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Elsaesser,S. 2013 

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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.

Chromatin ‘readers’ are now an accepted aspect of chromatin biology and its functional readout. Moreover, a growing list of chromatin-associated effector proteins or complexes continue to be identified at a rapid pace, many with solved co-crystal structures of protein modules with binding ligand (see Taverna et al., 2007; Ruthenburg et al., 2007).  Noteworthy are recent results wherein bromodomains, the first documented acetyl-lysine binding module, have proven to be an effective drug targets in several human disease settings (reviewed in Dawson et al., 2012).

The molecular basis for the discrimination of distinct repressive methyl-lysine marks in histone H3 by chromodomains within (repressive) Polycomb and HP1 proteins is now well described (Fischle et al., 2003; 2005), as well as the role that phosphorylation of nearby phosphorylations play in releasing bound effectors from its chromatin association in what is now described as ‘phospho-methyl’ switching. Moreover, some of these general concepts have now been shown to apply to non-histone proteins supporting the general notion of a ‘protein code’ or what some have called ‘histone mimicry’.

Following the discovery of certain PHD fingers as methyl ‘reading’ modules (Wysocka et al. 2006), disease links soon followed.  For example, Allis and colleagues (Wang et al., 2009) provided the first clear demonstration between chromatin ‘mis-reading’ and tumorigenesis.  Here, a human translocation involving a single PHD finger from the JARID1A lysine demethylase, when fused to NUP98, was shown to induce acute myeloid leukemia (AML) in mouse models.  Importantly, when point mutations were introduced into the translocated PHD finger, which disrupted H3K4me binding, cancer did not occur.  Critical downstream genes, such as HoxA9, were shown to gain repressive H3K27 methyl marks, only when the above PHD finger was mutated, not when the PHD finger was ‘wild type’. 

Histone variant (H3.3) related with human disease links

Allis has maintained a long-time interest in minor histone variants following his 1980 discovery of two histone variants in the ciliated protozoan Tetrahymena (Allis et al. 1980).  Building upon studies from Henikoff and others, who had rekindled interest in the histone variant H3.3 as a ‘active’ variant in Drosophila cells, Allis and colleagues used, for the first time, zinc finger-mediated genome ‘editing’ to replace endogenous alleles of the histone variant H3.3 with tagged alleles in the genome of mouse ES cells.  Chromatin immunoprecipitation (ChIP)-sequencing showed that H3.3 localizes to some active loci, but also documented unexpected locations, such as intergenic transcription factor binding sites and telomeres.  Moreover, the location of H3.3 in ES cells changed upon differentiation and was dependent upon the primary amino acid sequence of H3.3, tested by mutagenizing H3.3 into H3.1 or H3.2.

Using epitope-affinity tags, Allis and colleagues went on in the above study to identify several new chaperones that are selective for H3.3, including the mental retardation-associated protein, ATRX, and its suspected binding partner, Daxx.  Future studies showed that ATRX and Daxx govern distinct, and non-overlapping locations of H3.3 in the mouse genome.  Recent studies from others (Jiao et al., 2011) have identified ATRX and Daxx as being mutated in a significant subset of pancreatic cancers (pancreatic neuroendocrine or panNET tumors).  In light of this ground-breaking study, Allis and colleagues have shifted much of their recent attention to how H3.3 deposition and exchange may be mis-regulated in this form of human cancer, contributing to oncogenesis by what they have referred to a ‘back-seat driver’ mutations (Elsaesser et al., 2011). 

Together with Patel and colleagues (MSKCC), Allis and co-workers recently reported the crystal structures of the Daxx histone-binding domain with a histone H3.3-H4 dimer, including mutants within Daxx and H3.3, together with in vitro and in vivo functional studies that elucidate the principles underlying H3.3 recognition specificity (Elsaesser et al., 2012). These structural studies identified recognition elements that read out H3.3-specific residues, and functional studies addressed the contributions of specific residues in H3.3 and in Daxx that contribute to chaperone-mediated H3.3 variant recognition specificity.  Not only is this one of the few co-crystal structures of a variant-specific chaperone in complex with its histone ‘passengers’, but also these structural studies give important insights into function (mis-function) that results from the missense mutations identified in panNET patients in the histone-binding domain of Daxx (ongoing work in the Allis laboratory).

Recent exome sequencing studies by others (Schwartzentruber et al., 2012; Wu et al., 2012) of pediatric gliomas identified quite unexpectedly missense mutations (K27M and G34R/V) in genes encoding H3.3 (H3F3A) and H3.1 (HIST3H1B).  In follow-up work, Allis and colleagues report that human diffuse intrinsic pontine gliomas (DIPGs) containing the K27M mutation display lower overall H3K27me3 levels relative to tumors without H3 mutations, and that histone H3K27M transgenes are sufficient to cause global reduction in H3K27me3 in vitro and in vivo (Lewis et al., 2013).  Moreover, we find that H3K27M interacts with the catalytic EZH2 subunit of PRC2, and this interaction inhibits the enzymatic activity of PRC2 both in cis and trans.  Additionally, transgenes containing lysine-to-methionine substitutions at other known methylated lysines (H3K9 and H3K36) are sufficient to cause specific reduction in methylation levels of their cognate lysines through inhibition of SET-domain enzymes.  From these collective studies, we propose a provocative new model that K-to-M substitutions may represent a novel and previously unrecognized mechanism to alter epigenetic states in a variety of pathologies through inhibition of a wide range of histone methyltransferases.  Ongoing studies aim to obtain co-crystal structures of the SET domain of relevant histone methyltransferases with their respective K-to-M histone peptides to better understand the mechanism of inhibition.  As well, we suggest that inhibitory K-to-M peptides provide us with new tools to perturb histone methylation in a wide variety of biological processes such as development, differentiation and somatic cell reprogramming.

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. Strahl, B.D. and Allis, C.D. (2000) The language of covalent histone modifications. Nature 403, 41-45
  2. Cheung, P., Allis, C.D. and Sassone-Corsi, P. (2000) Signaling to chromatin through histone modifications. Cell 103, 263-271
  3. Jenuwein, T. and Allis, C.D. (2001) Translating the histone code. Science 293, 1074-1080
  4. Sun, Z.-W. and Allis, C.D. (2002) Ubiquitylation of histone H2B regulates H3 methylation and gene silencing in yeast. Nature 418, 104-108
  5. 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
  6. Fischle, W., Wang, Y. and Allis, C.D. (2003) Binary switches and modification cassettes in histone biology and beyond. Nature 425, 475-479
  7. 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)
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. Ruthenburg, A., Allis, C.D., Wysocka, J. (2007) Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol. Cell. 25, 15-37.
  14. Ruthenburg, A.J., Li, H., Patel, D.J., Allis, C.D. (2007) Multivalent engagement of chromatin modifications by linked binding modules. Nat Rev Mol Cell Biol, 12: 983-994
  15. 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 
  16. Goldberg, A.D., Allis, C.D., Bernstein, E. (2007) Epigenetics: a landscape takes shape. Cell 128, 635-638
  17. Wang, G.G., Allis, C.D., Chi, P. (2007) Chromatin remodeling and cancer: part II - ATP-dependent chromatin remodeling. Trends in Molecular Medicine 13, 373-380
  18. 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
  19. 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
  20. Borrelli, E., Nestler, E. Allis, C.D., Sassone-Corsi, P. (2008) Decoding the epigenetic language of neuronal plasticity. Neuron 60, 961-974
  21. 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
  22. 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 459, 847-851   
  23. Goldberg A.D., Banaszynski L.A., Noh K.M., Lewis P.W., Elsässer S.J.,Stadler S., Dewell S., Law M., Guo X., Li X., Wen D., Chapgier A., DeKelver, R.C., Miller J.C., Lee Y.L., Boydston E.A., Holmes M.C., Gregory P.D., Greally J.M., Rafii S., Yang C., Scambler P.J., Garrick D., Gibbons R.J., Higgs D.R.,Cristea I.M., Urnov F.D., Zheng D., Allis C.D. (2010) Distinct factors controlhistone variant H3.3 localization at specific genomic regions. Cell 140, 678-691 
  24. Allis, C.D. and Muir, T.W. (2011) Spreading chromatin into chemical biology. ChemBioChem. 12, 264-279
  25. Elsässer, S.J., Huang, H., Lewis, P.W., Allis, C.D. and Patel, D.J. (2012) DAXX envelops a histone H3.3-H4 dimer for H3.3 specific recognition.  Nature 491, 560-565
  26.  Kim, J., Kim, J.A., McGinty, R.K., Nguyen, U.T.T., Muir, T.W., Allis, C.D. and Roeder,R.G. (2013) The n-SET domain of Set1 regulates H2B ubiquitylation-dependent H3K4 methylation. Mol. Cell, February 26 (Epub ahead of print)
  27. Lewis, P.W., Mueller, M.M., Koletsky, M.S., Cordero, F., Lin, S., Banaszynski, L.A.,Garcia, B.A., Muir, T.W., Becher, O.J. and Allis C.D. (2013) Inhibition of PRC2 activity by gain-of-function mutations in pediatric glioblastoma. Science, Mar 28. (Epub ahead of print)

    Textbooks

    Allis, C.D., Jenuwein, T., Reinberg, D. (eds.), Caparros, M.L. (assoc. ed.) Epigenetics Cold Spring Harbor Laboratory Press. Cold Spring Harbor, NY, 2006