regulation of gene expression part ii molecular biology – regulation of gene expression ii

Regulation of gene expression

Part II

MOLECULAR BIOLOGY – Regulation of gene expression II

Figure 7-92 Molecular Biology of the Cell (© Garland Science 2008)


There are MULTIPLE opportunities to regulated gene expression (derivation of functional protein) after the initiation of transcription !


Riboswitch … short sequences of RNAthat 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

Riboswitch can can activate ‘self cleaving’ ribozyme activity


5’AUG

STOP

H2N COOH3’ ON

AUG

H2N COOH3’ OFF

5’small molecule

Autolytic ribozyme activitySTOP

Figure 7-106c Molecular Biology of the Cell (© Garland Science 2008)

Riboswitch can affect the translation initiation from Shine-Dalgarno sequence


Figure 7-106b Molecular Biology of the Cell (© Garland Science 2008)

THERMOSENSOR


Figure 7-106d Molecular Biology of the Cell (© Garland Science 2008)


Antisense RNA


ALTERNATIVE SPLICING


e.g.Drosophila Dscam

axon guidance receptors


Thousands of possible different functional protein sequence combinations



Splicing is subject to tight regulatory control


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:

Altered amino acid codons

C - U deaminations also possible do not rely on RNA duplexes e.g. ApoB100 mRNA

in liver and intestine


Extensive RNA editing in mitochondria of trypanosomes


Uracil insertions


Nonsense-mediated mRNA decay


EJC ribonucleoprotein complexes are remnants

of splicing

DNA gene

transcription

EJC displacement during translation

Premature termination of translation leaves ‘beacon’ EJC leading to abnormal mRNA

degradation

Nanos proteinBicoid protein

Some mRNAs are localized to specific regions of the cytoplasm

bicoid mRNA nanos mRNA

mRNAs for secretedproteins targeted to

ER by SRP


Drosophila oocyte polarity and embryo patterning

A P

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

http://cellbio.utmb.edu/CELLBIO/cit2.htm

PROMOTER

AATAAA

exon 1 exon 2 exon 3

ATG TAA

AAUAAAAUG UAA

AAUAAAAUG UAA

intron intron

TRANSCRIPTION

Pre-mRNA

mRNA

DNA

RNA SPLICING

protein

TRANSLATION

coding sequence

MAPSSRGG…..

OPEN READING FRAME

5’UTR 3’UTR

CAP AAAAA

NUCLEUS

CYTOPLASM


Central genetic dogma

Regulation of gene expression via regulation of mature mRNAs


mRNA stability as a way to regulate gene expression

in bacteria – half life couple minutesin eukaryotes – half life minutes to tens of hours


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

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


mRNA stability as a way to regulate gene expression

in bacteria – half life couple minutesin eukaryotes – half life minutes to tens of hours


Cytoplasmic deadenylases e.g. PARN



PARN binds exposed 5‘ cap of non-translated mRNAs, leading to poly-A tail deadenylation and eventual degradation

mRNA’s with longer poly-A tails more likely to be translated

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



mRNA stability mechanisms in

action

e.g. ferritin/ transferrin receptor system

PROMOTER

AATAAA

exon 1 exon 2 exon 3

ATG TAA

AAUAAAAUG UAA

AAUAAAAUG UAA

intron intron

TRANSCRIPTION

Pre-mRNA

mRNA

DNA

RNA SPLICING

protein

TRANSLATION

coding sequence

MAPSSRGG…..

OPEN READING FRAME

5’UTR 3’UTR

CAP AAAAA

NUCLEUS

CYTOPLASM



microRNA (miRNA) ... small noncoding RNA regulators recognizing 3’UTRs

● one miRNA recognizes many mRNAs (even hundreds if they share common 3’UTRs)● more than one miRNA can bind to one mRNA (combinatorial regulation)

RNA-induced silencing complex


● >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

Drosha & Prasha (DGCR8)

Pri-miRNA

Dicer

Pre-miRNA

RNA induced silencing complex (RISC) miRNA (imperfect duplex 22nts - guide strand

incorporated, passenger strand degraded)

3’UTR sequence homology


RNA interference (RNAi)

small interfering RNA (21-23nt)

RISC re-used

RNA-inducedtranscription silencing


Dicer mediated processing

dsRNA viral genomesPre-miRNA transcripts

Experimentally introduced RNA

n.b. sequence homology not limited to 3’UTR

Argonaut mediated target mRNA degradationCo-transcriptional degradation

of transcript

Origin of life - RNA world

active RNAs involved in:

• RNA splicing

• Protein synthesis

• Expression regulation – siRNA, riboswitches


regulation of gene expression part ii molecular biology – regulation of gene expression ii

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