Eukaryotic Gene ExpressionEukaryotic Gene Expression
Managing the Complexities of Managing the Complexities of Controlling Eukaryotic GenesControlling Eukaryotic Genes
Prokaryotes vs. EukaryotesProkaryotes vs. EukaryotesProkaryotesProkaryotes EukaryotesEukaryotes
Closely related genes are Closely related genes are clustered togetherclustered together
Related genes are located on Related genes are located on different chromosomesdifferent chromosomes
Largely transcriptional Largely transcriptional controlcontrol
Significant transcriptional Significant transcriptional control; other levels of control control; other levels of control possiblepossible
Larger number of larger-sized Larger number of larger-sized genesgenes
Trans-acting sequence-Trans-acting sequence-specific DNA binding specific DNA binding proteinsproteins
Trans-acting sequence-Trans-acting sequence-specific DNA binding proteinsspecific DNA binding proteins
Proximal Cis-acting Proximal Cis-acting sequencessequences
Cis-acting sequences can be Cis-acting sequences can be located at significant located at significant distancesdistances
Control Points for Control Points for Gene Expression in EukaryotesGene Expression in Eukaryotes
DNADNA
RNARNA
ProteinProtein
transcriptiontranscription
translationtranslation
Transcriptional ControlTranscriptional Control
Translational ControlTranslational Control
Post-Translational ControlPost-Translational Control
Post-Transcriptional ControlPost-Transcriptional Control
Levels of Eukaryotic Chromatin StructureLevels of Eukaryotic Chromatin Structure
First level of chromatin coiling Nucleosome = DNA + histone proteins
Variations in chromatin condensation affect gene activity.Variations in chromatin condensation affect gene activity.
Transcriptional Regulation: Transcriptional Regulation: Effects of Chromatin StructureEffects of Chromatin Structure
Decompaction of chromatin: Decompaction of chromatin: • Transcription factors unwindTranscription factors unwind
nucleosomes in the area where nucleosomes in the area where transcription will begin, creating transcription will begin, creating DNAse I hypersensitive sites DNAse I hypersensitive sites
• RNA polymerase unwinds moreRNA polymerase unwinds more nucleosomes as transcription nucleosomes as transcription proceeds proceeds
Transcriptional Regulation: Transcriptional Regulation:
Effects of Chromatin StructureEffects of Chromatin Structure Acetylation of histone proteins (adding -CHAcetylation of histone proteins (adding -CH33CO) CO)
reduces DNA-histone interaction, permitting reduces DNA-histone interaction, permitting transcription factors to bind. transcription factors to bind.
Transcriptional Regulation: Transcriptional Regulation: Effects of Chromatin StructureEffects of Chromatin Structure
DNA MethylationDNA Methylation• DNA Methylation (adding -CHDNA Methylation (adding -CH33) can occur on ) can occur on
cytosines at CpG groupings near transcription cytosines at CpG groupings near transcription start sites start sites
•Inactive genes have methylated cytosines Inactive genes have methylated cytosines •Active genes have demethylated cytosinesActive genes have demethylated cytosines
• Acetylation of histones is associated withAcetylation of histones is associated with cytosine demethylation cytosine demethylation
Transcriptional Regulation: Control of InitiationTranscriptional Regulation: Control of Initiation
•Transcriptional Activator Proteins assist in the Transcriptional Activator Proteins assist in the formation or action of the basal transcription formation or action of the basal transcription apparatus apparatus
Transcriptional Regulation: Control of InitiationTranscriptional Regulation: Control of Initiation
• Transcriptional Activator Proteins bind to Transcriptional Activator Proteins bind to Enhancer sequences that increase Enhancer sequences that increase transcriptiontranscription– Enhancers can influence Enhancers can influence
promoters at distances promoters at distances of 50 kb or greater of 50 kb or greater due to DNA looping due to DNA looping mechanismmechanism
– Insulators control the direction of enhancer actionInsulators control the direction of enhancer action
Transcriptional Regulation: Control of InitiationTranscriptional Regulation: Control of Initiation
• Transcriptional Repressor Proteins have three Transcriptional Repressor Proteins have three possible modes of action possible modes of action
– compete with activators for DNA binding compete with activators for DNA binding sitessites
– bind to sites near activator site andbind to sites near activator site and inhibit inhibit activator contact with basal transcription activator contact with basal transcription apparatusapparatus
– interfere with assembly of basal transcription interfere with assembly of basal transcription apparatusapparatus
Applying Your KnowledgeApplying Your Knowledge
What effect does each of the following have on What effect does each of the following have on transcription? transcription?
• Methylation of Cytosines in CpG groups near Methylation of Cytosines in CpG groups near transcription initiation sitestranscription initiation sites
• Binding of an Activator Protein to an Enhancer Binding of an Activator Protein to an Enhancer SequenceSequence
• Acetylation of Histones in the nucleosomes Acetylation of Histones in the nucleosomes covering a gene sequencecovering a gene sequence
Thumbs Up: Increases TranscriptionThumbs Up: Increases TranscriptionThumbs Down: Decreases TranscriptionThumbs Down: Decreases TranscriptionThumbs Horizontal: No change Thumbs Horizontal: No change
Post-Transcriptional Regulation: Post-Transcriptional Regulation:
Alternative RNA SplicingAlternative RNA Splicing
Post-Transcriptional Regulation: Post-Transcriptional Regulation: RNA EditingRNA Editing
Base substitution after transcription =
Translational Regulation: Translational Regulation: RNA StabilityRNA Stability
• Degradation of mRNA can occur from the Degradation of mRNA can occur from the 5’ or 3’ end5’ or 3’ end
• Stability of mRNA depends on Stability of mRNA depends on – 5’ cap5’ cap– 3’ poly-A tail3’ poly-A tail– 5’ and 3’ UTRs: serve as binding sites for 5’ and 3’ UTRs: serve as binding sites for
regulatory factorsregulatory factors– Coding regionCoding region
• Example: Hormone prolactin increases Example: Hormone prolactin increases the longevity of casein mRNA coding for the longevity of casein mRNA coding for milk protein in lactating mammalsmilk protein in lactating mammals
Translational RegulationTranslational Regulation
• Masking of mRNAsMasking of mRNAs– Many species store mRNAs in the cytoplasm Many species store mRNAs in the cytoplasm
of the egg. These mRNAs are inactive due of the egg. These mRNAs are inactive due to masking by proteins. Fertilization of the to masking by proteins. Fertilization of the egg initiates unmasking and translation of egg initiates unmasking and translation of these mRNAs.these mRNAs.
• Availability of specific tRNAsAvailability of specific tRNAs– In the embryonic development of a In the embryonic development of a
hornworm, an mRNA is present from day 1 hornworm, an mRNA is present from day 1 but a specific tRNA needed for its translation but a specific tRNA needed for its translation is not produced until day 6.is not produced until day 6.
Translational Regulation:Translational Regulation:RNA SilencingRNA Silencing
Small interfering
RNAs
RNA-induced silencing complex
microRNAs
Post-Translational Modification: Post-Translational Modification: PhosphorylationPhosphorylation
Addition or removal of a Addition or removal of a phosphate group is a phosphate group is a common way to change common way to change protein activity. protein activity.
Post-Translational Modification: Post-Translational Modification: Peptide cleavagePeptide cleavage
Proteins that have an inactive form after Proteins that have an inactive form after
synthesis are activated by removal of a synthesis are activated by removal of a small number of amino acids. small number of amino acids. ProthrombinProthrombin
ThrombinThrombin
Cleavage
FibrinFibrinpolymer polymer (blood clot)(blood clot)
FibrinogenFibrinogen
FibrinFibrin
Cleavage
Activation of blood clotting factors by cleavage
Applying Your KnowledgeApplying Your Knowledge
Which type of control is demonstrated by Which type of control is demonstrated by • Alternative RNA splicing mechanisms that give rise Alternative RNA splicing mechanisms that give rise
to different protein products? to different protein products? • Addition of a phosphate group to activate a protein?Addition of a phosphate group to activate a protein?• Increased stability of mRNA in the presence of a Increased stability of mRNA in the presence of a
regulator molecule? regulator molecule? • Binding of a repressor protein to the regulatory Binding of a repressor protein to the regulatory
promoter so that an activator protein is unable to promoter so that an activator protein is unable to bind to this site?bind to this site?
1.1. Transcriptional ControlTranscriptional Control2.2. Post-Transcriptional ControlPost-Transcriptional Control3.3. Translational ControlTranslational Control4.4. Post-Translational Control Post-Translational Control