REGULATION OF GENE EXPRESSION Chapter 18

Gene expression A gene that is expressed is “turned on”. It is actively making a product (protein or RNA). Gene expression is often regulated at transcription. Newly discovered roles of RNA in gene expression

Regulation of a metabolic pathway

Prokaryotic Gene Regulation Adjust activity of enzymes already present –Often through negative feedback Adjust production level of certain enzymes

OPERONS Regulation in prokaryotes –Operator – switch segment of DNA in promoter –Operon – the promoter, the operator, and the genes they control –Regulatory gene – long distance from gene that is regulated

The trp operon: regulated synthesis of repressible enzymes trp animationtrp animation trp tutorialtrp tutorial

The trp operon: regulated synthesis of repressible enzymes

The lac operon: regulated synthesis of inducible enzymes lac operon animationlac operon tutorial

The lac operon: regulated synthesis of inducible enzymes

Regulatory gene makes protein (repressor) that inhibits operator Regulatory protein has inactive and active shape –Corepressor – makes repressor active –Inducer – inactivates repressor

Repressible enzymes usually used when cell makes something (ex. tryptophan) Inducible enzymes usually used when cell breaks something down (ex. lactose)

Positive control: cAMP receptor protein

POSITIVE GENE REGULATION an example… Cyclic AMP (cAMP) accumulates when low sugar cAMP receptor protein (CRP) attaches to cAMP and changes shape so it becomes and activator CRP binds to DNA at lac operon so cell can break down lactose

Eukaryotic Gene Regulation Expression can be regulated at any stage Differential gene expression – different cells in an organism express different genes from the genome Much regulation occurs at transcription like prokaryotes, but even more possibilities in eukaryotes

CHROMATIN Composed of DNA and proteins called histones Nucloesome – DNA wrapped around a histone Forms looped domains Heterochromatin – highly compacted DNA so generally is not transcribed

Levels of chromatin packing

GENOME ORGANIZATION 1.5% of DNA in humans codes for protein 24% introns and regulatory Most is repetitive DNA (59%) Unique noncoding is 15%

Opportunities for the control of gene expression in eukaryotic cells

Eukaryotic Regulation At DNA level –Chromatin modification, DNA unpacking with histone acetylation and DNA demethylation At RNA level –Transcription, RNA processing, transport to cytoplasm At protein level –Translation, protein processing, transport to cellular destination, protein degradation

GENE EXPRESSION Not all genes are turned on all of the time!

GENE REGULATION Regulation of chromosome structure –Histone acetylation (-COCH 3 ) loosens chromatin so transcription can occur –DNA methylation (-CH 3 ) inactivates DNA Responsible for X-inactivation Genomic imprinting – in mammals, methylation turns off paternal or maternal allele of certain genes at start of development Epigenetic inheritance – inheritance of traits not directly involving DNA sequence (all of the above)

Regulation of transcription –Control elements– upstream of promoter; help regulate transcription by binding certain transcription factors –Transcription factors – mediate the binding of RNA polymerase to the promoter –Enhancers – far upstream of gene; bind to transcription factors; called distal control element

Figure 19.8 A eukaryotic gene and its transcript

–Activator – transcription factors bound to enhancer that stimulate transcription –Not many different control elements so the combination of control elements regulates gene action Different combos of activators makes different genes turned on Different genes can be turned on by same activator

Cell-type specific transcription based on available activators

Coordinate gene expression –Genes that should be turned on together have same enhancers so that same transcription factor(s) is(are) needed Ex. estrogen activates multiple genes to prepare the uterus for pregnancy

Post transcription regulation –RNA processing (alternative splicing) –Lifespan of mRNA in cell controls expression –Removal of caps leads to mRNA destruction Translation Regulation –Translation prevented by regulatory proteins by not letting ribosome to attach to mRNA

–Once a protein is made, ubiquitin can be added to signal its destruction –Proteasomes – degrade proteins with ubiquitin

Degradation of a protein by a proteasome

Noncoding RNAs and gene expression Discovering more about RNA’S that do not make protein MicroRNAs (miRNA) – small, single stranded RNA generated from a hairpin on precursor RNA; associates with proteins that can degrade or prevent translation of mRNA with complementary sequence Small interfering RNAs (siRNA) – like miRNA, but made from longer sections of double stranded RNA (not hairpins) Other small RNA’s are involved in remodleing chromatin structure and other regulatory processes

DIFFERENTIAL GENE EXPRESSION = DIFFERENT CELL TYPES Cell differentiation – process by which cells become specialized in structure and function Morphogenesis – process that gives an organism its form (shape) How do different sets of activators come to be present in two cells? –Cytoplasmic determinants (materials in cyctoplasm) –Environment surrounding a cell

Sources of Developmental Info for early embryo

Pattern formation Pattern formation – development of spatial organization in which tissues and organs are in their correct places Positional information – molecular cues that control pattern formation Homeotic genes – control pattern formation

CANCER Oncogenes- cancer causing genes in retroviruses Proto-oncogenes – normal genes that code for proteins that stimulate cell growth and division Tumor suppressor genes - make proteins that help prevent uncontrolled cell growth

Converting proto-oncogene into oncogene

Movement of DNA within a chromosome –May place a more active promoter near a proto-oncogene (= more cell division) Amplification of a proto-oncogene Point mutations in control element or proto-oncogene (= more expression or makes abnormal protein that doesn’t get degraded or is more active)

GENES INVOLVED IN CANCER Ras gene – makes ras (G) protein that starts cascade reactions that initiate cell division –Mutations in Ras gene cause ~30% cancers p53 tumor suppressor gene – “guardian of genome” –Activates p21 which halts cell cycle –Turns on genes to repair DNA –Activates suicide proteins that cause cell death (apoptosis) –Mutations in P53 gene cause ~50% cancer

Multistep Model of Cancer Development Approximately half dozen changes have to occur at the DNA level for cancer to develop. Need at least one oncogene and loss of tumor suppressor gene(s) Most oncogenes are dominant and most tumor suppressor genes recessive so must knock out both alleles Typically telomerase is activated

A multi-step model for the development of colorectal cancer

Inherited Predisposition to Cancer 15% colorectal cancers are inherited –Most from mutated APC gene (tumor suppressor gene) 5-10% breast cancers are inherited –Most with mutated BRCA1 and BRCA2 –A woman with one mutant BRCA1 gene (tumor suppressor gene) has a 60% chance of getting breast cancer by age 50