Chromatin Control of Viral Infection Edited by Thomas M. Kristie Printed Edition of the Special Issue Published in Viruses www.mdpi.com/journal/viruses Thomas M. Kristie (Ed.) Chromatin Control of Viral Infection This book is a reprint of the special issue that appeared in the online open access journal Viruses (ISSN 1999-4915) in 2013 (available at: http://www.mdpi.com/journal/viruses/special_issues/chromatin). Guest Editor Thomas M. Kristie National Institute of Allergy and Infectious Diseases (NIAID) Bethesda, MD, USA Editorial Office MDPI AG Klybeckstrasse 64 Basel, Switzerland Publisher Shu-Kun Lin Production Editor Matthias Burkhalter 1. Edition 2013 MDPI • Basel • Beijing ISBN 978-3-906980-73-7 © 2013 by the authors; licensee MDPI, Basel, Switzerland. All articles in this volume are Open Access distributed under the Creative Commons Attribution 3.0 license (http://creativecommons.org/licenses/by/3.0/), which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. However, the dissemination and distribution of copies of this book as a whole is restricted to MDPI, Basel, Switzerland. Table of Contents Preface ....................................................................................................................................................vii Jodi L. Vogel and Thomas M. Kristie The Dynamics of HCF-1 Modulation of Herpes Simplex Virus Chromatin during Initiation of Infection.................................................................................................................................................... 1 Reprinted from Viruses 2013, 5(5), 1272-1291; doi:10.3390/v5051272 http://www.mdpi.com/1999-4915/5/5/1272 Guoying Zhou, Te Du and Bernard Roizman The Role of the CoREST/REST Repressor Complex in Herpes Simplex Virus 1 Productive Infection and in Latency......................................................................................................................... 22 Reprinted from Viruses 2013, 5(5), 1208-1218; doi:10.3390/v5051208 http://www.mdpi.com/1999-4915/5/5/1208 Kristen L. Conn and Luis M. Schang Chromatin Dynamics during Lytic Infection with Herpes Simplex Virus 1.......................................... 34 Reprinted from Viruses 2013, 5(7), 1758-1786; doi:10.3390/v5071758 http://www.mdpi.com/1999-4915/5/7/1758 Zachary Watson, Adit Dhummakupt, Harald Messer, Dane Phelan and David Bloom Role of Polycomb Proteins in Regulating HSV-1 Latency.................................................................... 65 Reprinted from Viruses 2013, 5(7), 1740-1757; doi:10.3390/v5071740 http://www.mdpi.com/1999-4915/5/7/1740 Alison A. McBride and Moon Kyoo Jang Current Understanding of the Role of the Brd4 Protein in the Papillomavirus Lifecycle...................... 84 Reprinted from Viruses 2013, 5(6), 1374-1394; doi:10.3390/v5061374 http://www.mdpi.com/1999-4915/5/6/1374 Margaret E. McLaughlin-Drubin and Karl Munger Biochemical and Functional Interactions of Human Papillomavirus Proteins with Polycomb Group Proteins...................................................................................................................................... 107 Reprinted from Viruses 2013, 5(5), 1231-1249; doi:10.3390/v5051231 http://www.mdpi.com/1999-4915/5/5/1231 iv Matthew Reeves and John Sinclair Regulation of Human Cytomegalovirus Transcription in Latency: Beyond the Major Immediate-Early Promoter ................................................................................................................... 127 Reprinted from Viruses 2013, 5(6), 1395-1413; doi:10.3390/v5061395 http://www.mdpi.com/1999-4915/5/6/1395 Amanda J. Guise, Hanna G. Budayeva, Benjamin A. Diner and Ileana M. Cristea Histone Deacetylases in Herpesvirus Replication and Virus-Stimulated Host Defense..................... 148 Reprinted from Viruses 2013, 5(7), 1607-1632; doi:10.3390/v5071607 http://www.mdpi.com/1999-4915/5/7/1607 Xue-feng Liu, Xueqiong Wang, Shixian Yan, Zheng Zhang, Michael Abecassis and Mary Hummel Epigenetic Control of Cytomegalovirus Latency and Reactivation ......................................................... 176 Reprinted from Viruses 2013, 5(5), 1325-1345; doi:10.3390/v5051325 http://www.mdpi.com/1999-4915/5/5/1325 Carmen M. Wong, Emily R. McFall, Joseph K. Burns and Robin J. Parks The Role of Chromatin in Adenoviral Vector Function....................................................................... 198 Reprinted from Viruses 2013, 5(6), 1500-1515; doi:10.3390/v5061500 http://www.mdpi.com/1999-4915/5/6/1500 Zsolt Toth, Kevin Brulois and Jae U. Jung The Chromatin Landscape of Kaposi’s Sarcoma-Associated Herpesvirus.......................................... 215 Reprinted from Viruses 2013, 5(5), 1346-1373; doi:10.3390/v5051346 http://www.mdpi.com/1999-4915/5/5/1346 Aaron Arvey, Italo Tempera and Paul M. Lieberman Interpreting the Epstein-Barr Virus (EBV) Epigenome Using High-Throughput Data....................... 244 Reprinted from Viruses 2013, 5(4), 1042-1054; doi:10.3390/v5041042 http://www.mdpi.com/1999-4915/5/4/1042 Daniela Boehm, Ryan J. Conrad and Melanie Ott Bromodomain Proteins in HIV Infection ............................................................................................. 258 Reprinted from Viruses 2013, 5(6), 1571-1586; doi:10.3390/v5061571 http://www.mdpi.com/1999-4915/5/6/1571 v Jessica N. Groen and Kevin V. Morris Chromatin, Non-Coding RNAs, and the Expression of HIV ............................................................... 275 Reprinted from Viruses 2013, 5(7), 1633-1645; doi:10.3390/v5071633 http://www.mdpi.com/1999-4915/5/7/1633 Ourania M. Andrisani Deregulation of Epigenetic Mechanisms by the Hepatitis B Virus X Protein in Hepatocarcinogenesis ........................................................................................................................... 289 Reprinted from Viruses 2013, 5(3), 858-872; doi:10.3390/v5030858 http://www.mdpi.com/1999-4915/5/3/858 Preface It is simplistic to state that the chromatin structure regulates accessibility to the genome. Ultimately that is the case. However, the complexity of the chromatin structure and its regulation by a plethora of protein and RNA complexes maintains the stability of the genome, controls the transcriptional program, modulates DNA replication throughout the cell cycle, and determines the identity or differentiation state of the cell. In addition to the linear organization of the genome into nucleosome arrays, multi-layered chromatin interactions define domains and enhance or suppress long-range coordinate regulatory foci. The control of cellular processes by chromatin-mediated regulatory paradigms has been intensely studied in recent years. This body of work has served to enhance recognition of the significance of the—chromatin structure and chromatin modulation machinery. It has also served to promote an appreciation for the immense complexity of chromatin regulation, a process which includes numerous families of proteins cooperating as regulatory complexes to direct nucleosome assembly/disassembly, post-transcriptional histone modification, and nucleosome recognition and positioning that ultimately controls functional access to the genome. Added to this complexity is the epigenetics of DNA modification that is often intertwined with nucleosome modulation. The field is rich with new insights into control of cellular processes from basic replication to differentiation and development. Arising from the discoveries of the enzymology of chromatin modulation, are novel translational-therapeutic approaches based on inhibition of histone and DNA modification and/or recognition proteins. This promising new field, while most evident in the oncology arena, has the potential to be applied to a wide range of diseases. In contrast to the investigation of chromatin regulation in cellular processes, the impacts of chromatin and/or chromatin modulation machinery on viral infection has been less well defined. Early studies focused on small DNA viruses that are packaged as nucleosomal genomes, or those that integrate into host cell chromatin, have recognized the importance of chromatin-based regulation as a determinant of infection. More recently, there has been a breadth of studies on chromatin-mediated control of viral infection, latency, and persistence in many systems. In addition, viruses represent unique models as many encode factors with functions that impact host cell epigenetics. The emerging picture is one of complex dynamics of pathogen and host cell mediated chromatin impacts that can ultimately determine the course of viral infection and/or the modulation of the cell state. The rapid development and use of pharmaceuticals targeting chromatin modulation machinery in oncology strongly suggests that understanding the components and the dynamic interplay of virus and host cell chromatin could also point to new directions in antiviral therapies. The collection of reviews included here, represents a selection of research at the forefront of chromatin regulation during viral infection. The papers cover a number of viral families and illustrate concepts including: (i) the initial dynamics of virus–host cell chromatin interactions; (ii) host cell viii chromatin machinery that serves to enhance or repress viral infection; (iii) viral factors that utilize or circumvent this machinery; and (iv) the significance of