Epigenetics and chromatin structure/function in genomic regulation
Translational modifications of histones and transcription factors problems: transcription, cancer, senescence and aging, behavioral epigenetics, gametogenesis.
epigenetics, chromatin, histone post-translational modifications, p53 tumor suppresor
Description of Research:
Research Overview --
Our research focuses on regulation of the nuclear genome in mammals and model organisms. The long strands of nuclear DNA are associated with packaging proteins, called histones, into a structure known as chromatin, akin to the way thread is organized around a spool. We are particularly interested in changes in this chromatin structure via chemical modification of the histone proteins, and how attachment of certain chemical groups onto the histones leads to altered chromatin function. These targeted structural changes are conceptually like the unraveling of the thread to reach specific, buried sections. We are also fascinated by functional changes in chromatin, caused by these histone modifications, that persist through cell division from one cell into two daughter cells; these persistent, or epigenetic, changes are of particular interest because they are key to normal and abnormal growth: they occur during organismal development into multicellular tissues and organs, and are typically disrupted during abnormal reversal of tissue specialization and growth control as in cancer, as well as during aging of cells and individuals.
Research Focus --
The basis of genome regulation is a fundamental biological question. Our past research findings have helped to establish the prevailing view that histone modifications regulate genomic functions, including transcription of genes, DNA replication during cell division, repair of DNA mutations as a result of DNA damage, and other processes. Our work has focused on transcription, or the turning on and off of gene expression, and the myriad of histone modifications that occur, such as acetylation, phosphorylation, methylation, among other chemical changes. We have identified many new modifications and the enzymes that carry them out, as well as understanding how the enzymes are recruited to certain locations in the genome. There is now an explosion of research in the field of chromatin regulation and how these histone modifications function to regulate the genome. We have contributed to the current ideas, including how histone PTMs function in combinatorial patterns, and in temporal sequences, to set up the intricate timing and spatial requirements of turning genes on and off, as depicted in the Figure. For example, we have extensively studied a pattern on histone H3 consisting of Serine10 phosphorylation and Lysine14 acetylation. We identified the enzymes that carry out the linked modifications, established the structural and biochemical basis of the cross-talk, and discovered a binding protein that specifically associates with the pattern, rather than the individual modifications. In a second example, we studied the timing of histone H2B ubiquitylation followed by deubiquitylation, identified the deubiquitylating enzyme, and determined the biochemical role of the dynamic switch, i.e. in regulating elongation by RNA polymerase II through transcribed genes.
Our work has also helped to reveal how some of these modifications, first characterized on histone substrates, such as acetylation and methylation, function to regulate non-histone proteins. In particular, we have identified new modifications on the tumor suppressor and transcription factor, p53; we focus on p53 because of its key function in regulating growth to prevent cancer, and so we wish to determine how these individual modifications turn p53 function on and off. As depicted in the Figure, our recent findings show that methylation and demethylation of p53 at a single lysine residue both activate and repress p53 function. This regulation occurs by promoting or inhibiting, respectively, the binding of a p53 coactivator protein, called 53BP1. We believe this type of regulation of p53 will prove to be common among non-histone proteins.
Research Future Directions --
Our current focus is to continue to discover novel chromatin and factor modifications and their mechanisms of action. However we are now endeavoring to elucidate the role and importance of these modifications in normal and abnormal cellular function. We are in particular keen to determine whether these modifications are important in persistent or epigenetic cellular states, as mentioned above. Thus, our emphasis is more biological in the sense of investigating how physical changes in chromatin impact biological processes such as gametogenesis and viral latency, as well as broader phenomenon such as aging, behavior and cancer. As one recent example, we have initiated a study of chromatin changes during replicative aging in the model S. cerevisiae. We discovered that telomeric changes in chromatin are centrally involved. Specifically, as depicted in the Figure, in old cells there is a reduction in the level of the histone deacetylase Sir2, which is crucial in maintaining compact chromatin in sub-telomeric regions, leading to an increase in histone H4 K16 acetylation by the acetylase Sas2. The result of this is decompaction of the teleomeric chromatin in the old cells.
Epigenetics is still an emerging field in biology, and is exerting an increasingly profound impact on medicine because of its potential explanatory power in development and disease. In spite of the broad interest, there is no clear consensus on a definition of epigenetics in chromatin research. To help to provide a framework for the field and beyond into the wider research community, we have recently published a short proposal defining Epigenetics, encompassing both established ideas in the chromatin field and providing some operational concepts, as shown in the Figure.
Research Associates --
Enrique Lin Shiao
K.M. Ahasan Al Tanim
Julian M Roessler
Bose Daniel A, Donahue Greg, Reinberg Danny, Shiekhattar Ramin, Bonasio Roberto, Berger Shelley L: RNA Binding to CBP Stimulates Histone Acetylation and Transcription. Cell 168(1-2): 135-149.e22, Jan 2017.
Bonini Nancy M, Berger Shelley L: The Sustained Impact of Model Organisms-in Genetics and Epigenetics. Genetics 205(1): 1-4, Jan 2017.
Mews P, Berger S L: Exploring the Dynamic Relationship Between Cellular Metabolism and Chromatin Structure Using SILAC-Mass Spec and ChIP-Sequencing. Methods in enzymology 574: 311-29, 2016.
Hur Stella K, Freschi Andrea, Ideraabdullah Folami, Thorvaldsen Joanne L, Luense Lacey J, Weller Angela H, Berger Shelley L, Cerrato Flavia, Riccio Andrea, Bartolomei Marisa S: Humanized H19/Igf2 locus reveals diverged imprinting mechanism between mouse and human and reflects Silver-Russell syndrome phenotypes. Proceedings of the National Academy of Sciences of the United States of America 113(39): 10938-43, Sep 2016.
Berger Shelley L, Sassone-Corsi Paolo: Metabolic Signaling to Chromatin. Cold Spring Harbor perspectives in biology 8(11), Nov 2016.
Shah PP, Donahue G, Otte GL, Capell BC, Nelson DM, Cao K, Aggarwala V, Cruickshanks HA, Rai TS, McBryan T, Gregory BD, Adams PD, Berger SL.: Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape. Genes Dev. 27(16): 1787-99, August 15 2013.
Simola DF, Ye C, Mutti NS, Dolezal K, Bonasio R, Liebig J, Reinberg D, Berger SL.: A chromatin link to caste identity in the carpenter ant Camponotus floridanus. Genome Res. 23(3): 486-96, March 2013.
Simola DF, Wissler L, Donahue G, Waterhouse RM, Helmkampf M, Roux J, Nygaard S, Glastad KM, Hagen DE, Viljakainen L, Reese JT, Hunt BG, Graur D, Elhaik E, Kriventseva EV, Wen J, Parker BJ, Cash E, Privman E, Childers CP, Muñoz-Torres MC, Boomsma JJ, Bornberg-Bauer E, Currie CR, Elsik CG, Suen G, Goodisman MA, Keller L, Liebig J, Rawls A, Reinberg D, Smith CD, Smith CR, Tsutsui N, Wurm Y, Zdobnov EM, Berger SL, Gadau J.: Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality. Genome Res. August 2013.
Berger SL.: Transgenerational inheritance of longevity: epigenetic mysteries abound. Cell Metab. January 2012.
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Last updated: 05/15/2017
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