Eukaryotic Gene Expression and

Regulation
 The organization of genes of a human
chromosome

Wednesday, November 11,

2
2020
 The organization of genes of a human
chromosome
• Most of the genes consist of; short coding
sequences or exons which are interrupted by a
longer intervening noncoding sequence or introns.

Wednesday, November 11,

3
2020
 Gene Expression
• To synthesize its proteins, a cell must be able to
access the information that is stored within its DNA.

• The process of using a gene sequence to affect the

characteristics of cells and organisms is referred to as
gene expression.
 Gene Expression
1. Transcription the DNA
sequence within a gene is
copied into a nucleotide
sequence of ribonucleic
acid (RNA).
2. Translation the sequence of
nucleotides in an mRNA
provides the information
(using the genetic code) to
produce the amino acid
sequence of a polypeptide.
Gene Expression
The Genetic Code
• In the code, a three-base
sequence specifies one
particular amino acid
• One or more polypeptides
→functional protein.
 Regulation of Gene
Expression
Levels at which expression of
protein-coding genes is
regulated in eukaryotes:
1. Epigenetic gene regulation
2. Transcription.
3. mRNA processing and transport.
4. Translation.
5. Degradation of mRNA.
6. Protein processing.
7. Protein degradation.

Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as

Benjamin Cummings.
Epigenetic gene regulation

•Epigenetics literally means "above" or "on top of"

genetics.

•It refers to external modifications to DNA that turn

genes "on" or "off."
Epigenetic gene regulation
Two forms of chromatin
• Euchromatin
A lesser coiled transcriptionally active region which can
be easily accessed by the RNA polymerases

• Heterochromatin
A highly condensed transcriptionally inactive region.
Genes cannot be accessed by RNA polymerases for
active transcription.
 Mechanisms which affect the chromatin
structure and hence the expression of
gene
• Histone modifications- these modifications make a
region of gene either transcriptionally active or
inactive.

1. Acetylation
↑Acetylation----↓condensation of DNA ------↑
transcription of genes in that region.
2. Methylation

• Methylation occurs most

often in genomic regions
with ↑ frequency of CG
dinucleotides (CpG islands) Cytosine
Methylated
Cytosine

• CpG islands particularly occur

at or near the transcription
start site of housekeeping
genes
 TF RNA pol

Active
transcription
Unmethylated CpG island

TF RNA pol

CH3 CH3 CH3 Repressed

transcription

Methylated CpG island

 Transcriptional Control
• Transcription of eukaryotic genes is regulated by
interactions between proteins and DNA sequences
within or near the genes.
1. Cis-acting elements
DNA sequences close to a gene that are required for
gene expression E.g.:
• Promoters
• Enhancers
• Terminators
• Insulators
Promoters
• Located immediately adjacent to the genes they
regulate, upstream of the transcription start site.
i. Consist of short nucleotide sequence that serve as
the recognition point for binding of RNA polymerase.
ii. Some promoter elements (e.g., TATA) are required to
specify the start of transcription, through binding of
transcription factor proteins.
iii. Promoters may be either positively or negatively
regulated.
Enhancers
• Enhancers are mostly located some distance
away, either upstream or downstream.
i. The binding of enhancer binding proteins
(transcription factors) ↑ the rate of transcription.
ii. Each enhancer has its own transcription factor that
it binds to.
iii. Effective only in the specific cell type in which
appropriate regulatory proteins (transcription factors)
are expressed.
 Distal control
element
Promoter
Activators
Gene

Enhancer TATA
box
1 General
Activator proteins bind transcription
to distal control elements factors
grouped as an enhancer in
the DNA. This enhancer has
three binding sites. DNA-bending
protein

2 Group of
A DNA-bending protein Mediator proteins
brings the bound activators
closer to the promoter.
Other transcription factors,
mediator proteins, and RNA RNA
polymerase are nearby. Polymerase II

Chromatin changes

3
Transcription
The activators bind to
certain general transcription RNA processing

factors and mediator RNA

proteins, helping them form Polymerase II
an active transcription mRNA
degradation
Translation

initiation complex on the promoter.

Protein processing
and degradation

Transcription RNA synthesis

Initiation complex
 Insulators
• Typically 300 bp to 2000
bp in length.
• Function either as
an enhancer-blocker or a
barrier, or both.
– By loop formation
and nucleosome modificatio
ns
Terminator
A DNA sequence just downstream of the coding segment
of a gene, which is recognized by RNA polymerase as a
signal to stop transcription.
5. Silencers
• Are control regions of
DNA, may be located
thousands of base pairs
away from the gene they
control.

• When transcription factors

(repressor) bind →
expression of gene is
repressed.
 Transcriptional Control
2. Trans-acting factor
Usually they are proteins, that bind to the cis-
acting elements to control gene expression.
– RNA polymerase
• RNA Pol
– Transcriptional factors
• Basal/general TFs, specific TFs
 Transcriptional Control
• These trans-acting factors can control gene
expression in different ways:
– may be expressed in a specific tissue
– may be expressed at specific time in development
– may be required for protein modification
 RNA Processing Regulation
Pre-mRNA processing includes 5' capping, 3’ polyadenylation, and
intron splicing. These reactions occur in the nucleus, and begin
while the primary transcript is being elongated (co-
transcriptional). Mature mRNAs then are transported to the
cytoplasm for translation.
RNA Processing Regulation

Spliceosome
 RNA Processing Regulation
• RNA processing regulates mRNA production from
precursor RNAs.
• In eukaryotes, one single gene can encode different
peptides by:
– Alternative polyadenylation
• In some genes proteins for synthesizing poly(A) tails can add a
poly(A) tail at one of several possible sites.
• Therefore polyadenylation can produce more than one transcript
from a single gene (alternative polyadenylation).
– Alternative splicing
• Process of selecting different combinations of splice sites within
a pre-mRNA to produce variably spliced mRNAs which can encode
proteins that vary in their sequence and activity, and yet arise
from a single gene.
Alternative polyadenylation and splicing of the human CACL
gene in thyroid and neuronal cells.
 Regulation of RNA Transport
• Only some RNAs function within the nucleus
whereas all other RNAs which are meant for
protein synthesis have to be transported from
the nucleus to the cytoplasm via nuclear pores.

• Some experiments show ~1/2 of primary

transcripts never leave the nucleus and are
degraded.
 Regulation of RNA Transport
• A mature mRNA,
complexed with RBPs
[mature RNA-protein
particles (RNP)], ready to
be transported to the
cytoplasm .

• Interaction with proteins

of the nuclear pore
complex

• In the cytoplasm, RNPs

attach to cytoplasmic
motor proteins, which
mediate the
microtubule-dependent
transport of mRNA to its
final destination
 mRNA translation control
• Presence or absence of the 5’ cap and the length of
the poly-A tail at the 3’ end can determine whether
translation takes place and how long the mRNA is
active.

• Conditions that affect the length of the poly-A tail or

leads to the removal of the cap may trigger the
destruction of an mRNA.
 mRNA degradation control
• All RNAs in the cytoplasm are subject to degradation.

• tRNAs and rRNAs usually are very stable; mRNAs vary

considerably (minutes to months).

• Stability may change in response to regulatory signals

and is thought to be a major regulatory control point.
 Post-translational control - protein
degradation
• Proteins can be short-lived (e.g., steroid receptors) or
long-lived (e.g., lens proteins in your eyes).

• This is a cells last change to affect gene expression.

• Protease, enzymes that break down proteins, are

confined to lysosomes and proteasomes.
 Post-translational control - protein
degradation
• When a protein is tagged by a signaling protein, it
enters a proteasome to be degraded.