Eukaryotic Gene Regulation Flashcards
(82 cards)
Eukaryotic vs Prokaryotic Gene Regulation
Eukaryotes have much greater levels of complexity for controlling of gene expression:
o Eukaryotic genomes are larger than prokaryotic genomes
o Chromatin structure in eukaryotes makes DNA unavailable to transcription machinery
o Additional RNA processing events occur in eukaryotes (Differential splicing)
o In eukaryotes, transcription takes place in the nucleus and translation takes place in the cytoplasm
What are Exons?
Sequences that end up in mature mRNA and reach the cytoplasm. However not all of them are translated.
Can be coding or non-coding.
What are Introns?
Segments of the gene that are in the primary transcript but are not included in the mRNA, they are removed during splicing
What is the cap site?
The beginning of the first exon
What is the Poly A site?
The end of the last exon (a sequence that causes synthesis of multiple Poly A sequences at the end of mRNA
Downstream Definition
3’-direction
upstream Definition
5’-Direction
TATA Box
- ±30bp (in mammals) in the 5’ direction.
- It directs where RNA polymerase will assemble
Cis-acting elements
Promoters & Enhancers
Promoters
- Usually directly adjacent to the gene (Usually on the 5’ flank)
- Include transcription initiation site
- Often have a TATA box
- Allows basal level of transcription
Enhancers
- Can be far away from the gene
- Augment or repress the basal level of transcription
Differences Promoters vs Enhancers
- Both contain binding sites for regulatory transcription factors
- Difference is their position in the genome
- Proximal-Promoter is found from -1000 to -100bp upstream of TSS
- Enhancers can be kilo bases up or downstream of TSS, or even within the gene itself
Levels of regulation in Eukaryotes
- Initiation of transcription
- Transcript processing (splicing, polyadenylation, stability)
- Export from nucleus
- Translation
- Modification/localisation of protein products.
Type of RNA Polymerases in Eukaryotes
- RNA Pol 1 - transcribes rRNA genes
- RNA Pol II - transcribes all protein-coding genes (mRNAs) and micro-RNAs
- RNA Pol III - transcribes tRNA genes and some small regulatory RNAs
Processing of RNA Pol II transcripts
- Most RNA Pol II transcripts undergo further processing to generate mature mRNA
- RNA splicing - removes introns
- Addition of 5’ GTP cap - protects RNA from degradation
- Cleavage of 3’ end and addition of 3’ PolyA tail
Basal Factors Definition
Basal transcription factors assist the binding of RNA pol II to promoters
Key components of Basal Factor Complex
- TATA-Box binding protein (TBP): Is the first of several proteins to assemble at promoter and it binds to TATA box
- TBP-associated factors (Transcription Ancillary Factors or ‘TAFs’): Binds to TBP assembled at TATA box
- RNA Pol II associates with basal complex to form the Transcription Initiation Complex (TIC) and initiates basal level of transcription
Steps in Basal factor binding to core promoters
(Happens in all protein encoding genes)
- TBP binds to TATA box
- TAFs (transcription ancillary factors) bind to TBP
- RNA Pol II binds to TAFs
- Together the complex is referred to as the transcription initiation complex (TIC)
Transcription Factors Definition
Proteins that bind to DNA sequences within the proximal promoter or an enhancer to control the rate of transcription of a gene
Transcription Factors Function
Facilitate expression of genes in specific tissues at certain times or in response to specific condition
- Can be tissue specific
- complement can vary over time and space
General Method of transcription regulation by Transcription Factors
- Interactions with components of the TIC
- Modifying chromatin structure to make the transcription start site (TSS) more or less accessible
- Regulatory TFs can be activators or repressors of transcription depending on the cell they are in (some are both).
Activators
- TFs that increase rate of transcription
- Either promote binding of TIC components/stabilising the TIC complex
- OR recruiting co-activators (proteins that open chromatin and allow transcription)
Repressors
- TFs that decrease rate of transcription
- They can recruit co-repressors that directly prevent RNA Pol II from binding to the promoter
- Can also recruit co-repressors that close chromatin structure
How do Transcription Factors bound to enhancers kb away from TSS interact with the TIC?
DNA is looped to a mediator complex