epigenetic and expression regulation -.ppt
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Epigenetic and Epigenetic and Expression Expression RegulationRegulation
Sofia MubarikaSofia Mubarika
Variability :
genomic variations
Gene expression, alternative splicing
Protein cleavage,modification
DNA RNA PROTEIN
Genome : 40.000 genes
Transcriptome > 100.000 RNA
Proteome > 400.000 proteins
Central Dogma
DNA
RNA
Protein
Transcription
Translation
A gene is expressed in 3 steps:
1) Transcription: RNA synthesis
2) Splicing: removal of intron sequence from RNA
3) Translation: Protein synthesis
Central Dogma
DNA
RNA
Protein
Genotype
RNA function & structure
Protein sequence
Protein structure
Protein Function
Phenotype
Transcriptional MechanismsTranscriptional Mechanisms Type of promoters & RNA polymeraseType of promoters & RNA polymerase Control of TranscriptionControl of Transcription
ConstitutiveConstitutive InducibleInducible RepressibleRepressible
Transcription Factors and TFBSTranscription Factors and TFBS Translational MechanismsTranslational Mechanisms
Micro RNAs (miRNAs and RITS complexes)Micro RNAs (miRNAs and RITS complexes) Translational controlTranslational control mRNA degradationmRNA degradation Promoter activationPromoter activation
Silencer RNAs (siRNAs & RISC complexes) degrading Silencer RNAs (siRNAs & RISC complexes) degrading mRNAmRNA
Epigenetic MechanismsEpigenetic Mechanisms Chromatin remodelingChromatin remodeling Histone modifications (acetylation, phosphorylation, Histone modifications (acetylation, phosphorylation,
methylation …)methylation …) DNA methylationDNA methylation
Gene Regulatory MechanismsGene Regulatory Mechanisms
Epigenetics ??Epigenetics ??
Epigenetics is:Epigenetics is: Reversible changes in Reversible changes in
gene expressiongene expression Without changes in Without changes in
DNA sequence DNA sequence Can be inherited Can be inherited
from precursor cellsfrom precursor cells
Epigenetic Epigenetic information is information is included in the included in the epigenomeepigenome
Genome
DNA
Gene Expression
Epigenome
Chromatin
Phenotype
Chromatin – Key Component of Chromatin – Key Component of Epigenetic MechanismsEpigenetic Mechanisms
Chromatin organizes genes to be accessible Chromatin organizes genes to be accessible for transcription, replication, and repairfor transcription, replication, and repair
nucleosomehistone
DNA
chromatin
Cellular DNA is packaged into a structure called chromatin
The unit of chromatin is the nucleosome, a complex of a histone tetramer with approx. 125 bp of DNA wound around it
DNA Methylation can Prevent Gene DNA Methylation can Prevent Gene ExpressionExpression
DNA methylation involves the transfer of methyl groups to DNA methylation involves the transfer of methyl groups to cytosine residues in DNA by DNA methyltransferases (DNMTs)cytosine residues in DNA by DNA methyltransferases (DNMTs)
May prevent transcription factors from binding to DNAMay prevent transcription factors from binding to DNA
May serve as binding site for methylated DNA-binding May serve as binding site for methylated DNA-binding proteins, proteins, such as MECP2, which then recruit HDACssuch as MECP2, which then recruit HDACs
MeMe
MeMe
MeMe
Me
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DNMT DNMT
DNMT DNMT
Geneexpression
Geneexpression
TF
TF
HMT
Histone Methylation can Affect Histone Methylation can Affect Chromatin StructureChromatin Structure
HMT
Histone methylation by histone methyltransferases Histone methylation by histone methyltransferases (HMTs) can recruit HDACs, leading to:(HMTs) can recruit HDACs, leading to: Closed chromatin structureClosed chromatin structure Gene silencingGene silencing
HDAC
HDAC
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MeMeMe
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Geneexpression
Geneexpression
Other Epigenetic Modifications of Other Epigenetic Modifications of Histones and DNAHistones and DNA
HistoneAcetylation
AcMeMeMeMe
HistoneMethylation
Me
DNAMethylation
Epigenetic Modifications to Histones and DNA Can Epigenetic Modifications to Histones and DNA Can Cooperate to Silence Gene ExpressionCooperate to Silence Gene Expression
Gene expression
• Epigenetic modifications can cooperate to silence gene expression
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Me
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DNMT DNMT
HDAC
HDAC
TF
Imbalanced Levels of Histone Imbalanced Levels of Histone Acetylation Acetylation Deregulate Gene Deregulate Gene
ExpressionExpression
Increased HDAC activity or decreased HAT activity may Increased HDAC activity or decreased HAT activity may result in aberrant gene expression, contributing to cancerresult in aberrant gene expression, contributing to cancer
HISTONE ACETYLATION
HISTONE DEACETYLATION
Acetylated Histones
Open chromatin Transcription factors can access DNA
Deacetylated Histones
Closed chromatin Transcription factors cannot access DNA
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HDAC
HAT
TF
TF
Epigenetics Play Important Roles in Normal Epigenetics Play Important Roles in Normal Cellular Development and in CancerCellular Development and in Cancer
Epigenetic mechanisms can regulate genes involved in Epigenetic mechanisms can regulate genes involved in differentiation, cell cycle, and cell survivaldifferentiation, cell cycle, and cell survival
Deregulation of epigenetic mechanisms results in aberrant gene Deregulation of epigenetic mechanisms results in aberrant gene expression, which can lead to cancerexpression, which can lead to cancer
Reversal of deregulated epigenetic changes is a rational Reversal of deregulated epigenetic changes is a rational strategy for targeting cancerstrategy for targeting cancer
EPIGENETICS
Normal differentiated cells, e.g. embryonic cells, hematopoetic cells
Malignant progenitor cell Tumor
Normal epigenetic mechanisms
Deregulated epigenetic mechanisms
Example: Replication errors
GENETIC
Altered DNA/mRNA/proteins
Altered DNA sequence
Historically, Cancer Was Considered to Historically, Cancer Was Considered to be Driven Mostly by be Driven Mostly by Genetic ChangesGenetic Changes
X X
Oncogenesis
Tumor
Example: Replication errors
GENETIC EPIGENETIC
Example: Chromatin modification errors
Altered DNA/mRNA/proteins
Altered DNA sequence
Altered levels ofmiRNA/proteins
Alteredchromatin structure
Epigenetic ChangesEpigenetic Changes Important in Important in Causing CancerCausing Cancer
X X
Oncogenesis
Tumor
Cancer epigeneticsCancer epigenetics Epigenetic alterationsEpigenetic alterations found in almost found in almost all all
types of cancerstypes of cancers 50% of genes50% of genes that cause that cause familial forms of cancerfamilial forms of cancer
are found are found silenced silenced in sporadic forms of cancerin sporadic forms of cancer Large number of Large number of epigenetic alterationsepigenetic alterations found found
in cancer cells in cancer cells due todue to:: Stochastic occurrencesStochastic occurrences that accumulate with that accumulate with
age, selected for during tumour formationage, selected for during tumour formation Caused by Caused by defectsdefects in components of the in components of the
epigenetic machineryepigenetic machinery Repair geneRepair gene (repair defects) (repair defects) alterationsalterations
Cancer epigeneticsCancer epigenetics
Changes in 5-me-C distribution in DNAChanges in 5-me-C distribution in DNA Hypermethylation Hypermethylation of of promoter CpG islands (found in promoter CpG islands (found in
~50% genes)~50% genes) associated with TSGs associated with TSGs Decreased expression levels/silencing of TSGsDecreased expression levels/silencing of TSGs Increased mutationsIncreased mutations
Global hypomethylation Global hypomethylation Chromosome instability (particularly pericentromeric Chromosome instability (particularly pericentromeric
repeats) repeats) Activation of virusesActivation of viruses Activation of proto-oncogeneActivation of proto-oncogene
Changes in chromatin structureChanges in chromatin structure Histone modifications:Histone modifications:
Histone deacetylationHistone deacetylation Histone methylation (H3-K9); demethylation (H3-K4)Histone methylation (H3-K9); demethylation (H3-K4) Histone sumoylationHistone sumoylation
Heterochromatin-associated proteinsHeterochromatin-associated proteins
GENETIC EPIGENETIC
Epigenetics & Genetic Mutations Can Epigenetics & Genetic Mutations Can Cooperate to Promote OncogenesisCooperate to Promote Oncogenesis
↓ Tumor suppressor function
Oncogene function
↓ Tumor suppressor levels
Oncogene levels
Oncogenesis
Tumor
Epigenetics Play Important Roles in Epigenetics Play Important Roles in Normal & Cancer DevelopmentNormal & Cancer Development
Epigenetic mechanisms can regulate genes involved in Epigenetic mechanisms can regulate genes involved in differentiation, cell cycle, and cell survivaldifferentiation, cell cycle, and cell survival
Deregulation of epigenetic mechanisms results in aberrant gene Deregulation of epigenetic mechanisms results in aberrant gene expression, which can lead to cancerexpression, which can lead to cancer
Reversal of deregulated epigenetic changes is a rational Reversal of deregulated epigenetic changes is a rational strategy for targeting cancerstrategy for targeting cancer
EPIGENETICS
Normal differentiated cells, e.g. embryonic cells, hematopoetic cells
Malignant progenitor cell Tumor
Normal epigenetic mechanisms
Deregulated epigenetic mechanisms
Cancer Stem Cell Theory: the ‘Root’ Cancer Stem Cell Theory: the ‘Root’ of Cancer Growthof Cancer Growth
Tumor
Epigenetically altered, self-renewing cancer stem cells
Tumor Development
and Growth
Conventional Therapies May Target Tumor Conventional Therapies May Target Tumor Cells, Cells,
Not Cancer Stem CellsNot Cancer Stem Cells
Target tumor Cancer stem cells survive
Tumor regrowth
Conventionaltherapy
Epigenetic Therapy May Target Cancer Stem Epigenetic Therapy May Target Cancer Stem Cells and Tumor CellsCells and Tumor Cells
Target tumor and cancer stem cells
Tumor and cancer stem
cell death
No regrowth
Epigenetic therapy
Section 3: Therapeutic Targeting of Epigenetics
Section 1: Importance of Epigenetics in Cancer
Section 2: Mechanisms of Epigenetics: Focus on Deacetylation
Basic Epigenetic Mechanisms: Post Basic Epigenetic Mechanisms: Post Translational Modifications to Histones and Translational Modifications to Histones and
Base Changes in DNABase Changes in DNA
Epigenetic modifications of histones and DNA include:Epigenetic modifications of histones and DNA include: Histone acetylation and methylation, and DNA methylationHistone acetylation and methylation, and DNA methylation
HistoneAcetylation
HistoneMethylation
DNA Methylation
MeMeMeMeAc Me
Histone Proteins in Chromatin Can be Histone Proteins in Chromatin Can be Modified by AcetylationModified by Acetylation
HistoneMethylation
DNA Methylation
MeMeMeMeAc
Me
Histone Acetylation
Geneexpression
Epigenetic Changes can Alter Epigenetic Changes can Alter Chromatin Structure and Regulate Chromatin Structure and Regulate
Gene ExpressionGene Expression
Gene expression (transcription) requires DNA to be physically Gene expression (transcription) requires DNA to be physically accessible to transcription factors (TF)accessible to transcription factors (TF)
Epigenetic changes alter the structure of the chromatin, which Epigenetic changes alter the structure of the chromatin, which determines whether DNA is accessibledetermines whether DNA is accessible Open chromatin allows gene expression Open chromatin allows gene expression Closed chromatin prevents gene expression Closed chromatin prevents gene expression
Geneexpression
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TFTF
In Cancer, Changes in Chromatin In Cancer, Changes in Chromatin Structure Can Structure Can
Silence Tumor Suppressor GenesSilence Tumor Suppressor Genes
Silencing of tumor suppressor genes, a major process in Silencing of tumor suppressor genes, a major process in tumorigenesis, may result from epigenetic changes that tumorigenesis, may result from epigenetic changes that condense chromatin structure condense chromatin structure
Cancer cells
Tumor suppressorgene expression
Tumor suppressor gene expression
Normal cells
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Balance of Histone Acetylation is a Key Balance of Histone Acetylation is a Key Factor in Transcriptional Regulation in Factor in Transcriptional Regulation in
Normal Cells Normal Cells
HISTONE ACETYLATION
Acetylated Histones
Open chromatin Transcription factors can access DNA
Deacetylated Histones
Closed chromatin Transcription factors cannot access DNA
Geneexpression
Geneexpression
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HAT
TF
TF
Balance of Histone Acetylation is a Key Balance of Histone Acetylation is a Key Factor in Transcriptional Regulation in Factor in Transcriptional Regulation in
Normal CellsNormal Cells
HISTONE ACETYLATION
HISTONE DEACETYLATION
Acetylated Histones
Open chromatin Transcription factors can access DNA
HDAC
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HDAC
Geneexpression
HAT
Deacetylated Histones
Closed chromatin Transcription factors cannot access DNA
Geneexpression
TF
TF
Section 3: Therapeutic Targeting of Epigenetics
Section 1: Importance of Epigenetics in Cancer
Section 2: Mechanisms of Epigenetics: Focus on Deacetylation
Increased HDAC activity Increased HDAC activity associated with certain associated with certain tumors, can alter tumors, can alter expression of genes expression of genes involved in normal cell involved in normal cell development, resulting in:development, resulting in:
Loss of cell-cycle arrestLoss of cell-cycle arrest
Inhibition of Inhibition of differentiationdifferentiation
Cell growth and Cell growth and proliferation proliferation
Evasion of apoptosisEvasion of apoptosis
Migration and metastasisMigration and metastasis
Increased HDAC Activity Can Alter Gene Increased HDAC Activity Can Alter Gene Expression and Result in CancerExpression and Result in Cancer
Gene expression
Cell nucleus
HDACTF
Inhibition of HDAC Inhibition of HDAC activity can restore activity can restore the balance of the balance of histone acetylationhistone acetylation
Targeting HDAC Targeting HDAC activity may activity may therefore allow therefore allow re-expression of re-expression of silenced genes to silenced genes to reverse reverse oncogenesisoncogenesis
HDAC Inhibition Can Reverse HDAC Inhibition Can Reverse Altered Gene ExpressionAltered Gene Expression
Gene expression
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Differentiation
Growth control
Cell-cycle arrest
Apoptosis
Adhesion
Cell nucleus
HDACTF
DACInhibitor
Since DNA Since DNA methylation and methylation and histone histone deacetylation deacetylation can co-operate can co-operate to silence tumor to silence tumor suppressors, suppressors, inhibition of both inhibition of both DNMT and DNMT and HDACHDAC activities activities can synergize to can synergize to restore restore expression of expression of silenced genes silenced genes
Therapeutic Targeting of Both Histone and Therapeutic Targeting of Both Histone and DNA Modifications Can SynergizeDNA Modifications Can Synergize
DACInhibitor
Gene expression
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Cell nucleus
HDAC
DNMT
DNMTInhibitor
TF
Differentiation
Growth control
Cell-cycle arrest
Apoptosis
Adhesion
