Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Regulation of transcription by the MLL2 complex and MLL complex–associated AKAP95

Nature Structural & Molecular Biology volume 20, pages 1156–1163 (2013)Cite this article

Subjects

Abstract

Although histone H3 Lys4 (H3K4) methylation is widely associated with gene activation, direct evidence for its causal role in transcription, through specific MLL family members, is scarce. Here we have purified a human MLL2 (Kmt2b) complex that is highly active in H3K4 methylation and chromatin transcription in a cell-free system. This effect requires S-adenosyl methionine and intact H3K4, thus establishing a direct and causal role for MLL2-mediated H3K4 methylation in transcription. We also show that human AKAP95, a chromatin-associated protein, physically and functionally associates with MLL complexes and directly enhances their methyltransferase activity. Ectopic AKAP95 stimulates expression of a chromosomal reporter gene in synergy with MLL1 or MLL2, whereas AKAP95 depletion impairs retinoic acid–mediated gene induction in embryonic stem cells. These results demonstrate an important role for AKAP95 in regulating histone methylation and gene expression, particularly during cell-fate transitions.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: An MLL2 complex that is highly active in methylating H3K4.
Figure 2: The MLL2 complex stimulates chromatin transcription in a SAM- and H3K4-dependent manner.
Figure 3: AKAP95 is associated with DPY30–MLL complexes.
Figure 4: AKAP95 strongly coactivates expression of a chromosomal reporter gene.
Figure 5: Transcriptional coactivation function of AKAP95 requires the region that binds DPY30–MLL complexes.
Figure 6: AKAP95 enhances the HMT activity of the MLL2 complex in vitro.
Figure 7: AKAP95 modulates ATRA-mediated gene induction in human ECCs and mouse ESCs.

Similar content being viewed by others

Accession codes

Primary accessions

Gene Expression Omnibus

References

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

    Article  CAS  PubMed  Google Scholar 

  2. Li, B., Carey, M. & Workman, J.L. The role of chromatin during transcription. Cell 128, 707–719 (2007).

    CAS  PubMed  Google Scholar 

  3. Shahbazian, M.D. & Grunstein, M. Functions of site-specific histone acetylation and deacetylation. Annu. Rev. Biochem. 76, 75–100 (2007).

    Article  CAS  PubMed  Google Scholar 

  4. Shilatifard, A. Molecular implementation and physiological roles for histone H3 lysine 4 (H3K4) methylation. Curr. Opin. Cell Biol. 20, 341–348 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Ruthenburg, A.J., Allis, C.D. & Wysocka, J. Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol. Cell 25, 15–30 (2007).

    Article  CAS  PubMed  Google Scholar 

  6. Shilatifard, A. The COMPASS family of histone H3K4 methylases: mechanisms of regulation in development and disease pathogenesis. Annu. Rev. Biochem. 81, 65–95 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Santos-Rosa, H. et al. Active genes are tri-methylated at K4 of histone H3. Nature 419, 407–411 (2002).

    Article  CAS  PubMed  Google Scholar 

  8. Schneider, R. et al. Histone H3 lysine 4 methylation patterns in higher eukaryotic genes. Nat. Cell Biol. 6, 73–77 (2004).

    Article  CAS  PubMed  Google Scholar 

  9. Bernstein, B.E. et al. Methylation of histone H3 Lys 4 in coding regions of active genes. Proc. Natl. Acad. Sci. USA 99, 8695–8700 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).

    Article  CAS  PubMed  Google Scholar 

  11. Dou, Y. et al. Regulation of MLL1 H3K4 methyltransferase activity by its core components. Nat. Struct. Mol. Biol. 13, 713–719 (2006).

    Article  CAS  PubMed  Google Scholar 

  12. Dou, Y. et al. Physical association and coordinate function of the H3 K4 methyltransferase MLL1 and the H4 K16 acetyltransferase MOF. Cell 121, 873–885 (2005).

    Article  CAS  PubMed  Google Scholar 

  13. Hughes, C.M. et al. Menin associates with a trithorax family histone methyltransferase complex and with the hoxc8 locus. Mol. Cell 13, 587–597 (2004).

    Article  CAS  PubMed  Google Scholar 

  14. Milne, T.A. et al. MLL targets SET domain methyltransferase activity to Hox gene promoters. Mol. Cell 10, 1107–1117 (2002).

    Article  CAS  PubMed  Google Scholar 

  15. Wysocka, J. et al. WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell 121, 859–872 (2005).

    Article  CAS  PubMed  Google Scholar 

  16. Demers, C. et al. Activator-mediated recruitment of the MLL2 methyltransferase complex to the β-globin locus. Mol. Cell 27, 573–584 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Vermeulen, M. et al. Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell 142, 967–980 (2010).

    Article  CAS  PubMed  Google Scholar 

  18. Vermeulen, M. & Timmers, H.T. Grasping trimethylation of histone H3 at lysine 4. Epigenomics 2, 395–406 (2010).

    Article  CAS  PubMed  Google Scholar 

  19. Lim, D.A. et al. Chromatin remodelling factor Mll1 is essential for neurogenesis from postnatal neural stem cells. Nature 458, 529–533 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Rathert, P., Dhayalan, A., Ma, H. & Jeltsch, A. Specificity of protein lysine methyltransferases and methods for detection of lysine methylation of non-histone proteins. Mol. Biosyst. 4, 1186–1190 (2008).

    Article  CAS  PubMed  Google Scholar 

  21. Zhang, K. et al. The Set1 methyltransferase opposes Ipl1 aurora kinase functions in chromosome segregation. Cell 122, 723–734 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Cho, Y.W. et al. PTIP associates with MLL3- and MLL4-containing histone H3 lysine 4 methyltransferase complex. J. Biol. Chem. 282, 20395–20406 (2007).

    Article  CAS  PubMed  Google Scholar 

  23. Jiang, H. et al. Role for Dpy-30 in ES cell-fate specification by regulation of H3K4 methylation within bivalent domains. Cell 144, 513–525 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Wong, W. & Scott, J.D. AKAP signalling complexes: focal points in space and time. Nat. Rev. Mol. Cell Biol. 5, 959–970 (2004).

    Article  CAS  PubMed  Google Scholar 

  25. Jungmann, R.A. & Kiryukhina, O. Cyclic AMP and AKAP-mediated targeting of protein kinase A regulates lactate dehydrogenase subunit A mRNA stability. J. Biol. Chem. 280, 25170–25177 (2005).

    Article  CAS  PubMed  Google Scholar 

  26. Eide, T. et al. Protein kinase A-anchoring protein AKAP95 interacts with MCM2, a regulator of DNA replication. J. Biol. Chem. 278, 26750–26756 (2003).

    Article  CAS  PubMed  Google Scholar 

  27. Li, Y. et al. A novel histone deacetylase pathway regulates mitosis by modulating Aurora B kinase activity. Genes Dev. 20, 2566–2579 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Collas, P., Le Guellec, K. & Tasken, K. The A-kinase-anchoring protein AKAP95 is a multivalent protein with a key role in chromatin condensation at mitosis. J. Cell Biol. 147, 1167–1180 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Bomar, J., Moreira, P., Balise, J.J. & Collas, P. Differential regulation of maternal and paternal chromosome condensation in mitotic zygotes. J. Cell Sci. 115, 2931–2940 (2002).

    CAS  PubMed  Google Scholar 

  30. Akileswaran, L., Taraska, J.W., Sayer, J.A., Gettemy, J.M. & Coghlan, V.M. A-kinase-anchoring protein AKAP95 is targeted to the nuclear matrix and associates with p68 RNA helicase. J. Biol. Chem. 276, 17448–17454 (2001).

    Article  CAS  PubMed  Google Scholar 

  31. van den Berg, D.L. et al. An Oct4-centered protein interaction network in embryonic stem cells. Cell Stem Cell 6, 369–381 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. An, W. & Roeder, R.G. Reconstitution and transcriptional analysis of chromatin in vitro. Methods Enzymol. 377, 460–474 (2004).

    Article  CAS  PubMed  Google Scholar 

  33. An, W., Kim, J. & Roeder, R.G. Ordered cooperative functions of PRMT1, p300, and CARM1 in transcriptional activation by p53. Cell 117, 735–748 (2004).

    Article  CAS  PubMed  Google Scholar 

  34. An, W., Palhan, V.B., Karymov, M.A., Leuba, S.H. & Roeder, R.G. Selective requirements for histone H3 and H4 N termini in p300-dependent transcriptional activation from chromatin. Mol. Cell 9, 811–821 (2002).

    Article  CAS  PubMed  Google Scholar 

  35. Tsukiyama, T. & Wu, C. Purification and properties of an ATP-dependent nucleosome remodeling factor. Cell 83, 1011–1020 (1995).

    Article  CAS  PubMed  Google Scholar 

  36. Carr, D.W., Hausken, Z.E., Fraser, I.D., Stofko-Hahn, R.E. & Scott, J.D. Association of the type II cAMP-dependent protein kinase with a human thyroid RII-anchoring protein: cloning and characterization of the RII-binding domain. J. Biol. Chem. 267, 13376–13382 (1992).

    CAS  PubMed  Google Scholar 

  37. Eide, T. et al. Distinct but overlapping domains of AKAP95 are implicated in chromosome condensation and condensin targeting. EMBO Rep. 3, 426–432 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Goo, Y.H. et al. Activating signal cointegrator 2 belongs to a novel steady-state complex that contains a subset of trithorax group proteins. Mol. Cell Biol. 23, 140–149 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Pavri, R. et al. Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II. Cell 125, 703–717 (2006).

    Article  CAS  PubMed  Google Scholar 

  40. Lin, J.J. et al. Mediator coordinates PIC assembly with recruitment of CHD1. Genes Dev. 25, 2198–2209 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Lauberth, S.M. et al. H3K4me3 interactions with TAF3 regulate preinitiation complex assembly and selective gene activation. Cell 152, 1021–1036 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Tang, Z. et al. SET1 and p300 act synergistically, through coupled histone modifications, in transcriptional activation by p53. Cell 154, 297–310 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Beene, D.L. & Scott, J.D. A-kinase anchoring proteins take shape. Curr. Opin. Cell Biol. 19, 192–198 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Dignam, J.D., Lebovitz, R.M. & Roeder, R.G. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 11, 1475–1489 (1983).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Guermah, M., Kim, J. & Roeder, R.G. Transcription of in vitro assembled chromatin templates in a highly purified RNA polymerase II system. Methods 48, 353–360 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Nelson, J.D., Denisenko, O. & Bomsztyk, K. Protocol for the fast chromatin immunoprecipitation (ChIP) method. Nat. Protoc. 1, 179–185 (2006).

    Article  CAS  PubMed  Google Scholar 

  47. Livak, K.J. & Schmittgen, T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25, 402–408 (2001).

    Article  CAS  PubMed  Google Scholar 

  48. Zhang, J., Kalkum, M., Chait, B.T. & Roeder, R.G. The N-CoR-HDAC3 nuclear receptor corepressor complex inhibits the JNK pathway through the integral subunit GPS2. Mol. Cell 9, 611–623 (2002).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank Kazusa DNA Research Institute (Japan) for providing the cDNA KIAA0304. We thank J. Kim (Rockefeller University (RU)) for histone H3 and H4 with mutations in acetylation sites, E. McIntush (Bethyl Laboratories) and C. Hughes (RU) for the antibody to DPY30, Q. Yang (RU) for multiple valuable reagents, J. Wysocka (Stanford University) for the antibody to WDR5, A. Goldberg and D. Allis (RU) for LIF and Z. Fu and Z. Yan (RU) for excellent technical assistance. H.J. was supported by a fellowship from the Leukemia and Lymphoma Society, and X.L. was supported as a recipient of the C.H. Li Memorial Scholar Award. This work was supported by grants from the US National Institutes of Health (CA129325 and DK071900) and the Ellison Medical Foundation (AG-SS-2665-11) to R.G.R. and by a Leukemia and Lymphoma Society SCOR grant (7132-08).

Author information

Author notes

  1. Hao Jiang and Xiangdong Lu: These authors contributed equally to this work.

Authors and Affiliations

  1. Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, New York, USA

    Hao Jiang, Xiangdong Lu, Miho Shimada, Yali Dou, Zhanyun Tang & Robert G Roeder

  2. Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA

    Hao Jiang

  3. UAB Stem Cell Institute, University of Alabama at Birmingham, Birmingham, Alabama, USA

    Hao Jiang

Authors
  1. Hao Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xiangdong Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Miho Shimada
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yali Dou
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Zhanyun Tang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Robert G Roeder
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

H.J. and X.L. conceived of the project, designed and performed the experiments, analyzed the data and wrote the paper. M.S. and Y.D. performed experiments. Z.T. generated the K4Q mutant octamer. R.G.R. conceived of the project, analyzed the data, wrote the paper, supervised the project and had overall responsibility for the joint research.

Corresponding author

Correspondence to Robert G Roeder.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8 and Supplementary Tables 1 and 2 (PDF 1580 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Jiang, H., Lu, X., Shimada, M. et al. Regulation of transcription by the MLL2 complex and MLL complex–associated AKAP95. Nat Struct Mol Biol 20, 1156–1163 (2013). https://doi.org/10.1038/nsmb.2656

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.2656

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing