Human Molecular Genetics Advance Access originally published online on February 19, 2004
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Human Molecular Genetics, 2004, Vol. 13, No. 8 819-828
DOI: 10.1093/hmg/ddh098
Tissue-specific imprinting of the G protein Gs
is associated with tissue-specific differences in histone methylation

Metabolic Diseases Branch, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
Received December 9, 2003; Accepted February 10, 2004
| ABSTRACT |
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The G protein Gs
is imprinted in a tissue-specific manner, being primarily expressed from the maternal allele in some tissues, such as renal proximal tubules. The Gs
promoter is unmethylated, but is downstream of a differentially methylated region [the exon 1A differentially methylated region (DMR)] that is methylated on the maternal allele. Maternal Gs
null mutations or loss of maternal-specific exon 1A methylation leads to pseudohypoparathyroidism types 1A or 1B, respectively. We now have examined the chromatin state of each parental allele within the exon 1A-Gs
promoter region by chromatin immunoprecipitation of samples derived from mice with heterozygous deletions within the region using antibodies to covalently modified histones. The exon 1A DMR had allele-specific differences in histone acetylation and methylation, with histone acetylation and H3 lysine 4 (H3K4) methylation of the paternal allele, and H3 lysine 9 (H3K9) methylation of the maternal allele. Both parental alleles had similar levels of histone acetylation and H3K4 methylation within the Gs
promoter and first exon, with no H3K9 methylation. In liver, where Gs
is biallelically expressed, both parental alleles had similar levels of tri- and dimethylated H3K4 within the Gs
first exon. In contrast, in renal proximal tubules there was a greater ratio of tri- to dimethylated H3K4 of Gs
exon 1 in the more transcriptionally active maternal as compared with the paternal allele. These results show that allele-specific differences in Gs
expression correlate in a tissue-specific manner with allele-specific differences in the extent of H3K4 methylation, and are the first demonstration that chronic transcriptional activation in mammals is correlated with trimethylation of H3K4. | INTRODUCTION |
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Genomic imprinting is a process by which specific genes undergo allele-specific epigenetic changes that lead to allele-specific differences in gene expression. One or more of these epigenetic changes is established in the male or female germline during gametogenesis. In many cases imprinting is associated with allele-specific differences in DNA methylation at CpG dinucleotides. Allele-specific DNA methylation of some regions is established during gametogenesis and maintained throughout development (referred to as gametic imprint marks). In many cases silencing of one parental allele is complete and associated with CpG methylation of the gene promoter on the same allele. These regions often have allele-specific differences in covalent modifications of histones, particularly acetylation and methylation of histones H3 and H4 (112). In other cases imprinting may be incomplete, with only partial silencing of one allele, or may be tissue-specific. How tissue-specific imprinting is established and whether there are concordant tissue-specific differences in the epigenetic state of the promoter regions in these genes is not well studied.
One example of incomplete and tissue-specific imprinting is provided by the heterotrimeric G protein
-subunit Gs
that couples seven transmembrane receptors to adenylyl cyclase and is required for receptor-stimulated intracellular cAMP production (13). Gs
is biallelically expressed in most tissues, but in a few tissues, such as renal proximal tubules and some endocrine organs, is expressed primarily from the maternal allele (1418). As a result of this tissue-specific imprinting, patients with Albright hereditary osteodystrophy who inherit Gs
null mutations from their mother develop multihormone resistance (a condition known as pseudohypoparathyroidism type 1A, PHP1A), while those who inherit the same mutations from their father fail to develop hormone resistance (19).
Gs
is one product of the GNAS locus at 20q13 (Gnas on distal chromosome 2 in mouse), a complex imprinted locus that generates multiple gene products through the use of multiple promoters and first exons that splice onto a common set of downstream exons (13) (Fig. 1). Far upstream of the Gs
promoter are two oppositely imprinted promoters that generate transcripts for the maternally expressed gene product NESP55 and paternally expressed gene product XL
s, respectively, as well as a promoter for paternally expressed antisense transcripts. For all of these promoters one allele is methylated and transcriptionally inactive. Recent studies show that a gametic imprint mark may be located within the antisense/XL
s promoter region that may be required to establish the imprinting patterns of these upstream promoter regions (20).
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The Gs
promoter, which is
35 kB downstream of XL
s, is within a CpG island that is unmethylated on both alleles in all tissues, despite the fact that in some of these tissues there are allele-specific differences in promoter activity (13,21). Just upstream of this CpG island is another
2 kb GC-rich region that appears to carry a maternal gametic imprint mark in that it is densely methylated on the maternal allele in all tissues and this methylation is established during oogenesis and maintained throughout development (21) (Figs 1 and 2). Within this differentially methylated region (DMR) is an alternative first exon (exon 1A) that generates untranslated transcripts from only the paternal allele, and we therefore refer to this region as the exon 1A DMR (21). The exon 1A DMR and unmethylated CpG island are separated by a
250 bp AT-rich region located 638889 bp upstream of the Gs
translational start site. In patients with PHP1B (pseudohypoparathyroidism type 1B), an isolated form of renal parathyroid hormone resistance, methylation of the exon 1A on the maternal allele is absent, and based upon this we have proposed that the exon 1A DMR has one or more cis-acting elements, such as a silencer or insulator, that negatively regulates Gs
expression on the same allele in a methylation-sensitive and tissue-specific manner (22).
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In this study we made use of mice with maternal or paternal deletions within the exon 1A DMR-Gs
promoter region to perform an initial characterization of allele-specific patterns of histone methylation and acetylation within this region. Our results show reciprocal patterns of histone modification within the exon 1A DMR. The paternal allele was associated with H3 and H4 acetylation and methylation of H3 lysine 4 (H3K4) but not H3 lysine 9 (H3K9), histone modifications that are generally associated with euchromatin, while the maternal allele was associated with H3K9 methylation and absence of H3K4 methylation or histone acetylation, a pattern typical for heterochromatin. In contrast, the unmethylated CpG island including the Gs
promoter had a euchromatic pattern on both alleles, with histone acetylation and methylation of H3K4 but not H3K9. While there were no allele-specific differences in the relative amount of tri- to dimethyled H3K4 in liver, a tissue in which Gs
is not imprinted, in renal proximal tubules higher Gs
transcriptional activity in the maternal allele is associated with a higher ratio of tri- to dimethylated H3K4 within Gs
exon 1. This is the first demonstration of the association of transcriptional activity with a specific increase in trimethylation of H3K4 in mammals and shows that tissue-specific imprinting can lead to tissue-specific epigenetic changes in the absence of DNA methylation. | RESULTS |
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H3K4 and H3K9 methylation patterns in the exon 1A-Gs
regionThe Gs
promoter and first exon are located within a CpG island that is unmethylated on both parental alleles (Fig. 2) (21). Located just upstream of this CpG island is a GC-rich DMR that includes exon 1A and that is a gametic imprint mark which is methylated on the maternal allele. These two regions are separated by a
250 bp AT-rich region. In this study we examined the chromatin states of both the exon 1A DMR and the unmethylated CpG island containing the Gs
promoter region by chromatin immunoprecipitation (ChIP) to determine the covalent modifications of their associated histones. In order to examine the histone modifications on each parental allele individually, we performed ChIP assays in tissues obtained from mice with heterozygous deletions of this region that were generated in our laboratory. One mutant allele (
6267/1601) had a deletion from position 6267 to 1601 relative to the translational start site of Gs
, while the other mutant (
1601/+419) had a deletion from 1601 to +419. In mice with paternal deletion (+/
), only the maternal allele of the region of interest is present while in the maternal deletion (
/+) only the paternal allele is present. Neither deletion had any effect on DNA methylation within the Gnas locus (unpublished data).
After crosslinking of chromatin in liver nuclei isolated from wild type (WT), +/
, and
/+ mice, ChIP assays were performed using anti-dimethyl H3K4 and -dimethyl H3K9 antibodies, respectively (Fig. 2). After ChIP and reverse crosslinking, PCR reactions were performed on immunoprecipitated DNA (C), negative controls in which ChIP was performed with no antibody (N), and input DNA (I; 1% of the DNA subjected to ChIP). For primer pairs A and B, DNA from
6267/1601 heterozygotes were used, while
1601/+419 heterozygotes were used for the primer pairs C-I which amplify segments downstream of position 1601.
ChIP of WT chromatin with anti-dimethyl H3K4 showed relatively weak amplification of the most upstream segments and stronger amplification of segments within the transition from DMR to unmethylated CpG island and within the unmethylated CpG island itself. For segments within the DMR (AE) the ChIP assay was positive in chromatin derived from
/+, but not +/
mice, consistent with H3K4 methylation only associated with the paternal allele. Sequencing of ChIPPCR products from WT CD1x129Sv mice using primer pair B, which contains a polymorphic HpaII site (21), confirmed that only the paternal allele was immunoprecipitated with the anti-dimethyl H3K4 antibody (data not shown). In contrast H3K4 was strongly methylated on both parental alleles within the unmethylated CpG island based upon the fact that products FI amplified to a similar extent from both +/
and
/ samples after ChIP with the anti-dimethyl H3K4 antibody. Results in experiments examining renal proximal tubule samples were similar to the results with liver samples (data not shown).
Similar analysis of WT samples using the anti-dimethyl H3K9 antibody showed strong amplification of segments within the exon 1A DMR (AC; Fig. 2). Segments A and B were amplified after ChIP in the +/
6267/1601, but not the
6267/1601/+ samples, indicating that H3K9 methylation within the DMR was only associated with the maternal allele. Segments GI failed to amplify after ChIP of the WT sample, indicating that H3K9 methylation is absent from both alleles downstream of the DMR within the unmethyated CpG island. Results in experiments examining renal proximal tubule samples were similar to the results with liver samples (data not shown). In summary, the exon 1A DMR had reciprocal methylation of H3K4 and H3K9 on the paternal and maternal alleles, respectively, while the unmethylated CpG island associated with the Gs
promoter had H3K4 methylation, but no H3K9 methylation, on both parental alleles.
H3 and H4 acetylation patterns in the exon 1A DMR-Gs
promoter region
Similar experiments were performed using antibodies to acetylated histones H3 and H4, respectively (Fig. 3). In these experiments duplex PCR was performed using primers for
-tubulin and primers for each respective Gnas segment. Negative controls, which are not shown, generated no bands. Both H3 and H4 acetylation was detected in WT samples in all segments examined throughout the exon 1A DMR-Gs
promoter region. Within the DMR (segments AC), H3 and H4 acetylation was easily detected in the
6267/1601/+ samples and minimally detected in the +/
6267/1601 samples, indicating that H3 and H4 acetylation is almost exclusively associated with the paternal allele within the DMR. Towards the downstream end of the DMR (segment E) H4 acetylation appears to be similar within the two parental alleles, but H3 acetylation is still present to a greater extent in the paternal allele. Within the unmethylated CpG island including the Gs
promoter and first exon (segments G, H and J), histones H3 and H4 are acetylated to similar extents on both parental alleles. Similar results were obtained in renal proximal tubules, despite the fact that Gs
is preferentially expressed from the maternal allele in this tissue (14) (data not shown).
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Quantitation of di- and trimethylated H3K4 within the exon 1A DMR-Gs
promoter regionGs
is imprinted in a tissue-specific manner with predominant expression from the maternal allele in a small number of hormone-responsive tissues. However no corresponding allele-specific differences in the chromatin state of the Gs
promoter region have been identified, as both parental alleles lack DNA methylation in somatic tissues (21,22) and there are no gross allele-specific differences in histone acetylation or methylation even in renal proximal tubules where Gs
is known to be expressed preferentially from the maternal allele. Recent studies in yeast suggest that transcriptional activation is correlated with the extent of H3K4 methylation and that in activated genes there is a greater conversion of dimethyated H3K4 to trimethylated H3K4 in the initial portion of the coding region (23,24). We therefore examined whether there were allele-specific differences in the ratio of tri- to dimethylated H3K4 that correlated with allele-specific differences in Gs
expression.
ChIP was performed using anti-dimethyl and -trimethyl H3K4 antibodies, respectively, on samples derived from +/
1601/+419 and
1601/+419/+ mice. The relative quantity of each Gnas segment that was immunoprecipitated was determined by performing duplex PCR with Gnas and
-tubulin primers and determining the ratio of Gnas segment/
-tubulin in the ChIP sample versus the same ratio in the input DNA sample. The number of PCR cycles was optimized to be sure that the reactions were not saturated and control experiments were performed to show that the readout of relative quantity was not significantly affected by cycle number. Using this approach we determined the relative amounts of tri- and dimethylated H3K4 in liver, a tissue where there are no allele-specific differences in Gs
expression, and in renal proximal tubules where Gs
is expressed primarily from the maternal allele. Because the dimethyl H3K4 antibody used has some cross-reactivity with monomethyl H3K4 (Technical Services, Upstate Biotechnology), the quantitative results using the dimethyl H3K4 antibody may to some extent also reflect the level of monomethyl H3K4.
Quantitative results from one representative experiment are shown in Figure 4. Within the DMR (segment C) levels of both di- and trimethyl H3K4 are relatively low with a higher level of methylation in the
1601/+419/+ samples, consistent with the results in Figure 2 and the fact that the paternal allele is not CpG methylated in this region. While the levels of H3K4 methylation are somewhat higher within the AT-rich region that is located between the exon 1A DMR and the unmethylated CpG island (segment G), the highest levels of di- and trimethylation are located within the most upstream portion of the CpG island (segment K). This high level of H3K4 methylation may serve as a barrier to prevent the spread of heterchromatization towards the Gs
promoter (25). In liver the levels of di- and trimethylated H3K4 and the tri/dimethylation ratio is similar in both
1601/+419/+ and +/
1601/+419 samples, indicative of the fact that the two parental alleles have similar epigenetic characteristics. In contrast, in proximal tubules there are differences in di- and trimethylated H3K4 within the Gs
exon 1 coding region (segment J) between the
1601/+419/+ and +/
1601/+419 samples, indicative of the two parental alleles having epigenetic differences with exon 1. Note that in the initial coding region (segment J) the ratios of tri- to dimethylation of H3K4 in the liver samples and +/
1601/+419 proximal tubule samples are similar whereas the ratio in the
1601/+419/+ proximal tubule sample is much lower. This is consistent with suppressed transcriptional activity of the Gs
promoter on the paternal allele in renal proximal tubules. The higher levels of trimethylated H3K4 of segment H in liver compared to proximal tubule possibly reflects the fact that Gs
expression levels are much higher in this tissue.
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Table 1 shows the combined results from two independent experiments with independently derived tissue samples which both gave similar results. Each parameter is expressed as the ratio of the quantity immunoprecipitated from the +/
1601/+419 versus
1601/+419/+ samples, which reflects the relative proportion of each parameter in the maternal versus paternal allele. There were no allele-specific differences in the amount of di- or trimethyl H3K4 or the ratio of tri- to dimethyl H3K4 within the AT-rich region (segment G) or the upstream portions of the unmethylated CpG island in either tissue. In liver there were no obviously allele-specific differences in the ratio of tri- to dimethylated H3K4 throughout the exon 1A DMR-Gs
promoter region including Gs
exon 1 (segment J), consistent with similar transcriptional activity of the Gs
promoter on both parental alleles. In contrast, the ratio of tri-to dimethyl H3K4 in the coding region of Gs
exon 1 (segment J) was 5-fold greater in the maternal allele as compared with the paternal allele in renal proximal tubules. These changes were due to a relatively lower level of dimethyl H3K4 and higher level of trimethyl H3K4 in the maternal allele relative to the paternal allele. The allele-specific differences in the extent of H3K4 methylation in proximal tubules were present only in the nucleosomes of Gs
exon 1, as there were no allele-specific differences observed in the other more upstream segments.
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| DISCUSSION |
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In this study we show that the region involved in the tissue-specific imprinting of Gs
has a complex pattern of histone modifications that correlate with its pattern of DNA methylation. Within the exon 1A DMR the maternal allele has H3 and H4 hypoacetylation and H3K9 methylation without H3K4 methylation, characteristics of heterochromatin that are often associated with DNA methylation (25,26) (Fig. 5). In contrast, the paternal allele in this region has histone acetylation and H3K4 methylation without H3K9 methylation, characteristics of euchromatin and active transcription. These epigenetic differences are consistent with the paternal-specific expression from the exon 1A promoter (21,22). Similar allele-specific differences in histone modifications have been identified in DMRs associated with other imprinted genes (112). Our results provide further evidence that imprinted genes are associated with allele-specific differences in histone modifications, and that these differences in the histone code may be important in the imprinting mechanism.
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Although DNA methylation is thought to be the primary epigenetic mark of imprinting, recent studies suggest that histone modifications may also be primary imprinting marks for some genes. Evidence in Neurospora crassa (27) and Arabidopsis (28) demonstrate that in these organisms DNA methylation is dependent upon H3K9 methylation, and the presence of such histone modifications could explain why some methylation imprints are lost during the blastocyst stage and reaquired during later development. In mouse embryonic stem (ES) cells deficient in G9a, a methylase for H3K9 and H3K27, DNA methylation and imprinting of the PraderWilli imprinting control region is lost, while ES cells deficient in the DNA methyltransferase Dnmt1 lose DNA methylation without affecting histone methylation or imprinting of the gene (5). Another study provided evidence that imprinting of the PraderWilli imprinting center is dependent upon an upstream region (the Angelman syndrome imprinting center) with allele-specific differences in histone modifications but not in DNA methylation (4). We have shown that methylation of the exon 1A DMR is established during oogenesis in mice (21). A recent study has identified a region 220 kb upstream of the exon 1A DMR that is deleted in familial PHPIB and is associated with loss of methylation within the DMR when present on the maternal allele (29). Further studies will be required to determine how this putative upstream cis-acting element leads to imprinting of the exon 1A DMR and whether histone modification or DNA methylation is the primary epigenetic event.
Spread of the heterochromatic state is believed to be mediated by binding of the chromodomain protein HP-1 to methylated H3K9, which then can recruit H3K9 methylases and possibly DNA methyltransferases (30). Downstream spread of heterochromatization from the exon 1A DMR on the maternal allele appears to be inhibited
1000 bp upstream of the Gs
translational start site. The short AT-rich region that separates the DMR and unmethylated CpG island may be a boundary that prevents the spread of heterochromatization into the CpG island (Fig. 5). Alternatively there may be a barrier to heterochromatin spreading within the most upstream portion of the CpG island, as we showed this region to have very high levels of H3K4 methylation, a characteristic present within a similar barrier region of the chicken ß-globin locus (25). In either case the CpG island containing the Gs
promoter region remains unmethylated and has histone modifications characteristic of euchromatin (histone hyperacetylation, H3K4 methylation, no H3K9 methylation), which is consistent with Gs
being ubiquitously and biallelically expressed in most tissues.
Gs
is imprinted in a tissue-specific manner, being primarily expressed from the maternal allele in some tissues (e.g. renal proximal tubules) despite an absence of DNA (21,22) or H3K9 methylation within its promoter. In yeast a complex containing the H3K4 methylase Set1 (the yeast analog of MLL) binds to RNA polymerase II during the initial phase of elongation, leading to trimethylation of H3K4 within the initial portion of the coding region (23,24,31), and similar patterns have also been observed in chicken genes (32). While both di- and trimethylation have been associated with inducible transcription in higher organisms (3335), there is no evidence that the extent of H3K4 methylation (tri- versus dimethylation) directly correlates with the transcriptional activity of mammalian genes in their native state. In liver, a tissue in which Gs
is not imprinted, we found no allele-specific differences in the extent of di- or trimethylation of H3K4 within the Gs
upstream region. In contrast, in renal proximal tubules lower Gs
expression from the paternal allele is associated with a decrease in the ratio of trimethyl versus dimethyl H3K4 within the Gs
exon 1 coding region, which is due to both a decrease in trimethyl H3K4 and an increase in dimethyl H3K4. The increased levels of dimethyl H3K4 in the paternal allele may be due to accumulation resulting from decreased conversion to trimethyl H3K4, or may be a reflection of the fact that the overall levels of bound histones in this region is greater due to lower rates of transcription and chromatin remodeling. This is the first demonstration that trimethylation of H3K4 in the initial coding region correlates with chronic expression levels of a mammalian gene and shows that genes that undergo tissue-specific imprinting can have corresponding allele-specific differences in histone methylation even in the absence of DNA methylation. Although it has been suggested that trimethylation of H3K4 in the initial coding region may act as a molecular memory for gene transcriptional activity (23,36), it has not been definitively established whether this histone modification leads to increased transcription or is a result of increased transcription.
Although our results define an association between tissue-specific imprinting and epigenetic differences within the Gs
promoter region, they do not answer the question of how these tissue-specific differences are established or maintained. We had previously proposed that tissue-specific imprinting is dependent upon a cis-acting negative regulatory element within the exon 1A DMR that is both methylation-sensitive and tissue-specific (13,22). This model predicts that a tissue-specific factor such as a repressor can bind to the unmethylated paternal allele and inhibit the Gs
promoter. Evidence for this model is provided by the fact that loss of methylation on the maternal allele in the DMR leads to PTH resistance in PHP1B patients, presumably due to loss of expression of the Gs
signaling protein from both parental alleles (22). More direct evidence for this model is provided by preliminary results suggesting that paternal deletion of the exon 1A DMR results in increased Gs
expression in the proximal tubules of mice (J.L. and L.S.W., unpublished data). Although there appears to be a barrier to the spread of heterochromatization between the exon 1A DMR and Gs
exon 1, results showing that the exon 1A DMR impacts on Gs
promoter activity suggests that there is no functional insulator between these two regions. Experiments examining the chicken ß-globin locus recently demonstrated that barrier and insulator functions are not dependent on identical sequence elements (37). Future studies to identify of the binding proteins and cis-acting elements that mediate the Gs
imprinting process will provide important insights into the mechanisms involved in tissue-specific imprinting.
| MATERIALS AND METHODS |
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Mice
Mice heterozygous for the
6267/1601 and
1601/+419 alleles were generated by the insertion of loxP sites at each respective position using targeted mutagenesis in embryonic stem cells and injection of mutant cells into blastocysts, followed by mating of offspring with EIIa-cre mice. The numbers indicate extent of the deletion based upon the position in bp relative to the Gs
translational start site. Details of how these mutant mice were generated will be provided elsewhere. All mice were mated to WT CD1 mice to generate mice with paternal (+/
) or maternal (
/+) deletions of the indicated regions, respectively. WT mice were CD1 background (Charles River Laboratories, Wilmington, MA, USA) unless indicated.
Tissue isolation and chromatin immunoprecipitation
Renal cortices were dissected and proximal tubule suspensions were prepared by collagenase digestion and isolation on a Percoll gradient as previously described (14). Proximal tubule fragments from five mice of the same genotype were combined and immediately suspended in formaldehyde for cross linking. Liver samples (300500 mg wet weight) were snap frozen and homogenized at 4°C in 10 ml Dulbecco's phosphate-buffered saline (DPBS without Ca and Mg), 5 mM EDTA and 40 µl proteinase inhibitor cocktail (P8340, Sigma, St Louis, MI, USA) using a Teflon/glass homogenizer (size AA). The homogenate was poured through cheese cloth and then centrifuged at 2000 g at 4°C for 5 min. The pellet was resuspended in 7 ml of 4% formaldehyde in DPBS, 5 mM EDTA, 10 µl proteinase inhibitor using a size A teflon/glass homogenizer (one stroke) and cross-linked on ice for 25 min and recentrifuged as before. Pellets were resuspended in 7 ml of homogenizing buffer (0.15 mM spermine, 0.5 mM spermidine, 60 mM KCl, 15 mM NaCl, 15 mM TrisHCl, pH 7.6, 2 mM EDTA, 0.5 mM EGTA, 0.5% NP-40, with 20 µl proteinase inhibitor), homogenized (three to five strokes), incubated for 10 min on ice, rehomogenized and recentrifuged. The pellets were resuspended in homogenizing buffer without NP-40 and separated into three microcentrifuge tubes, centrifuged at 3000 rpm for 5 min at 4°C, and rewashed with the same buffer. Pellets were resuspended in SDS lysis buffer (Upstate Biotechnology, Lake Placid, NY, USA) using the manufacturer's instructions and sonicated four times for 10 s at 30% maximal power to generate fragments <500 bp in length with peak length of 2300 bp, as determined by agarose gel electrophoresis. Sonicated samples were centrifuged (13 000 rpm for 10 min at 4°C) and supernatants were stored at 80°C in 200 µl aliquots. Chromatin precipitation and reverse crosslinking were performed using the protocol and reagents provided by Upstate Biotechnology. After dilution to 2 ml with ChIP dilution buffer and two precleanings with protein A-agarose beads, half the sample (1 ml) was incubated with antibody to modified histone, and the other half was treated identically but without addition of antibody (negative control). Prior to the second precleaning 10 µl of sample was removed and saved as the input DNA sample. This sample was diluted to 500 µl with water prior to reverse crosslinking. The antibodies used for ChIP assay (with volume used in parentheses) were anti-acetyl-H3 (10 µl, Upstate, 06-599), anti-acetyl-H4 (20 µl, Upstate, 06-866), anti-dimethyl-H3K4 (5 µl, Upstate, 07-030), anti-trimethyl-H3K4 (3 µl, Abcam, Cambridge, MA, USA, ab8898) and anti-dimethyl-H3K9 (70 µl, United States Biological, Swampscott, MA, H5110-14E). ChIP performed with normal rabbit IgG (Santa Cruz Biotechnology, Santa Cruz, CA, USA; 2.5 µg/ml final concentration) consistently gave negative results (data not shown).
PCR
DNA derived after reverse crosslinking (1 µl) was amplified by PCR in 25 µl reactions consisting of 1xPCR buffer (Invitrogen, Carlsbad, CA, USA), 0.3 µl Platinum Taq polymerase (Invitrogen), 2 mM MgCl2, oligonucleotide primers (0.4 µM each), and dNTPs (400 µM each). The sequences of oligonucleotides used are listed in Table 2. In some reactions 6 µl betaine (Sigma) was included to allow amplification of GC-rich regions. The PCR cycling profile included an initial denaturation at 94°C for 5 min, followed by 3035 cycles of annealing (62°C, 30 s), extension (72°C, 1 min), and denaturation (94°C, 30 s) and a final cycle with a 7 min extension. Cycle number was adjusted to be two cycles beyond the cycle in which a band was first seen for the input DNA, and ranged from 30 to 32 cycles for liver tissue and 3234 cycles for proximal tubules. Products were assessed by acrylamide gel electrophoresis (6% TBE gels, Invitrogen) and ethidium bromide staining. Duplex PCR was performed using the same procedure as for monoplex PCR except for the annealing temperature, which was 58°C, and cycle numbers, which ranged from 30 to 35 and were adjusted to avoid saturation of either product. Gnas and
-tubulin primer concentrations were 0.2 and 0.4 µM, respectively, for the
1601/+419 samples and 0.4 and 0.2 µM, respectively, for the
6267/1601 samples. Ethidium bromide stained bands were quantified using Alpha Ease FC software (Alpha Innotech, San Leandro, CA, USA). To determine the relative amount of histone modification in a given Gnas segment, the ratio of intensities of the Gnas-specific to
-tubulin-specific band in the ChIP sample was divided by the Gnas/
-tubulin ratio in the input DNA sample (26). We confirmed that the quantitative analysis was not affected by the PCR cycle number, the amount of PCR product that was loaded or the exposure time.
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| ACKNOWLEDGEMENTS |
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This work was supported by the Intramural Research Program of the National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, US Department of Health and Human Services.
| FOOTNOTES |
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* To whom correspondence should be addressed. Tel: +1 3014022923; Fax: +1 3014020374; Email: leew{at}amb.niddk.nih.gov
Present address: Columbia University College of Physicians and Surgeons, New York, USA. ![]()
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