Shelley L. Berger , Ph.D. Professor of Biology Ph.D., University of Michigan , 1987 Departments of Cell & Developmental Biology; Biology; Genetics; Director, Epigenetics Program University of Pennsylvania 1051 BRBII/III 421 Curie Boulevard Philadelphia, PA 19104 USA V +1 215 898.3922 F +1 215 746.8791 E bergers@upenn.edu

research : publications

cell and developmental biology 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

publications Dang, W, Steffers KK, Perry R, Dorsey JA, Johnson FB, Shilatifard A, Kaeberlein M, Kennedy BK, Berger SL.   (2009) Histone H4 lysine 16 acetylation regulates cellular lifespan. Nature in press. Berger SL , Kouzarides T, Shiekhattar R, Shilatifard A.   (2009) An operational definition of epigenetics.   Genes & Development , 23:781-3. Lin YY, Lu, JY, Zhang J, Walter W, Dang W, Wan J, Tao SC, Qian J, Zhao Y, Boeke JD, Berger SL , Zhu H.   (2009) Protein acetylation microarray reveal NuA4 controls key metabolic target regulating gluconeogenesis. Cell 136:1073-84. Berger SL .   (2008) Out of the jaws of death: Prmt5 steers p53.   Nature Cell Biology 10:1389-90. Zediak V and Berger SL .   (2008) Hit and Run:   Transient activation of deubiquitylase activity in a chromatin remodeling complex.   Molecular Cell 31:773-4. Walter W, Clynes D, Tang Y, Marmorstein R, Mellor J, Berger SL .   (2008) 14-3-3 interaction with histone H3 involves dual modification pattern of phosphoacetylation. Molecular and Cellular Biology , 28:2840-9. Huang J and Berger SL . (2008) The emerging field of lysine methylation of non-histone proteins. Current Opinion in Genetics , 18:152-8. Huang J, Sengupta R, Espejo A, Lee MG, Dorsey JA, Richter M, Opravil S, Shiekhattar R, Bedford MT, Jenuwein T, and Berger SL .   (2007) p53 is regulated by the lysine demethylase LSD1.   Nature , 449:105-8. Wyce AW, Whelan KA, Xiao T, Walter W, Krogan NJ, Strahl B, Berger SL .   (2007) H2B ubiquitylation acts as a barrier to Ctk1 nucleosomal recruitment prior to removal by SALSA-associated Ubp8.   Molecular Cell , 27:275-88. Berger SL . (2007) The complex language of chromatin regulation during transcription. Nature , 447:407-12. Allis CD, Berger SL , Cote J, Dent SY, Jenuwein T, Kouzarides T, Pillus L, Reinberg, D, Shi Y, Shiekhattar R, Shilatifard A, Workman J and Zhang Y. (2007) New nomenclature for chromatin-modifying enzymes. Cell , 131:633-6. Ingvarsdottir K, Edwards C, Lee MG, Lee JS, Schultz DC, Shilatifard A, Shiekhattar R, and Berger SL . (2007) Histone K4 demethylation during activation and attenuation of GAL1 transcription in S. cerevisiae. Molecular and Cellular Biology , 27:7856-64. Huang J, Perez-Burgos L, Placek BJ, Sengupta R, Richter M, Dorsey JA, Kubicek S, Opravil S, Jenuwein T, and Berger SL . (2006) Repression of p53 activity by Smyd2-mediated methylation.   Nature , 444:629-32. Krishnamoorthy T, Chen X, Govin J, Cheung WL, Dorsey J, Schindler K, Winter E, Allis CD, Khochbin S, Fuller MT, Berger SL . (2006) Phosphorylation of histone H4 Ser1 regulates sporulation in yeast and is conserved in fly and mouse spermatogenesis. Genes & Development, 20:2580-92. Nathans D, Ingvarsdottir K, Sterner DE, Bylebyl GR, Dorsey JA, Meluh PB, Lane WS, Johnson ES, Berger SL . (2006) Histone sumoylation represses transcription and shows dynamic interplay with histone acetylation in Saccharomyces cerevisiae. Genes & Development , 20:966-76. Kouzarides T and Berger SL . (2006) Chromatin modifications and their mechanism of action.   In "Epigenetics" , CSH Press. Editors: Jenuwein T, Allis CD, Reinberg D.