Transcript Gene Regulation

Introns and Exons
• DNA is interrupted by short sequences that are
not in the final mRNA
– Called introns
– Exons = RNA kept in the final sequence
Gene Regulation
• Ability of an organisms to control which genes
are present in response to the environment
Prokaryotic cells turn genes on and off by
controlling transcription.
• A promotor is a DNA segment that allows a gene to
be transcribed.
• An operator is a part of DNA that turns a gene “on”
or ”off.”
• An operon includes a promoter, an operator, and
one or more structural genes that code for all the
proteins needed to do a job.
– Operons are most common in prokaryotes.
– The lac operon was one of the first examples of gene
regulation to be discovered.
– The lac operon has three genes that code for enzymes
that break down lactose.
•
The lac operon acts like a switch.
– The lac operon is “off” when lactose is not present.
– The lac operon is “on” when lactose is present.
Trp operon
lac operon
Points of control
• The control of gene expression
can occur at any step in the
pathway from gene to functional
protein
1. packing/unpacking DNA
2. transcription
3. mRNA processing
4. mRNA transport
5. translation
6. protein processing
7. protein degradation
1. DNA packing as gene control
• Degree of packing of DNA regulates transcription
– tightly wrapped around histones
• no transcription
• genes turned off
 heterochromatin
darker DNA (H) = tightly packed
 euchromatin
lighter DNA (E) = loosely packed
H
E
DNA methylation
• Methylation of DNA blocks transcription factors
– no transcription
 genes turned off
– attachment of methyl groups (–CH3) to cytosine
• C = cytosine
– nearly permanent inactivation of genes
• ex. inactivated mammalian X chromosome = Barr body
• Methylation results in a human disease called fragile X syndrome; FMR-1
gene is silenced by methylation.
Histone acetylation

Acetylation of histones unwinds DNA

loosely wrapped around histones



enables transcription
genes turned on
attachment of acetyl groups (–COCH3) to histones


conformational change in histone proteins
transcription factors have easier access to genes
Fig. 18.13
Methylation of H19 inactivates transcription
(involved in expression of insulin like growth factor)
Fig. 18.10a
Chromatin remodeling
Acetylation of histones enhances
access to promoter region and
facilitates transcription.
Epigenetic Inheritance
• Although the chromatin modifications just discussed
do not alter DNA sequence, they may be passed to
future generations of cells
• The inheritance of traits transmitted by mechanisms
not directly involving the nucleotide sequence is called
epigenetic inheritance
• http://learn.genetics.utah.edu/content/epigenetics/intro/
2. Transcription initiation
• Control regions on DNA
– promoter
• nearby control sequence on DNA (TATA box )
• binding of RNA polymerase & transcription factors
• “base” rate of transcription
– enhancer
• distant control
sequences on DNA
• binding of activator
proteins
• “enhanced” rate (high level)
of transcription
Model for Enhancer action
• Enhancer DNA sequences
– distant control sequences
• Activator proteins
– bind to enhancer sequence &
stimulates transcription
• Silencer proteins
– bind to enhancer sequence &
block gene transcription
Turning on Gene movie
Transcription complex
Activator Proteins
• regulatory proteins bind to DNA at distant
Enhancer Sites
enhancer sites
• increase the rate of transcription
regulatory sites on DNA distant
from gene
Enhancer
Activator
Activator
Activator
Coactivator
A
E
F
B
TFIID
RNA polymerase II
H
Core promoter
and initiation complex
Initiation Complex at Promoter Site binding site of RNA polymerase
Fig. 18-9-3
Promoter
Activators
DNA
Enhancer
Distal control
element
Gene
TATA
box
General
transcription
factors
DNA-bending
protein
Group of
mediator proteins
RNA
polymerase II
RNA
polymerase II
Transcription
initiation complex
RNA synthesis
3. Post-transcriptional control
• Alternative RNA splicing
– variable processing of exons creates a family of
proteins
•
•
RNA processing is also an important part of gene regulation in eukaryotes.
mRNA processing includes three major steps.
– Introns are removed and exons are spliced together.
– A cap is added.
– A tail is added.
Regulation by alternative splicing
Calcitonin generelated peptide
4. Regulation of mRNA degradation
• Life span of mRNA determines amount of
protein synthesis
– mRNA can last from hours to weeks
RNA processing movie
5. Control of translation
• Block initiation of translation stage
– regulatory proteins attach to 5' end of mRNA
• prevent attachment of ribosomal subunits & initiator
tRNA
• block translation of mRNA to protein
Control of translation movie
6-7. Protein processing & degradation
• Protein processing
– folding, cleaving, adding sugar groups,
targeting for transport
• Protein degradation
– ubiquitin tagging
– proteasome degradation
Protein processing movie
Concept 18.3: Noncoding RNAs play
multiple roles in controlling gene
expression
• Only a small fraction of DNA codes for proteins,
rRNA, and tRNA
• A significant amount of the genome may be
transcribed into noncoding RNAs
• Noncoding RNAs regulate gene expression at two
points: mRNA translation and chromatin
configuration
RNA interference
• Small interfering RNAs (siRNA)
– short segments of RNA (21-28 bases)
• bind to mRNA
• create sections of double-stranded mRNA
• “death” tag for mRNA
– triggers degradation of mRNA
– cause gene “silencing”
• post-transcriptional control
• turns off gene = no protein produced
siRNA
Action of siRNA
dicer
enzyme
mRNA for translation
siRNA
double-stranded
miRNA + siRNA
breakdown
enzyme
(RISC)
mRNA degraded
functionally turns
gene off
6
7
Gene Regulation
protein
processing &
degradation
1 & 2. transcription
- DNA packing
- transcription factors
5
initiation of
translation
4
mRNA
processing
5. translation
- block start of
translation
2
1
initiation of
transcription
3
mRNA splicing
3 & 4. post-transcription
- mRNA processing
- splicing
- 5’ cap & poly-A tail
- breakdown by siRNA
6 & 7. post-translation
- protein processing
- protein degradation
mRNA
4 protection
Cancers result from a series of genetic
changes in a cell lineage
– The incidence of cancer increases with age because multiple
somatic mutations are required to produce a cancerous cell
– As in many cancers, the development of colon cancer is gradual
Eukaryotic Gene Regulation
• Hox genes – controls
differentiation of genes
– Responsible for general body
pattern of most animals
– Order of genes is order of
body parts
Review questions
What does DNA polymerase do?
What does Helicase do?
What does ligase do?
Match the bases below.
5’ – A T C G T A – 3’
List 3 differences between RNA/DNA.
What are the 3 types of RNA?
Where does RNA go after it is made?
Transcribe the DNA below.
ATCGTA
What does RNA attach to when it leaves the
nucleus?
Amino Acids are the building block of ________.
What type of RNA brings an amino acid?
When does translation stop?
Where is the codon located? Anticodon?
What is a codon?
Translate the mRNA strand below.
AGCGAG
Translate the DNA strand below
ATG CTA TGCA