MOLECULAR BIOLOGY – Regulation of gene expression II
Regulation of gene expression
Part II
MOLECULAR BIOLOGY – Regulation of gene expression II
There are MULTIPLE opportunities
to regulated gene expression
(derivation of functional protein)
after the initiation of transcription !
Figure 7-92 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
Riboswitch … short sequences of RNA
that change their conformation upon binding
small molecules such as metabolites, usually
reside in 5’ UTR
Mostly observed in bacteria but also documented in fungi and plants
MOLECULAR BIOLOGY – Regulation of gene expression II
Riboswitch can can activate ‘self cleaving’ ribozyme activity
5’
STOP
AUG
H2N
COOH
3’ ON
Autolytic ribozyme activity
STOP
AUG
5’
small molecule
H2N
COOH
3’ OFF
MOLECULAR BIOLOGY – Regulation of gene expression II
Riboswitch can affect the translation initiation from Shine-Dalgarno sequence
Figure 7-106c Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
THERMOSENSOR
Figure 7-106b Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
Antisense RNA
Figure 7-106d Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
Figure 7-92 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
ALTERNATIVE SPLICING
Figure 7-94 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
e.g.
Drosophila Dscam
axon guidance receptors
Thousands of possible different functional protein sequence combinations
MOLECULAR BIOLOGY – Regulation of gene expression II
Splicing is subject to tight regulatory control
Figure 7-96 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
Figure 7-92 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
RNA editing
- specific to eukaryotes (and viruses)
Non-templated changes to the genetic information that affect the protein sequence and
possibly function and are therefore not predictable from genomic DNA sequence
Deamination reactions e.g. A - I/G in RNA duplexes by ADAR:
C - U deaminations also possible do not
rely on RNA duplexes e.g. ApoB100 mRNA
in liver and intestine
Altered amino acid codons
Figure 7-101 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
Extensive RNA editing in mitochondria of trypanosomes
Uracil insertions
Figure 7-100 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
Figure 7-92 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
Nonsense-mediated mRNA decay
DNA gene
EJC ribonucleoprotein
complexes are remnants
of splicing
EJC displacement during
translation
Figure 6-80 Molecular Biology of the Cell (© Garland Science 2008)
transcription
Premature termination of translation leaves
‘beacon’ EJC leading to abnormal mRNA
degradation
MOLECULAR BIOLOGY – Regulation of gene expression II
Some mRNAs are localized to specific regions of the cytoplasm
mRNAs for secreted
proteins targeted to
ER by SRP
Drosophila oocyte polarity and embryo patterning
nanos mRNA
bicoid mRNA
A
Bicoid protein
P
Nanos protein
bicoid and nanos proteins inhibit translation of other homogenously
distributed cell fate genes which in turn affects the expression of other
cell fate mRNAs along the A-P axis as development proceeds
MOLECULAR BIOLOGY – Regulation of gene expression II
Figure 7-92 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
Central genetic dogma
PROMOTER
exon 1
DNA
exon 2
exon 3
ATG
TAA AATAAA
TRANSCRIPTION
5’UTR
Pre-mRNA
intron
AUG
CAP
3’UTR
intron
UAA AAUAAA
NUCLEUS
RNA SPLICING
CYTOPLASM
mRNA
AUG
UAA AAUAAA
coding sequence
TRANSLATION
protein
OPEN READING FRAME
MAPSSRGG…..
Regulation of gene expression via regulation of mature mRNAs
AAAAA
MOLECULAR BIOLOGY – Regulation of gene expression II
mRNA stability as a way to regulate gene expression
in bacteria – half life couple minutes
in eukaryotes – half life minutes to tens of hours
3’ UTR contains regulatory
elements that participate in
transcript stability
5‘ Cap:
• aids mRNA nuclear export
• protects from 5‘ - 3‘ exonuclease
degradation in cytoplasm
• targets transcripts to ribosome for
translation
Figure 7-109 Molecular Biology of the Cell (© Garland Science 2008)
poly-A tail:
• participates in termination of
transcription
• aids mRNA nuclear export
• protects from 3‘ - 5‘ exonuclease
degradation in cytoplasm
• targets transcripts to ribosome for
translation
MOLECULAR BIOLOGY – Regulation of gene expression II
mRNA stability as a way to regulate gene expression
in bacteria – half life couple minutes
in eukaryotes – half life minutes to tens of hours
Cytoplasmic deadenylases
e.g. PARN
Figure 7-109 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
mRNA’s with longer poly-A tails
more likely to be translated
PARN binds exposed 5‘ cap
of non-translated mRNAs,
leading to poly-A tail
deadenylation and eventual
degradation
Regulatory potential to influence this equilibrium
e.g. cytoplasmic polyadenylation of short poly-A tails e.g. fertilized mammalian oocytes and
post-synaptic neurone sites
Figure 7-110 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
mRNA stability
mechanisms in
action
e.g. ferritin/ transferrin
receptor system
Figure 7-111 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
PROMOTER
exon 1
DNA
exon 2
exon 3
ATG
TAA AATAAA
TRANSCRIPTION
5’UTR
Pre-mRNA
intron
AUG
CAP
3’UTR
intron
UAA AAUAAA
NUCLEUS
RNA SPLICING
CYTOPLASM
mRNA
AUG
UAA AAUAAA
coding sequence
TRANSLATION
protein
OPEN READING FRAME
MAPSSRGG…..
AAAAA
MOLECULAR BIOLOGY – Regulation of gene expression II
microRNA (miRNA) ... small noncoding RNA regulators recognizing 3’UTRs
Drosha & Prasha (DGCR8)
● one miRNA recognizes many mRNAs
(even hundreds if they share
common 3’UTRs)
● more than one miRNA can bind
to one mRNA
(combinatorial regulation)
Pri-miRNA
Dicer
Pre-miRNA
RNA-induced
silencing
complex
RNA induced
silencing
complex (RISC)
3’UTR sequence
homology
miRNA (imperfect duplex 22nts - guide strand
incorporated, passenger strand degraded)
● >1000 miRNA genes targeting approx
60% of genes
● estimated 16% of pre-miRNAs can be
altered by ADAR mediated editing
● miRNA can be derived from spliced
introns in non-mammalian species,
known as mirtons
Figure 7-112 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
RNA interference (RNAi)
dsRNA viral genomes
Pre-miRNA transcripts
Experimentally introduced RNA
Dicer mediated processing
small interfering RNA
(21-23nt)
RNA-induced
transcription silencing
Argonaut mediated target mRNA degradation
RISC re-used
n.b. sequence homology not limited to 3’UTR
Figure 7-115 Molecular Biology of the Cell (© Garland Science 2008)
Co-transcriptional degradation
of transcript
MOLECULAR BIOLOGY – Regulation of gene expression II
Origin of life - RNA world
active RNAs involved in:
• RNA splicing
• Protein synthesis
• Expression regulation
– siRNA, riboswitches