-Ac (acetyl lysines 5, 8, 12, and 16, catalog no. 06-866), H3-Ac (diacetyl lysines 9, and 14, catalog no. 06-599), H3 K4-Me (methyl lysine 4 of histone H3, catalog no. 07-030), and H3 K9-Me (dimethyl lysine 9, catalog no. 07-212). Antibodies against H3 K9-Ac (acetyl lysine 9 of histone H3, catalog no. 9617) and antibodies against H3-S10-P (phosphorylated serine 10 of histone H3, catalog no. 9701) were from Cell Signaling Technology (Beverly, MA). The specificity of antibodies against H3-S10-P was not affected by the modification of the adjacent lysine 9 (unmodified, acetylated, or methylated lysine 9) (data from Cell Signaling Technology). Antibodies against mono-, and trimethyl lysine 4, and lysine 9 of histone H3 were obtained from Abcam, Cambridge, UK (monomethyl K4, no. ab8895; trimethyl K4, catalog no. ab8580; monomethyl K9, catalog no. ab9045; trimethyl K9, catalog no. ab8898). All antibodies recognize the specific histone modifications (data from the suppliers). ChIP assays were carried out according to the protocol supplied by Upstate Biotechnology (Lake Placid, NY). Briefly, sonicated chromatin was diluted 10-fold in ChIP dilution buffer (200 µl), precleared with 80 µl salmon sperm DNA/protein A agarose for 1 h at 4 C with rotation. A portion of the protein A-purified chromatin (20 µl) was used to prepare DNA as the "input" sample. Antibodies (2–5 µl) were added to the clarified chromatin (180 µl) and incubated overnight with rotation. Sixty microliters of protein A agarose were added to the antibody-histone mix and incubated at 4 C for 1 h with rotation. The protein A-agarose/histone complex was collected by gentle centrifugation and washed three times with ChIP buffers, and the bound chromatin was eluted in 500 µl elution buffer. After adding 20 µl of 5 M NaCl, protein-DNA cross-linking was reversed by heating at 65 C for 4 h. Samples were treated with proteinase K, purified by MiniElute PCR purification kit (QIAGEN, Valencia, CA), and then eluted in 100 µl of low-TE buffer (1 mM Tris, 0.1 mM EDTA).

Analysis of modified histones
The relative enrichment of modified histones associated with DNA, obtained from ChIP, was determined as described previously (37) using ß-actin or Ig-k as an internal control (38). Each sample was quantified in duplicate. All primer sets were tested for the absence of primer-dimer products by conventional PCR using radioisotope and polyacrylamide-urea gel.

Quantitative real-time (Q)-PCR
Enrichments of modified histones in DNA, obtained from some of the ChIP assays, were also determined by (Q)-PCR using the ABI Prism 7900HT sequence detector, following the ABI protocol. The Q-PCR assays were run in triplicate on 384-well plates. We designed allele-specific oligonucleotide primers to amplify specifically each parental allele (Table 1Go). All primer sets for Q-PCR were free of primer-dimer products. We used SYBR Green in our Q-PCR assays. At the end of the Q-PCR amplification, we ran a melting curve analysis, to confirm the homogeneity of all Q-PCR products. Relative enrichment of a given target sequence by a specific antibody is determined by a delta Ct and delta-delta Ct calculation, by an ABI protocol, with reference to ß-actin or mouse ribosomal L7 protein gene control (Table 1Go).


   Results
Top
 Abstract
 Introduction
 Materials and Methods
 Results
Discussion
 References
 
Histone acetylation is enriched in the DMRs
Recent studies have shown that acetylated histones are associated with the chromatin regions of genes that are actively transcribed. Whereas acetylation of lysine residues of the histone tails of both H3 and H4 histones (H3-Ac and H4-Ac) has been found in active chromatin regions, deacetylation of H3, but not H4, is linked to allele-specific DNA methylation and allelic silencing in the imprinted genes Snrpn and U2af1-rs1 (39). On the paternal allele, the Igf2r antisense transcript is active, and the Igf2r sense transcript is silenced (22). Therefore, on each parental allele, active and silenced chromosomal domains are juxtaposed within the 13-Kb DNA separating the two DMRs.

To investigate the histone modifications in the chromatin region of the mouse Igf2r gene, by ChIP assay, we made PCR primers to amplify short DNA fragments of approximately 100 bases crossing various regions of the Igf2r gene. These primers were designed to amplify DNA fragments enriched in the chromatin immunoprecipitated fraction; and therefore, they can determine the presence of the histone modification specified by the antibody used in the assay at specific nucleosomes associated with the specific genomic DNA fragments. We used the primers to amplify selected sequences in the DMRs, 3.2 kb upstream of the Igf2r gene, exon 2 (where the sense and antisense transcripts overlap), and exon 48 of the 3' region of Igf2r (Fig. 1AGo, and Table 1Go).

We scanned the acetylation of H3 in nucleosomes across the overlapping sense and antisense region using the ChIP assay with a multiplex PCR containing target DNA primers and internal control primers. As shown in Fig. 1BGo, all target DNAs of predicted sizes (listed in Table 1Go) were amplified along with the internal controls in the input DNA. After immunoprecipitation using the anti-H3-Ac antibodies, no target DNAs were observed at 3.2 kb upstream (Fig. 1BGo, amplicon a1) and at exon 48 (Fig. 1BGo, amplicon e) while consistent amplification of internal controls were evident (Fig. 1BGo, compare bottom panel to top panel). Histone H3 acetylation was enriched in the DMR1, DMR2, and exon 2 to levels comparable with that of ß-actin (Fig. 1BGo, amplicons b through d, compare top and bottom panels).

Though histone acetylation was found in the active chromosomal domain, our results indicate that the acetylation modification is more enriched in the promoter region of the Igf2r (DMR1) and the Air (DMR2). The regions upstream of the Igf2r (amplicon a1) and upstream of Air (amplicon e, exon 48) or downstream of the Igf2r (exon 48) were nearly deficient of the acetylation modification.

Allele-specific histone modification in DMR1 and DMR2
We then investigated allele-specific histone modification using a panel of antibodies against histone acetylation and histone methylation. To differentiate histone modifications in the two parental alleles of the F1 interspecific mice, we sequenced the DMR1 and DMR2 of the wild-derived M. spretus (the paternal allele in the F1 mice) by standard PCR cloning and sequencing. We compared the DMR sequences of the M. spretus with those of the M. musculus (maternal allele, available in the GenBank database) and found six allelic differences between these strains (Table 1Go, amplicons c1, a, b, c, d, and e). Three of these polymorphisms involve small insertion/deletion differences that are readily quantified by PCR fragment length polymorphism without amplification bias. The remaining three polymorphisms are RFLPs that require restriction digestion. In previous publications, we have used three of these polymorphisms to distinguish the parental alleles (Table 1Go, amplicons b, d, and e) (34).

We ran PCRs of the ChIP assay along with input DNA (before immunoprecipitation) using ß-actin or Ig-k as internal PCR controls. The active ß-actin gene was used in the ChIP assay with anti H4-Ac, H3-Ac, and H3 K4-Me (methylation) antibodies. The inactive Ig-k gene was used in the ChIP assay with anti H3 K9-Me, because it has been reported that H3 K9-methylation associates with inactive genes (7, 27). Representative data of duplicate PCR from each ChIP assay are shown in Fig. 2Go, A and B. Calculation of the relative enrichment of specific histone modifications in each parental allele, compared with those of input DNA before immunoprecipitation, was based on the formula in Fig. 2CGo (40). Relative enrichments as mean values from duplicate PCR are shown at the bottom panels in Fig. 2Go, A and B and are plotted in Fig. 2DGo.



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  		FIG. 2. Allele-specific histone modifications across DMR1 and DMR2. A, ChIP-PCR using anti-H4-Ac, H3-Ac, H3 K4-Me antibodies. B, ChIP-PCR using anti-H3 K9-Me antibodies. C, Calculation of relative enrichment of parental-specific alleles vs. control, and input DNA. The calculated relative enrichments are listed under each panel in A and B. Significant data are highlighted. Interspecific F1 fibroblast cells were treated with medium (-/-) or with medium containing AzaC and/or TSA (+/+). Duplicate ChIP-PCRs were assayed across DMR1 (panels a and b), DMR2 (panels c and d), and exon 48 (panel e). Specific paternal (Pat) and maternal (Mat) alleles in each panel are listed in Table 1Go. Active alleles are underlined, and in bold. ß-actin or Ig-k was used as internal PCR control. Average relative enrichments from duplicate PCRs are listed at the bottom of each panel. D, Graphic depicts the allele-specific enrichments. White columns, Active allele (maternal in DMR1, paternal in DMR2). Black columns, Silenced allele (paternal in DMR1, maternal in DMR2). Both parental alleles are shown as shaded columns in exon 48 region. Enrichment of modified histone in input DNA was set as 1.00. Arrows indicate control F1 skin cells before AzaC/TSA treatment. M, Maternal allele; P, paternal allele; E, ChIP-Q-PCR. Relative enrichment of modified histone in each parental allele in DMR1 and DMR2 was quantified by Q-PCR using allele-specific primers (Table 1Go). White columns indicate active allele, and black columns indicate silenced allele, as in D. Enrichment of modified histone in input DNA was set as 1.00. Mean values from triplicate PCR are on the top of each column.

 
As shown in the panels marked by arrows in Fig. 2DGo, in control F1 cells without AzaC and TSA treatment (-/-), H4-Ac, H3-Ac, and H3 K4-Me associated strongly with the expressed alleles across the DMR1 and DMR2 [expressed (white columns) vs. silenced (black columns)]. In the region near the Igf2r transcription site (panel b) and in DMR2 (panels c and d), H3 K9-Me was in low abundance in nucleosomes from both parental alleles.

We further quantified the relative enrichment of histone modifications in each parental allele in DMR1 (amplicon b region) and DMR2 (amplicon d region) by Q-PCR using allele-specific primers (Table 1Go, ChIP-Q-PCR). As shown in Fig. 2EGo, acetylated histone (H3-Ac) and methylated lysine 4 (H3 K4-Me) were exclusively enriched in nucleosomes from the expressed alleles (white columns, maternal allele in DMR1 and paternal allele in DMR2). The silenced alleles (black columns, paternal allele in DMR1 and maternal allele in DMR2) were devoid of H3-Ac and H3 K4-Me. Both parental alleles had low levels of lysine 9 methylation (H3 K9-Me). The Q-PCR results are in accordance with the ChIP-PCR data in Fig. 2DGo and show absolute allele-specific histone modification, reflecting the high specificity of the antibodies employed in the ChIP experiments, and the sensitivity of the real-time PCR assay.

Reactivation of silenced alleles by AzaC and TSA associates with biallelic histone acetylation
We investigated the pharmacological modulation of allele-specific histone modifications in the reactivation of the silenced allele. We treated the F1 fibroblast cells with AzaC (0.2 µM) and/or TSA (0.33 µM) and then quantified Igf2r and Air allelic abundance using RT-PCR, and we assessed the histone modifications in DMR1 and DMR2 using the ChIP assay. Combined treatment with AzaC+TSA led to approximately 1% reactivation of the imprinted Igf2r paternal allele and to approximately 6% of the imprinted maternal Air allele (Fig. 3Go). Although the magnitudes of the reactivation were low, the detection of reactivation was not artifactual. In the case of Igf2r, the reactivated paternal allele was detected positively as a specific band by restriction enzyme digestion; and in the case of Air, the reactivated maternal allele was detected by insertion/deletion PCR analysis.



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  		FIG. 3. Reactivation of silenced allele by AzaC and TSA treatment. Expression of active and silenced alleles in Igf2r and Air were assayed by standard PCR at 65 C annealing temperature and quantified by PhosphoImager. The average values of relative expression from each parental allele are shown at the bottom of each panel. Active alleles are underlined, and in bold.

 
We analyzed the relative enrichment (compared with input DNA) of specific histone modifications (H4-Ac, H3-Ac, H3 K4-Me, and H3 K9-Me) in each parental allele across DMR1, DMR2, and exon 48 (Fig. 2Go, A, B, and D). As shown in Fig. 2DGo, AzaC alone did not significantly change histone acetylation (both H4-Ac and H3-Ac) or histone methylation at H3 K4 and H3 K9 across the DMR and exon 48 regions [Fig. 2DGo, compare nontreatment (-/-) with AzaC treatment (+/-) in a, b, c, d, and e]. In the silenced allele, TSA or TSA+AzaC slightly increased H3-Ac in the DMR1 region and H4-Ac in the DMR2 region (Fig. 2DGo, DMR1 and DMR2, H4-Ac and H3-Ac, black columns).

Tissue-specific reactivation of Igf2r silenced allele in CNS correlates with biallelic acetylation and biallelic H3 K4 methylation
To understand mechanisms underlying the CNS-specific biallelic expression of Igf2r sense transcript despite maintenance of Air imprinting, we analyzed histone modifications in the DMR1 and DMR2 in peripheral tissues, and in CNS. Representative data showing duplicate ChIP-PCR assays, using anti-H3-Ac and anti-H4-Ac antibodies in DMR1 (amplicon b) and DMR2 (amplicon d) from the F1 mice, are shown in Fig. 4AGo.



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  		FIG. 4. Allele-specific histone modifications (acetylation and methylation) in CNS and in peripheral tissues. Duplicate ChIP-PCR in liver, kidney, and CNS F1 mice were assayed using PCR primers b (DMR1) and primers d (DMR2) in Table 1Go. A, ChIP-PCR with anti-H4-Ac and anti-H3-Ac antibodies. B, ChIP-PCR with anti-H3 K4-Me and H3 K9-Me antibodies. The average enrichment values of each parental allele vs. control (ß-actin) quantified by PhosphoImager are shown at the bottom of each panel. Note equal enrichment of H4-Ac, H3-Ac, H3 K4-Me in both parental alleles in DMR1, but not DMR2, in CNS tissue. Active alleles are underlined, and in bold. Representative data from two F1 mice are shown.

 
The ChIP assays using liver and kidney resulted in data similar to those from the cultured fibroblasts, showing enrichments of H3-Ac and H4-Ac in nucleosomes near the transcription site (DMR1, amplicon b). The enrichments were restricted to the maternal, expressed allele (1.17- to 2.54-fold), whereas the paternal, silenced allele was depleted of acetylated histone (0.22- to 0.56-fold). The ratios of acetylated histone in expressed-maternal/silenced-paternal allele varied from 2.20–7.68 (Fig. 4AGo, DMR1). In contrast, at the same nucleosome location in CNS, where Igf2r was not imprinted, there was no allele-specific histone acetylation; both parental alleles had the relative enrichments of approximately 1.0 (0.85–1.22), and the allelic acetylated histone ratios were approximately1.0 (0.77–0.93) (Fig. 4AGo).

Despite the loss of Igf2r imprinting, imprinting of the Igf2r antisense (Air) was maintained in CNS. ChIP assays demonstrated predominant allele-specific H3-Ac and H4-Ac in DMR2 in all tissues including CNS (Fig. 4AGo, DMR2). The ratios of acetylated histone in expressed-paternal/silenced-maternal allele varied from 1.50–5.56.

Methylation of histone 3 at lysine 4 (H3 K4-Me), but not at lysine 9, was predominantly associated with the expressed allele in the DMRs in liver (and skin fibroblasts, see above) where Igf2r was imprinted. The allele-specificity of H3 K4-Me was not present in CNS where there was loss of Igf2r imprinting: both parental alleles had equal enrichment of H3 K4-Me in the DMR1 (Fig. 4BGo, top panel).

To correlate the histone modifications (acetylation and methylation) of nucleosomes in the DMRs to the DNA methylation status of the two parental alleles, we performed MR-PCR, a modified COBRA (combined bisulfite restriction analysis) method (41, 42), on the bisulfite-treated DNAs from liver, kidney, and CNS of F1 mice. As shown in Fig. 5Go the maternal allele was always unmethylated, whereas the paternal allele was predominantly methylated in liver and in kidney, but not in CNS.



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  		FIG. 5. Allele-specific DNA methylation in CNS and in peripheral tissues. Genomic DNAs from liver, kidney, and CNS were treated with bisulfite and amplified by methylation and restriction PCR primers (Table 1Go). PCR products from the two parental alleles (maternal, 263 b; paternal, 247 b) were purified by acrylamide gel, reamplified, and digested with Hinf I or Aci I to probe for the methylation status of CpG at nucleotide location nos. 957 and 968 (GenBank no. L 06445). Unmethylated DNA was modified by bisulfite and therefore resisted the restriction digestion. Note both parental alleles in CNS are unmethylated.

 
Allele-specific histone code in Igf2r imprinting
Histone methylation at lysine residues can occur in states of mono-, di-, or trimethylation. In Saccharomyces cerevisiae (S. cerevisiae), it has been recently reported that H3 K4 dimethylation occurs at both inactive and active genes, whereas H3 K4 trimethylation is present exclusively at active genes (43). Because S. cerevisiae has no detectable H3 K9 methylation, it may use differential states of K4 methylation to mark active and inactive genes; the three states of mono-, di-, and trimethylation may likely represent the complexity of histone modification in higher eukaryotes.

Most of the published data (including the data reported herein) concerning H3 K4 and H3 K9 methylation refer to dimethyl lysine. To test whether the three states of methylation of lysine 4 and lysine 9, and H3 K4 and H3 K9 correlate with the imprinting and loss of imprinting of Igf2r, we used antibodies directed against mono- and trimethyl H3 K4 and H3 K9 in our ChIP assays. In all tissue tested (liver, kidney, and CNS), antibodies directed against trimethyl lysine yielded results virtually identical to those from antibodies directed against dimethyl lysine: in DMR1, the active maternal allele in liver and kidney was associated predominantly with H3 K4 di- and trimethylation (Fig. 6AGo). In CNS, both active maternal and active paternal alleles were associated with H3 K4 di-and trimethylation. Low levels of H3 K9 di- and trimethylation were associated with both parental alleles in liver, kidney, and CNS, which may represent, as discussed above, basal levels of association. ChIP assays using anti-monomethylated H3 K4 and H3 K9 antibodies yielded much weaker signals, although more sensitive ChIP-Q-PCR assays revealed patterns of modification similar to those from dimethyl lysine antibodies (Li et al., unpublished). Therefore, it is likely that, in the case of Igf2r, the histone code makes no distinction between the three states of mono-, di-, and trimethylation of H3 K4 and H3 K9.



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  		FIG. 6. Allele-specific histone modifications (di- and trimethylation, H3 K9-Ac and H3-S10-P) in CNS and in peripheral tissues. Duplicate ChIP-PCRs in liver, kidney, and CNS from F1 mice were assayed using PCR primers a and b (DMR1), primers c and d (DMR2), and primers e (exon 48) in Table 1Go. A, ChIP-PCR with antidimethylated (di-) and antitrimethyl (tri-) lysine 4 and lysine 9 of histone H3 antibodies (H3 K4-Me and H3 K9-Me). B, ChIP-PCR with H3 K9-Ac vs. H3-Ac (acetylated lysines 9 and 14) antibodies. C, ChIP-PCR with anti-H3-S10-P in liver, kidney, and CNS. The average enrichment values (vs. input and ß-actin) quantified by PhosphoImager are shown at the bottom of each panel. Note similar patterns of di- and trimethylation in (A), exclusive association of H3 K9-Ac with active alleles in (B), and association of H3-S10-P with active paternal allele in DMR2, but not DMR1, in (C). Active alleles are underlined and in bold.

 
The modification of lysine 9 of histone 3 is quite unique. Unlike other lysines in H3 and H4 tails, H3 K9 can be bivalently modified, because it can be either methylated or acetylated. By using antibodies directed against the acetylated lysine 9, we could delineate the allele-specific H3 K9-Ac in the DMRs of Igf2r (Fig. 6BGo). It is interesting to note that acetylated lysine 9 (H3 K9-Ac) was detected exclusively in the active allele in liver (DMR1 and DMR2) and CNS (DMR2). Inactive or imprinted alleles in liver and in CNS (DMR2) were devoid of H3 K9-Ac. It seems, therefore, that the acetylation status of H3 K9 serves as a marker of allelic activation or silencing in Igf2r sense and antisense (DMR1 and DMR2), at least in liver and in CNS. Biallelic expression of Igf2r sense in CNS correlates with biallelic acetylation of H3 K9 in DMR1.

Phosphorylated serine 10 of H3 (H3 S10-P) has been reported to be associated with active genes (44, 45). To investigate allele-specific modifications of H3 S10-P across the Igf2r gene, we used antibodies against H3 S10-P in our ChIP assays that recognize phosphorylated serine 10 independent of modifications of the adjacent lysine 9 (data from Cell Signaling Technology). As shown in Fig. 6CGo, H3 S10-P was found only in the DMR2. No H3 S10-P was seen in the DMR1 in liver, kidney, and CNS; whereas consistent amplification of positive control (ß-actin) was seen in all ChIP assays. The results were consistent at polymorphic sites in the DMR1 (amplicons a and b) and in the DMR2 (amplicons c and d). In liver, kidney, and CNS, H3 serine 10 phosphorylation associated exclusively with the active paternal allele in DMR2. There were no H3 S10-P modifications on the silenced maternal allele in DMR2. However, in DMR1, both active and silenced parental alleles (in liver and kidney) and both active parental alleles (in CNS) were devoid of the H3 S10-P modifications. Outside of the DMRs, in exon 48, H3 S10-P was detected equally in both parental alleles (Fig. 6CGo), indicating that H3 S10-P modifications outside of the DMRs did not correlate with allelic-specific expression.


   Discussion
Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
References
 
The IGF-II receptor is a multifunctional molecule that binds mannose-6-phosphate-containing proteins, numerous lysosomal enzymes, the latent complex of TGF-ß, granzyme B (46), retinoids (47), and leukemia inhibitory factor (48) in addition to IGF-II. The gene for this protein is imprinted in rodents and many other mammals, but it is biallelically expressed in humans, because the human gene does not produce an equivalent of Air, the Igf2r-related transcript that controls imprinting in that region. However, one of the IGF2R alleles is frequently lost in malignant tissues (49), leading to a nonimprinted form of monoallelic expression of this tumor suppressor gene. Moreover, the IGF2R gene is often mutated in hepatic cancer, leading to greatly diminished activity of the expressed gene (50).

The epigenetic regulation of Igf2r expression by DNA methylation has been extensively studied. In this report, we have expanded our knowledge concerning the histone modifications regulating gene expression. It has been postulated that a histone code, encompassing numerous posttranslational covalent modifications to these evolutionarily conserved proteins, determines the pattern of gene expression. In general, increases in histone acetylation have been associated with an open chromatin conformation and enhanced gene expression. Histone methylation may induce an active or inactive chromatin state, depending on the particular amino acid that is modified. Studying the Igf2r gene locus allows us to test and refine this histone code hypothesis by studying a gene that has two promoters, one of which is expressed only by the maternal allele, whereas the other is expressed only by the paternal allele. Thus, examination of histone modifications of this gene in various tissues, including CNS, will allow us to determine whether there are consistent epigenetic changes along the gene that correlate with tissue-specific gene expression.

In most tissues, reciprocal imprinting of Igf2r sense and antisense is associated with DNA methylation of the DMRs: methylated DNA is found with the silenced allele, whereas unmethylated DNA is found with the active allele. In CNS, despite the biallelic expression of Igf2r sense, allelic expression of both Igf2r sense and Air is still strictly dictated by allelic DNA methylation (51). The allelic DNA methylation also correlates with a specific set of histone modifications. In general, the methylated DNA of the silenced allele is associated with H3 K9 Me, and the unmethylated DNA of the active allele is associated with H4 Ac, H3 Ac, and H3 K4 Me. This "universal" histone code for silenced and active genes is found in silenced and active alleles in the imprinted Igf2r in this report. Fournier et al. (10), in a recent independent study, also reported the universal histone code in imprinted loci in Snrpn, U2af1-rs1, and Igf2r.

It is interesting to note that H3 and H4 histones in the DMR1 and DMR2 were acetylated differentially after TSA treatment. TSA (with and without AzaC) leads to equal biallelic acetylation in histone H3 (but not in H4-Ac) in DMR1 and equal biallelic acetylation in histone H4 (but not in H3-Ac) in DMR2 (Fig. 2DGo, H4-Ac and H3-Ac, b and d panels). It is likely that, in the DMR1 promoter region, histone H3 is more susceptible to pharmacologic modulation than histone H4, leading to increased H3-Ac. In the DMR2, however, histone H4 is more susceptible than H3, reflecting differential structure of local nucleosomes in the two DMRs.

Biallelic acetylation of one (H3 or H4, but not both) of these histones may correlate with partial reactivation of the silenced allele to levels of 1–6% of those of the active allele in Fig. 3Go. The reactivation of the silenced allele by AzaC and/or TSA is therefore associated with (but not completely controlled by) increased H3-, H4-acetylation, and H3 K4 methylation in the DMR1 and DMR2.

Biallelic H3 K9-methylation at DMR1 was observed in CNS that demonstrated biallelic expression of Igf2r. The loss of Igf2r imprinting in CNS, however, was not directly correlated with biallelic H3 K9 methylation, because this was also observed in liver, a tissue that demonstrated maintenance of Igf2r imprinting (Fig. 4BGo, DMR1). It is likely that the low levels of biallelic H3 K9-methylation observed in liver and CNS reflect the basal levels of the H3 K9-Me in the DMR1 location. (Q)-PCR-ChIP assays also confirmed the basal, low levels of H3 K9-Me in this DMR1 location (Fig. 2EGo).

In DMR2, H3 K4-Me was found associated predominantly with the expressed paternal allele, whereas H3 K9-Me associated exclusively with the silenced maternal allele (Fig. 4BGo, DMR2). The association of H3 K9-Me with the silenced allele was more profound in tissues (liver and CNS) than in the cultured fibroblast cells.

In Igf2r imprinting, DMR2, which harbors the gametic methylated CpG pattern, has been referred to as the gametic or primary imprint, whereas DMR1, which is established after implantation, is considered to be a secondary imprint. Because allele-specific H3 S10-P modifications were observed only in DMR2, but not in DMR1 or outside of the DMRs (biallelic modification), we speculate that the allele-specific H3 S10-P modification exclusively marks the primary imprint. Further investigation of the H3 S10 phosphorylation in other imprinting loci having both primary and secondary DMRs (or imprints), such as Igf2-H19 and Nesp55-Gnas, will shed light on this hypothesis.

Are there any unique features of the histone code in imprinted genes? Our present data on Igf2r imprinting indicate the following features of the code (1). Histone modifications occur predominantly in the nucleosomes in the promoter region near the transcription site (2). H3 K9 acetylation is associated exclusively with the active allele, whereas deacetylation of H3 K9 is associated with the silenced allele (3). H3 K9 methylation and H3 S10 phosphorylation are associated exclusively with the silenced and active alleles, respectively, of the primary imprint but not of the secondary imprint. Though data on H3 S10 phosphorylation in imprinted genes are scarce, H3 K9 methylation has been demonstrated to be an epigenetic imprint of the inactive X chromosome in female mammals. H3 K9 methylation also occurs predominantly in the inactive allele in the primary (gametic methylated CpG) DMRs of Snrpn, U2af1-rs1, and Igf2r genes (10).

In Fig. 7Go, we propose a model of allelic histone modification in the primary (DMR2) and secondary (DMR1) imprints of Igf2r. In regard to the expression of Igf2r, DNA methylation and histone deacetylation in DMR1 are found in the silenced allele, whereas in unmethylated DNA, histone acetylation (including H3 K9-Ac) and H3 K4 methylation are present in the active allele. Air contains similar epigenetic DNA and histone marks; and in addition, it contains specific modifications, which we believe to be the characteristic of the primary imprint: H3 K9 methylation in the silenced allele, and H3 S10 phosphorylation in the active allele.



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  		FIG. 7. Model of allele-specific histone code in tissue-specific imprinting of Igf2r. In liver and CNS (brain) tissues, transcription of Igf2r and Igf2r-as (Air) is restricted to the active DNA unmethylated allele marked by the yellow box in the DMR1 and DMR2. Methylated DNA (dark blue box) marks the silenced imprinted allele. Histone acetylation, including H3 K9-Ac (red lollipops), and histone methylation at lysine 4 (H3 K4-Me) (blue triangle lollipops) are universal histone code for active allele, whereas deacetylated H3 (especially at H3 K9), deacetylated H4, and unmethylated H3 K4 (white lollipops) are universal histone code for silenced allele. The promoter of Air contains primary imprint (DMR2) that is marked exclusively with H3 K9-Me (orange triangle lollipops) in the silenced maternal allele and with H3-S10-P (orange square lollipops) in the active paternal allele. During early development, Air from the paternal allele may act in cis and induce DNA methylation, and histone deacetylation in the promoter of Igf2r, creating the secondary DMR1. Once established, DMR1 mediates paternal-specific silencing of Igf2r and is not constrained by Air. We speculate that, in the early development of CNS, Air may fail to establish the secondary DMR1. Later, in CNS tissue, biallelic expression of Igf2r persists, even in the presence of the imprinted Air. m, Methylated DNA.

 
Barlow and her colleagues (21, 22) have demonstrated that imprinting of Igf2r depends on the intronic DMR2 or the presence of imprinted Igf2r antisense or Air. That biallelic expression of Igf2r is seen in conjunction with monoallelic expression of Air in CNS seems to contradict the crucial role of the imprinted antisense in regulating the imprinting of the sense transcript. However, considering the differential histone modifications in the primary and secondary DMR imprints, one could speculate that there are distinct functions of the two DMRs during development. The imprinted Air, which is driven by its promoter in the primary imprint region DMR2 on the paternal allele, may induce DNA methylation and histone deacetylation on the paternal Igf2r promoter region during early development, thereby creating the secondary DMR1. Once DMR1 has been established, transcription from DMR1 is driven by the local chromatin structure and is no longer constrained by Air. To explain the biallelic expression of Igf2r in CNS, we speculate that, during the early development of the CNS, Air failed to establish the secondary DMR1, i.e. it failed to induce DNA methylation and histone deacetylation on the paternal Igf2r promoter region. As a result, in the absence of allele-specific DNA methylation and histone modifications in the Igf2r promoter region, biallelic expression of Igf2r persists, even in the presence of the imprinted Air. Human IGF2R is biallelically expressed, and no AIR antisense transcripts have been found. In conjunction with these findings, there is no DMR1 in the IGF2R promoter region. The absence of AIR transcripts from a DMR2 in intron 2 may be attributable to the hypo-acetylation and hypo-methylation of histones H3 and H4 in the human DMR2 (Vu et al., unpublished).

In an analogous situation at the Igf2/H19 imprinted locus, the methylated CpG primary imprint located 2–4 kb upstream of the H19 gene can generate secondary epigenetic DNA modifications in the H19 promoter region (secondary imprint). It is the secondary imprint (not the primary one) that mediates paternal-specific silencing of H19 (52). Interestingly, the secondary methylation imprint is stable through multiple cell divisions, even in the absence of the primary imprint (52), suggesting the functional independence of the secondary imprint once it has been established. Further explication of the histone code will likely provide new clues to specific epigenetic marks that constitute a unique histone code for imprinted genes.


   Footnotes
 
This work was supported by NIH Grant DK36054 and the Medical Research Service of the Department of Veterans Affairs.

Y.Y. and T.L. contributed equally.

Abbreviations: AzaC, 5-Aza deoxycytidine; ChIP, chromatin immunoprecipitation; CNS, central nervous system; DMR, differentially methylated region; H4-Ac, acetyl lysines 5, 8, 12, and 16 of histone H4; H3-Ac, acetyl lysines 9 and 14 of histone H3; H3 K9-Ac, acetyl lysine 9 of histone H3; H3 K4-Me, methyl lysine 4 of histone H3; H3 K9-Me, methyl lysine 9 of histone H3; H3 S10-P, phosphorylated serine 10 of histone H3; Igf2, mouse IGF 2; Me, methylation; Q-PCR, quantitative, real-time PCR; RFLP, restriction fragment length polymorphism; RT, reverse transcription; TSA, Trichostatin A.

Received June 26, 2003.

Accepted for publication September 3, 2003.


   References
Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 

  1. Hu JF, Oruganti H, Vu TH, Hoffman AR 1998 The role of histone acetylation in the allelic expression of the imprinted human insulin-like growth factor II gene. Biochem Biophys Res Commun 251:403–408[CrossRef][Medline]
  2. Saitoh S, 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[CrossRef][Medline]
  3. Xin Z, Allis CD, Wagstaff J 2001 Parent-specific complementary patterns of histone H3 lysine 9, and H3 lysine 4 methylation at the Prader-Willi syndrome imprinting center. Am J Hum Genet 69:1389–1394[CrossRef][Medline]
  4. Grandjean V, O’Neill L, Sado T, Turner B, Ferguson-Smith A 2001 Relationship between DNA methylation, histone H4 acetylation, and gene expression in the mouse imprinted Igf2–H19 domain. FEBS Lett 488:165–169[CrossRef][Medline]
  5. Gregory RI, O’Neill LP, Randall TE, Fournier C, Khosla S, Turner GM, Feil R 2002 Inhibition of histone deacetylases alters allelic chromatin conformation at the imprinted U2af1-rs1 locus in mouse embryonic stem cells. J Biol Chem 277:11728–11734[Abstract/Free Full Text]
  6. Fulmer-Smentek SB, Francke U 2001 Association of acetylated histones with paternally expressed genes in the Prader-Willi deletion region. Hum Mol Genet 10:645–652[Abstract/Free Full Text]
  7. Peters AH, Mermoud JE, O’Carroll D, Pagani M, Schweizer D, Brockdorff N, Jenuwein T 2002 Histone H3 lysine 9 methylation is an epigenetic imprint of facultative heterochromatin. Nat Genet 30:77–80[CrossRef][Medline]
  8. Bird A 2002 DNA methylation patterns, and epigenetic memory. Genes Dev 16:6–21[Free Full Text]
  9. Boggs BA, Cheung P, Heard E, Spector DL, Chinault AC, Allis CD 2002 Differentially methylated forms of histone H3 show unique association patterns with inactive human X chromosomes. Nat Genet 30:73–76[CrossRef][Medline]
  10. Fournier C, Goto Y, Ballestar E, Delaval K, Hever AM, Esteller M, Feil R 2002 Allele-specific histone lysine methylation marks regulatory regions at imprinted mouse genes. EMBO J 21:6560–6570[CrossRef][Medline]
  11. Killian JK, Byrd JC, Jirtle JV, Munday BL, Stoskopf MK, MacDonald RG, Jirtle RL 2000 M6P/IGF2R imprinting evolution in mammals. Mol Cell 5: 707–716
  12. Killian JK, Nolan CM, Stewart N, Munday BL, Andersen NA, Nicol S, Jirtle RA 2001 Monotreme IGF2 expression, and ancestral origin of genomic imprinting. J Exp Zool 291:205–212[CrossRef][Medline]
  13. Killian JK, Nolan CM, Wylie AA, Li T, Vu TH, Hoffman AR, Jirtle RL 2001 Divergent evolution in M6P/IGF2R imprinting from the Jurassic to the Quaternary. Hum Mol Genet 10:1721–1728[Abstract/Free Full Text]
  14. Lau MM, Stewart CE, Liu Z, Bhatt H, Rotwein P, Stewart CL 1994 Loss of the imprinted IGF2/cation-independent mannose 6-phosphate receptor results in fetal overgrowth, and perinatal lethality. Genes Dev 8:2953–2963[Abstract/Free Full Text]
  15. Hassan AB 2003 Keys to the hidden treasures of the mannose 6-phosphate/insulin-like growth factor 2 receptor. Am J Pathol 162:3–6[Free Full Text]
  16. Jirtle RL 1999 Genomic imprinting, and cancer. Exp Cell Res 248:18–24[CrossRef][Medline]
  17. De Souza AT, Yamada T, Mills JJ, Jirtle RL 1997 Imprinted genes in liver carcinogenesis. FASEB J 11:60–67[Abstract]
  18. Yao X, Hu JF, Daniels M, Shiran H, Zhou X, Yan H, Lu H, Zeng Z, Wang Q, Li T, Hoffman AR 2003 A methylated oligonucleotide inhibits IGF2 expression, and enhances survival in a model of hepatocellular carcinoma. J Clin Invest 111:265–273[CrossRef][Medline]
  19. Barlow DP, Stoger R, Herrmann BG, Saito K, Schweifer N 1991 The mouse insulin-like growth factor type-2 receptor is imprinted, and closely linked to the Tme locus. Nature 349:84–87[CrossRef][Medline]
  20. Stoger R, Kubicka P, Liu CG, Kafri T, Razin A, Cedar H, Barlow DP 1993 Maternal-specific methylation of the imprinted mouse Igf2r locus identifies the expressed locus as carrying the imprinting signal. Cell 73:61–71[CrossRef][Medline]
  21. Sleutels F, Zwart R, Barlow DP 2002 The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415:810–813[Medline]
  22. Wutz A, Smrzka OW, Schweifer N, Schellander K, Wagner EF, Barlow DP 1997 Imprinted expression of the Igf2r gene depends on an intronic CpG island. Nature 389:745–749[CrossRef][Medline]
  23. Hu JF, Balaguru KA, Ivaturi RD, Oruganti H, Li T, Nguyen BT, Vu TH, Hoffman AR 1999 Lack of reciprocal genomic imprinting of sense, and antisense RNA of mouse insulin-like growth factor II receptor in the central nervous system. Biochem Biophys Res Commun 257:604–608[CrossRef][Medline]
  24. Smrzka OW, Fae I, Stoger R, Kurzbauer R, Fischer GF, Henn T, Weith A, Barlow DP 1995 Conservation of a maternal-specific methylation signal at the human IGF2R locus. Hum Mol Genet 4:1945–1952[Abstract/Free Full Text]
  25. Oudejans CB, Westerman B, Wouters D, Gooyer S, Leegwater PA, van Wijk IJ, Sleutels F 2001 Allelic IGF2R repression does not correlate with expression of antisense RNA in human extraembryonic tissues. Genomics 73:331–337[CrossRef][Medline]
  26. Vu TH, Hoffman AR 2000 Comparative genomics sheds light on mechanisms of genomic imprinting. Genome Res 10:1660–1663[Free Full Text]
  27. Jenuwein T, Allis CD 2001 Translating the histone code. Science 293:1074–1080[Abstract/Free Full Text]
  28. Strahl BD, Allis CD 2000 The language of covalent histone modifications. Nature 403:41–45[CrossRef][Medline]
  29. Spotswood HT, Turner BM 2002 An increasingly complex code. J Clin Invest 110:577–582[CrossRef][Medline]
  30. Hu JF, Vu TH, Hoffman AR 1996 Promoter-specific modulation of insulin-like growth factor II genomic imprinting by inhibitors of DNA methylation. J Biol Chem 271:18253–18262[Abstract/Free Full Text]
  31. Hu JF, Vu TH, Hoffman AR 1997 Genomic deletion of an imprint maintenance element abolishes imprinting of both insulin-like growth factor II, and H19. J Biol Chem 272:20715–20720[Abstract/Free Full Text]
  32. Cameron EE, Bachman KE, Myohanen S, Herman JG, Baylin SB 1999 Synergy of demethylation, and histone deacetylase inhibition in the re-expression of genes silenced in cancer. Nat Genet 21:103–107[CrossRef][Medline]
  33. Pedone PV, Pikaart MJ, Cerrato F, Vernucci M, Ungaro P, Bruni CB, 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[CrossRef][Medline]
  34. Hu JF, Pham J, Dey I, Li T, Vu TH, Hoffman AR 2000 Allele-specific histone acetylation accompanies genomic imprinting of the insulin-like growth factor II receptor gene. Endocrinology 141:4428–4435[Abstract/Free Full Text]
  35. El Kharroubi A, Piras G, Stewart CL 2001 DNA demethylation reactivates a subset of imprinted genes in uniparental mouse embryonic fibroblasts. J Biol Chem 276:8674–8680[Abstract/Free Full Text]
  36. Vu TH, Hoffman A 1996 Alterations in the promoter-specific imprinting of the insulin-like growth factor-II gene in Wilms’ tumor. J Biol Chem 271:9014–9023[Abstract/Free Full Text]
  37. Hall IM, Shankaranarayana GD, Noma K, Ayoub N, Cohen A, Grewal SI 2002 Establishment, and maintenance of a heterochromatin domain. Science 297:2232–2237[Abstract/Free Full Text]
  38. Eden S, Hashimshony T, Keshet I, Cedar H, Thorne AW 1998 DNA methylation models histone acetylation. Nature 394:842[CrossRef][Medline]
  39. Gregory RI, Randall TE, Johnson CA, Khosla S, Hatada I, O’Neill LP, Turner BM, Feil R 2001 DNA methylation is linked to deacetylation of histone H3, but not H4, on the imprinted genes Snrpn, and U2af1-rs1. Mol Cell Biol 21:5426–5436[Abstract/Free Full Text]
  40. Noma K, Allis CD, Grewal SI 2001 Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 293:1150–1155[Abstract/Free Full Text]
  41. Li T, Vu TH, Lee KO, Yang Y, Nguyen CV, Bui HQ, Zeng ZL, Nguyen BT, Hu JF, Murphy SK, Jirtle RL, Hoffman AR 2002 An imprinted PEG1/MEST antisense expressed predominantly in human testis, and in mature spermatozoa. J Biol Chem 277:13518–13527[Abstract/Free Full Text]
  42. Ulaner GA, Vu TH, Li T, Hu JF, Yao XM, Yang Y, Gorlick R, Meyers P, Healey J, Ladanyi M, Hoffman AR 2003 Loss of imprinting of IGF2, and H19 in osteosarcoma is accompanied by reciprocal methylation changes of a CTCF-binding site. Hum Mol Genet 12:535–549[Abstract/Free Full Text]
  43. Santos-Rosa H, Schneider R, Bannister AJ, Sherrif J, Bernstein BE, Emre NC, Schreiber SL, Mellor J, Kouzarides T 2002 Active genes are tri-methylated at K4 of histone H3. Nature 419:407–411[CrossRef][Medline]
  44. Strelkov IS, Davie JR 2002 Ser-10 phosphorylation of histone H3, and immediate early gene expression in oncogene-transformed mouse fibroblasts. Cancer Res 62:75–78[Abstract/Free Full Text]
  45. Lefebvre B, Ozato K, Lefebvre P 2002 Phosphorylation of histone H3 is functionally linked to retinoic acid receptor ß promoter activation. EMBO Rep 3:335–340[CrossRef][Medline]
  46. Wylie AA, Pulford DJ, McVie-Wylie AJ, Waterland RA, Evans HK, Chen YT, Nolan CM, Orton TC, Jirtle RL 2003 Tissue-specific inactivation of murine M6P/IGF2R. Am J Pathol 162:321–328[Abstract/Free Full Text]
  47. Kang JX, Bell J, Beard RL, Chandraratna RA 1999 Mannose 6-phosphate/insulin-like growth factor II receptor mediates the growth-inhibitory effects of retinoids. Cell Growth Differ 10:591–600[Abstract/Free Full Text]
  48. Blanchard F, Duplomb L, Raher S, Vusio P, Hoflack B, Jacques Y, Godard A 1999 Mannose 6-phosphate/insulin-like growth factor II receptor mediates internalization, and degradation of leukemia inhibitory factor but not signal transduction. J Biol Chem 274:24685–24693[Abstract/Free Full Text]
  49. Yamada T, De Souza AT, Finkelstein S, Jirtle RL 1997 Loss of the gene encoding mannose 6-phosphate/insulin-like growth factor II receptor is an early event in liver carcinogenesis. Proc Natl Acad Sci USA 94:10351–10355[Abstract/Free Full Text]
  50. De Souza AT, Hankins GR, Washington MK, Orton TC, Jirtle RL 1995 M6P/IGF2R gene is mutated in human hepatocellular carcinomas with loss of heterozygosity. Nat Genet 11:447–449[CrossRef][Medline]
  51. Hu JF, Oruganti H, Vu TH, Hoffman AR 1998 Tissue-specific imprinting of the mouse insulin-like growth factor II receptor gene correlates with differential allele-specific DNA methylation. Mol Endocrinol 12:220–232[Abstract/Free Full Text]
  52. Srivastava M, Frolova E, Rottinghaus B, Boe SP, Grinberg A, Lee E, Love PE, Pfeifer K 2003 Imprint control element-mediated secondary methylation imprints at the Igf2/H19 locus. J Biol Chem 278:5977–5983[Abstract/Free Full Text]



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B. A. Garcia, S. B. Hake, R. L. Diaz, M. Kauer, S. A. Morris, J. Recht, J. Shabanowitz, N. Mishra, B. D. Strahl, C. D. Allis, et al.
Organismal Differences in Post-translational Modifications in Histones H3 and H4
J. Biol. Chem., March 9, 2007; 282(10): 7641 - 7655.
[Abstract] [Full Text] [PDF]

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 Mol. Cell. Biol.Home page
Y. Yamasaki-Ishizaki, T. Kayashima, C. K. Mapendano, H. Soejima, T. Ohta, H. Masuzaki, A. Kinoshita, T. Urano, K.-i. Yoshiura, N. Matsumoto, et al.
Role of DNA Methylation and Histone H3 Lysine 27 Methylation in Tissue-Specific Imprinting of Mouse Grb10
Mol. Cell. Biol., January 15, 2007; 27(2): 732 - 742.
[Abstract] [Full Text] [PDF]

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 Proc. Natl. Acad. Sci. USAHome page
D. Monk, P. Arnaud, S. Apostolidou, F. A. Hills, G. Kelsey, P. Stanier, R. Feil, and G. E. Moore
From the Cover: Limited evolutionary conservation of imprinting in the human placenta
PNAS, April 25, 2006; 103(17): 6623 - 6628.
[Abstract]