Regulating Gene Expression Bonus 1 due today Bonus

Regulating Gene Expression • Bonus #1 due today • Bonus #2 due 7/30 • Exams back M 6/30

What makes us who we are? Nature and Nurture Based on “Nature via Nurture” by Matt Ridley (2003)

Genes Traits Genes code for proteins. These proteins give rise to traits…

Genes Traits Genes code for proteins. These proteins give rise to traits… It is rarely this simple.

Imprinting: exposure to movement (environment) sets “mother”

X/Y chromosomes in humans: genes = traits

This article, shows how even today people see nature and nurture as opposing each other: The Pathogenesis of the Glaucomas: Nature versus Nurture Mackey, et al. , Clinical & Experimental Opthamology vol 36, pg 297, April 2008

Twin studies have been used to determine the heritability of various traits.

Types of twins: http: //pennhealth. com/health_info/pregnancy/000199. htm

Twin studies have been used to determine the heritability of various traits, but there are some caveats: How many twins have been studied? How different are the environments?

Correlation of weight and relatedness Correlation of weight (BMI) % Identical twins reared together 80 Identical twins reared apart 72 Fraternal twins reared together 43 Biological siblings 34 Parents and children living together 26 Adopted children and parents 4 Unrelated children living together 1 *But food preference shows little genetic correlation The nature of environmental influences on weight and obesity: A behavior genetic analysis. Grilo, Carlos M. ; Pogue-Geile, Michael F. ; Psychological Bulletin, Vol 110(3), Nov 1991. pp. 520 -537. And two books by Matt Ridley: Nature via Nurture (2003) and Genome: the Autobiography of a Species in 23 Chapters (1999)

Intelligence Correlation of IQ Inheritance : The same person tested twice Identical twins reared together Identical twins reared apart Fraternal twins reared together Biological siblings Parents and children living together Parents and children living apart Adopted children living together Unrelated people living apart % 87 86 76 55 47 40 31 0 0 From two books by Matt Ridley: Nature via Nurture (2003) and Genome: the Autobiography of a Species in 23 Chapters (1999)

When the environment is equal (everyone has access to resources), genetic differences are magnified. When environments are different (only a few have access to resources), environmental differences are magnified.

Proof or disproof? Correlation of IQ Inheritance : The same person tested twice Identical twins reared together Identical twins reared apart Fraternal twins reared together Biological siblings Parents and children living together Parents and children living apart Adopted children living together Unrelated people living apart % 87 86 76 55 47 40 31 0 0 From two books by Matt Ridley: Nature via Nurture (2003) and Genome: the Autobiography of a Species in 23 Chapters (1999)

Can we see a genetic basis for complex behaviors?

Voles Prairie Montane • Monogamous • Nonmonogamous • Both parents care • Mother cares for young briefly

Oxytocin and Vasopressin (hormones) Water/salt balance Contraction of womb and milk production Encourages bonding between individuals

Hormones are molecules produced in one cell and signal another.

Oxytocin and Vasopressin (hormones) Water/salt balance Contraction of womb and milk production Encourages bonding between individuals

Voles Prairie Montane • Monogamous • Nonmonogamous • Both parents care • Mother cares for young briefly

Voles Prairie Montane • Monogamous • Nonmonogamous • Both parents care for • Mother cares for young briefly Same levels of oxytocin and vasopressin

Hormones are molecules produced in one cell and signal another.

Voles Prairie Montane • Monogamous • Nonmonogamous • Both parents care for • Mother cares for young briefly Same levels of oxytocin and vasopressin • More receptors • Less receptors

Voles Prairie Montane • Monogamous • Nonmonogamous • Both parents care for • Mother cares for young briefly Same levels of oxytocin and vasopressin • More receptors • Less receptors Inject hormone into brain • ?

Voles Prairie Montane • Monogamous • Nonmonogamous • Both parents care for • Mother cares for young briefly Same levels of oxytocin and vasopressin • More receptors • Less receptors Inject hormone into brain • Monogamous • Nonmonogamous

Voles Prairie Montane • Monogamous • Nonmonogamous • Both parents care for • Mother cares for young briefly Same levels of oxytocin and vasopressin • More oxytocin • Less oxytocin receptors Block receptors • ?

Voles Prairie Montane • Monogamous • Nonmonogamous • Both parents care for • Mother cares for young briefly Same levels of oxytocin and vasopressin • More oxytocin • Less oxytocin receptors Block receptors • Nonmonogamous

Voles Prairie Montane • Monogamous • Nonmonogamous • Both parents care for • Mother cares for young briefly Same levels of oxytocin and vasopressin • More oxytocin • Less oxytocin receptors Increase levels of receptors (genetically) in ventral pallidum • Monogamous

Voles Prairie Montane • Monogamous • Nonmonogamous • Both parents care for • Mother cares for young briefly Same levels of oxytocin and vasopressin • More receptors • Less receptors

Why might these voles use different reproductive strategies? Prairie voles Montane voles • Monogamous • Nonmonogamous • Both parents care • Mother cares for young briefly

Why might these voles use different reproductive strategies? Prairie voles: Montane voles: Resource poor Resource rich habitat • Monogamous • Nonmonogamous • Both parents care • Mother cares for young briefly

We looked at the mechanisms of gene expression, now we will look at its regulation. Combinations of 3 nucleotides code for each 1 amino acid in a protein.

Exons are a very small part of DNA

Fig 15. 1 Each step in gene expression presents an opportunity to regulate when and how much of a gene product will be produced.

Fig 15. 1 Why change gene expression? • Different cells need different components • Responding to the environment • Replacement of damaged/worn-out parts

Two points to keep in mind: 1. Cellular components are constantly turnedover. 2. Gene expression takes time: Typically more than an hour from DNA to protein. Most rapidly 15 minutes. Fig 15. 1

Blood clotting must happen within minutes

m. RNA levels change in response to cold acclimation Fowler and Thomashow The Plant Cell, Vol. 14, 1675 -1690, 2002

DNA damage inhibits r. RNA transciption Fig 1 b The ATM repair pathway inhibits RNA polymerase I transcription in response to chromosome breaks Nature Vol 447 pg 730 -734 (7 June 2007)

• Gene expression can be controlled at many points between DNA and making the final proteins. • Changes in the various steps of gene expression control when and how much of a product are produced. Fig 15. 1

In bacteria, transcription and translation occur simultaneously. So most regulation of gene expression happens at transcription. Fig 13. 22

Transcription initiation in prokaryotes: sigma factor binds to the -35 and -10 regions and then the RNA polymerase subunits bind and begin transcription Fig 12. 7

Fig 14. 3 Operon: several genes whose expression is controlled by the same promoter

Fig 14. 3 E. coli lactose metabolism

Fig 14. 4 In the absence of lactose, the lac operon is repressed.

Fig 14. 4 Lactose binds to the repressor, making it inactive, so that transcription can occur.

Fig 14. 5 Repression or induction of the lac operon

Fig 14. 3 There is more to lac gene expression than repression

Fig 14. 8 Glucose is a better energy source than lactose

Fig 14. 8 Low glucose leads to high c. AMP binds to CAP which increases lac operon transcription

High glucose leads to low c. AMP, CAP inactive, low lac operon transcription Fig 14. 8

Fig 14. 3 The lac operon: one example of regulating gene expression in bacteria

Overview of transcriptional regulation Fig 14. 1 and 15. 1

Gene Expression is controlled at all of these steps: • DNA packaging • Transcription • RNA processing and transport • RNA degradation • Translation • Post-translational Fig 15. 1 Fig 16. 1

Gene Expression is controlled at all of these steps: • DNA packaging • Transcription • RNA processing and transport • RNA degradation • Translation • Post-translational Fig 15. 1 Fig 16. 1

Tightly packaged DNA is unavailable. DNA packaging changes as the need for different genes changes. Fig 10. 21

Different levels of DNA packaging Fig 10. 21

Histones can be posttranslationally modified, which affects their abililty to bind DNA.

Fig 12. 15 Acetylation (-COCH 3): post-translational modifications of the histones loosen DNA binding

Acetylation of histones ( -COCH 3) causes a loosening of the DNA/histone bond…unpackaging the DNA.

Fig 15. 13 DNA methylation

DNA methylation often inhibits transcription Fig 15. 14

Epigenetics: the inheritance of DNA modifications, including methylaton Fig 15. 15

Four-stranded DNA: cancer, gene regulation and drug development by Julian Leon Huppert Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences Triennial Issue of 'Chemistry and Engineering’ DOI: 10. 1098/rsta. 2007. 0011 Published: September 13, 2007

Four-stranded DNA forms between sequences of guanines…G-quadruplexes 4 strand DNA Fig 1

Four-stranded DNA forms between sequences of guanines…G-quadruplexes 4 strand DNA Fig 1

The Gquadruplexes can form from 4, 2, or 1 DNA strand. 4 strand DNA Fig 2

Fig 10. 11 During DNA replication, the ends of the DNA are not completely copied.

Fig 10. 11 Telomeres are non-gene DNA at the ends of DNA strands. Telomeres are shortened during DNA replication.

Fig 11. 25 Telomeres can be lengthened by telomerase.

The telomeric cap structure is one place where G-quadruplexes can be found

Fig 10. 11 Telomeres are non-gene DNA at the ends of DNA strands. Short telomeres will cause cells to stop replicating or cell death. The critical size is unknown.

Drugs that can block the action of telomerase, by binding the G-quadruplexes, are being investigated to treat cancer.

Fig 12. 13 Eukaryotic promoters often contain G-rich areas

G-quadruplex in promoters 4 strand DNA Fig 5

If the promoter is defined as 1 kbase upstream of the transcription start site: • Quadruplex motifs are significantly overrepresented relative to the rest of the genome, by almost an order of magnitude. • almost half of all known genes have a putative quadruplex-forming motif • By comparison, the TATA box motif—probably the best-known regulatory motif and a staple of undergraduate textbooks—is found in only approximately 10% of genes. Four-stranded DNA: cancer, gene regulation and drug development by Julian Leon Huppert in Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences Triennial Issue of 'Chemistry and Engineering’ DOI: 10. 1098/rsta. 2007. 0011 Published: September 13, 2007

Oncogenes, the genes involved in cancer, are especially rich in potentially regulatory quadruplexes— 69% of them have such motifs Four-stranded DNA: cancer, gene regulation and drug development by Julian Leon Huppert in Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences Triennial Issue of 'Chemistry and Engineering’ DOI: 10. 1098/rsta. 2007. 0011 Published: September 13, 2007

Werner syndrome, which causes premature aging, is caused by the lack of a helicase that binds to G-quadruplexes. Four-stranded DNA: cancer, gene regulation and drug development by Julian Leon Huppert in Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences Triennial Issue of 'Chemistry and Engineering’ DOI: 10. 1098/rsta. 2007. 0011 Published: September 13, 2007

G-quadruplex ligands TMPy. P 4 BRACO-19 Down regulates telomerase and some oncogene transcription G-quadruplex telomestatin Specifically binds to telomeres, naturally occurring in Streptomyces anulatus 4 strand DNA Fig 6

Model of specific G-quadruplex ligand binding to G-quadruplex and a specific DNA sequence 4 strand DNA Fig 7

Gene Expression is controlled at all of these steps: • DNA packaging • Transcription • RNA processing and transport • RNA degradation • Translation • Post-translational Fig 15. 1 Fig 16. 1