Regulation of Gene Expression Chapter 18 (18.1 & 18.2)

Gene Expression All cells contain the entire genome In theory, every cell could make every single protein encoded in the genome But that doesn’t happen! e.g. Lymphocytes of immune system are the only cells that make antibodies while red blood cells are the only cells that make the oxygen transport protein hemoglobin Or sometimes the environment will influence which proteins are made and when The spatial (space) and temporal (time) select transcription of certain genes is called gene expression

Gene Expression So how do different cells know which genes to use and which genes to ignore? It’s a little complicated so let’s start with the prokaryotes!

Regulation in Prokaryotes Bacterial cells only make gene products when they are needed Bacteria can use 2 methods to regulate this production: Feedback regulation of enzymes Gene expression regulation by the operon model

Regulation by Operons: Enzyme Production Basic idea: Clusters of functionally related genes are under coordinated control A single “on-off switch” The switch is a DNA segment called an operator Usually found inside the promoter An operon is everything involved: operator, promoter and genes the operon controls

Regulation by Operons Operons can be switched off by proteins called repressors Repressors prevent gene transcription by binding to operators and blocking RNA polymerase Repressors are gene products of separate regulatory genes Repressors can be active or inactive Corepressors make repressors active so they can turn operons off (allosteric regulation)

Regulation by Operons If repressor present and active: No transcription No gene products made If repressor absent or inactive: Transcription occurs Gene products made

Negative Gene Regulation Operons can be repressible or inducible Repressible operons are usually ON An active repressor can shut them off Inducible operons are usually OFF Inducer molecule inactivates repressor and therefore turns on operon Ex. lac operon is an inducible operon

Negative Gene Regulation Repressible operons usually found in anabolic pathways (i.e. Pathways that make bigger molecules) When enough product made, operon turns off Inducible operons usually found in catabolic pathways (i.e. Pathways that break down molecules) Presence of reactant molecule will turn on operon when necessary

Example of Inducible Operon: lac operon E.coli can metabolize both glucose or lactose as energy sources but it prefers glucose If environmental glucose is low and lactose is high, lac operon transcribes genes for enzymes used to break down lactose 3 genes needed for lactose metabolism: lacZ gene codes for b-galactosidase: Breaks lactose into glucose and galactose lacY gene codes for permease: Allows lactose into cell lacA gene codes for transacetylase: Unknown role

lac operon: If no lactose Since the lac operon is inducible, it is normally OFF when no lactose Would be a waste to make enzymes to break down lactose if no lactose available lac operon normally switched off by ACTIVE repressor which binds to operator Repressor made by regulatory gene lacI Repressor prevents RNA polymerase from transcribing operon’s genes (lacZ, lacY, lacA)

Lactose absent, repressor active, operon off Regulatory gene Promoter Operator lacI lacZ No RNA made 3 RNA polymerase 5 Figure 18.4 The lac operon in E. coli: regulated synthesis of inducible enzymes. Active repressor Lactose absent, repressor active, operon off i.e. No genes transcribed for lactose metabolism

lac operon: Lactose present If lactose present, b-galactosidase breaks down lactose into allolactose first Allolactose binds to repressor, making it inactive Inactive repressor can’t block RNA polymerase so operon transcribes genes (lacZ, lacY, lacA) Allolactose acts as an inducer in this role

(b) Lactose present, repressor inactive, operon on lac operon lacI lacZ lacY lacA RNA polymerase 3 5 -Galactosidase Permease Transacetylase Figure 18.4 The lac operon in E. coli: regulated synthesis of inducible enzymes. Inactive repressor Allolactose (inducer) (b) Lactose present, repressor inactive, operon on i.e. Genes transcribed to metabolize lactose

Regulation by Inducible Operons If lactose present: Allolactose (inducer) made Inducer makes repressor INACTIVE Operon ON Genes for lactose metabolism transcribed If lactose absent: No allolactose (no inducer) made Repressor stays ACTIVE Operon stays OFF Genes for lactose metabolism NOT transcribed

Eukaryotic Gene Regulation Remember that all cells are genetically identical Yet each typical human cell only expresses 20% of its genes on average at a given time How do cells have such differential gene expression?

Eukaryotic Gene Regulation Remember that all cells are genetically identical Yet each typical human cell only expresses 20% of its genes on average at a given time How do cells have such differential gene expression? Lots of levels of eukaryotic gene expression control, from transcription to translation and beyond!

Summary of stages of gene expression in eukaryotes Signal NUCLEUS Chromatin Summary of stages of gene expression in eukaryotes Chromatin modification: DNA unpacking involving histone acetylation and DNA demethylation DNA Gene available for transcription Gene Transcription RNA Exon Primary transcript Intron RNA processing Tail Cap mRNA in nucleus Transport to cytoplasm CYTOPLASM mRNA in cytoplasm Degradation of mRNA Translation Figure 18.6 Stages in gene expression that can be regulated in eukaryotic cells. Polypeptide Protein processing, such as cleavage and chemical modification Active protein Degradation of protein Transport to cellular destination Cellular function (such as enzymatic activity, structural support)

Regulation of Chromatin Structure Recall from Chapter 16 that eukaryotic DNA is wrapped around histone proteins, forming chromatin Chromatin does more than just compact DNA to fit in nucleus Amount of wrapping can control whether or not gene expression occurs Tight wrapping = reduced transcription Looser wrapping = more transcription Heterochromatin regions very tightly wrapped with little transcription (telomere & centromere regions)

Regulation of Chromatin Structure Chemical modification to histones and DNA can also influence gene expression Acetylation (adding acetyl groups, -COCH3) to positively charged histone tails reduces attraction to negatively charged DNA Acetylation loosens chromatin = more transcription Deacetylation (removing acetyl groups) = less transcription

Acetylation of Histones Histone tails (+ charged) DNA double helix (- charged) Nucleosome (a) Positive tails attracted to negative DNA; Prevents transcription Figure 18.7 A simple model of histone tails and the effect of histone acetylation. Unacetylated histones Acetylated histones (b) Acetylation makes histones less positive so less attraction to DNA; Permits transcription

DNA Methylation Methylation (adding methyl groups, -CH3) can occur on DNA itself, usually to cytosine nucleotides In general, more methylation = less transcription i.e. Methylation turns genes “off” Ex. Inactivated genes on mammalian X chromosome that becomes Barr body are heavily methylated Remember those tortoise shell cats?

DNA Methylation Methylation patterns can be passed on from cell to cell Helps cells differentiate into cell types during embryonic development But methylation patterns can ALSO change, thus altering gene expression

Epigenetics But wait a minute! That’s a big deal! Think about this: You inherit your gene sequence BUT the expression of those genes could change over time with DNA methylation changes

Epigenetics Epigenetics has profound implications for human health Inheritance of traits not involving the nucleotide sequence is called epigenetic inheritance Epigenetics has profound implications for human health Ex. Could explain why one identical twin has a particular disease and one doesn’t Ex. Some cancers shown to have a connection to epigenetic modification