Transcription from DNA Templates
📌 Transcription, the production of mRNA from double-stranded DNA (dsDNA), is the required first biosynthetic event for DNA viruses to create proteins necessary for DNA replication.
📌 Viruses with single-stranded DNA (ssDNA) or gapped dsDNA genomes (like Parvoviruses or Hepadnaviruses) must first have their genomes converted into fully double-stranded DNA by the host cell's DNA repair response before transcription can occur.
📌 Most DNA viruses utilize the host cell's DNA-dependent RNA polymerases (Pol I, Pol II, or Pol III), with Pol II being the enzyme responsible for making messenger RNA precursors.
📌 Viruses replicating in the cytoplasm (e.g., Poxviruses) must encode their own RNA polymerase as the host enzymes reside in the nucleus.

Transcriptional Control and Regulation
📌 Transcription initiation is the most regulated step, controlled by sequences within the transcriptional control region, including the core promoter (initiator sequence and TATA-like sequences) and upstream regulatory sequences.
📌 Enhancers, distal sequences up to 10,000 base pairs away, stabilize the initiation complex (RNA Polymerase II and associated proteins) to enhance transcription rate.
📌 Regulatory proteins often possess a modular structure: a Nuclear Localization Signal, a domain for dimerization (like a Leucine Zipper), a sequence-specific DNA binding domain (e.g., zinc fingers), and an activation domain.
📌 Transcription can be regulated by proteins that modulate nucleosome structure through histone methylation or acetylation, affecting how tightly DNA is wrapped around histones.

Viral Gene Expression Strategies (Temporal Regulation)
📌 Many DNA viruses employ a cascade regulation system involving sequential gene expression (Immediate Early $\rightarrow$ Early $\rightarrow$ Late) to coordinate DNA replication and structural protein synthesis.
📌 SV40 uses an early promoter to express T antigen, which then triggers DNA replication, subsequently activating the late promoter for structural protein synthesis; the late promoter is initially repressed by the cellular protein IBP until genome replication increases the target number, titrating out the IBP.
📌 Adenovirus relies on the E1A protein (an immediate early product) to bind the Retinoblastoma protein (RB), freeing up E2F transcription factors needed to activate the early gene expression, which includes DNA replication machinery.
📌 Herpesviruses require the virion-carried protein VP16 to activate their immediate early promoter because the host cell machinery cannot recognize it directly.

mRNA Processing and Export
📌 mRNA transcripts are matured in the nucleus via co-transcriptional capping at the 5' end (a 5' to 5' triphosphate linkage with GTP) and polyadenylation at the 3' end following cleavage of the pre-mRNA.
📌 Splicing, the removal of introns (intervening sequences) between exons, was discovered in Adenovirus studies and is largely carried out by the spliceosome, which is an RNA-driven ribozyme.
📌 Alternative splicing allows viruses like Adenovirus to produce a larger variety of proteins (e.g., structural proteins) from a limited genome size by including or excluding specific exons.
📌 Splicing often marks mRNA for nuclear export; however, some viral RNAs (like unspliced retroviral RNAs) bypass this requirement using specific RNA elements recognized by export machinery, such as the Constitutive Transport Element (CTE) or the Rev Responsive Element (RRE) bound by the Rev protein in HIV.

Other RNA Biology Aspects
📌 RNA editing, exemplified by Hepatitis Delta Virus, involves non-templated changes (like $\text{A} \rightarrow \text{I}$ by deaminase), altering codons and producing different proteins (Small vs. Large Delta Antigens).
📌 MicroRNAs ($\text{miRNAs}$) are short regulatory RNAs that target complementary mRNA sequences, leading to translational suppression or degradation; $\text{Hep C}$ virus replication is liver-specific because it absolutely requires the host liver-specific $\text{miRNA-122}$ for genome stabilization.
📌 RNA methylation, specifically $n^6$ methylation of adenosines, is used by host cells (e.g., against Hep C) as an antiviral mechanism, where methylation tags on the viral RNA inhibit its incorporation into new virions.

Key Points & Insights
➡️ For dsDNA viruses, the initial requirement before replication is transcription to produce necessary proteins, necessitating a double-stranded DNA template.
➡️ Viral temporal gene expression is regulated in phases (e.g., Early/Late) to ensure structural proteins are only synthesized after DNA replication has begun.
➡️ E1A protein from Adenovirus manipulates the host cell cycle by binding $\text{RB}$ to release $\text{E2F}$ transcription factors, demonstrating a crucial link between viral transcription and host cell regulation that facilitates oncogenesis.
➡️ Splicing evolved to expand the coding capacity of genomes through alternative splicing, yielding multiple proteins from a single precursor RNA.

📸 Video summarized with SummaryTube.com on Nov 27, 2025, 04:48 UTC