7 Chapter 7Figure 7.1 Conversion of viral genomes to templates for transcription by cellula...Figure 7.2 RNA polymerase II transcriptional control elements. The site of ini...Figure 7.3 Initiation of transcription by RNA polymerase II. Assembly of the c...Figure 7.4 Variations in core RNA polymerase II promoter architecture. Variati...Figure 7.5 Local regulatory sequences of three viral transcriptional control reg...Figure 7.6 Organization of the archetypal simian virus 40 enhancer. The positi...Figure 7.7 Modular organization of sequence-specific transcriptional activators....Figure 7.8 Widespread cellular transcriptional activators of an avian retrovirus...Figure 7.9 Mechanisms of stimulation of transcription by viral proteins. Cellu...Figure 7.10 Cell-type-specific regulators bind to the transcriptional control re...Figure 7.11 The cellular regulator NF-κB and its participation in viral transcri...Figure 7.12 Human immunodeficiency type-1 TAR and the Tat protein. (A) The reg...Figure 7.13 Stimulation of transcription elongation by the human immunodeficienc...Figure 7.14 Molecular mechanisms of stimulation of human immunodeficiency virus ...Figure 7.15 Common features of the simian virus 40 (SV40), human adenovirus type...Figure 7.16 Organization and regulation of the Epstein-Barr virus Zta gene promo...Figure 7.17 Models for transcriptional activation by the herpes simplex virus ty...Figure 7.18 Conformational changes and recruitment of VP16 to herpes simplex vir...Figure 7.19 The adenoviral E1A proteins bind to multiple transcriptional regulat...Figure 7.20 Indirect stimulation of transcription by adenoviral E1A proteins. Figure 7.21 Cellular repressors regulate the activity of the simian virus 40 lat...Figure 7.22 The latency-associated transcripts of herpes simplex virus type 1. ...Figure 7.23 Organization of viral RNA polymerase III promoters. (A) The human ...Figure 7.24 Assembly of an initiation complex on a vaccinia virus early promoter...
8 Chapter 8Figure 8.1 Processing of a viral or cellular pre-mRNA synthesized by RNA polymer...Figure 8.2 The 5′ cap structure and its synthesis by cellular or viral enzymes. ...Figure 8.3 A viral unimolecular assembly line for capping. The structure of th...Figure 8.4 Cleavage and polyadenylation of vertebrate pre-mRNAs. The 3′ end of...Figure 8.5 The vaccinia virus capping enzyme and 2′-O-methyltransferase process ...Figure 8.6 Reversible N6 methylation of internal adenosine nucleosides. Intern...Figure 8.7 Inhibition of assembly and release of virus particles by N6 A methyla...Figure 8.8 Splicing of pre-mRNA. (A) Consensus splicing signals in cellular an...Figure 8.9 The conserved mechanism of eukaryotic pre-mRNA splicing. (A) Pathwa...Figure 8.10 Constitutive and alternative splicing. (A) In constitutive splicin...Figure 8.11 Alternative polyadenylation and splicing control the production of b...Figure 8.12 Control of RNA-processing reactions during retroviral gene expressio...Figure 8.13 Alternative polyadenylation and splicing of adenoviral major late tr...Figure 8.14 Cotranscriptional editing of measles virus mRNAs. (A) Proposed mec...Figure 8.15 Editing of hepatitis delta virus RNA by double-stranded RNA adenosin...Figure 8.16 Regulation of export of human immunodeficiency virus type 1 mRNAs by...Figure 8.17 Features and mechanism of Rev protein-dependent export. (A) The fu...Figure 8.18 Export of unspliced RNA of retroviruses with simple genomes and cell...Figure 8.19 Regulation of alternative splicing of viral pre-mRNA. (A) The poly...Figure 8.20 Inhibition of cellular pre-mRNA processing by viral proteins. The ...Figure 8.21 Mechanisms of intrinsic cellular and viral mRNA decay. A major pat...Figure 8.22 Viral proteins initiate mRNA degradation by different mechanisms. ...Figure 8.23 Major pathways of nonsense-mediated mRNA degradation. Nonsense-med...Figure 8.24 Synthesis and function of miRNAs. The precursors of miRNAs (pri-mi...Figure 8.25 The miRNAs of simian virus 40. The circular simian virus 40 genome...Figure 8.26 Cellular lncRNAs that facilitate or impair virus reproduction. Cel...
9 Chapter 9Figure 9.1 Viral and cellular proteins that synthesize viral DNA genomes. The ...Figure 9.2 Properties of replicons. (A) Electron micrographs of replicating si...Figure 9.3 Semidiscontinuous DNA synthesis from a bidirectional origin. Synthe...Figure 9.4 The 5′-end problem in replication of linear DNAs. (A) Incomplete sy...Figure 9.5 The origin of simian virus 40 DNA replication. The positions in the...Figure 9.6 Model of the recognition and unwinding of the simian virus 40 origin....Figure 9.7 Synthesis of leading and lagging strands. The DNA polymerase (POL) ...Figure 9.8 A model of the simian virus 40 replication machine. A replication m...Figure 9.9 Function of topoisomerases during simian virus 40 DNA replication. ...Figure 9.10 Replication of parvoviral DNA. (A) Sequence and secondary structur...Figure 9.11 Replication of adenoviral DNA. Assembly of the viral preterminal p...Figure 9.12 Features of the herpes simplex virus type 1 genome. The long (L) a...Figure 9.13 Common features of viral origins of DNA replication. The simian vi...Figure 9.14 Functional organization of simian virus 40 LT. The domains of LT a...Figure 9.15 Structural homology among DNA-binding domains of viral origin recogn...Figure 9.16 Model of origin loading of the papillomaviral E1 initiation protein ...Figure 9.17 Crystal structure of the adenoviral single-stranded-DNA-binding prot...Figure 9.18 Regulation of production of cellular and viral replication proteins....Figure 9.19 Discrete sites of viral replication. (A) Cytoplasmic vaccinia viru...Figure 9.20 Reorganization of PML bodies by the adenoviral E4 Orf3 protein. Mo...Figure 9.21 Common features of the adenovirus-associated virus type 2 lTR and th...Figure 9.22 Licensing of replication from Epstein-Barr virus OriP. (A) Organiz...Figure 9.23 Regulation of papillomaviral DNA replication in epithelial cells. ...Figure 9.24 Proofreading during synthesis. If permanently fixed into the genom...Figure 9.25 The DNA damage response. Damage to the DNA genome, such as a doubl...Figure 9.26 Association of cellular DNA damage response proteins with herpesvira...Figure 9.27 General model for initiation of recombination-dependent replication....Figure 9.28 Isomers of the herpes simplex virus type 1 genome. The organizatio...
10 Chapter 10Figure 10.1 Human immunodeficiency type 1 capsid hexamers showing open and close...Figure 10.2 The diploid retroviral genome and a dimerization domain. (A) The d...Figure 10.3 Primer tRNA binding to a retroviral RNA genome. (Top) Linear repre...Figure 10.4 Retroviral reverse transcription: initiation of (–) strand DNA synth...Figure 10.5 Retroviral reverse transcription: first template exchange, mediated ...Figure 10.6 Retroviral reverse transcription: (+) strand DNA synthesis primed fr...Figure 10.7 Retroviral reverse transcription: the second template exchange and f...Figure 10.8 Two models for recombination during reverse transcription. Virtual...Figure 10.9 Domain and subunit relationships of the RTs of different retroviruse...Figure 10.10 Ribbon representation of HIV-1 RT bound to a model RNA template-DNA...Figure 10.11 Model for a DNA-RNA hybrid bound to HIV-1 RT. The RNA template-DN...Figure 10.12 Evolutionary relatedness of RT-like enzymes in bacteria, archaea, e...Figure 10.13 Retroelements resident in eukaryotic genomes and their representati...Figure 10.14 Comparison of the structures of two RTs. (A) The DNA polymerase d...Figure 10.15 Characteristic features of retroviral integration. Unintegrated l...Figure 10.16 Three steps in the retroviral DNA integration process. Endonucleo...Figure 10.17 Sequence preferences of integration sites. The figure shows the 5...Figure 10.18 Models for chromatin tethering of retroviral preintegration complex...Figure 10.19 Host proteins affect the integration process. The abundant host b...Figure 10.20 Domain maps of integrase proteins from different retroviral genera,...Figure 10.21 Crystal structure of the prototype foamy virus integrase tetramer b...Figure 10.22 Arrangement