Transcript Q: Which of the following graphs represents the proportion of

The Life and Death of
Eukaryotic mRNA
G.E. Whiz
(Gene Expression)
Learning goals
Students will:
•Explain the role of post-transcriptional regulatory processes in
establishing cell diversity.
•Describe the steps that regulate the production of a functional mRNA.
•Use information on splicing to explain the paradox that there are fewer
genes than proteins.
•Use a (mathematical) simulation of synthesis and degradation of
mRNA to predict the quantitative regulation of mRNA levels.
Teaching Challenges
Students often confuse transcription and translation.
Discussion of the regulatory events that occur between
these two steps may help differentiate transcription and
translation in the students’ minds.
Control of gene expression at the post-transcriptional level
is often overlooked in introductory biology.
Biology students do not often apply quantitative
approaches (math) to biological questions.
Assessment
•Content mastery
•clicker questions
•problem solving - RNA splicing
•Peer instruction (group work) – lots of proteins, few genes
•Data analysis – northern blot
•Quantitative application/synthesis – mRNA decay
Active Learning Exercise
Contribution to Diversity
Clicker questions
Individual participation
Splicing exercises
Tactile/kinesthetic
Data analysis
Peer instruction & visual learning
RNA stability simulation
Interdisciplinary approach (quantitative)
Context
Introductory (general biology, genetics, cell biology)
Large class size (>250).
DNA to RNA to protein
General features of transcription and translation
Biological macromolecules
Cellular structure
Differential gene expression determines cell type
Which genes are expressed determines the phenotype of the organism
Green
A
Blue
B
Genotype
Genes
Transcription
mRNA
Translation
protein
Phenotype
Gene expression is regulated at multiple levels
1. Transcriptional
Green
A
Blue
B
Genes
DNA structure
Repressors
Enhancers
2. Post-transcriptional
Transcription
mRNA
Translation
RNA splicing
RNA trafficking
RNA degradation
3. Translational
protein
Ribosome binding
Termination
4. Post-Translational
P
P
Folding
Modification
Trafficking
Schedule of Activities for the Entire Teachable Unit
Step 1: Background:
Importance of mRNA splicing in gene expression – hook, group work.
Step 2: Mini lecture on pre-mRNA processing:
Mini-lecture and animation – clicker question.
Step 3: Alternative splicing:
Question-driven discussion and a small group activity.
Step 4: Export from the nucleus:
A mini-lecture with animation.
Step 5: Simulation of mRNA levels in the cytoplasm
Clicker questions employing graphs and mathematical simulation.
Post-transcriptional processing
Transcription
DNA
exon Intron
exon
Intron
exon Intron
exon
Pre-mRNA
RNA splicing, capping, polyadenylation
AAAAA
mRNA
cap
Export from nucleus
AAAAA
cap
degradation
AAAAA
cap
storage
AA
Splicing
Exon
Intron
Intron
Intron
Exon
Exon
Exon
IAMAPREMRNQRSTVAWHICHHQPBASTRVASBEEQABDFCTVNSPLICED
IAMAPREMRNAWHICHHASBEENSPLICED
I AM A PRE MRNA WHICH HAS BEEN SPLICED
Alternative Splicing of Tropomyosin
Exon
Intron
Exon
Intron
Exon
Intron
Exon
IAMTHEQSRTVHEARTQPBASRTVBRAINQABDEVTROPOMYOSIN
In the heart
IAMTHEHEARTTROPOMYOSIN
(I am the heart tropomyosin)
In the brain
IAMTHEBRAINTROPOMYOSIN
(I am the brain tropomyosin)
Schedule of Activities for the Entire Teachable Unit
Step 1: Background:
Importance of mRNA splicing in gene expression – hook, group work.
Step 2: Mini lecture on pre-mRNA processing:
Mini-lecture and animation – clicker question.
Step 3: Alternative splicing:
Question-driven discussion and a small group activity.
Step 4: Export from the nucleus:
A mini-lecture with animation.
Step 5: Simulation of mRNA levels in the cytoplasm
Clicker questions employing graphs and mathematical simulation.
Northern Blot of mRNA
Northern Blot of mRNA


What do you notice
about the patterns of
the different RNAs
over time?
Describe one
mechanism that
could account for
these patterns
Q: Which of the following curves
represents the proportion of remaining
ND-5 in the blot?
B
A
C
D
Half-life of mRNA

What does “halflife” mean?

What is the half-life
of the mRNA
shown for curve C?
A. About 1 hour
B. About 2 hours
C. About 15 minutes
C
Half-life of mRNA
B
A
D
C
Half-life of mRNA


If the half-life
increases, will the
curve become more
steep, less steep, or
remain the same?
Illustrative simulation
B
A
D
C
Synthesis and degradation
of mRNA
The amount of any specific mRNA in a
cell doesn’t only depend on its half-life
 Often, new mRNA molecules are also
being synthesized, processed, and
exported from the nucleus

Homework

Download the simulation from the course website.

BEFORE moving any of the controls, describe the
shape of the curve. Does it always increase, always
decrease, or does it reach a limit at some point?

Increase the half-life of the mRNA and describe how
changing this parameter changes the shape of the
curve. Save this curve by pressing the “Save Data”
button.
• Decrease the production rate of the mRNA and
describe how changing this parameter changes
the shape of the curve.
• Click on the “Mystery curve” button, and adjust
the parameters so that the blue curve matches
the green curve. Record the corresponding
parameter values.
• Explore the simulation to your heart’s content
and WRITE A QUESTION that you can ask your
groupmates tomorrow.
• Be prepared to share your answers with the rest
of the class.
• Decrease the production rate of the mRNA and
describe how changing this parameter changes
the shape of the curve.
• Click on the “Mystery curve” button, and adjust
the parameters so that the blue curve matches
the green curve. Record the corresponding
parameter values.
• Explore the simulation to your heart’s content
and WRITE A QUESTION that you can ask your
groupmates tomorrow.
• Be prepared to share your answers with the rest
of the class.