Molecular Virology

1. RNApol I- cellular pre-mRNA2. RNApol II- transcript proteins coding gene and mRNA3. RNApolIII- transcribe tRNA

1. PolII binds to promoter and begins initiation2. Elongates by adding NTP and creating a 5' nascent RNA3. Once processivity is initiated, full transcription gene occurs4. Termination occurs by RNApol falling off

1. viral and cellular factors2. Core promoter (TATA and +1)3. Initiation complex4. RNApol I

1

1. use specific cellular proteins that bind to help with transcription2. use cellular proteins that recognize this region and their availability in cells determine permissively3. enhance transcription of very fist genes transcribed i.e enhancer-binding proteins bridge DNA to initiate transcription

1. contain regions that specify binding to each other, DNA sites and cellular transcription2. Viral transcription factors are configured the same ways as cellular transcription factors3. DNA binding is specific protein-protein interaction4. cellular transcription factors is often not sufficient, need viral transcription factors

A. a plasmid encoding a promoter linked to a reporter gene are transfected along with plasmid expressing regulatory proteinsb. the reported gene expresses on easily assayed for in-vitroc. allow for the examination of mutated promoter or regulatory protein in a controlled way

A. reconstituted cellular transcription with purified transcription factors in a tube (with or without viral regulatory proteins present or with altered promoter/templates

A. northern blotb. RT-pcrc. primer extensiond. nuclear run-one. microarray analysis

1. gel shift and DNAse footprinting2. ChiP (chromatin Immunoprecipitation

1. Pox virus: very large and replicates in cytoplasm; contains own unique regulatory signals in promoter;transcription is initiated on the virion structure before complete uncoating and mediated by vRNApol

Retroviruses: integrates into cellular genome and do not express viral regulatory proteins.
Lentiviruses: "DO" express regulatory proteins because it is treated like any cellular gene when transcribed.
A. 1. complicated promoter/enhancer region (contains many binding sites for cellular factors)2. availability of factors in cell3. physical state of chromatin in the integration region

Most viruses are expressed in a cascade effect. First genes expressed are cellular promoters that have complicated promoter enhancer regions. Proteins products of these genes are regulatory proteins that activates transcription of alter genes. DNA replication to increase number of templates or change physical state of template to activate late viral genes.

Some viruses induce cellular pathways by specific interaction with viral surface proteins with receptors on cell surface. This activates kinase cascade inside cell resulting in altered activity or abundance of cellular transcription factors. Then activates vgene transcription.

1. activity is dependent on availability of cellular proteins. Reason why HIV grows in activated T cells and monocytes lineage cells. (NF-kb)
2. increase transcription from LTR creating positive regulatory loop. a. binds to structure at 5'end of nascent RNA called TAR b. has modular structure like many transcription factors.