Research

 

Summary

Although every gene exists within every cell in the human body, only a small percentage of genes are activated in any given cell. To manage this genetic information efficiently, nature has evolved a sophisticated system that facilitates access to specific genes. Dr. Allis and his colleagues study the DNA-histone protein complex called "chromatin" that packages the genetic information that exists within each cell and serves as a means of gene regulation that lies outside of the DNA itself (the basis of "epigenetics"; see Allis et al., 2006 for a textbook dedicated to this field).

Chromatin, the repeating polymer of DNA and associated histone proteins, is the physiological template of our genome. As such, elaborate mechanisms have evolved to introduce meaningful variation into chromatin for purposes of altering gene expression and other important biological processes. Introduction of covalent histone modifications, chromatin remodeling by ATP-dependent complexes, and the utilization of histone variants are three major mechanisms by which variation can be introduced into the chromatin fiber. At some level all of these mechanisms are under study in the Allis lab, but our group is best know for its work on post-translational modifications (PTMs) of histone proteins.

Dr. Allis and his colleagues favor the general view that distinct patterns of covalent histone modifications form a "histone or epigenetic code" that is then read by effector proteins to bring about distinct downstream events (Strahl and Allis, 2000; Cheung et al., 2000; Jenuwein and Allis, 2001). Since histone proteins are highly conserved through evolution, their post-translational modifications, and the enzyme systems responsible for bringing them about, are also well conserved. Thus, members of the Allis lab are currently investigating different PTMs and their biological roles in a variety of unicellular and multicellular eukaryotic models, ranging from yeast to human. One useful way to summarize much of our work is as follows - What are the relevant "marks" in histone proteins, who "writes" these marks, who "erases" them, and who "reads" the marks. In pursuing these questions, we exploit the biological strengths of many experimental models, a "perk" of working with such a conserved structure as the chromatin polymer.

The research performed in the Allis laboratory focuses on how chemical changes to histone proteins affect essentially all DNA-templated processes such as gene expression, DNA replication and repair. Through such enzymatic processes as acetylation, methylation, phosphorylation or ubiquitylation, histones are believed to function like a master "on/off switches", determining whether particular genes are active or inactive, and how these states are maintained and propagated in developmental contexts. Knowing how to control which genes to turn on or off, using targeted therapies, could reduce the risk of certain diseases by activating genes that suppress tumor growth and deactivating genes that support it. The implications of this research for human diseases, notably cancer, are now clear (see below).

One example of a current Allis lab "pipeline approach" that underscores the fundamental nature of our work, as well as its relatedness to human biology and disease is provided below. This example also underscores an advantage of being at The Rockefeller University (RU) and being in the Tri-Institutional "neighborhood", which includes RU, Memorial Sloan-Kettering Cancer Center (MSKCC) and Cornell-Weill Medical School. In 2006, research from the Allis lab showed that a robust "on" epigenetic mark, H3 lysine 4 tri-methylation (H3K4me3), a mark "written" by the human mixed lineage leukemia protein (MLL), was "read" by the nucleosome remodeling complex NURF (nucleosome remodeling factor). Specific "reading" of the tri-methylated lysine 4 in H3, but not other tri-methylated marks, such as H3K9 or H3K27, both repressive marks, occurs using a specific PHD finger module (Wysocka et al. 2006;Taverna et al., 2006). In collaboration with the laboratory of Dr. Dinshaw Patel at MSKCC, the co-crystal structure of this PHD finger in complex with the H3K4me3 peptide had been solved at atomic resolution, giving new insights into how these modules function in reading the "histone code" (Li et al., 2006; Taverna et al., 2006). Past work by the Allis laboratory and others have identified proteins containing bromodomains as gene-activating histone code readers and chromodomain-containing proteins as gene-silencing "histone code" readers (see Ruthenburg et al., 2007a; 2007b and Taverna et al., 2007; Baker et al., 2007 for reviews on this general topic).

In keeping with Dr. Allis' view that, "every amino acid in histone matters", Allis and his colleagues hypothesized - and experimentally verified - that lysine/threonine or lysine/serine pairs act like "binary molecular switches" in modifying histone:effector interactions (Fischle et al., 2003; 2005). More specifically, they propose that phosphorylation of an adjacent or neighboring serine or a threonine somehow weakens the bond that the effector protein has with the methylated lysines. Dr. Allis and his colleagues also observed that post-translational modifications of histones often appear frequently and in high density. The researchers call such clusters of high-density marks "cassettes" or "modification hot spots" and hypothesize that these high-density marks are placed in strategic locations along the histone tail as a way for the cell to deal, in a reversible way, with gene silencing or perhaps gene activation. Allis and colleague have documented "cross-talk" relationships in the same histone tails ("cis") or across distinct histone ("trans") tails. Outside of governing gene expressing, it appears that these regulatory pathways govern chromatin function during DNA replication and repair, during chromosome segregation (in meiosis and mitosis) and during chromatin compaction as cells undergo programmed cell death or apoptosis (See Cheung et al., 2003; Ahn et al., 2005; 2006; reviewed in Wang et al., 2007a; 2007b).

Recent studies in budding yeast documented a histone modification pathway associated with RNA polymerase II (polII) transcription, whereby ubiquitylation of histone H2B leads to methylation of histone H3 on specific lysine residues, such as H3K4 and H3K79 in a pathway that has now been termed, "trans-tail" cross-talk (see Sun and Allis, 2002; Briggs et al., 2002). Experiments by members of Dr. Allis's lab showed that loss of H2B ubiquitylation results in defects in cell growth, septation, and nuclear structure, phenotypes not observed in cells lacking methylation of lysine 4 on histone H3. Chromatin immunoprecipitation experiments demonstrated that loss of H2B ubiquitylation alters the distribution of polII and histones in gene coding regions. The findings suggest that ubiquitylation of H2B affects transcription elongation and nuclear architecture through its effects on chromatin dynamics (Tanny et al., 2007).

As the Allis lab has "aged", Allis in particular, so has their ideas about the "histone code". Most recently, a theoretical advance suggests that the "code" may be more tied to multiple PTM marks, in one or more histone "tails", in one or more nucleosomes. Importantly, this hypothesis, known as the "multivalency hypothesis" suggest that linked protein modules (PHD fingers, chromodomains, bromodomains, etc.) may work together in reading this histone code (Ruthenburg et al. 2007b). In addition, research in the Allis lab has led to a recent proposal that the mammalian genome is indexed by histone H3 variants in a nonrandom fashion that reflects the assembly mechanisms of dedicated "personalized'' chaperone proteins and exchange factors. In this model (Hake and Allis, 2006; Shechter et al., 2009), the family of H3 variants control whether genes are constitutively expressed or remain silent. Their model suggests that vertebrate organisms, and mammals in particular, have evolved an additional way of regulating their genetic information over many cell generations. Efforts are underway to examine this "histone variant barcode" in the vertebrates (i.e. frogs and mammals) during defined pathways of differentiation. Quite recently, the Allis lab identified a novel H3 "clippase" as Cathepsin L in mouse embryonic stem (ES) cells whose activity is developmentally regulated as part of ES cell differentiation (Duncan et al., 2008). We suspect, and seek to test, that one function of this activity is to generate "new ends" that, in turn, change the "epigenetic landscape" (Goldberg et al., 2007) with respect to the binding of effector proteins or the complexes that they reside in.

In sum, the Allis laboratory favors the general view that chromatin remodeling, in part governed by covalent modification of histone proteins, is at the heart of normal development as well as abnormal situations leading to pathological conditions (Baker et al., 2008; Borrelli et al., 2008). Recent studies from the lab have shown that a DNA damage "sensor", the histone variant H2A.X, is phosphorylated on a C-terminal tyrosine residue in a pathway required for DNA repair and genomic stability (Xiao et al., 2009). Unexpectedly, this work lead to the identification of a novel H2A.X phospho-tyrosine (Tyr142ph)-binding complex as the WICH chromatin remodeling complex, and more remarkably, the finding that its WSTF subunit has novel tyrosine kinase activity towards H2A.X at its extreme C-terminal tyrosine 142. Most recently, the lab has linked the translocation of several H3K4me3-binding PHD fingers to cell type identity and leukemogenesis in mouse and human models (Wang et al., 2009). Thus, implications of their work for human biology and human disease, notably cancer (Wang et al., 2007a; 2007b), are clear and far-reaching.

Career

Dr. Allis received his Ph.D. in 1978 from Indiana University and performed postdoctoral work with Martin Gorovsky at the University of Rochester. Before he joined The Rockefeller University in 2003 as the Joy and Jack Fishman Professor and Head of the Laboratory of Chromatin Biology and Epigenetics and Epigenetics, Allis held several academic positions elsewhere, including ones at Baylor College of Medicine and the University of Virginia Health System. Dr. Allis is a member of the National Academy of Sciences and the American Academy of Arts and Sciences. Among his many honors are the 2002 Dickson Prize in Biomedical Sciences, the 2003 Massry Prize, the 2004 Wiley Prize in Biomedical Sciences, the 2007 Gairdner Foundation International Award and the 2008 Merck-ASBMB Award.

Selected Publications (2000-present)

  1. Allis, C.D., Jenuwein, T., Reinberg, D. (eds.), Caparros, M.L. (assoc. ed.) Epigenetics Cold Spring Harbor Laboratory Press. Cold Spring Harbor, NY, 2006
  2. Strahl, B.D. and Allis, C.D. (2000) The language of covalent histone modifications. Nature 403, 41-45
  3. Cheung, P., Allis, C.D. and Sassone-Corsi, P. (2000) Signaling to chromatin through histone modifications. Cell 103, 263-271
  4. Jenuwein, T. and Allis, C.D. (2001) Translating the histone code. Science 293, 1074-1080
  5. Wysocka, J., Swigut, T., Xiao, H., Landry, J., Kauer, M., Tackett, A., Chait, B., Brivanlou, A.H., Wu, C. and Allis, C.D. (2006) A PHD finger in the largest subunit of NURF couples histone H3 K4 trimethylation with chromatin remodeling. Nature 442, 86-90
  6. Taverna, S.D., Ilin, S., Rogers, R.S., Tanny, J.C., Lavender, H., Li, H., Baker, L., Boyle, J., Blair, L.P., Chait, B.T., Patel, D.J., Aitchison, J.D., Tackett, A.J. and Allis, C.D. (2006) Yng1 PHD finger binding to histone H3 trimethylated at lysine 4 targets lysine 14 specific NuA3 HAT activity to a subset of promoters for transcriptional activation. Mol. Cell 24, 1-12
  7. Li, H., Ilin, S., Wang, W.-K., Wysocka, J., Allis, C.D. and Patel, D.J. (2006) Molecular basis for site/state-specific readout of histone lysine-methylation marks by the PHD domain of BPTF. Nature 442, 91-95
  8. Ruthenburg, A., Allis, C.D., Wysocka, J. (2007a) Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol. Cell. 25, 15-37.
  9. Ruthenburg, A.J., Li, H., Patel, D.J., Allis, C.D. (2007b) Multivalent engagement of chromatin modifications by linked binding modules. Nat Rev Mol Cell Biol, 12: 983-994
  10. Taverna, S.D., Li, H., Ruthenburg, A.J., Allis, C.D., Patel, D.J. (2007) How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol, 14: 1025-1040
  11. Baker, L.A., Allis, C.D. and Wang, G.G. (2008) PHD fingers in human diseases: disorders arising from misinterpreting epigenetic marks. Mutat. Res. 647, 3-12
  12. Fischle, W., Wang, Y. and Allis, C.D. (2003) Binary switches and modification cassettes in histone biology and beyond. Nature 425, 475-479
  13. Fischle, W., Tseng, B.S., Dormann, H., Ueberheide, B.M., Garcia, B.A., Shabanowitz, J., Hunt, D.F., Funabiki, H. and Allis, C.D. (2005) Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature 438, 1116-1122
  14. Cheung, W.L., Ajiro, K., Kloc, M., Cheung P., Mizzen, C.A., Beeser, A., Etkin, L.D., Chernoff, J. and Allis, C.D. (2003) Apoptotic phosphorylation of histone H2B is mediated by mammalian sterile twenty kinase. Cell 16, 507-517 (featured article)
  15. Ahn, S.-H., Cheung, W.L., Hsu, J.-Y., Smith, M.M. and Allis, C.D. (2005) Sterile 20 kinase phosphorylates histone H2B at serine10 during hydrogen peroxide-induced apoptosis in S. cerevisiae. Cell 120, 25-36
  16. Ahn, S., Diaz, R.L., Grunstein, M., Allis, C.D. (2006) Histone H2B deacetylation at lysine 11 is required for yeast apoptosis induced by phosphorylation of H2B at serine 10. H2B. Mol. Cell 24, 211-220
  17. Wang, G.G., Allis, C.D., Chi, P. (2007a) Chromatin remodeling and cancer: part I - covalent histone modifications. Trends in Molecular Medicine 13, 363-372
  18. Wang, G.G., Allis, C.D., Chi, P. (2007b) Chromatin remodeling and cancer: part II - ATP-dependent chromatin remodeling. Trends in Molecular Medicine 13, 373-380
  19. Sun, Z.-W. and Allis, C.D. (2002) Ubiquitylation of histone H2B regulates H3 methylation and gene silencing in yeast. Nature 418, 104-108
  20. Briggs, S.D., Xiao, T., Sun, Z.-W., Caldwell, J.A., Shabanowitz, J., Hunt, D.F., Strahl, B.D. and Allis, C.D. (2002) Gene silencing: trans-histone regulatory pathway in chromatin. Nature 418, 498
  21. Hake S.B. and Allis, C.D. (2006) Histone H3 variants and their potential role in indexing mammalian genomes: The "H3 barcode hypothesis" Proc. Natl. Acad. Sci. USA 103, 6428-6435
  22. Shechter, D., Nicklay, J., Chitta, R., Shabanowitz, J., Hunt, D.F., Allis, C.D. (2009) Analysis of histones in Xenopus laevis, Part I: A distinct index of enriched variants and modifications exists in each cell type and is remodeled during developmental transitions. J Biol Chem 284, 1064-1074
  23. Duncan, E.M., Muratore-Shroeder, T.L., Cook, R.G., Shabanowitz, J., Hunt, D.F., Allis, C.D. (2008) Cathepsin L proteolytically processes histone H3 during mouse embryonic stem cell differentiation. Cell 135, 284-294
  24. Goldberg, A.D., Allis, C.D., Bernstein, E. (2007) Epigenetics: a landscape takes shape. Cell 128, 635-638
  25. Borrelli, E., Nestler, E. Allis, C.D., Sassone-Corsi, P. (2008) Decoding the epigenetic language of neuronal plasticity. Neuron 60, 961-974
  26. Xiao, A., Li, H., Shechter, D., Ahn, S.H., Fabrizio, L.A., Erdjument-Bromage, H., Murakami-Ishibe, S., Wang, B., Tempst, P., Hofmann, K., Patel, D.J., Elledge, S.J., Allis, C.D. (2009) WSTF regulates the DNA damage response of H2A.X via a novel tyrosine kinase activity. Nature 457, 57-62
  27. Wang, G.W., Song, J., Wang, Z., Dormann, H., Casadio, F., Li, H., Patel, D. and Allis, C.D. (2009) Engaging histone H3 Lys4 methylation marks by aberrant PHD fingers perturbs cellular identities and initiates tumorigenesis. (2009) Nature, in press