Download Chapter 18 – Eukaryotic Gene Regulation Cell Differentiation • All

Chapter 18 – Eukaryotic Gene Regulation
Cell Differentiation
 All cells have complete DNA set
o 6 billion nucleotide pairs
 Roughly 6 ft laid end to end
 Differential Gene Expression
o Varying sites & levels of control account for different cell types
o Starts at embryonic development
Chromatin (DNA + Protein)
 Histones
o Most common chromatin protein
o Large amounts of (+) charged amino acids (arg & lys)
 Interact w/ (-) charged DNA
o 5 types (4 core & 1 linker)
 Nucleosome
o DNA loops twice around 4 dimers of core histones (8 histones)
 Histone tails extend outwards
o Linker histone will help to link neighboring nucleosomes
o Scaffolding proteins can further condense chromatin
 Degrees of Condensation
o Euchromatin
 Loosely packed & can be transcribed
o Heterochromatin
 Densely packed & can’t be transcribed
 Some structural (centromere & telomere)
o Can be altered back & forth
Regulation Methods
 Chromatin Modification
o Histone Acetylation
 Acetyl group added to histone tails
 Enzyme catalyzes transfer from an acetyl CoA to lysine (now neutral)
 Nucleosomes not as strongly attracted & chromatin loosens for transcription
 Deacetylation has opposite effect
o Histone Phosphorylation loosens & Methylation tightens
o Histone Code Hypothesis – condensation from order & combinations of change
 DNA Methylation
o Enzyme attaches a methyl to cytosine
 Usually next to a guanine (CpG site)
 Promotes condensing & inactivity
o Proteins bind methylated DNA & recruit deacetylation enzymes
 Inactive DNA highly methylated
 Genes more methylated in cells where they aren’t expressed
o Once methylated, genes usually keep it thru synthesis (e.g. imprinting)
o Epigenetic Inheritance
 Genome = DNA Sequence (largely static)
 Epigenome incorporates all the changes to chromatin that occur thru lifetime
 Helps controls gene expression
 Affected by development, diet, drugs, environmental chemicals, aging
 Reversible & unpredictable
 Can be passed on to offspring
o Lamarck…We’re Sorry
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Transcriptional Regulation
o Transcription factors (TFs) must bind to DNA for transcription to occur
o Control Elements
 Noncoding DNA stretches of DNA that are binding sites of TFs
 General Transcription factors required for all transcription
 Discussed in Ch 17
 Specific Transcription Factors
 Needed for high levels of transcription at certain specific times
 Enhancers
o Distal control elements that can be 1000s of nucleotides away
o One gene may have many enhancers
 Each enhancer associated w/ only one gene
o Activator
 TF that binds to enhancer & activates transcription
 Repressors (TFs) bind to silence
 Have two domains
 DNA-binding domain
 Activation domain – initiates protein to protein
binding w/ TFs (mediators)
 DNA-bending protein aligns activators w/ general TF
(transcription complex forms)
o Only a few types of enhancer sequences
Alternate RNA Splicing
o Different mature mRNA transcripts can be made from the same pre-mRNA
 Spliceosomes regulate by removing different introns
 1 Drosophila gene found that can make 19,000 different membrane proteins
mRNA Degradation
o Often regulated by areas in the untranslated regions (UTR) of mRNA
o Longer lived mRNA is translated more
 Hemoglobin transcripts are long-lived as they are used continuously
 Growth factor transcripts often short-lived
Translational Regulation
o Regulatory proteins can bind to UTR & prevent attachment to ribosomes
o Poly-A tail too short for translation to start
 At correct time, tail lengthened
o Global control – a protein factor needed for all translation is activated (e.g. just after
fertilization)
Posttranslational Modification
o Different methods
 Polypeptide cleaved
 Phosphate (other functional group) added
 Sugars added
 Cofactor added (e.g. heme)
o Once structurally ready, must be sent to destination
Protein Degradation
o Protein life span has a large role in regulation
 Cyclins (cell cycle) short-lived, while hemoglobin & neurotransmitters not
o Proteosome
 Large complex that breaks down proteins
 ‘Dying’ proteins marked w/ ubiquitin
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Noncoding RNA
o Non-protein coding RNA
 Very small amount of DNA is for proteins (mRNA), tRNA, rRNA
 1% segment of human genome studied closely transcribed 90% of DNA
 Noncoding RNA found to regulate gene expression at two points
 MicroRNA (miRNA)
 Halt translation by binding to mRNA
 Formation
o Long transcript made & folds over itself creating hairpins w/ loops
o Dicer (enzyme) cuts each end of hairpin
o Protein complex picks up hairpin
o One strand degraded, other can bind
 miRNA-protein complex will bind mRNA & either degrade it or bind to it
 Small Interfering RNA (siRNA)
 Inhibit gene expression by altering chromatin configuration
o Called RNA interference
 Can block large regions of chromosome or a few genes
 Formed from long, double-stranded, & linear RNA precursor
Genetic Program
 Cell Division – increase # of cells
 Cell Differentiation – process of cell becoming specialized
 Morphogenesis – physical processes that give shape
 Cytoplasmic Determinants
o Maternal substances already in egg are spread unevenly
o Proteins, organelles, RNA, etc.
o After zygote divides, different cells have different substances
o Different gene expression
 Induction
o Nearby embryonic cells send out signal molecules
o Hit receptor molecules & trigger a signal transduction pathway
o Transcription altered
o Starts process of determination
 Cells go from totipotent to some determinant level
 Determination commits cell to its final state (like a switch)
 Cell will now undergo differentiation
 Differentiation marked by production of tissue-specific proteins
 myoD Gene (One of Master Regulatory Gene for Muscle Cells)
o Once turned on, cell is ‘determined’ & differentiation will begin
 MyoD protein is a TF (activator) that binds to many enhancers (itself, other TFs for
muscle proteins) & it blocks cell cycle
o Embryonic precursor – gene inactive
o Myoblast – gene active (determined)
o Muscle fiber – cell fully differentiated
 Pattern Formation
o Development of spatial organization of tissues & organs
o Animals start w/ major axes
 Anterior/Posterior, Dorsal/Ventral, Right/Left
o Lewis, Nüsslein-Volhard, & Eric Wieschaus (Nobel Prize in 1995)
 1,200 Pattern Development Genes in Embryo
 120 Essential Genes for Normal Segmentation
Cancer
 Results from genetic changes affecting cell cycle control
o Tumor
 HPV, Epstein-Barr, HHV-8
o Mutations
 Oncogenes are genes that cause cancer
 Proto-Oncogenes
o Normal versions of oncogenes that are responsible for cell growth & division
o Proto-Oncogenes can be converted to oncogenes
 DNA moves within genome, if it ends up near an active promoter, transcription
may increase
 Amplification of a proto-oncogene increases the number of copies of the gene
 Point mutations in the proto-oncogene or its control elements can cause an increase
in gene expression
 Tumor-Suppressor Genes
o Help prevent uncontrolled cell growth
o Their proteins function…
 Repair damaged DNA
 Control cell adhesion
 Inhibit cell cycle in cell-signaling pathway
o Mutations that decrease their proteins may contribute to cancer onset
 ras Gene
o Proto-Oncogene
o Protein product is a G protein
 Molecular switch that is activated by external signal
 Turned ‘on’ by GTP & starts a protein kinase cascade stimulating cell cycle
o Mutations can cause hyperactivity
 p53 Tumor-Suppressor Gene
o Normally it halts cell cycle when DNA damage occurs
 Prevents passing of mutations to daughter cells
o Mutations prevent suppression of the cell cycle
o Mutations of ras & p53 genes are very common in all cancers
 Multistep Model of Cancer
o Multiple mutations are generally needed for full-fledged cancer; thus the incidence
increases with age
 At DNA level, a cancerous cell is usually characterized by at least one active
oncogene & mutation of several tumor-suppressor genes
o Oncogenes and/or mutant alleles of tumor-suppressor genes can be inherited
 Tumor-suppressor gene adenomatous polyposis coli common w/ colorectal cancer
 BRCA1 or BRCA2 gene are found in at least half of inherited breast cancers