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Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36

Abstract

Several lines of recent evidence support a role for chromatin in splicing regulation. Here, we show that splicing can also contribute to histone modification, which implies bidirectional communication between epigenetic mechanisms and RNA processing. Genome-wide analysis of histone methylation in human cell lines and mouse primary T cells reveals that intron-containing genes are preferentially marked with histone H3 Lys36 trimethylation (H3K36me3) relative to intronless genes. In intron-containing genes, H3K36me3 marking is proportional to transcriptional activity, whereas in intronless genes, H3K36me3 is always detected at much lower levels. Furthermore, splicing inhibition impairs recruitment of H3K36 methyltransferase HYPB (also known as Setd2) and reduces H3K36me3, whereas splicing activation has the opposite effect. Moreover, the increase of H3K36me3 correlates with the length of the first intron, consistent with the view that splicing enhances H3 methylation. We propose that splicing is mechanistically coupled to recruitment of HYPB/Setd2 to elongating RNA polymerase II.

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Figure 1: Patterns of H3K36 trimethylation in intron-containing and intronless genes.
Figure 2: In an intronless gene, H3K36me3 remains low irrespective of transcriptional activation.
Figure 3: H3K36me3 is highly dynamic in intron-containing genes.
Figure 4: Splicing inhibition reduces H3K36me3 and HYPB/Setd2 recruitment in intron-containing genes.
Figure 5: Exon inclusion by alternative splicing increases HYPB/Setd2 recruitment and H3K36me3.
Figure 6: H3K36me3 does not mirror Ser2P Pol II occupancy.

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Acknowledgements

We are grateful to K. Koide (University of Pittsburgh), for kindly providing the meayamycin used in this study. We are also thankful to S. Marinho (Faculdade de Medicina, Universidade de Lisboa) for technical assistance. This work was supported by grants from Fundação para a Ciência e Tecnologia (PTDC-BIA-BCM-101575-2008 to M.C.-F. and PTDC-BIA-BCM-111451-2009 to S.F.deA.) and the European Commission (MRTN-CT-2006-035733 to M.C.-F. and P.F.). S.F.deA. and A.R.G. are supported by fellowships from Fundação para a Ciência e Tecnologia (SFRH-BPD-34679-2007 and SFRH-BPD-62911-2009). Work in the P.F. laboratory is supported by institutional grants from Institut National de la Santé et de la Recherche Médicale (INSERM) and Centre National de la Recherche Scientifique (CNRS), and by specific grants from Fondation Princesse Grace de Monaco, the Agence Nationale de la Recherche (ANR), the Institut National du Cancer (INCa) and the Commission of the European Communities. F.K. was supported by a Marie Curie research training fellowship (MRTN-CT-2006-035733); and is now supported by Association pour la Recherche sur le Cancer (ARC). R.F. was supported by Marseille-Nice Genopole; and is now supported by a grant from CNRS.

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Contributions

S.F.deA. and M.C.-F. conceived the project and designed the experiments. S.F.deA., S.C., J.A., H.L. conducted and analyzed the wet-lab experiments. F.K., I.G., J.-C.A. and P.F. conceived the framework of the ChIP-seq studies. F.K. and J.-C.A. designed the ChIP-seq experiments. D.E. produced and provided the Ser2P and Ser5P Pol II antibodies. R.F. and F.K. carried out the bioinformatics preprocessing of ChIP-seq data. ChIP-seq and RNA-seq preprocessing materials were prepared by F.K.. M.G. and I.G. conducted all ChIP-seq– and RNA-sequencing experiments. A.R.G carried out the bioinformatic analysis of microarray, ChIP-seq and RNA-seq data. S.F.deA., A.R.G. and M.C.-F. wrote the manuscript. All authors reviewed the manuscript.

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Correspondence to Jean-Christophe Andrau, Pierre Ferrier or Maria Carmo-Fonseca.

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de Almeida, S., Grosso, A., Koch, F. et al. Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36. Nat Struct Mol Biol 18, 977–983 (2011). https://doi.org/10.1038/nsmb.2123

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