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J. Biol. Chem., Vol. 280, Issue 18, 17732-17736, May 6, 2005
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¶
**
From the
Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Pathology, Tennis Court Road, Cambridge, CB2 1QN, United Kingdom, the ¶Max Planck Institute for Immunbiology, 79108 Freiburg, Germany, and the ||Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom
Received for publication, January 21, 2005 , and in revised form, March 9, 2005.
| ABSTRACT |
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| INTRODUCTION |
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In vivo histone lysines may be mono-, di-, or tri-methylated, but little is known concerning the functional interplay between these different levels of methylation. In metazoa the levels of the di- and tri-methyl forms of lysine 4 of histone H3 (K4/H3) have been shown to peak in the 5' transcribed region of active genes, implicating both in the early phases of transcriptional elongation (7). Consistent with this the yeast Set1p enzyme that is responsible for methylating K4/H3 is found associated with the initiation-elongation phosphorylated form of RNA pol II,1 RNAPII-5P (8). Another H3 modification, di-methyl K36/H3, also has been found in the transcribed region of active genes in yeast (9, 10). In this case, the Set2p enzyme that methylates K36/H3 associates with the elongation-termination form of RNA pol II, RNAPII-2P (9, 10).
Recently, the mammalian NSD1 protein has been shown to possess K36/H3 methyltransferase activity (6). Haploinsufficiency of the NSD1 gene leads to Sotos syndrome, which is a neurological disorder characterized by overgrowth in childhood, advanced bone age, craniofacial abnormalities, mental retardation, and possibly a susceptibility to cancer (11, 12). In addition, translocation of the NSD1 gene leads to the development of certain leukemias (13). Taken together, these facts suggest that deregulation of K36/H3 methylation and the resulting effect on transcription may be crucial events in cellular transformation.
Mapping studies have analyzed the spatial distribution of di-methyl K36/H3 in active yeast genes and have found that this modification is generally enriched in transcribed regions, but no definitive trend within transcribed regions has been observed (9, 10). Furthermore, recent experiments performed in mammalian cells have mapped di-Me K36/H3 to active genes but not inactive genes (14). However, to date nothing is known concerning the role of tri-Me K36/H3. Here, we describe the characterization of anti tri-Me K36/H3 antisera and use the antibody to map tri-Me K36/H3 to active metazoan genes. Analysis of the spatial distribution of di- and tri-Me K36/H3 within active genes indicates that the levels of these modifications increase toward the 3' end of actively transcribing genes.
| MATERIALS AND METHODS |
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Nucleosome Preparation and Chromatin Immunoprecipitation Chicken mononucleosomes were prepared and chromatin immunoprecipitations (ChIPs) performed essentially as described previously (20, 21). Typically, 150 µg of sucrose gradient-purified input mononucleosomes (as DNA) were dialyzed into the immunoprecipitation buffer (150 mM NaCl, 0.02% SDS, 20 mM Tris·HCl, pH 8.0, 2 mM EDTA, 0.9% Triton X-100) and immunoprecipitated at 4 °C with 10 µg of affinity-purified antibodies in the presence of protein A/G beads (Amersham Biosciences). The beads were then washed five times with immunoprecipitation buffer and twice with wash buffer (350 mM NaCl, 0.02% SDS, 20 mM Tris·HCl, pH 8.0, 2 mM EDTA, 0.9% Triton X-100). The histones and DNA from the input, unbound (supernatant), and bound fractions were recovered as described (20).
Quantitative Real-time PCRUsing an ABI 7000 real-time PCR system and the TaqMan PCR Master Mix protocol (Applied Biosystems), differences in the DNA content of the bound and input fractions were determined. Bound to input (B/I) ratios were determined for each amplicon by taking a fixed aliquot of the DNA extracted from the input and bound nucleosomal samples. These were amplified together with a defined amount of genomic DNA on the same plate, using the latter to construct the standard curve. B/I values for any one amplicon are thus in the correct quantitative ratio to B/I values for other amplicons measured for the same ChIP, because this procedure compensates for differences in the PCR efficiencies of different probe/primer combinations and for nucleosome representation. However, B/I values derived using different ChIPs cannot be quantitatively compared because of variations in the efficiency of individual immunoprecipitations. All data within each graphical representation are derived from a single representative ChIP experiment; repeat ChIPs were found to give the same relative spatial distributions of B/I values across all amplicons. PCR reactions were carried out in triplicate using fixed amounts of template DNA from each fraction: 50 °C for 2 min and 95 °C for 10 min followed by 40 cycles of 15 s at 95 °C and 1 min at 60 °C. The threshold (CT) was set such that the fluorescence signal was above the base-line noise but as low as possible in the exponential amplification phase. For each amplicon a standard curve was determined by plotting the number of cycles at which the fluorescence crossed the threshold (crossing values) against increasing amounts of genomic DNA template. Based on this standard curve, the DNA sequence content of the input and bound fractions was determined. All primers and TaqMan probes were designed using ABI Primer Express software. The PCR products were substantially shorter than 200 bp, the length of DNA in a nucleosome. Primer and TaqMan sequences are available on request.
| RESULTS |
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First, the specificity of the antibody against tri-Me K36/H3 was verified. This was done by using the antibodies in Western blots of various histone preparations (Fig. 1). We prepared total cellular extracts from three strains of Schizosaccharomyces pombe: wild type; a set1 knock-out lacking the Set1p K4/H3 methyltransferase; and a set2 knock-out, which lacks the Set2p K36/H3 methyltransferase. The antibody specifically recognizes a band corresponding to histone H3 in the wild type strain. Importantly, this recognition is maintained in the set1 knock-out strain but is lost in the set2 knock-out strain (Fig. 1A). This confirms the specificity of the antibodies for Me K36/H3. Furthermore, recognition of the H3 epitope is specifically blocked by an H3 peptide containing tri-Me Lys-36 but not by peptides bearing mono-Me or di-Me Lys-36, nor is it affected by peptides containing tri-Me lysine at positions other than Lys-36 (Fig. 1B and data not shown). We conclude that the antibody is specific for the tri-methylated form of K36/H3.
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-globin locus were the first target to be analyzed (15). These genes were chosen because they are a highly characterized model gene system that includes both active and inactive genes. In 15-day chicken embryo erythrocytes the adult and hatching genes (
A,
H) are active, whereas the embryonic rho and epsilon genes (
, 
) are inactive (Fig. 2a). Although there is little detectable tri-Me K36/H3 either in the 16 kb of heterochromatin that lies upstream of the locus (Fig. 2b, bar 1) or in the promoters or transcribed regions of the inactive 
and 
genes (Fig. 2b, bars 2, 3, 8, and 9), at the promoters (bars 4 and 6) and in particular within the transcribed regions of the active
A and
H genes (bars 5 and 7) the levels are substantial. These data imply that tri-Me K36/H3 is enriched mostly in the transcribed region of active genes. This hypothesis was tested by analyzing the upstream (5') transcribed regions of a number of constitutively active and tissue-specific genes and comparing enrichments of tri-Me K36/H3 to those found in similar regions of inactive genes. Fig. 2c clearly shows that tri-Me K36/H3 is enriched at active genes, whereas at several tissue-specific genes not expressed in erythrocytes, very low but not zero levels of tri-Me K36/H3 are present in their transcribed regions.
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A gene when compared with the level at the other active globin gene,
H (Fig. 2b). This might have two explanations: (i) more tri-Me K36/H3 is found associated with the
A gene because it is the most active gene in the
-globin locus in 15-day embryos; or (ii) because the amplicon analyzed in the
A gene is near the 3' end of the transcribed region but that analyzed for the
H gene is more toward the 5' end of its transcribed region, the distribution of tri-Me K36/H3 might increase toward the 3'-ends of transcribed regions. If the latter assumption is correct and it is a general phenomenon, then the levels of tri-Me K36/H3 at other active genes should increase toward the 3' ends of their transcribed regions. Analysis of a further four active genes, vimentin, DNAPKcs, L30, and MHCII demonstrated that this was indeed the case (Fig. 3). Each of the four genes displayed significantly increased levels of tri-Me K36/H3 toward the 3' ends of their transcribed regions.
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| DISCUSSION |
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The above data clearly show that in metazoans di- and tri-Me K36/H3 is associated with the process of active transcription, but what process could require Me K36/H3? We previously reported that di- and tri-Me K4/H3 levels peak in the early transcribed region of the active genes analyzed here (7). This led us to suggest that methyl K4/H3 has an important role in the early phase of transcriptional elongation. In contrast, in the present study we find that di- and tri-Me K36/H3 peak toward the 3' end of actively transcribing regions, implying that methyl K36/H3 has a different role than that of di- and tri-Me K4/H3. Furthermore, we detect no significant differences between the spatial distributions of di- and tri-Me K36/H3, suggesting that these modifications may have very similar or overlapping functions. Me K36/H3 modification levels reach a maximum right at the end of the 4-kb GAPDH gene but
15 nucleosomes before the end of the four times longer CA gene, so the peak might occur at an approximately fixed distance from the start of transcription. However, the DNAPKcs gene is
85 kb long, and the 3' amplicon monitored (Fig. 3) is in the last of 86 exons; so the peak of tri-Me K36/H3 is clearly located close to the end of the transcribed region, whatever its length, and might therefore be directly involved in transcription termination or have a role in transcriptionally linked early mRNA processing. Consistent with the second possibility, the transcribing RNA polymerase (to which Set2p binds) has been shown to be involved in the early phase of RNA processing (18). Furthermore, the yeast Set2 protein contains a WW motif, a motif recently shown to be essential in proteins involved in pre-mRNA splicing, which is a process that occurs in vivo in concert with transcription (19). Whatever the detailed explanations, the mapping studies reported here suggest that methylated K4/H3 and methylated K36/H3 have distinct roles at active genes.
| FOOTNOTES |
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These authors contributed equally. ![]()
** To whom correspondence should be addressed: Wellcome Cancer Research UK Gurdon Institute, Tennis Ct. Rd., Cambridge CB2 1QN, UK. Tel.: 44-1223-334112; Fax: 44-1223-334089; E-mail: tk106{at}mole.bio.cam.ac.uk.
1 The abbreviations used are: pol II, polymerase II; ChIP, chromatin immunoprecipitation. ![]()
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