Transcript Regulation of Gene Expression

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
Gene regulatory
protein
• Short DNA segments of defined sequence
• Gene regulatory proteins that bind to a specific sequence
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
General function: promote assembly of RNA polymerase II
and general transcription factors at the
promoter to allow transcription to begin
Can facilitate:
• Recruitment of RNA polymerase II
holoenzyme complex
• Assembly of general transcription factors
• Alterations in chromatin structure
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 Genome
1962 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 Islands
• CG dinucleotides deficient,
preferentially found at promoters of
many genes
• 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
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
Attenuation of trp
operon:
• Coupled to
translation
• Depends upon
levels of tryptophan
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 editing
ADAR recognizes
RNA structure
C to U editing
ApoB 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 PostTranscriptional Regulation
Aconitase:
• 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