Lecture 3: Post transcriptional RNA modification

What 5 structures do almost all mRNA molecules have that helps them regulate translation

A 5’ cap, a 5’ untranslated region (UTR), an open reading frame (ORF), a 3’ UTR and a poly(A) tail

What is an ORF

Contains codons that determine the amino acid sequence of the protein

What is the function of the 5’ cap

Protects the mRNA from degradation due to high reactivity of RNA and helps ribosomes recognise the start of translation

What is the function of the poly(A) tail

stabilises the mRNA by acting as a fuse to avoid immediate degradation in the cytoplasm and aids in export from the nucleus

What is the function of the 5’ UTR

Proteins can bind here to transport the mRNA to particular locations in the cell OR affect translation initiation directly throug providing binding sites for regulatory proteins

Function of the 3’ UTR

Translation regulated by sequences in this region by binding with specific proteins

What is the function of the polyA binding proteins

They cause a loop to be formed by binding to the Poly A tail and the 5’ cap, which increases the efficiency of translation initiation

What is the transcriptome

The arrray of all mRNA transcripts produced in a cell

What is RNA splicing

The removal of non-coding segments of the mRNA transcript (introns) which turns it from pre-mRNA to mRNA

What is the spliceosome

consists of 5 small ribonuclear proteins (snRNPs) which joins the exons together in their linear order, and remove introns to form processed mRNA

What is alternative splicing, why is it a way of regulating gene expression

The same primary transcript can be spliced in different ways to yield different proteins (some exons are also recognised as introns in different primary transcripts)

What is the C-value paradox

The number of genes in a human genome doesn’t correlate with organismal complexity (too few genes for how complex we are)

What percentage of genes in a human genome are alternatively spliced

75%, so there are on average 4 variants per gene

What is RNA editing

A post-transcriptional process that modifies RNA molecules (specifically their bases), leading to changes in their sequence

What are the usual bases edited in RNA editing, what do they turn into

A → I - inosine (G equivalent in DNA)

C → U (T equivalent in DNA)

What are the 2 types of small regulatory RNAs

siRNA (small interfering RNA) and microRNA

How + where are these made

Transcribed from DNA and form hairpin structures in the nucleus (stabilised by base pairing in the stem, which is then cleaved by enzymes in the cytoplasm)

What then happens to the stem of the pre-miRNA

The pre-miRNA further cut into small, double-stranded fragments to form miRNA duplex

What is the RISC, what is loaded here

RNA Induced Silencing Complex - the miRNA is loaded here

What is the function of the siRNA in this, what does this cause

Guides the RISC complex to the mRNA, causing inhibition of translation, chromatin remodelling OR RNA degradation

What is the main difference between siRNA and miRNA

siRNA is exogenous (produced by other organisms than the host) and miRNA is endogenous

siRNA leads to specific degradation of mRNAs

miRNAs bind to complementary sequences in target mRNAs to inhibit translation OR promote degradation

How can siRNAs be used in therapeutic applications

siRNAs for genes of interest can be generated, which can be used to lower expression of specific genes in vivo by degrading mRNA (i.e. for cancer genes)

What is translational control

Regulatory mechanism determining the efficiency and timing of translation of mRNAs into proteins

What roles do UTR 5’ and 3’ play in this

5’ contains elements influencing translation initiation

3’ contain regulatory sequences that impact efficiency of translation and mRNA stability

What are initiation factors

Proteins that facilitate the assembly of the ribosome machinery at the start codon of mRNA