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Genomes and Genes | S L BergerSummaryAffiliation: University of Pennsylvania Country: USA Publications
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Publications
The complex language of chromatin regulation during transcriptionShelley L Berger
The Wistar Institute, 3601 Spruce Street, Room 201, Philadelphia, Pennsylvania 19104, USA
Nature 447:407-12. 2007..Although such modifications were initially thought to be a simple code, a more likely model is of a sophisticated, nuanced chromatin 'language' in which different combinations of basic building blocks yield dynamic functional outcomes...- Chromatin goes globalS L Berger
Molecular Genetics Program, The Wistar Institute, Philadelphia, PA 19104, USA
Mol Cell 8:263-8. 2001..The latest findings on the structure of chromatin, its organization in the nucleus, and its involvement in regulating gene expression were presented at a recent meeting at the Juan March Foundation in Madrid, Spain... - Histone modifications in transcriptional regulationShelley L Berger
The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania 19104, USA
Curr Opin Genet Dev 12:142-8. 2002..This multiplicity of modifications, and their occurrence in patterns and dependent sequences, argues persuasively for the existence of a histone code... - Gene activation by histone and factor acetyltransferasesS L Berger
Molecular Genetics Program, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
Curr Opin Cell Biol 11:336-41. 1999..Finally, enzymatic acetyltransferase activities are themselves regulated by phosphorylation and interaction with other proteins... - Acetylation of p53 activates transcription through recruitment of coactivators/histone acetyltransferasesN A Barlev
Molecular Genetics Program, The Wistar Institute, Philadelphia, PA 19104, USA
Mol Cell 8:1243-54. 2001..Therefore, we propose that an acetylation cascade consisting of p53 acetylation-dependent recruitment of coactivators/HATs is crucial for p53 function... 
Inhibition of TATA-binding protein function by SAGA subunits Spt3 and Spt8 at Gcn4-activated promotersR Belotserkovskaya
The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
Mol Cell Biol 20:634-47. 2000..These results suggest that the composition of SAGA may be dynamic in vivo and may be regulated through dissociable inhibitory subunits...- Functional organization of the yeast SAGA complex: distinct components involved in structural integrity, nucleosome acetylation, and TATA-binding protein interactionD E Sterner
The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
Mol Cell Biol 19:86-98. 1999..Loss of either of these causes slight impairment in vivo, but loss of both is highly detrimental to growth and transcription... - Phosphorylation of serine 10 in histone H3 is functionally linked in vitro and in vivo to Gcn5-mediated acetylation at lysine 14W S Lo
Molecular Genetics Program, Wistar Institute, Philadelphia, Pennsylvania 19024, USA
Mol Cell 5:917-26. 2000..These observations suggest that transcriptional regulation occurs by multiple mechanistically linked covalent modifications of histones... - Histone acetyltransferase activity is conserved between yeast and human GCN5 and is required for complementation of growth and transcriptional activationL Wang
Wistar Institute, Philadelphia, Pennsylvania 19104, USA
Mol Cell Biol 17:519-27. 1997..These findings directly link enzymatic histone acetylation and transcriptional activation and show evolutionary conservation of this potentially crucial pathway in gene regulation... - Snf1--a histone kinase that works in concert with the histone acetyltransferase Gcn5 to regulate transcriptionW S Lo
Molecular Genetics Program, The Wistar Institute, Philadelphia, PA 19104, USA
Science 293:1142-6. 2001.... - Histone acetyltransferase activity and interaction with ADA2 are critical for GCN5 function in vivoR Candau
The Wistar Institute, Philadelphia, PA 19104, USA
EMBO J 16:555-65. 1997..These results suggest that both functions of GCN5, HAT activity and interaction with ADA2, are necessary for targeting and acetylation of nucleosomal histones... - Repression of GCN5 histone acetyltransferase activity via bromodomain-mediated binding and phosphorylation by the Ku-DNA-dependent protein kinase complexN A Barlev
The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
Mol Cell Biol 18:1349-58. 1998..These findings suggest a possible regulatory mechanism of HAT activity... - Identification of human proteins functionally conserved with the yeast putative adaptors ADA2 and GCN5R Candau
Wistar Institute, Philadelphia, Pennsylvania 19104, USA
Mol Cell Biol 16:593-602. 1996..These data indicated that the human proteins correspond to functional homologs of the yeast adaptors, suggesting that these cofactors play a key role in transcriptional activation... - The acidic transcriptional activation domains of herpes virus VP16 and yeast HAP4 have different co-factor requirementsL Wang
Wistar Institute, Philadelphia, PA 19401, USA
Gene 158:163-70. 1995..These results strongly suggest that HAP4 and VP16 have distinct cofactor requirements, although they are both acidic activators... - p53 sites acetylated in vitro by PCAF and p300 are acetylated in vivo in response to DNA damageL Liu
The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
Mol Cell Biol 19:1202-9. 1999..These data indicate that site-specific acetylation of p53 increases under physiological conditions that activate p53 and identify CBP/p300 and PCAF as the probable enzymes that modify p53 in vivo... - CREB-binding protein and p300/CBP-associated factor are transcriptional coactivators of the p53 tumor suppressor proteinD M Scolnick
Department of Molecular Genetics, The Wistar Institute, University of Pennsylvania, Philadelphia 19104 4268, USA
Cancer Res 57:3693-6. 1997..These studies link two tumor suppressor families and provide a framework for understanding the molecular mechanism by which p53 activates transcription... - Structural and functional analysis of yeast putative adaptors. Evidence for an adaptor complex in vivoR Candau
Wistar Institute, Philadelphia, Pennsylvania 19104, USA
J Biol Chem 271:5237-45. 1996.... - Acetylation of histones and transcription-related factorsD E Sterner
The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
Microbiol Mol Biol Rev 64:435-59. 2000..Thus, we also detail these known factor acetyltransferase (FAT) substrates and the demonstrated or potential roles of their acetylation in transcriptional processes... - Structure and function of bromodomains in chromatin-regulating complexesR Marmorstein
Structural Biology Program, The Wistar Institute, Philadelphia, PA, USA
Gene 272:1-9. 2001..Interactions between bromodomains and modified histones may be an important mechanism underlying chromatin structural changes and gene regulation... - Histone H2B ubiquitylation and deubiquitylation in genomic regulationN C T Emre
Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
Cold Spring Harb Symp Quant Biol 69:289-99. 2004 - BAP1: a novel ubiquitin hydrolase which binds to the BRCA1 RING finger and enhances BRCA1-mediated cell growth suppressionD E Jensen
The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
Oncogene 16:1097-112. 1998..BAP1 may be a new tumor suppressor gene which functions in the BRCA1 growth control pathway... 
Cell signaling and transcriptional regulation via histone phosphorylationS L Berger
Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
Cold Spring Harb Symp Quant Biol 75:23-6. 2010..These results lead to a gathering appreciation of the potential role of signal transduction kinase-mediated direct histone phosphorylation in regulating transcription...- Characterization of physical interactions of the putative transcriptional adaptor, ADA2, with acidic activation domains and TATA-binding proteinN A Barlev
Wistar Institute, Philadelphia, Pennsylvania 19104, USA
J Biol Chem 270:19337-44. 1995..In addition, ADA2 physically associated with TBP, but not with TFIIB. These results suggest that the role of ADA2 in transcriptional activation is to promote physical interaction between activation domains and TBP... - Gene array analysis reveals changes in peripheral nervous system gene expression following stimuli that result in reactivation of latent herpes simplex virus type 1: induction of transcription factor Bcl-3D Tsavachidou
The Wistar Institute, Philadelphia, Pennsylvania 19104-4268, USA
J Virol 75:9909-17. 2001..We discuss a potential role for this factor in upregulating ICP0 transcription, which is an important viral event for initiation of HSV-1 reactivation... - The histone H2B-specific ubiquitin ligase RNF20/hBRE1 acts as a putative tumor suppressor through selective regulation of gene expressionEfrat Shema
Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
Genes Dev 22:2664-76. 2008..Furthermore, frequent RNF20 promoter hypermethylation was observed in tumors. RNF20 may thus be a putative tumor suppressor, acting through selective regulation of a distinct subset of genes... - Histone sumoylation is a negative regulator in Saccharomyces cerevisiae and shows dynamic interplay with positive-acting histone modificationsDafna Nathan
Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
Genes Dev 20:966-76. 2006..These results indicate that sumoylation is the first negative histone modification to be identified in S. cerevisiae and further suggest that sumoylation may serve as a general dynamic mark to oppose transcription... - Trimethylation of histone H3 lysine 4 by Set1 in the lytic infection of human herpes simplex virus 1Jing Huang
The Wistar Institute, Philadelphia, PA 19104, USA
J Virol 80:5740-6. 2006.... - Phosphorylation of histone H4 Ser1 regulates sporulation in yeast and is conserved in fly and mouse spermatogenesisThanuja Krishnamoorthy
Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
Genes Dev 20:2580-92. 2006..Thus, H4 S1ph may be an evolutionarily ancient histone modification to mark the genome for gamete-associated packaging... - Repression of p53 activity by Smyd2-mediated methylationJing Huang
Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
Nature 444:629-32. 2006..Thus, similar to histones, p53 is subject to both activating and repressing lysine methylation. Our results also predict that Smyd2 may function as a putative oncogene by methylating p53 and repressing its tumour suppressive function... - Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction mapSean R Collins
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, USA
Nature 446:806-10. 2007..This modification, in turn, enables a ubiquitin ligase complex containing the cullin Rtt101 to ensure genomic integrity during DNA replication... - A feed-forward repression mechanism anchors the Sin3/histone deacetylase and N-CoR/SMRT corepressors on chromatinMichiel Vermeulen
NCMLS, Radboud University Nijmegen, Department of Molecular Biology, Geert Grooteplein Zuid 30, Nijmegen, The Netherlands
Mol Cell Biol 26:5226-36. 2006.... - Histone H3 K4 demethylation during activation and attenuation of GAL1 transcription in Saccharomyces cerevisiaeKristin Ingvarsdottir
Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
Mol Cell Biol 27:7856-64. 2007..Thus, analysis of lysine demethylation in yeast provides new insight into the physiological roles of jumonji demethylase enzymes... - 14-3-3 interaction with histone H3 involves a dual modification pattern of phosphoacetylationWendy Walter
Division of Molecular Genetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3 QU, United Kingdom
Mol Cell Biol 28:2840-9. 2008..The importance of acetylation in this interaction is also seen in vivo, where K14 acetylation is required for optimal Bmh1 recruitment to the GAL1 promoter during transcriptional activation... - New nomenclature for chromatin-modifying enzymesC David Allis
Cell 131:633-6. 2007 - Histone H3 phosphorylation can promote TBP recruitment through distinct promoter-specific mechanismsWan Sheng Lo
Division of Biological Sciences and UCSD Cancer Center, University of California, San Diego, CA, USA
EMBO J 24:997-1008. 2005..Our results emphasize that histone modifications share general functions between promoters, but also acquire distinct roles tailored for promoter-specific requirements... - Structural basis for histone and phosphohistone binding by the GCN5 histone acetyltransferaseAdrienne Clements
The Wistar Institute, Philadelphia, PA 19104, USA
Mol Cell 12:461-73. 2003..Together, these studies reveal how one histone modification can modulate another to affect distinct transcriptional signals... - Maintenance of low histone ubiquitylation by Ubp10 correlates with telomere-proximal Sir2 association and gene silencingN C Tolga Emre
Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19024, USA
Mol Cell 17:585-94. 2005..Our results suggest that these H2B-deubiquitylating enzymes have distinct genomic functions... - Activating signal cointegrator 2 belongs to a novel steady-state complex that contains a subset of trithorax group proteinsYoung Hwa Goo
Department of Life Science, Pohang University of Science and Technology, Korea
Mol Cell Biol 23:140-9. 2003..Further characterization of ASCOM will lead to a better understanding of how nuclear receptors and other transcription factors mediate transcriptional activation... - Histone modification patterns during gene activationWan-Sheng Lo
Wistar Institute, Philadelphia, Pennsylvania 19104, USA
Methods Enzymol 377:130-53. 2004 - Good fences make good neighbors: barrier elements and genomic regulationJumin Zhou
The Wistar Institute, Philadelphia, Pennsylvania 19014, USA
Mol Cell 16:500-2. 2004..In a recent issue of Molecular Cell, West et al. (2004) shed light on mechanisms underlying these molecular "fences.".. - Trans-tail histone modifications: wedge or bridge?Karl W Henry
Nat Struct Biol 9:565-6. 2002 - The SANT domain of Ada2 is required for normal acetylation of histones by the yeast SAGA complexDavid E Sterner
Wistar Institute, Philadelphia, Pennsylvania 19104, USA
J Biol Chem 277:8178-86. 2002..These results suggest that histone and nucleosomal substrate recognition by SAGA involves multiple conserved domains and proteins, beyond those that have been previously identified... - The putative cancer stem cell marker USP22 is a subunit of the human SAGA complex required for activated transcription and cell-cycle progressionXiao Yong Zhang
The Department of Cancer Biology, The Kimmel Cancer Center, Thomas Jefferson Medical College, Philadelphia, PA 19107, USA
Mol Cell 29:102-11. 2008..In support of a functional role within the Polycomb/cancer stem cell signature, USP22 is required for appropriate progression through the cell cycle... - SALSA, a variant of yeast SAGA, contains truncated Spt7, which correlates with activated transcriptionDavid E Sterner
The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
Proc Natl Acad Sci U S A 99:11622-7. 2002..These data clarify a mechanism by which a transcriptional regulatory complex can switch between positive and negative modulation... - The emerging field of dynamic lysine methylation of non-histone proteinsJing Huang
Gene Expression and Regulation Program, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19087, United States
Curr Opin Genet Dev 18:152-8. 2008..Taking into account combinatorial activity with numerous other PTMs, lysine methylation provides enormous functional diversity and regulatory complexity... - A novel human Ada2 homologue functions with Gcn5 or Brg1 to coactivate transcriptionNickolai A Barlev
Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania, USA
Mol Cell Biol 23:6944-57. 2003.... - Histone modifications: Now summoning sumoylationDafna Nathan
Gene Expression and Regulation Program, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
Proc Natl Acad Sci U S A 100:13118-20. 2003 - H2B ubiquitylation acts as a barrier to Ctk1 nucleosomal recruitment prior to removal by Ubp8 within a SAGA-related complexAnastasia Wyce
Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
Mol Cell 27:275-88. 2007..These findings reveal a mechanism by which H2B ubiquitylation acts as a barrier to Ctk1 association with active genes, while subsequent deubiquitylation by Ubp8 triggers Ctk1 recruitment at the appropriate point in activation... - Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8Karl W Henry
The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
Genes Dev 17:2648-63. 2003..These results suggest that the histone H2B ubiquitylation state is dynamic during transcription, and that the sequence of histone modifications helps to control transcription... - LKB1 is recruited to the p21/WAF1 promoter by p53 to mediate transcriptional activationPing Yao Zeng
Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania and Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, Hunan Province, P R China
Cancer Res 66:10701-8. 2006..Finally, a genetic fusion of LKB1 to defective p53, deleted for its activation domains, promotes activation of p21/WAF1. These results indicate that LKB1 has a direct role in activation of p21/WAF1 gene... - Temporal and spatial changes in transcription factor binding and histone modifications at the steroidogenic acute regulatory protein (stAR) locus associated with stAR transcriptionHisahiko Hiroi
Center for Research on Reproduction and Women s Health, University of Pennsylvania Medical Center, 1354 Biomedical Research Building, 421 Curie Boulevard, Philadelphia, PA 19104, USA
Mol Endocrinol 18:791-806. 2004..Our findings demonstrate that increased StAR transcription can occur in the context of different patterns of transcription factor binding and histone modification... - H2B ubiquitylation and de-ubiquitylation in gene activationAnastasia Wyce
The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
Novartis Found Symp 259:63-73; discussion 73-7, 163-9. 2004..These results suggest that ubiquitylation of histones has a unique role among histone modifications, possibly to orchestrate an ordered pathway of chromatin alterations... - Sumoylation of the yeast Gcn5 proteinDavid E Sterner
Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
Biochemistry 45:1035-42. 2006..Taken together with recent identification of multiple additional subunits of SAGA as sumoylated proteins in vivo, these data suggest that Gcn5 sumoylation may have an inhibitory role in transcriptional regulation... - H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complexKristin Ingvarsdottir
The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
Mol Cell Biol 25:1162-72. 2005..These data indicate that Ubp8 and Sgf11 likely represent a new functional module within SAGA that is involved in gene regulation through H2B deubiquitylation... - Phosphorylation of histone H4 serine 1 during DNA damage requires casein kinase II in S. cerevisiaeWang L Cheung
Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland 21210, USA
Curr Biol 15:656-60. 2005..CK2 has been implicated in regulating a DNA-damage response; our data suggest that histone H4 S1 is one of its physiological substrates. These data suggest that this modification is a part of the DNA-repair histone code... - p53 is regulated by the lysine demethylase LSD1Jing Huang
The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania 19104, USA
Nature 449:105-8. 2007..Lysine methylation therefore provides similar regulatory complexity for non-histone proteins and for histones...