gene Control And Cellular Signalling Flashcards
Two different methods of regulating transcription factors
- Method 1: slower ( regulation of transcription factor)
2. Method 2: faster ( regulation of TF activity)
Explain method 1 regulation of transcription factors
- Regulation of TF synthesis
- Frequently used for expression over a one time.
- Second TF required to regulate transcription of 1st TF
Explain method 2 of Regulation of transcription factors.
- Regulation of TF activity
- Alteration of re-existing protein
- More rapid response.
Multiple mechanism that regulate TF activity.
- Direct binding of ligand to TF
- Phosphorylation of TF
- Proteolytic cleavage
- Regulation of protein-protein interaction
What happens to steroid receptors when a ligand binds.
The steroid receptors often from dimers.
Binding of a hormone to HSP90 results in ?
- HSP90 dissociation
- Exposure of nuclear localisation signal of receptor and interaction with nuclear-import proteins
- Exposes domains essential for binding to DNA and transcription.
What happens to the conformation of a TF when a ligand binds.
Binding of ligand produces a conformational change so that the C-terminal domain can form a lid over the ligand and the activation domain can interact with co-activator molecules.
How glucocorticoid receptor can activate gene transcription.
- Glucocorticoid-hormone receptor complex binds to GRE( glucocorticoid response element) DNA sequence as a dimer.
- The dimer recruits correct factors to activate transcription.
How glucocorticoid receptor can repress gene transcription.
- Trimers bind to nGRE (naive glucocorticoid response element) sequence.
- NGRE sequences resemble naive GRE sequences, but are not identical.
- Blocks binding of other activating factors and thus represses transcription .
How glucocorticoid receptors can repress transcription elongation.
- Activated glucocorticoid receptor prevent recruitment of the pTEF-b kinase.
- No phosphorylation of ser 2 of RNA pol2 that is a prerequisite for transcriptional elongation.
Phosphorylation by receptor-associated kinases.
- Signalling molecules bind to receptor on plasma membrane.
- Receptor structure change and this activates the intracellular G protein.
- This activate adenylate cyclase to convert ATP to cAMP (second messenger)
- CAMP activates protein kinase A.
- CREB (transcription factor) is phosphorylated, activating transcription
Function of CBP.
- Intrinsic histone acetyltransferase activity and acetylate both histone and non-histone proteins.
- Acts as a scaffold to stabilise additional protein interactions with the transcription complex.
What results from the acetylation of NFkB
- Acetylation reduce interaction of NFkB with IkB
2. Activating transcription along with the phosphorylation of IkB
What is result of ubiquinition of IkB.
- Addition of ubiquitin targets proteins for degradation.
2. In the NFkB/IkB system, ubiquitination of IkB release activate NFkB and gene expressing is enhanced.
Results of sumoylation of IkB
- Sumoylation of IkB protects it against ubiquitination.
- This stabilises IkB (not targeted for degradation )
- Which suppresses signalling into the nucleus
Post transcriptional modifications of TF via.
- Phosphorylation
- Proteolytic cleavage
- Regulation of protein to protein interactions
Regulation of post-transcriptional processes by the PL3-kinase/ Akt system.
- Insulin binds to the cell receptor.
- This activates PI3-kinase which phosphorylates PIP2 into PIP3.
- PIP3 activates PDK1 which is responsible for activation Akt.
- Akt is responsible for the phosphorylation of factors involved in transcription, splicing, and mRNA translation.
AKT phosphorylates which molecules?
- A polycomb factor (EZH2)
- The DNA methyltransferase enzyme (DNMT)
- Chromatin remodelling structure (ISW1)
What is Akts role in RNA splicing.
Phosphorylation of SF2 enhances its ability to recruit U1 snRNP to 5’splice sites induce splicing of an exon into the mature mRNA.
How does AKT/TOR influence translation.
It phosphorylates eLF4Ebp releasing it from ALF4E allowing for the recruitment of eLF4A and eLF4G allowing or translation to take place.
What are all the functions of AKT
- Activates proteins that influence chromatin structure
- Activate/ enhance splicing
- Activate TOR which enhances translation.
Tor influence coupling of splicing and translation
- The SF2 splicing factor can recruit TOR kinase to an mRNA.
- TOR then phosphorylates elF4bp
- This then opens up eLF4E to bind to the cap and initiate translation.
The affects of Akt/TOR on transcription factors and repressors.
- The activation of TIF-IA which enhance synthesis of rRNAs this leads to RNA polymerase 1.
- Inhibit CRF1 which function as a repressor of ribosomal protein transcription. So inhabitation will result in an increase RNA polymerase 2 which will increase rRNA.
- Inhibit MAF1 which is a repressor of RNA pol 3 activity. So inhibition will result in an increase RNA pol 3 which will increase tRNA.
Function of argonaute proteins.
Argonaute are Endonuclease that mediate the degradation of mRNA.
Function of AKt in modulating miRNA activity.
When Akt phosphorylates Argo :
- Blocks MiRNA-mediated RNA degradation.
- Activates miRNA-mediated translation repression.
Unfertilised egg have a large number of maternal mRNA, bound to what protein?
RNP (Ribonucleoproteins)
Fertilisation causes what to happen in the zygote ?
Fertilisation causes dissociation of mRNA and RNPs (ribonucleoproteins) and translation is initiated.
The maternal/embryonic switch is regulated by?
- Activation of TAF4
- This then leads to increased levels of TBP, that increase embryonic genome transcription.
- By increasing the expression of a miRNA gene responsible for de-adenylation and degradation maternal mRNA.
What is a bitcoid?
Is a maternal encoded transcription factor that contains a homeodomain (helix-turn-helix) for DNA binding.
Define morphogen
Any substance produced in developing embryo that diffuses to form a gradient and affects morphological development.
Genes activated by binding TF have:
- An upstream control region that contains a biocid binding domain ( 5’-TCTAATCCC-3’)
- Have high or low affinity binding sites in their promoters, so different genes are activated at different concentrations of the bicoid TF.
Function of the receptor tyrosine kinase torso (Tor)
A key component of this system, is active in the pole regions of the embryo, its activity Down regulates the maternally deposited repressor capsicua (Cic)
What is CIC and what is its function.
Cic is a repressor protein that bind to the DNA. And suppresses expression of the bicoid responsive gene.
What are homeobox genes
Encode homeodomain protein that are transcription factors.
Function of homeodomain proteins.
They regulate gene expression and cell differentiation during early embryonic development. Ultimately determining the structure each segment form.
Homeotic sector genes are organised into what 2 clusters
- Antennapedia cluster: development of head (H) and anterior Thoriax (T1,T2)
- Bithorax cluster: development of posterior thorax (T3) and abdomen (A1 to A8)
What are the four cluster of Hox genes in mammals
- Hox A
- Hox B
- Hox C
- Hox D
Expression of HoxB genes revealed that
- Most anterior gene expressed first.
2. As time pass, the most posterior genes are expressed.
Expression of Hox genes is mediated by?
Retinoic acids (RA) gradient
Signalling via RA
- Retinol enter the cell (permeable), gets converted into RA
- RA moves into nucleus and binds to RA-receptor (RAR)
- RAR binds to RA-response element sequences in the 3’-regulatory region of thee Hox gene.
- Affects transcription of Hox
Retinoic acid gradient is higher in the posterior or anterior
Posterior
HoxB1 are activated by low or high RA concentration?
Low RA will activate HoxB1 gene activation
What are inner cell mass (ICM)
Cells can give rise to all different cell types
