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Gene Expression
• Expression of different set of genes in each cell type
Steps For Regulating Gene Expression
• Transcriptional control is most common
Components For Regulating Transcription
• Short DNA segments of defined sequence• Gene regulatory proteins that bind to a specific sequence
Gene regulatoryprotein
Specific Binding of Gene Regulatory Proteins
• Structural motifs recognize specific DNA sequences• Amino acids interact with outside of bases
Trp Operon
• Multiple genes transcribed as one mRNA molecule• Transcribed from a single promoter
Regulation Of Tryptophan Operon
• On only when tryptophan is absent• Negative regulation by tryptophan repressor• Repressor is active only when tryptophan is bound to
it
Regulation Of Lac Operon
• On only when lactose is present and glucose is absent• Positive regulation by CAP in response to glucose• Negative regulation by lac repressor in response to lactose
Transcriptional Control Region Of Eucaryotic Gene
• Multiple binding sites for gene regulatory proteins• Regulatory sequences known as enhancers can be
thousands of nucleotides from promoter
Eucaryotic Gene Activator Proteins
• Recruitment of RNA polymerase II holoenzyme complex
• Assembly of general transcription factors• Alterations in chromatin structure
Can facilitate:
General function: promote assembly of RNA polymerase II and general transcription factors at the
promoter to allow transcription to begin
Recruitment Of RNA Polymerase II Holoenzyme
• Gene activators attract holoenzyme complex to promoter
Assembly Of General Transcription Factors
• Gene activators promote assembly of some general transcription factors
Alterations In Chromatin Structure
• Recruitment of histone modifying proteins, histone chaperones, and chromatin remodeling complexes
• Can make chromatin more accessible to transcription machinery
Histone Code
• Proteins recognize specific patterns of histone modification• Acetylation promotes activation• Methylation: some residues promote activation some residues promote repression
An example of writing and reading the histone code
Gene Repressor Proteins
TFs in Human Genome1962 estimated (8% of genome)
Gene regulatory proteins, general transcription factors, coactivators, corepressors, chromatin and histone modifiers
Common structural classes of gene regulatory proteins
Zinc finger (762)Homeobox (199)Basic helix-loop-helix (117)Beta-scaffold (87) Basic-leucine zipper (72)Nuclear hormone receptor (49) Forkhead (40) Ets (31)
Examples of TF Classes
Zinc finger Basic helix-loop-helix
• Classes have common motif for DNA binding• Differences within a class determine specificity
Regulating Activity Of Gene Regulatory Proteins
• Modulates pattern of gene expression in response to cell’s environment
DNA Methylation
• Methylation of C at certain CG• Pattern maintained by
maintenance methyl transferases
Effect Of DNA Methylation
• Reinforce inactivation of genes that are not expressed
Genomic Imprinting
• Expression of few genes occurs only from paternal or maternal allele
• Methylation pattern established in germ cells and maintained in offspring
CG IslandsCG
Met
hyl gr
oup
• Many CG lost during vertebrate evolution due to accidental deamination, inefficient repair of methylated CG found at inactive DNA in germ cells
• Promoters of active (often housekeeping) genes in germ cells not methylated, deamination repaired accurately, preserved as CG islands
• CG dinucleotides deficient, preferentially found at promoters of many genes
Epigenetic Mechanisms• Epigenetic inheritance- daughter cells maintain
memory of gene expression pattern of parent cells• Histone modifications, DNA methylation, and
positive feedback loops contribute to epigenetic inheritance
Epigenetic Mechanisms
Histone reader-writers that recognize same histone modification they catalyze
Gene regulatory proteins that activate their own expression
Coordinating Gene Expression
• Decisive event within combinatorial control• Single gene regulatory protein can be decisive,
can control set
Generate Specialized Cell Types
Myogenic helix-loop-helix proteins (MyoD, etc.) and skeletal muscle•Trigger becoming muscle cell•Muscle-specific expression•Coordinately activate muscle genes•Specific for muscle genes
Transcription Attenuation
• Coupled to translation
• Depends upon levels of tryptophan
Attenuation of trp operon:
Alternative Splicing
• Alternative choices for certain splice sites in primary RNA transcript
Regulation Of Alternative Splicing
• Splicing decision controlled by regulatory protein that binds primary RNA transcript
Regulation Of RNA Cleavage In Antibody Genes
• First cleavage site encountered is suboptimal and skipped in unstimulated cells
• Antigen stimulation increases CstF levels to promote cleavage at first site
RNA Editing
A to I editingADAR recognizes RNA structure
C to U editingApoB example
HIV Genome
• Several products through alternative splicing• Some have introns that normally cannot be exported
Regulation Of Nuclear Export Of HIV RNA
• Rev directs export of viral RNAs that contain introns
• Rev levels sufficient to promote export late in infection
Gene Silencing by microRNAs
• miRNAs are dsRNAs processed from hairpin precursors
• miRNA complex binds 3’ UTR of mRNA targets
• Translation repression / mRNA degradation
Translational Repressors
• Bind specific sequences in 5’ or 3’ UTR of RNA
Phosphorylation Of eIF-2
• Activation of specific protein kinases• Reduction of overall protein synthesis by inhibiting
eIF-2B-mediated exchange of GDP→GTP on eIF-2
Regulation Of Translation In Reticulocytes
• Globin translation coordinated with Heme levels• HRI phosphorylates eIF-2• HRI active in absence of heme, inactive in presence of heme
Mechanisms Of mRNA Decay
• Deadenylation-dependent- gradual polyA shortening followed by rapid degradation
• Deadenylation-independent- endonucleolytic removal of polyA
Iron-Mediated Post-Transcriptional Regulation
• Protein that binds to ferritin & transferrin receptor mRNAs• Disassociates from RNA when bound to iron• Blocks translation when bound to 5’ UTR of ferritin mRNA• Stabilizes mRNA when bound to 3’ UTR of transferrin receptor
Aconitase: