human genome
Tags & Description
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)
types of epigenetic modifications
DNA methylation - at cytosine in CpG dinucleotide area (5mCpG)
histone modification - chromatin remodeling via post-translational modification of histones
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
DNMT1
preserve and maintain methylation patterns during replication
TET1-3
removes the epigenetic modification
DNMT3A/B
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
histone subunits and their products
H3 + H4 -> H3-H4 dimer -> H3-H4 tetramer
H2A + H2B -> H2A-H2B dimer ->
tetramer + dimer = histone octamer
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
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)
HAT
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)
HDAC
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
transformation
conversion of a normal cell into a tumor cell
changes at cellular, genetic, and epigenetic levels and abnormal cell division
6 hallmarks of cancer
sustaining proliferative signaling
evading growth suppressors
activating invasion and metastasis
enabling replicative immorality
inducing angiogenesis
resisting cell death
sustaining proliferative signaling
the accelerator signals instruct cells to grow and divide chronically
formation of oncogenes
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
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
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
how proto-oncogenes beome oncogenes
mutation (point/delete/inser) -> hyperactive protein
gene amplification -> greatly overproduced
chromosome translocation (promoter/gene fusion) -> abnormal production of normal protein or novel protein
classification of oncogenes
growth factors (PDGF)
growth factor receptors (EGFR, PDGFR)
signal transducers (Ras, Src, Abl)
cell cycle regulators (cyclin D, CDK4)
transcription factors (Myc, MITF)
anti-apoptotic regulators
BCL-2
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
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
Gleevec/imatinib
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)
Rb
cell cycle regulator; first human tumor suppressor gene ID'd
retinoblastoma requires loss of both functional copies of Rb gene
p53
inactivated in many cancers; mutations of p53 in about 50% of all cancers
normally responsible for cell cycle arrest and apoptosis
PTEN
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)
enabling replicative immorality
circumventing a counting mechanism that disrupts continuing cell division when a set limit is reached
telomere activity related
telomere
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
hTERT
telomerase reverse transcriptise
in HEK cells: without hTERT, eventually die. with hTERT, HEK cells keep growing
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
tumor secretes VEGF
VEGF increases blood vessel expression and movement to tumor
tumor has increased blood supply
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
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
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