Article | Published:

H2B Tyr37 phosphorylation suppresses expression of replication-dependent core histone genes

Nature Structural & Molecular Biology 19, 930–937 (2012) | Download Citation

Subjects

Abstract

Histone gene transcription is actively downregulated after completion of DNA synthesis to avoid overproduction. However, the precise mechanistic details of the cessation of histone mRNA synthesis are not clear. We found that histone H2B phosphorylation at Tyr37 occurs upstream of histone cluster 1, Hist1, during the late S phase. We identified WEE1 as the kinase that phosphorylates H2B at Tyr37. Loss of expression or inhibition of WEE1 kinase abrogated H2B Tyr37 phosphorylation with a concomitant increase in histone transcription in yeast and mammalian cells. H2B Tyr37 phosphorylation excluded binding of the transcriptional coactivator NPAT and RNA polymerase II and recruited the histone chaperone HIRA upstream of the Hist1 cluster. Taken together, our data show a previously unknown and evolutionarily conserved function for WEE1 kinase as an epigenetic modulator that marks chromatin with H2B Tyr37 phosphorylation, thereby inhibiting the transcription of multiple histone genes to lower the burden on the histone mRNA turnover machinery.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

Rent or Buy

All prices are NET prices.

References

  1. 1.

    , , , & The human and mouse replication-dependent histone genes. Genomics 80, 487–498 (2002).

  2. 2.

    , & Regulation of human histone gene expression: kinetics of accumulation and changes in the rate of synthesis and in the half-lives of individual histone mRNAs during the HeLa cell cycle. Mol. Cell. Biol. 3, 539–550 (1983).

  3. 3.

    The regulation of histone synthesis in the cell cycle. Annu. Rev. Biochem. 60, 827–861 (1991).

  4. 4.

    , , , & Further evidence of transcriptional and translational control of histone messenger RNA during the HeLa S3 cycle. Cell 4, 59–67 (1975).

  5. 5.

    , & Periodic transcription of yeast histone genes. Cell 30, 305–310 (1982).

  6. 6.

    , , & Cell-cycle regulation of yeast histone mRNA. Cell 24, 367–375 (1981).

  7. 7.

    & Identification of a sequence responsible for periodic synthesis of yeast histone 2A mRNA. Proc. Natl. Acad. Sci. USA 79, 7689–7693 (1982).

  8. 8.

    & Trans-acting regulatory mutations that alter transcription of Saccharomyces cerevisiae histone genes. Mol. Cell. Biol. 7, 4204–4210 (1987).

  9. 9.

    , & Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail. Nat. Rev. Genet. 9, 843–854 (2008).

  10. 10.

    et al. Hsk1- and SCF(Pof3)-dependent proteolysis of S. pombe Ams2 ensures histone homeostasis and centromere function. Dev. Cell 18, 385–396 (2010).

  11. 11.

    , & Histone transcription in cell cycle mutants of fission yeast. EMBO J. 6, 1093–1097 (1987).

  12. 12.

    & Histone tyrosine phosphorylation comes of age. Epigenetics 6, 153–160 (2011).

  13. 13.

    Cell signaling and transcriptional regulation via histone phosphorylation. Cold Spring Harb. Symp. Quant. Biol. 75, 23–26 (2010).

  14. 14.

    & Negative regulation of mitosis by wee1+, a gene encoding a protein kinase homolog. Cell 49, 559–567 (1987).

  15. 15.

    & Fission yeast p107wee1 mitotic inhibitor is a tyrosine/serine kinase. Nature 349, 808–811 (1991).

  16. 16.

    & Cell cycle regulation of human WEE1. EMBO J. 14, 2166–2175 (1995).

  17. 17.

    et al. mik1 and wee1 cooperate in the inhibitory tyrosine phosphorylation of cdc2. Cell 64, 1111–1122 (1991).

  18. 18.

    et al. Small-molecule inhibition of Wee1 kinase by MK-1775 selectively sensitizes p53-deficient tumor cells to DNA-damaging agents. Mol. Cancer Ther. 8, 2992–3000 (2009).

  19. 19.

    et al. Ack1 mediated AKT/PKB tyrosine 176 phosphorylation regulates its activation. PLoS ONE 5, e9646 (2010).

  20. 20.

    et al. A high-resolution map of active promoters in the human genome. Nature 436, 876–880 (2005).

  21. 21.

    & The human histone gene cluster at the D6S105 locus. Hum. Genet. 101, 284–294 (1997).

  22. 22.

    , , , & Human histone gene organization: nonregular arrangement within a large cluster. Genomics 40, 314–322 (1997).

  23. 23.

    et al. Characterization of the mouse histone gene cluster on chromosome 13: 45 histone genes in three patches spread over 1 Mb. Genome Res. 6, 688–701 (1996).

  24. 24.

    et al. Effect of Ack1 tyrosine kinase inhibitor on ligand-independent androgen receptor activity. Prostate 70, 1274–1285 (2010).

  25. 25.

    et al. Ack1-mediated androgen receptor phosphorylation modulates radiation resistance in castration-resistant prostate cancer. J. Biol. Chem. 287, 22112–22122 (2012).

  26. 26.

    Chromatin modifications and their function. Cell 128, 693–705 (2007).

  27. 27.

    The complex language of chromatin regulation during transcription. Nature 447, 407–412 (2007).

  28. 28.

    , & H2B ubiquitylation in transcriptional control: a FACT-finding mission. Genes Dev. 21, 737–743 (2007).

  29. 29.

    et al. Signaling kinase AMPK activates stress-promoted transcription via histone H2B phosphorylation. Science 329, 1201–1205 (2010).

  30. 30.

    , & Rad6-dependent ubiquitination of histone H2B in yeast. Science 287, 501–504 (2000).

  31. 31.

    , , , & Identification of lysine 37 of histone H2B as a novel site of methylation. PLoS ONE 6, e16244 (2011).

  32. 32.

    , , & Chromatin remodelling at a DNA double-strand break site in Saccharomyces cerevisiae. Nature 438, 379–383 (2005).

  33. 33.

    et al. A comprehensive library of histone mutants identifies nucleosomal residues required for H3K4 methylation. Nat. Struct. Mol. Biol. 15, 881–888 (2008).

  34. 34.

    , & Properties of Saccharomyces cerevisiae wee1 and its differential regulation of p34CDC28 in response to G1 and G2 cyclins. EMBO J. 12, 3417–3426 (1993).

  35. 35.

    et al. Swe1Wee1-dependent tyrosine phosphorylation of Hsp90 regulates distinct facets of chaperone function. Mol. Cell 37, 333–343 (2010).

  36. 36.

    , & The cyclin E/Cdk2 substrate and Cajal body component p220(NPAT) activates histone transcription through a novel LisH-like domain. Mol. Cell. Biol. 23, 3669–3680 (2003).

  37. 37.

    et al. NPAT links cyclin E-Cdk2 to the regulation of replication-dependent histone gene transcription. Genes Dev. 14, 2283–2297 (2000).

  38. 38.

    , , , & Identification of sequences in a yeast histone promoter involved in periodic transcription. Cell 45, 537–544 (1986).

  39. 39.

    , , & Identification of a new set of cell cycle-regulatory genes that regulate S-phase transcription of histone genes in Saccharomyces cerevisiae. Mol. Cell. Biol. 12, 5249–5259 (1992).

  40. 40.

    , , , & The HIR corepressor complex binds to nucleosomes generating a distinct protein/DNA complex resistant to remodeling by SWI/SNF. Genes Dev. 19, 2534–2539 (2005).

  41. 41.

    et al. Replication-independent histone deposition by the HIR complex and Asf1. Curr. Biol. 15, 2044–2049 (2005).

  42. 42.

    , , , & A role for transcriptional repressors in targeting the yeast Swi/Snf complex. Mol. Cell 4, 75–83 (1999).

  43. 43.

    , & Characterization of HIR1 and HIR2, two genes required for regulation of histone gene transcription in Saccharomyces cerevisiae. Mol. Cell. Biol. 13, 28–38 (1993).

  44. 44.

    , , , & Hir1p and Hir2p function as transcriptional corepressors to regulate histone gene transcription in the Saccharomyces cerevisiae cell cycle. Mol. Cell. Biol. 17, 545–552 (1997).

  45. 45.

    et al. Two-color cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression. Mol. Cell 35, 340–351 (2009).

  46. 46.

    , & Hir proteins are required for position-dependent gene silencing in Saccharomyces cerevisiae in the absence of chromatin assembly factor I. Mol. Cell. Biol. 18, 4793–4806 (1998).

  47. 47.

    et al. Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci. Mol. Cell 41, 56–66 (2011).

  48. 48.

    et al. Coupling of DNA synthesis and histone synthesis in S phase independent of cyclin/cdk2 activity. Mol. Cell. Biol. 22, 7459–7472 (2002).

  49. 49.

    et al. WSTF regulates the H2A.X DNA damage response via a novel tyrosine kinase activity. Nature 457, 57–62 (2009).

  50. 50.

    et al. Tyrosine dephosphorylation of H2AX modulates apoptosis and survival decisions. Nature 458, 591–596 (2009).

  51. 51.

    et al. JAK2 phosphorylates histone H3Y41 and excludes HP1alpha from chromatin. Nature 461, 819–822 (2009).

  52. 52.

    , , & Histone levels are regulated by phosphorylation and ubiquitylation-dependent proteolysis. Nat. Cell Biol. 11, 925–933 (2009).

  53. 53.

    , , , & SPT10 and SPT21 are required for transcription of particular histone genes in Saccharomyces cerevisiae. Mol. Cell. Biol. 14, 5223–5228 (1994).

  54. 54.

    , , , & Spt10-dependent transcriptional activation in Saccharomyces cerevisiae requires both the Spt10 acetyltransferase domain and Spt21. Mol. Cell. Biol. 24, 135–143 (2004).

  55. 55.

    , , & Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal. Chem. 67, 1426–1436 (1995).

  56. 56.

    , , & Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551–3567 (1999).

  57. 57.

    et al. Activated Cdc42-associated kinase Ack1 promotes prostate cancer progression via androgen receptor tyrosine phosphorylation. Proc. Natl. Acad. Sci. USA 104, 8438–8443 (2007).

  58. 58.

    , , & Activated tyrosine kinase Ack1 promotes prostate tumorigenesis: role of Ack1 in polyubiquitination of tumor suppressor Wwox. Cancer Res. 65, 10514–10523 (2005).

Download references

Acknowledgements

We thank A. Shilatifard (Stowers Institute) for WT and the Y40A mutant of S. cerevisiae, M. Mollapour (US National Institutes of Health) for WT and the swe1Δ mutant of S. cerevisiae and G. Enders (Fox Chase Cancer Center) for myc-tagged WEE1 constructs. We thank X. Qu for bioinformatics analysis; L. Hall and J. Repass for qRT-PCR analysis; K. Shapland and J. Kroeger for flow cytometry; and E. Seto for critical reading of the manuscript. We thank the Moffitt Flow Cytometry, Molecular Biology core facilities, Lung Cancer Spore and the Comprehensive Melanoma Research Center. The project was supported by a Moffitt Support grant to N.P.M.

Author information

Affiliations

  1. Drug Discovery, Moffitt Cancer Center, Tampa, Florida, USA.

    • Kiran Mahajan
    •  & Nupam P Mahajan

  2. Proteomics Facility, Moffitt Cancer Center, Tampa, Florida, USA.

    • Bin Fang
    •  & John M Koomen

  3. Department of Oncologic Sciences, University of South Florida, Tampa, Florida, USA.

    • Nupam P Mahajan

Authors

  1. Search for Kiran Mahajan in:

  2. Search for Bin Fang in:

  3. Search for John M Koomen in:

  4. Search for Nupam P Mahajan in:

Contributions

K.M. and N.P.M. conceived the idea and designed all the experiments. K.M. and N.P.M. performed all the experiments except the mass spectrometric identification of H2B Tyr37 phosphorylation, which was performed by B.F. and J.M.K. K.M. and N.P.M. analyzed data and wrote the manuscript.

Competing interests

K.M. and N.P.M. are named as inventors on US patent application 61/583,864 titled “Antibodies specific for phosphorylated histones and uses thereof.”

Corresponding author

Correspondence to Nupam P Mahajan.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–9, Supplementary Tables 1–7 and Supplementary Note.

To obtain permission to re-use content from this article visit RightsLink.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nsmb.2356