Eukaryotic Gene Regulation Flashcards
what is the 5’ flank of gene
5’ (upstream) to transcription start site, contains important regulatory elements
true/false: Eukaryotic genomes are larger than prokaryotic genomes
true
cis-acting elements
name them + brief desc + level of transcription
- promoters → adjacent to gene, include transcription initiation, TATA box, basal level of transcription
- enhancers → can be far from gene, amplify or repress basal level transcription
difference between proximal promoter and enhancer
their position in genome
* promoter = -1000 to -100 bp upstream of TSS
* enhancer = can be kilobases up/downstream of TSS, or within gene itself
TSS = transcription start site
exons
segments of gene that end up in mature transcript that reaches cytoplasm, include UTRs
introns
segments of gene in primary transcript but not in mRNA
5’ capping function
to protect against nucleases
why do eukaryotes have more levels of regulation? (3)
they have chromatin & transcripts require more processing & transcripts are exported from nucleus to cytoplasm
function of each type of RNA polymerase in eukaryotes
- RNA pol I → transcribes rRNA genes
- RNA pol II → transcribes all protein-coding genes (mRNAs) & microRNAs
- RNA pol III → transcribes tRNA genes & some small regulatory RNAs
processing that RNA pol II transcripts undergo to generate mature mRNA (4)
- RNA splicing (removes introns)
- add 5’ GTP cap (prevent RNA degradation)
- cleave 3’ end
- add 3’ polyA tail
basal transcription factors
definition
assist binding of RNA poll II to promoters
key components of basal factor complex (2)
- TBP (tata box binding protein)
- TAFs (tbp-associated factors)
components of TIC (transcription initiation complex) (2)
RNA pol II + basal complex
TFs (regulatory transcription factors)
definition
proteins that bind to DNA seqs within proximal promoter or enhancer to control rate of transcripition of a gene (activate/inhibit transcription)
how do TFs regulate? (3)
- interact w TIC components
- modify chromatin struc to make TSS more/less accessible
- can be activators/respressors (sometimes both)
two ways activators can increase transcription
- promote binding of TIC components or stabilising TIC complex
- recruit co-activators
co-activators → proteins that open chromatin & allow transcription
two ways repressors can decrease transcription
- recruit corepressors that directly prevent RNA pol II complex from binding
- recruit corepressors that close chromatin
what type of proteins are TFs
modular proteins
what does a typical TF consist of?
name them + brief definition
- DNA binding domain → facilitates binding to specific DNA seq
- Activation/Repression domain → interacts w TIC components or co-activators/repressors
- Ligand-binding domain → some have (e.g. steroid receptors)
DNA-binding domains of activator proteins (2)
- have α helices to interact w major groove of DNA
- 3 motifs: HLH, HTH, Zinc finger
HLH = helix-loop-helix, HTH = helix-turn-helix
dimerisation domains
+ common dimerisation motif in euks
specialized for polypeptide-polypeptide interactions
leucine zippers
the 3 levels TF activity can be controlled at
- allosteric interaction w small molecules
- post-translational modifications to TFs
- transcription factor cascades
combinatorial regulation (3)
how its made possible
made possible by:
* 1 gene regulated by many TFs
* 1 TF regulate many genes
* many co activators/repressors
2 examples of reporter genes used in eukaryotes
- lacZ gene, blue colour when X-gal is used
- gene for GFP (green fluorescent protein)
in vivo vs in vitro
vivo: whole orgs → stably integrate reporter gene in transgenic orgs (seeds, eggs)
vitro: cells in culture → transfect reporter gene into cells in culture (stable/transient)
