chapter 7: Transcription and RNA processing Flashcards
What kind of viruses require transcription? What are the factors for transcription?
All DNA viruses:
- dsDNA : adenovirus, HSV, papillo
- ssDNA : parvovirus
- gapped DNA : hep B virus
- (+)ssRNA w/ ssDNA : retrovirus
Why?
- In cells infected with DNA virus, one protein must be made before transcription
- Not all DNA viruses are ready for transcription (ssDNA or gapped DNA)
- most viruses use DdRp (nucleus)
- some viruses don’t have access to DdRp (cytoplasm)
Overview of Transcription
- DNA is transcribed into RNA that is co-transcriptionally 5’ capped to form pre-mRNA
- polyadenylation and alternative splicing is needed to transport mRNA into cytoplasm
- Cellular and viral preMRNAs are synthesized by RNA pol II
- host mRNA and most viral RNA are spliced before leaving nucleus but some viral mRNA can override this and just be polyadenylated- (unspliced RNA have proteins that don’t allow it)
- (spliced RNA have nuclear export protein)
How is transcription highly regulated?
- Transcriptional control region
(promotor region + distant regulatory seq.)
transcription factors bind DNA seq. - Promotor (core promotor + local regulatory seq)
- Core Promotor: accurate initiation of transcription
( TATA sequence - binding site for TF11D) :modulated by local regulatory sequences
:distant regulatory sequences - stimulate enhancers
What is an enhancer in transcription?
Proteins bound to distance enhancers interact with the transcription initiation complex and stabilize it which initiates transcription
What are promoter regions between IE, E and L infection phase?
(Immediate early) : cell components activate transcription of viral genes (make mRNA)
(Early) : viral DNA synthesis
(Late) : structural proteins, require capsid formation
What proteins regulate transcription? How is it done?
- Host/Viral sequence-specific DNA binding proteins
- Viral co-activating molecules (don’t bind)
- Co-activators (regulate nucleosome)
- Viruses can completely/partially on host transcriptional machinery
- Cytoplasm depend completely on viral transcription machinery
Cellular transcriptional components interact with viral gene encoding protein X to transcribe
Human Adenovirus Type 2 Transcription Program
How does E1A activate Early Transcription?
- Particle enters via receptor mediated endocytosis, enters nucleus
The host cell RNA pol 2 transcribes
IE: E1A protein
E: TF- E2 protein: viral DNA synthesis
L: 1Va and L4 proteins expression of structural capsid proteins
E2 is needed for transcription of viral DNA: 1. RB binds to E2F complex
2. Hdacs tightly wraps removes the acetyl group inactivates transcription.
3.Then E1A binds to RB activates E2 protein
Simian Virus (SV40) Transcription Program (circular dsDNA with ORI)
Early transcription is by host cell RNA pol 2. Alternative splicing exports mRNA to cytoplasm
(E) : LT protein made by transcription of viral DNA
(L): transcriptions of genes codes for structural proteins
How does viral DNA replication activate the late phase in SV40?
IBP repressor binds the late promotor -> more viral DNA and empty sites (cellular TF)
What are post-transcriptional modification? SPLICING
- Capping: added co-transcriptionally 5’ region of pre-mRNA
- Polyadenylation: adding poly-A tail to the 3’ end of pre-mRNA after cleavage
- Splicing:
* multiple proteins
*cellular/viral pre-mRNAs
Alternative Splicing: exon skipping, alternative parts of introns 3’ or 5’ can be joined
Constitutive: all joined sequentially
Hydroxyl group attacks phosphodiester bond nucleotide to produce lariat, then another nucleophilic releases the lariat and joins 5’ and 3’ exons.
What are non-coding RNAs
microRNA (miRNA)
small nuclear RNA (snRNA)
long non-coding RNA (lncRNA)
Viral genome codes for non-coding RNAS
