Gene Expression and Regulation Flashcards
At what points can gene regulation occur?
Chromatin structure Transcription initiation mRNA processing RNA export Translation RNA degradation
How can chromatin structure affect gene regulation?
Heterochromatin cannot be accessed by transcription machinery
Histone modifications affect how densely compacted DNA is
Methylation = turns genes off
Acetylation = turns genes on
Features of direct DNA methylation
Form of epigenetics
Cytosine can become methylated, typically when it is adjacent to Guanine (known as a CpG island)
Tends to repress gene expression
What is needed to initiate transcription?
Transcription requires the transcription initiation complex, made of RNA Pol + TFIID
TFIID = TATA Box binding protein (TBP) + 11 TBP associated factors
TFIID binds to TATA Box promoter region
What is the function of enhancer regions?
Located far upstream of the gene
Bind tissue-specific transcription factors and activators
DNA folds over so it can interact with the pre-initiation complex via a mediator protein
Can function in either direction
What is the function of insulator regions?
Regulate activity of enhancer regions
Act as chromatin boundary markers e.g. to prevent formation of heterochromatin from spreading along a chromosome
Bind insulator proteins
What happens during 5’ mRNA capping?
Addition of a 7-methylguanine cap onto the 5’ end via a 5’ to 5’ linkage
The cap recruits a cap-binding-complex that is recognised by a nuclear pore to allow export
Also prevents degradation by exonucleases
What happens during splicing?
Introns start with GU and end AG Carried out by spliceosome (U1, U2, U4, U5, U6) 1. U1 binds to 5' Splice site 2. U2 binds to branch point adenine (AG) 3. U4/5/6 bind area in between 4. Branch point attacks 5' splice site 5. Introns lost as a lariat loop
How is alternative splicing regulated?
Exons and introns have enhancer and silencer elements. There are Intron splicing enhancers (ISEs) Intron splicing silencers (ISSs) Exon splicing enhancers (ESEs) Exon splicing silencers (ESEs)
What proteins do splicing enhancers and silencers bind?
ISEs and ESEs Enhancer elements bind serine and arginine rich (SR) proteins
ISSs and ESSs silencer regions bind heterogenous ribonucleoprotein particles (hnRNPs)
Use of splice site depends on balance of SR proteins and hnRNPs
What happens during Poly adenylation?
- PolyA site (AAUAAA) recognised by cleavage and polyA specificity factor (CPSF)
- Cleavage factors CF1 and CF2 make cute
- Cleavage stimulation factor (CstF) promotes cleavage
- PolyA tail added by polyadenylate polymerase
- PolyA binding proteins PAB1 and PAB2 regulate mRNA stability
What happens during RNA export?
RNA exits through nuclear pore
RNA transport proteins hnRNP, p15 and TAP
Sequences in 3’UTR tell transcript where to go
What happens during translation?
tRNA molecules bring amino acids relevant to the specific anticodon amino acid attached to 3' end of tRNA Initiation Elongation Termination
What is mRNA turnover?
The rate at which mRNA is degraded intracellularly
What is the shape of mRNA?
Circular - the 5’ cap interacts with the PolyA binding protein (PABP) on the polyA tail
How is mRNA degraded after being translated?
As the ribosome reaches the end of the mRNA, it displaces the Poly A binding protein, in turn displacing the cap binding protein. The RNA is then vulnerable to degradation
Exonucleases degrade from 3’ to 5’
How do RNA binding proteins regulate stability?
Bind specific sequences
AU-Rich Elements (AREs) cause degredation
C-rich elements bind alphaCP proteins, causing stabilisation
How is nonsense mediated decay initiated?
Ribosome stalls at termination codon, scans downstream to see if any exon junction complexes are still present. If there is, this indicates the the termination codon is premature, so degradation happens
What is the exon junction complex?
Complex present on mRNA at the junction of two exons that have been joined by RNA splicing
Process of nonsense mediated decay
UPF1 binds ribosome
UPF3 binds the exon junction complex
UPF2 joined UPF1 and UPF3 together
Termination factors eRF1 and eRF3 associate with the ribosome
Recruit decapping proteins and exonucleases
How do small RNAs regulate gene expression?
About 20 nucleotides long
Recognise sequences in the 3’ UTR
Bind to and blocks ribosome binding site
What is does SMA stand for?
Spinal Muscular Atrophy
Inherited neuromuscular disease
What mutation is responsible for SMA?
Deletions of exon 7 or 8 in the SMN1 gene
How is SMA inherited?
Autosomal recessive
How common is SMA?
Affects 1 in 6,000-10,000
Second most common autosomal recessive condition after cystic fibrosis
What is the function of the SMN1 gene?
Encodes Survival Motor Neuron Protein
Required for assembly of small nuclear ribonucleo proteins (snRNPs)
What are snRNPs?
Small nuclear ribonucleoproteins
Made of RNA and proteins
Forms part of the spliceosome
What happens when the SMN1 gene is non-functional?
Reduced availability of SMN protein
Gradual death of alpha-motor neurons in the anterior horn of the spinal cord
Muscles that depend on these motor neurons undergo atrophy
Symptoms of SMA in adults
Progressive muscle weakness
Respiratory failure
Death
Symptoms of SMA in babies/children
'Floppy' Cannot sit up without help Several respiratory illnesses Problems swallowing Weak cry
Why is SMA not usually fatal?
The SMN2 is almost identical
One functioning copy of SMN2 is enough to allow some motor neurons to survive
Why can siblings with SMA vary in their symptoms?
Phenotypic heterogeneity
Different mutations in the same gene can lead to different phenotypes
