Pauli Lectures 2013

Over a decade has passed since the scientific community first inspected an early draft of the DNA sequence or “blueprint” of the human genome. The logic underlying the Human Genome Project was clear -- genes determine disease, genes determine aging, and genetic analyses would provide new windows to explore the diagnosis and therapy of human disorders. The first chapter towards “personalized medicine” had been written. As DNA sequencing costs have fallen, a variety of human diseases from collections of individual patients have been fully or partially sequenced, yielding valuable information into the identification of genetic mistakes (or mutations) that drive, or closely correlate with, a variety of disease pathologies.

Despite this exciting progress, the questions can be asked -- is DNA sequence, founded in classical genetics, the whole story? In this lecture, Dr. Allis will describe biological processes where DNA alone is not enough; where it alone can not explain differences in outward appearances (phenotypes). Beyond the genetic code lies a second level of complexity above the genome itself; what is now being referred to the “epigenome”. Epigenetics refers to an exciting new area of research wherein the collective covalent modifications of DNA and chromatin control inheritable states of gene expression, without changes in DNA sequence. In some cases, these gene states can be influenced by “outside factors” such as environment, diet and even social interactions. The science of epigenetics suggests the provocative thought that the choices we make now not only affect us, but may also affect or children or even our grandchildren. A rapidly emerging literature suggests then that DNA alone does not dictate our destiny; Mendel would be surprised.

In this opening lecture, Dr. Allis will attempt to describe some of the molecular “signals” that are added to DNA and chromatin that underly some epigenetic phenomena. Since the molecules that “write”, “read” and “erase” this language do not alter the DNA sequence, the real hope, and in some case realized hope, remains that mistakes made in establishing the epigenome can be reversed with drugs, giving rise to what is described as epigenetic-based therapies. In some cases, drugs against epigenetic regulators have proven effective in giving promising clinical outcomes, notably tumor loss and remission in cancer patients. Given this, the inheritance of something besides DNA itself, will continue to cause excitement and receive much attention in years to come.

Chromatin is the physiological template of our genome. The packaging of DNA within chromatin, the orderly replication and distribution of chromosomes, the maintenance of genome integrity, and the regulated expression of genes depend upon the highly conserved histone proteins. Professor Richmond and colleagues have given the chromatin field its best look into the atomic structure of the fundamental repeating unit of chromatin, the nucleosome. While conserved, the repeating chromatin polymer is not static. It must respond to a variety of upstream signals and inputs that dictate whether the packaged DNA template is more or less accessible to the machinery that with act upon it. Variability is introduced by several well-studied mechanisms, including the enzymatic addition or subtraction of covalent post-translations modifications (PTMs). Work from Dr. Allis and many others have given valuable insights into the functions of some of these “marks”, and their work has contributed to the general concept of “writers”, “readers” and “erasers” that serve to alter the readout of the chromatin fiber in response to cellular demands.

Post-translational modifications of proteins provide vast indexing potential and expanded protein utility. The “histone code hypothesis” was proposed to account for the emerging complexity and combinatorial nature of PTMs associated with histone proteins; it has recently been extended to non-histone proteins. In this lecture, Dr. Allis will discuss some of the history and general principles underlying the histone or protein code. Experimental evidence supporting key tenets of this general hypothesis have now appeared in the literature with far-reaching implications for human biology and disease.

As predicted by the original histone code hypothesis, the bromodomain was first identified as a specific acetyl-lysine binding “reader”. Since that time, a variety of chromatin-associated effectors have been identified, with co-crystal structures solved, giving molecular insights into how the exquisite specificity governing these interactions is brought about. In this second lecture, Dr. Allis will review some of this exciting progress, along with new data suggesting that some of these “pockets” can “picked” or drugged with promising clinical outcomes. Mistakes made in mis-reading the “histone code” can lead to human disease underscoring the importance of deciphering the histone code.

The journey from embryonic stem cell to a fully developed liver, heart or muscle cell requires not only having the right set of genes, but also having genes that are turned on and off at the right time — a job that is handled in part by DNA-packaging proteins known as histones.

Cells use a number of mechanisms to establish and maintain the activation or silencing of specific genes. Among these is the chemical modification of histones, discussed in the second lecture. In addition, histone variants, which differ from other histone proteins by just a handful of amino acids, can be inserted at specific locations in the genome to provide a cell with another mechanism for fine-tuning gene regulation. Dr. Allis’ group has shown that histone variants play an important role in determining how and when genes are read or are silenced.

Recent work from Dr. Allis’ laboratory has focused upon one member of the histone H3 family known as H3.3. In comparing the genome-wide localization of H3.3, Allis and coworkers found that histone H3.3 is prevalent in regions of the genome where active genes are found, as well as in silent regions, such as at the ends of chromosomes, called telomeres. They went on to identify several additional proteins associated with H3.3. Two of them, ATRX and Daxx, were then discovered to be frequently mutated in a sporadic, non-functional pancreatic cancers, known as panNETs. Current experiments seek to determine whether genetic deficiency of Daxx and ATRX in pancreatic neuroendocrine cells is sufficient to induce tumorigenesis.

Mutations in histone H3.3 itself have also been found in pediatric brain tumors (gliomas). Allis and co-workers have recently asked -- how one of these mutations might act cause cancer in young children? Surprisingly they find that a specific mutation in H3.3 often found in the pediatric brain tumors inhibits histone methylation of all histone H3 at this site, a site methylated to induce gene silencing. Moreover, the specific mutation in H3.3 acts by inhibiting the enzyme responsible for bringing about methylation at this site. These data indicate that this specific type of mutation in histones might be more broadly applicable to the development and progression of other tumour types. It is not yet clear why aberrant epigenetic silencing of this enzyme results in the development of pediatric brain tumors, and further research is needed in an attempt to develop a better understanding of these difficult to treat childhood cancers.