Module 1.

Basic genetic principles and technologies

Lecture 1.3 Gene expression

and regulation
Tongli Wang
Questions for the last lecture
• How many chromosomes in a bacterial cell?
• What parts of a plant cell contain DNA?
• What is the association btw the number of chromosomes and
complexity of an organism?
• Is ploidy associated with performance in crop plants?
• What are the components of a chromatin?
• Chromatin makes DNA from linear form into 3D structure
• What is the direction in synthesizing a new DNA strand, 3’ -> 5’ or 5’ ->
3’ ?
• What is the major difference between DNA synthesis on the leading
strand and lagging strand?
• What happens if an error occur during the DNA replication?
Telomere
• What are the two factors causing the shortening
of our telomeres?
 Diet affects telomere length
• The main results suggest that a
higher consumption of fish, nuts
and seeds, fruits and vegetables,
green leafy, …, is beneficial.
• On the contrary, a higher intake
of dairy products, simple sugar,
sugar-sweetened beverages, …,
has a negative effect.
• A good sleeping habit
is important for
maintaining your
telomeres
• My point: to catch up
your homework at the
last moment with
sleepless nights
should be avoided as
much as possible
PCR
• What are the basic
elements need in
the test tube?
• What is the function
of primers?
Module 1. Basic genetic principles and technologies

Lecture 1.3 Gene expression

and regulation
Tongli Wang
Learning objectives
• Describe gene structure
• List RNA types and their functions
• Describe gene expression
• Interpret gene regulation
• Describe the components of non-coding
DNA
Outline
• Genes
• RNAs
• Gene expression
• Gene regulation
• Non-coding DNA
Genes
• A gene is a section of DNA that controls a
certain trait by encoding a protein
• Proteins do much of the work in the cell and
the body as a whole in all the organisms
• Some proteins give cells their shape and structure
• Others help cells carry out biological processes,
such as energy conversion and photosynthesis in
plants
Gene structure
 Promoters

• Usually located at 25-bp upstream

of transcription start site
• Contains specific sequences bind
to proteins to initiate transcription
 Gene - Coding region
• Exon – DNA/RNA sequence carrying coding information
• Intron – non-coding sequence located in between coding
sequences

Coding region
How to identify a gene in DNA sequence?

• 1. to search for start

and stop codons
• Start codon: ATG
• Stop codon: TAG, TAA,
or TGA
• 2. Based on gene
product
• The direct product of a
gene is a messenger
RNA (mRNA)
Some facts about genes
• Genes are 10-15kb long on average,
• varies from a few hundred bases to more than
2 million bases
• We all have the same genes
• Each person has the same set of genes -
about 21,000 in all
• The differences between people come
from slight variations in these genes
• all people have a gene for hair color
• different versions of this gene (alleles) dictate
whether someone will have red or brown hair
Some facts about genes – cont’d
• The total number of genes varies a lot among species
• It is not associated with the complexity of organisms
Outline
• Genes
• RNAs
• Gene expression
• Gene regulation
• Non-coding DNA
RNA
• Ribonucleic acid (RNA) is a nucleic acid
present in all living cells
• It has structural similarities to DNA
(backbone), but it is most often single-
stranded. (q)
• It also has four letters: A (adenine), U
(uracil), C (cytosine) and G ( guanine).
• U replaced T (in DNA)
• U pairs with A in matching DNA sequence
in
• Transcription to produce mRNA
• Making cDNA
RNA types
• mRNAs – messenger RNAs transcribed from
genes
• tRNAs – transfer RNAs for transferring amino
acids
• rRNAs – ribosome RNA involved in protein
synthesizing
• Most abundant
• lncRNAs – long non-coding RNAs (>100 base)
involved in epigenetics (gene regulation)
• miRNAs – microRNAs (21-23 bases) involved in
mRNA silencing (gene regulation)
• ncRNAs – non-coding RNAs.
• Except mRNA, all other types of RNAs
• All RNAs are encoded by DNA, but not all DNA
encodes RNA.
Outline
• Genes
• RNAs
• Gene expression
• Gene regulation
• Non-coding DNA
Gene expression

• Gene expression is the process by

which information from a gene is used
to synthesize a functional
gene product.
• It has two major steps:
• Transcription: DNA -> RNA (mRNA and
other RNA)
• Translation: mRNA -> protein
The central dogma of molecular biology
• "DNA makes RNA, and
RNA makes protein“
• Francis Crick (1957)
• It means that the
genetic "information"
cannot go backward in
nature
• Exceptions do exist,
• such as the reverse
transcription process in
retroviruses where RNA
is used to make DNA.
Transcription – from DNA to mRNA

• Transcription is carried
out by RNA polymerase,
which uses available
bases from the nucleus
of the cell to form the
mRNA.
Transcription – from DNA to mRNA
• A gene produces a Gene

pre-mRNA, which
contains exons and
Pre-mRNA
introns
• Introns are removed
in post-transcription
modification step Post-transcription modifications

• Mature mRNA is used

to make a protein
Translation – from mRNA to protein
• Translation is the
process in which
ribosomes (rRNA) in
the cytoplasm
synthesize protein
• mRNA serves as the
template
• tRNAs match both
amino acids based
genetic code and
mRNA template
 Translation: Genetic Code
• The genetic code is universal.
• Virtually all species use the same
genetic code for protein synthesis

• What is this evidence for?

• All life on Earth shares a common

origin.

(Not required to remember these codes)

26
Gene expression

https://youtu.be/gG7uCskUOrA
 “… has discovered an
unprecedented pathway
producing telomerase RNA
from a protein-coding
messenger RNA (mRNA)” in the
model fungal organism.

Julian Chen and his group in Arizona State University's

School of Molecular Sciences and the Biodesign Institute's
Center for the Mechanism of Evolution
Outline
• Genes
• RNAs
• Gene expression
• Gene regulation
• Non-coding DNA
Gene regulation
• It is the process used to control the timing,
location and amount in which genes are
expressed.
• Every cell contains the same genes in a
multicellular organism, How do cells know
whether to make an eye or a foot; shoot or
root?
• The set of genes expressed in a cell determines
the properties and the functions of the cell
• In eukaryotes, gene regulation can occur at
many steps.
Steps of gene regulation
• Chromatin accessibility
• Transcription
• Promoters, enhancer, and
silencers
• RNA processing
• Different mRNAs may be
made from the same pre-
mRNA by alternative
splicing
• RNA stability
• The longer it stays, the more
copies of the protein
• Translation
• Protein activity
Gene regulation
• Although all stages of gene
expression can be regulated, the
main control point for many
genes is transcription.
• Regulatory elements in DNA near
the gene: enhancers/silencers
• Protein transcription factors
Enhancers
• An enhancer in DNA is a specific
sequence of DNA that can "enhance"
or increase the expression of a gene.
• Located further away from the
starting point
• Attract activators and increase
transcription rate
• Often used in genetic modifications
by inserting extra enhancers
Silencers
• A silencer in DNA refers to a specific sequence of DNA that can
"silence" or inhibit the expression of a gene.
Promoter and enhancers

https://youtu.be/aq8PAM5Sa0s
Transcription factors
• A transcription factor (TF) is a
protein that controls the rate of
transcription of genes
• The TF turns on a transcription called
activator
• The TF turns off a transcription called
repressor
• TFs can turn on and off genes, and
they can work in a coordinated
fashion to direct cell division, cell
growth, and cell death throughout
life
 Transcription factors

https://youtu.be/vGTRiGHBMHU
Outline
• Genes
• RNAs
• Gene expression
• Gene regulation
• Non-coding DNA
Noncoding DNA
• Noncoding DNA sequences are
components of an organism's DNA
that do not encode proteins
• Noncoding DNA makes up about
98.5% of the total DNA, varied a lot
among species.
• Some noncoding DNA is transcribed
into functional non-coding RNAs
• transfer RNA,
• ribosomal RNA, and
• regulatory RNAs.
Noncoding DNA
• Other functional parts of noncoding DNA:
• transcriptional and translational regulation of “protein-coding”
sequences, including
• Promoters, enhancers, telomeres, centromeres.
• The rest of the non-coding DNA is considered as “junk
DNA”
• It varies among species
• Some parts are found relevant to epigenetic functions
• More and more is found to have regulatory functions
Non-coding DNA may
have important
functions
• The 30 loci identified, many of
them are within intronic regions
(47%) as well as non-coding RNA
introns (29%). Only 1.2% were
found in exons
• This is quite exceptional, as most
important loci are within exons in
other studies
Human vs. conifer trees
Conifer genome size
20 billion DNA “letters”;
~30,000 genes

Can study genetic

Human genome size
3 billion DNA “letters”;
variation within genes or
21,000 genes in non-coding regions

Genes
<1% of DNA
Genes
<2% of DNA
 Facts about conifer trees

Norway spruce

Conifer genomes are huge due to:

• highly repetitive elements
• long introns
• much larger proportion of junk DNA
• ~1.5 to 2 times as many genes as other plants

Loblolly pine
White spruce
 Learning objectives
• Describe gene structure
• List RNA types and their functions
• Describe gene expression
• Interpret gene regulation
• Describe the components of non-coding DNA