MCDB 436 (15): Epigenetic Modifications

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human genome
98% shared with chimps - human genome encodes for 30k genes, C elegans 20k (many human analogues)
organization of the genome
DNA (2nm) < nucleosome (11nm; histone core and DNA) < chromatin (30nm, 300nm, 700nm) < chromosome (1400nm)
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types of epigenetic modifications
1) DNA methylation - at cytosine in CpG dinucleotide area (5mCpG) 2) histone modification - chromatin remodeling via post-translational modification of histones
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DNA methylation
(for mammals); REVERSIBLE PROCESS DNMT enzyme catalyzes the covalent attachment of a methyl group to the C5 position residues in CpG dinuc DNA sequences introduced methylation patterns are preserved and maintained by DNMT1 during replication
preserve and maintain methylation patterns during replication
removes the epigenetic modification
responsible for de novo methylation - C5 position of cytosine residues in CpG dinucleotide DNA sequences
effect of DNA methylation on chromatin
results in condensed chromatin, leading to transcription inactivation
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histone subunits and their products
H3 + H4 -> H3-H4 dimer -> H3-H4 tetramer H2A + H2B -> H2A-H2B dimer -> tetramer + dimer = histone octamer
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histone protein structure
histone tail: can be acetylated, methylated, phosphorylated, or ubiquitinated histone fold
four major types of histone modifications
histone acetylation - on Lys (K) phosphorylation - on Ser/Thr (S/T) methylation - on His/Lys/Arg (H/K/R) ubiquitination
effects of histone modification on chromatin
modifications to histone tails render chromatin into open or closed conformation - tighter wrapping = less accessible; looser wrapping = accessible DNA -> transcription methyl = condensed acetyl = loosened
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histone methylation
catalyzed by histone methyltransferase enzyme (HMT) - associated with activation OR repression of gene expression (depends on histone protein + AA residue) - occurs on Arg, Lys, His
Lys methylation
monomethylated (me1), dimethylated (me2), or trimethylated (me3) on epsilon-amine group
Arg methylation
monomethylated (me1), symmetrically dimethylated (me2s), or asymmetrically dimethylated (me2a) on guanidinyl group
His methylation
monomethylated (me1)
histone methylation abbreviations
H3K4me3 - Histidine 3 methylated - Lysine 4 trimethylated H4K20me1 - histidine 4 methylated - lysine 20 monomethylated
histone acetylation
dynamic process regulated by histone aceyltransferase (HAT) and histone deacetylase enzyme (HDAC)
RELAX chromatin -> promote interaction of RNA-polymerase and other TFs with DNA and activation of gene expression (relax; take your hat off, stay a while)
mediate CLOSED chromatin conformation -> downregulation of gene expression (c = closed/condensed)
cell differentiation
a biological process wherein a cell develops and acquires a more specialized form and function - changes may include cell shape, size, membrane potential, metabolic activities, responsiveness, etc - changes brought about by modifications in gene expressions; crucial component of the cell differentiation process
differentiated cell
a cell that has changed in form and matured from being generalized into being more specific in terms of function
undifferentiated cell
a progenitor cell that is yet to undergo cellular differentiation
T cell differentiation
CD4 and CD8 T cells leave the thymus and enter circulation as resting cells in the G0 stage - 2x as many CD4 than CD8
naive T cell activation/proliferation
characteristics: condensed chromatin, very little cytoplasm, and little transcriptional activity can activate by recognizing Ag-MHC complex on APC/target cell - IL-2 -> IL2R -> proliferation -> 48hrs, enlarges into blast cell and undergoes rounds of cell division -> effector or memory cells
conversion of a normal cell into a tumor cell - changes at cellular, genetic, and epigenetic levels and abnormal cell division
6 hallmarks of cancer
1) sustaining proliferative signaling 2) evading growth suppressors 3) activating invasion and metastasis 4) enabling replicative immorality 5) inducing angiogenesis 6) resisting cell death
sustaining proliferative signaling
- the accelerator signals instruct cells to grow and divide chronically - formation of oncogenes
genes that transform normal cells into cancer cells
discovery of Rous Sarcoma Virus
by peyton rous, nobel prize/physiology or medicine chicken with sarcoma in breast muscle -> remove sarcoma and break up into small chunks of tissue -> grind up sarcoma with sand -> collect filtrate that has passed through fine-pore filter -> inject filtrate into young chicken -> observe sarcoma in injected chicken
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result of RSV discovery
RSV can transform infected cells into tumor cells - with sand, the cell membrane broke -> no individual cells result: tumor is not caused by another tumor cells. trigger of sarcoma = RSV, a single viral particle
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RSV genome
contains core proteins, reverse transcriptase, envelope protein, and Src
first human oncogene
Ras oncogene
Ras oncogene
a constitutively activated form of RAS (KRAS, HRAS, NRAS). can stimulate cell growth without any growth factor - proto-oncogene = ras, oncogene = mutated ras
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how proto-oncogenes beome oncogenes
1) mutation (point/delete/inser) -> hyperactive protein 2) gene amplification -> greatly overproduced 3) chromosome translocation (promoter/gene fusion) -> abnormal production of normal protein or novel protein
classification of oncogenes
1) growth factors (PDGF) 2) growth factor receptors (EGFR, PDGFR) 3) signal transducers (Ras, Src, Abl) 4) cell cycle regulators (cyclin D, CDK4) 5) transcription factors (Myc, MITF) 6) anti-apoptotic regulators
oncogene; translocations lead to over-expression -> favors prolonged survival of the cell and confers resistance to the cytotoxic effect of chemotherapeutic agents
MYC expression
transcription factor oncogene patients: > 10 copies of N-myc = lower rate of survival mice: bcl-2 alone = lived myc alone = less likely to live myc + bcl-2 = guaranteed death
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Philadelphia chromosome
ABL translocation from normal chromosome 9 onto chromosome 22 - found in 90% of chronic myeloid leukemia (CML) - gives rise to a BCR-ABL fusion protein (p210) with constitutive tyrosine kinase activity - inhibited by Gleevec
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competitive inhibitor of BCR-ABL blocks ATP binding to enzyme -> block chromosome formation -> block downstream signaling cascade
tumor suppressor genes
encoded proteins that negatively regulate cell proliferation in their normal state - lost or inactivated in many tumors, contributing to abnormal proliferation of tumor cells (P53, PTEN, etc)
cell cycle regulator; first human tumor suppressor gene ID'd - retinoblastoma requires loss of both functional copies of Rb gene
inactivated in many cancers; mutations of p53 in about 50% of all cancers - normally responsible for cell cycle arrest and apoptosis
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lipid a protein phosphatase mutated in many cancers
oncogenes vs tumor suppressor genes
- oncogenes: activation increases cancer risk. mutated form of proto-onco gene. gain-of-function mutation can overactivate a proto-oncogene to make it an oncogene - tumor suppressor genes (TSG): activation decreases cancer risk; loss-of-funcion can lead to loss of activity, allowing for cancer to occur
resisting cell death
avoiding assisted suicide of outlaw cells; abrogation of the inborn willingness of cells to die for the benefit of the organism - increases expression of anti-apoptotic Bcl-2 family proteins - down regulating pro-apoptotic Bcl-2 family members
Bcl-2 and B cell lymphoma
alterations in the Bcl-2 family of proteins (increased expression -> anti-apoptosis)
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enabling replicative immorality
circumventing a counting mechanism that disrupts continuing cell division when a set limit is reached - telomere activity related
a region of repetitive nucleotide sequences at each end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes
telomeres and cancer
- cancer cells maintain their telomeres (90% by increasing production of telomerase) - telomerase: adds telomeric DNA to the ends of chromosomes
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telomerase reverse transcriptise - in HEK cells: without hTERT, eventually die. with hTERT, HEK cells keep growing
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inducing angiogenesis
turning on new blood vessel growth to feed and nurture the growing mass of cancer cells - hypoxia-inducible transcription factor (HIF) system
hypoxia-inducible transcription factor (HIF) system
genes that indirectly/directly induce angiogenesis and other stress-adaptive capabilities of cancer cells 1) tumor secretes VEGF 2) VEGF increases blood vessel expression and movement to tumor 3) tumor has increased blood supply
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activating invasion and metastasis
- malignant tumor cells tend to invade locally and metastasize to other organs - EMT and seed and soil hypothesis
epithelia mesenchymal transition (EMT)
epithelia cells acquire mesenchymal traits - loss of adherent junctions, change in cellular morphology, increased motility - roughly 90% of cancers arise as carcinomas in epithelial (surface) tissue
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tumor cell invasion and metastasis
tumor splits into mesenchymal-like cancer cells of a collective invasion of epithelial-like + mesenchymal-like cancer cells -> intravasation -> metastasis -> extravasation
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seed and soil hypothesis
tumor cells grow preferentially in the microenvironment of select organs - metastases resulted only when the appropriate seed was implanted in its suitable soil - 50% related to brain; might be because brain is a hospitable environment