Regulation of Gene Expression Chapter 18 Regulation of Gene Expression

Overview: Conducting the Genetic Orchestra Prokaryotes and eukaryotes alter gene expression in response to their changing environment In multicellular eukaryotes, gene expression regulates development and is responsible for differences in cell types RNA molecules play many roles in regulating gene expression in eukaryotes © 2011 Pearson Education, Inc.

Figure 18.1 Figure 18.1 What regulates the precise pattern of gene expression in the developing wing of a fly embryo?

Concept 18.1: Bacteria often respond to environmental change by regulating transcription Natural selection has favored bacteria that produce only the products needed by that cell A cell can regulate the production of enzymes by feedback inhibition or by gene regulation Gene expression in bacteria is controlled by the operon model © 2011 Pearson Education, Inc.

Regulation of gene expression Figure 18.2 Precursor Feedback inhibition trpE gene Enzyme 1 trpD gene Regulation of gene expression Enzyme 2 trpC gene  trpB gene  Figure 18.2 Regulation of a metabolic pathway. Enzyme 3 trpA gene Tryptophan (a) Regulation of enzyme activity (b) Regulation of enzyme production

Operons: The Basic Concept A cluster of functionally related genes can be under coordinated control by a single “on-off switch” The regulatory “switch” is a segment of DNA called an operator usually positioned within the promoter An operon is the entire stretch of DNA that includes the operator, the promoter, and the genes that they control © 2011 Pearson Education, Inc.

The operon can be switched off by a protein repressor The repressor prevents gene transcription by binding to the operator and blocking RNA polymerase The repressor is the product of a separate regulatory gene © 2011 Pearson Education, Inc.

For example, E. coli can synthesize the amino acid tryptophan The repressor can be in an active or inactive form, depending on the presence of other molecules A corepressor is a molecule that cooperates with a repressor protein to switch an operon off For example, E. coli can synthesize the amino acid tryptophan © 2011 Pearson Education, Inc.

By default the trp operon is on and the genes for tryptophan synthesis are transcribed When tryptophan is present, it binds to the trp repressor protein, which turns the operon off The repressor is active only in the presence of its corepressor tryptophan; thus the trp operon is turned off (repressed) if tryptophan levels are high © 2011 Pearson Education, Inc.

Figure 18.3 trp operon Promoter Promoter Genes of operon DNA trpR trpE trpD trpC trpB trpA Operator Regulatory gene RNA polymerase Start codon Stop codon 3 mRNA 5 mRNA 5 E D C B A Protein Inactive repressor Polypeptide subunits that make up enzymes for tryptophan synthesis (a) Tryptophan absent, repressor inactive, operon on DNA No RNA made Figure 18.3 The trp operon in E. coli: regulated synthesis of repressible enzymes. mRNA Protein Active repressor Tryptophan (corepressor) (b) Tryptophan present, repressor active, operon off

Polypeptide subunits that make up enzymes for tryptophan synthesis Figure 18.3a trp operon Promoter Promoter Genes of operon DNA trpR trpE trpD trpC trpB trpA Operator Regulatory gene RNA polymerase Start codon Stop codon 3 mRNA 5 mRNA 5 E D C B A Protein Inactive repressor Figure 18.3 The trp operon in E. coli: regulated synthesis of repressible enzymes. Polypeptide subunits that make up enzymes for tryptophan synthesis (a) Tryptophan absent, repressor inactive, operon on

Tryptophan (corepressor) Figure 18.3b-1 DNA mRNA Protein Active repressor Figure 18.3 The trp operon in E. coli: regulated synthesis of repressible enzymes. Tryptophan (corepressor) (b) Tryptophan present, repressor active, operon off

Tryptophan (corepressor) Figure 18.3b-2 DNA No RNA made mRNA Protein Active repressor Figure 18.3 The trp operon in E. coli: regulated synthesis of repressible enzymes. Tryptophan (corepressor) (b) Tryptophan present, repressor active, operon off

Repressible and Inducible Operons: Two Types of Negative Gene Regulation A repressible operon is one that is usually on; binding of a repressor to the operator shuts off transcription The trp operon is a repressible operon An inducible operon is one that is usually off; a molecule called an inducer inactivates the repressor and turns on transcription © 2011 Pearson Education, Inc.

By itself, the lac repressor is active and switches the lac operon off The lac operon is an inducible operon and contains genes that code for enzymes used in the hydrolysis and metabolism of lactose By itself, the lac repressor is active and switches the lac operon off A molecule called an inducer inactivates the repressor to turn the lac operon on © 2011 Pearson Education, Inc.

Figure 18.4 Regulatory gene Promoter Operator DNA DNA lacI lacZ No RNA made 3 mRNA RNA polymerase 5 Active repressor Protein (a) Lactose absent, repressor active, operon off lac operon DNA lacI lacZ lacY lacA RNA polymerase Figure 18.4 The lac operon in E. coli: regulated synthesis of inducible enzymes. 3 mRNA mRNA 5 5 Protein -Galactosidase Permease Transacetylase Allolactose (inducer) Inactive repressor (b) Lactose present, repressor inactive, operon on

(a) Lactose absent, repressor active, operon off Figure 18.4a Regulatory gene Promoter Operator DNA DNA lacI lacZ No RNA made 3 mRNA RNA polymerase 5 Figure 18.4 The lac operon in E. coli: regulated synthesis of inducible enzymes. Active repressor Protein (a) Lactose absent, repressor active, operon off

Allolactose (inducer) Figure 18.4b lac operon DNA lacI lacZ lacY lacA RNA polymerase 3 mRNA mRNA 5 5 -Galactosidase Permease Transacetylase Protein 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

Inducible enzymes usually function in catabolic pathways; their synthesis is induced by a chemical signal Repressible enzymes usually function in anabolic pathways; their synthesis is repressed by high levels of the end product Regulation of the trp and lac operons involves negative control of genes because operons are switched off by the active form of the repressor © 2011 Pearson Education, Inc.

Positive Gene Regulation Some operons are also subject to positive control through a stimulatory protein, such as catabolite activator protein (CAP), an activator of transcription When glucose (a preferred food source of E. coli) is scarce, CAP is activated by binding with cyclic AMP (cAMP) Activated CAP attaches to the promoter of the lac operon and increases the affinity of RNA polymerase, thus accelerating transcription © 2011 Pearson Education, Inc.

When glucose levels increase, CAP detaches from the lac operon, and transcription returns to a normal rate CAP helps regulate other operons that encode enzymes used in catabolic pathways © 2011 Pearson Education, Inc.

RNA polymerase binds and transcribes Operator Figure 18.5 Promoter DNA lacI lacZ CAP-binding site RNA polymerase binds and transcribes Operator Active CAP cAMP Inactive lac repressor Inactive CAP Allolactose (a) Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized Promoter DNA lacI lacZ Figure 18.5 Positive control of the lac operon by catabolite activator protein (CAP). CAP-binding site Operator RNA polymerase less likely to bind Inactive CAP Inactive lac repressor (b) Lactose present, glucose present (cAMP level low): little lac mRNA synthesized

RNA polymerase binds and transcribes Operator Figure 18.5a Promoter DNA lacI lacZ CAP-binding site RNA polymerase binds and transcribes Operator Active CAP cAMP Figure 18.5 Positive control of the lac operon by catabolite activator protein (CAP). Inactive lac repressor Inactive CAP Allolactose (a) Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized

RNA polymerase less likely to bind Figure 18.5b Promoter DNA lacI lacZ Operator CAP-binding site RNA polymerase less likely to bind Inactive CAP Inactive lac repressor Figure 18.5 Positive control of the lac operon by catabolite activator protein (CAP). (b) Lactose present, glucose present (cAMP level low): little lac mRNA synthesized

Concept 18.2: Eukaryotic gene expression is regulated at many stages All organisms must regulate which genes are expressed at any given time In multicellular organisms regulation of gene expression is essential for cell specialization © 2011 Pearson Education, Inc.

Differential Gene Expression Almost all the cells in an organism are genetically identical Differences between cell types result from differential gene expression, the expression of different genes by cells with the same genome Abnormalities in gene expression can lead to diseases including cancer Gene expression is regulated at many stages © 2011 Pearson Education, Inc.

Figure 18.6 Signal NUCLEUS Chromatin 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)

Gene available for transcription Figure 18.6a Signal NUCLEUS Chromatin Chromatin modification: DNA unpacking involving histone acetylation and DNA demethylation DNA Gene available for transcription Gene Transcription RNA Exon Primary transcript Intron Figure 18.6 Stages in gene expression that can be regulated in eukaryotic cells. RNA processing Tail mRNA in nucleus Cap Transport to cytoplasm CYTOPLASM

Protein processing, such as cleavage and chemical modification Figure 18.6b CYTOPLASM mRNA in cytoplasm Translation Degradation of mRNA Polypeptide Protein processing, such as cleavage and chemical modification Active protein Degradation of protein Figure 18.6 Stages in gene expression that can be regulated in eukaryotic cells. Transport to cellular destination Cellular function (such as enzymatic activity, structural support)

Regulation of Chromatin Structure Genes within highly packed heterochromatin are usually not expressed Chemical modifications to histones and DNA of chromatin influence both chromatin structure and gene expression © 2011 Pearson Education, Inc.

Histone Modifications In histone acetylation, acetyl groups are attached to positively charged lysines in histone tails This loosens chromatin structure, thereby promoting the initiation of transcription The addition of methyl groups (methylation) can condense chromatin; the addition of phosphate groups (phosphorylation) next to a methylated amino acid can loosen chromatin Animation: DNA Packing © 2011 Pearson Education, Inc.

Amino acids available for chemical modification Figure 18.7 Histone tails DNA double helix Amino acids available for chemical modification Nucleosome (end view) (a) Histone tails protrude outward from a nucleosome Figure 18.7 A simple model of histone tails and the effect of histone acetylation. Unacetylated histones Acetylated histones (b) Acetylation of histone tails promotes loose chromatin structure that permits transcription

The histone code hypothesis proposes that specific combinations of modifications, as well as the order in which they occur, help determine chromatin configuration and influence transcription © 2011 Pearson Education, Inc.

DNA Methylation DNA methylation, the addition of methyl groups to certain bases in DNA, is associated with reduced transcription in some species DNA methylation can cause long-term inactivation of genes in cellular differentiation In genomic imprinting, methylation regulates expression of either the maternal or paternal alleles of certain genes at the start of development © 2011 Pearson Education, Inc.

Epigenetic Inheritance Although the chromatin modifications just discussed do not alter DNA sequence, they may be passed to future generations of cells The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence is called epigenetic inheritance © 2011 Pearson Education, Inc.

Regulation of Transcription Initiation Chromatin-modifying enzymes provide initial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery © 2011 Pearson Education, Inc.

Organization of a Typical Eukaryotic Gene Associated with most eukaryotic genes are multiple control elements, segments of noncoding DNA that serve as binding sites for transcription factors that help regulate transcription Control elements and the transcription factors they bind are critical to the precise regulation of gene expression in different cell types © 2011 Pearson Education, Inc.

Enhancer (distal control elements) Proximal control elements Figure 18.8-1 Enhancer (distal control elements) Proximal control elements Poly-A signal sequence Transcription start site Transcription termination region DNA Exon Intron Exon Intron Exon Upstream Downstream Promoter Figure 18.8 A eukaryotic gene and its transcript.

Enhancer (distal control elements) Proximal control elements Figure 18.8-2 Enhancer (distal control elements) Proximal control elements Poly-A signal sequence Transcription start site Transcription termination region DNA Exon Intron Exon Intron Exon Upstream Downstream Promoter Transcription Poly-A signal Primary RNA transcript (pre-mRNA) Exon Intron Exon Intron Exon Cleaved 3 end of primary transcript 5 Figure 18.8 A eukaryotic gene and its transcript.

Enhancer (distal control elements) Proximal control elements Figure 18.8-3 Enhancer (distal control elements) Proximal control elements Poly-A signal sequence Transcription start site Transcription termination region DNA Exon Intron Exon Intron Exon Upstream Downstream Promoter Transcription Poly-A signal Primary RNA transcript (pre-mRNA) Exon Intron Exon Intron Exon Cleaved 3 end of primary transcript 5 RNA processing Intron RNA Figure 18.8 A eukaryotic gene and its transcript. Coding segment mRNA G P P P AAA  AAA 3 Start codon Stop codon 5 Cap 5 UTR 3 UTR Poly-A tail

The Roles of Transcription Factors To initiate transcription, eukaryotic RNA polymerase requires the assistance of proteins called transcription factors General transcription factors are essential for the transcription of all protein-coding genes In eukaryotes, high levels of transcription of particular genes depend on control elements interacting with specific transcription factors © 2011 Pearson Education, Inc.

Enhancers and Specific Transcription Factors Proximal control elements are located close to the promoter Distal control elements, groupings of which are called enhancers, may be far away from a gene or even located in an intron © 2011 Pearson Education, Inc.

An activator is a protein that binds to an enhancer and stimulates transcription of a gene Activators have two domains, one that binds DNA and a second that activates transcription Bound activators facilitate a sequence of protein-protein interactions that result in transcription of a given gene Animation: Initiation of Transcription © 2011 Pearson Education, Inc.

Activation domain DNA-binding domain DNA Figure 18.9 Figure 18.9 The structure of MyoD, a specific transcription factor that acts as an activator.

Some transcription factors function as repressors, inhibiting expression of a particular gene by a variety of methods Some activators and repressors act indirectly by influencing chromatin structure to promote or silence transcription © 2011 Pearson Education, Inc.

Distal control element Enhancer TATA box Figure 18.10-1 Promoter Activators Gene DNA Distal control element Enhancer TATA box Figure 18.10 A model for the action of enhancers and transcription activators.

Distal control element Enhancer TATA box General transcription factors Figure 18.10-2 Promoter Activators Gene DNA Distal control element Enhancer TATA box General transcription factors DNA- bending protein Group of mediator proteins Figure 18.10 A model for the action of enhancers and transcription activators.

Distal control element Enhancer TATA box General transcription factors Figure 18.10-3 Promoter Activators Gene DNA Distal control element Enhancer TATA box General transcription factors DNA- bending protein Group of mediator proteins RNA polymerase II Figure 18.10 A model for the action of enhancers and transcription activators. RNA polymerase II Transcription initiation complex RNA synthesis

Albumin gene not expressed Figure 18.11 Enhancer Promoter Control elements Albumin gene Crystallin gene LIVER CELL NUCLEUS LENS CELL NUCLEUS Available activators Available activators Albumin gene not expressed Figure 18.11 Cell type–specific transcription. Albumin gene expressed Crystallin gene not expressed Crystallin gene expressed (a) Liver cell (b) Lens cell

Albumin gene expressed Figure 18.11a Enhancer Promoter Control elements LIVER CELL NUCLEUS Albumin gene Available activators Crystallin gene Albumin gene expressed Figure 18.11 Cell type–specific transcription. Crystallin gene not expressed (a) Liver cell

Albumin gene not expressed Figure 18.11b Enhancer Promoter Control elements LENS CELL NUCLEUS Albumin gene Available activators Crystallin gene Albumin gene not expressed Figure 18.11 Cell type–specific transcription. Crystallin gene expressed (b) Lens cell

Coordinately Controlled Genes in Eukaryotes Unlike the genes of a prokaryotic operon, each of the co-expressed eukaryotic genes has a promoter and control elements These genes can be scattered over different chromosomes, but each has the same combination of control elements Copies of the activators recognize specific control elements and promote simultaneous transcription of the genes © 2011 Pearson Education, Inc.

Nuclear Architecture and Gene Expression Loops of chromatin extend from individual chromosomes into specific sites in the nucleus Loops from different chromosomes may congregate at particular sites, some of which are rich in transcription factors and RNA polymerases These may be areas specialized for a common function © 2011 Pearson Education, Inc.

Chromosomes in the interphase nucleus Chromosome territory Figure 18.12 Chromosomes in the interphase nucleus Chromosome territory 10 m Figure 18.12 Chromosomal interactions in the interphase nucleus. Chromatin loop Transcription factory

Chromosomes in the interphase nucleus Figure 18.12a Chromosomes in the interphase nucleus Figure 18.12 Chromosomal interactions in the interphase nucleus. 10 m

Mechanisms of Post-Transcriptional Regulation Transcription alone does not account for gene expression Regulatory mechanisms can operate at various stages after transcription Such mechanisms allow a cell to fine-tune gene expression rapidly in response to environmental changes © 2011 Pearson Education, Inc.

RNA Processing In alternative RNA splicing, different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns Animation: RNA Processing © 2011 Pearson Education, Inc.

Primary RNA transcript Figure 18.13 Exons DNA 1 2 3 4 5 Troponin T gene Primary RNA transcript 1 2 3 4 5 Figure 18.13 Alternative RNA splicing of the troponin T gene. RNA splicing mRNA or 1 2 3 5 1 2 4 5

mRNA Degradation The life span of mRNA molecules in the cytoplasm is a key to determining protein synthesis Eukaryotic mRNA is more long lived than prokaryotic mRNA Nucleotide sequences that influence the lifespan of mRNA in eukaryotes reside in the untranslated region (UTR) at the 3 end of the molecule Animation: mRNA Degradation © 2011 Pearson Education, Inc.

Initiation of Translation The initiation of translation of selected mRNAs can be blocked by regulatory proteins that bind to sequences or structures of the mRNA Alternatively, translation of all mRNAs in a cell may be regulated simultaneously For example, translation initiation factors are simultaneously activated in an egg following fertilization Animation: Blocking Translation © 2011 Pearson Education, Inc.

Protein Processing and Degradation After translation, various types of protein processing, including cleavage and the addition of chemical groups, are subject to control Proteasomes are giant protein complexes that bind protein molecules and degrade them Animation: Protein Processing Animation: Protein Degradation © 2011 Pearson Education, Inc.

Proteasome and ubiquitin to be recycled Ubiquitin Figure 18.14 Proteasome and ubiquitin to be recycled Ubiquitin Proteasome Protein to be degraded Ubiquitinated protein Protein fragments (peptides) Protein entering a proteasome Figure 18.14 Degradation of a protein by a proteasome.

© 2011 Pearson Education, Inc. Concept 18.3: Noncoding RNAs play multiple roles in controlling gene expression Only a small fraction of DNA codes for proteins, and a very small fraction of the non-protein-coding DNA consists of genes for RNA such as rRNA and tRNA A significant amount of the genome may be transcribed into noncoding RNAs (ncRNAs) Noncoding RNAs regulate gene expression at two points: mRNA translation and chromatin configuration © 2011 Pearson Education, Inc.

Effects on mRNAs by MicroRNAs and Small Interfering RNAs MicroRNAs (miRNAs) are small single-stranded RNA molecules that can bind to mRNA These can degrade mRNA or block its translation © 2011 Pearson Education, Inc.

(a) Primary miRNA transcript miRNA miRNA- protein complex Figure 18.15 Hairpin Hydrogen bond miRNA Dicer 5 3 (a) Primary miRNA transcript miRNA miRNA- protein complex Figure 18.15 Regulation of gene expression by miRNAs. mRNA degraded Translation blocked (b) Generation and function of miRNAs

© 2011 Pearson Education, Inc. The phenomenon of inhibition of gene expression by RNA molecules is called RNA interference (RNAi) RNAi is caused by small interfering RNAs (siRNAs) siRNAs and miRNAs are similar but form from different RNA precursors © 2011 Pearson Education, Inc.

Chromatin Remodeling and Effects on Transcription by ncRNAs In some yeasts siRNAs play a role in heterochromatin formation and can block large regions of the chromosome Small ncRNAs called piwi-associated RNAs (piRNAs) induce heterochromatin, blocking the expression of parasitic DNA elements in the genome, known as transposons RNA-based mechanisms may also block transcription of single genes © 2011 Pearson Education, Inc.

The Evolutionary Significance of Small ncRNAs Small ncRNAs can regulate gene expression at multiple steps An increase in the number of miRNAs in a species may have allowed morphological complexity to increase over evolutionary time siRNAs may have evolved first, followed by miRNAs and later piRNAs © 2011 Pearson Education, Inc.

© 2011 Pearson Education, Inc. Concept 18.4: A program of differential gene expression leads to the different cell types in a multicellular organism During embryonic development, a fertilized egg gives rise to many different cell types Cell types are organized successively into tissues, organs, organ systems, and the whole organism Gene expression orchestrates the developmental programs of animals © 2011 Pearson Education, Inc.

A Genetic Program for Embryonic Development The transformation from zygote to adult results from cell division, cell differentiation, and morphogenesis © 2011 Pearson Education, Inc.

(a) Fertilized eggs of a frog (b) Newly hatched tadpole Figure 18.16 Figure 18.16 From fertilized egg to animal: What a difference four days makes. 1 mm 2 mm (a) Fertilized eggs of a frog (b) Newly hatched tadpole

(a) Fertilized eggs of a frog Figure 18.16a Figure 18.16 From fertilized egg to animal: What a difference four days makes. 1 mm (a) Fertilized eggs of a frog

(b) Newly hatched tadpole Figure 18.16b Figure 18.16 From fertilized egg to animal: What a difference four days makes. 2 mm (b) Newly hatched tadpole

© 2011 Pearson Education, Inc. Cell differentiation is the process by which cells become specialized in structure and function The physical processes that give an organism its shape constitute morphogenesis Differential gene expression results from genes being regulated differently in each cell type Materials in the egg can set up gene regulation that is carried out as cells divide © 2011 Pearson Education, Inc.

Cytoplasmic Determinants and Inductive Signals An egg’s cytoplasm contains RNA, proteins, and other substances that are distributed unevenly in the unfertilized egg Cytoplasmic determinants are maternal substances in the egg that influence early development As the zygote divides by mitosis, cells contain different cytoplasmic determinants, which lead to different gene expression © 2011 Pearson Education, Inc.

(a) Cytoplasmic determinants in the egg (b) Induction by nearby cells Figure 18.17 (a) Cytoplasmic determinants in the egg (b) Induction by nearby cells Unfertilized egg Early embryo (32 cells) Sperm Nucleus Fertilization Molecules of two different cytoplasmic determinants NUCLEUS Zygote (fertilized egg) Signal transduction pathway Mitotic cell division Figure 18.17 Sources of developmental information for the early embryo. Signal receptor Two-celled embryo Signaling molecule (inducer)

(a) Cytoplasmic determinants in the egg Figure 18.17a (a) Cytoplasmic determinants in the egg Unfertilized egg Sperm Nucleus Fertilization Molecules of two different cytoplasmic determinants Zygote (fertilized egg) Figure 18.17 Sources of developmental information for the early embryo. Mitotic cell division Two-celled embryo

© 2011 Pearson Education, Inc. The other important source of developmental information is the environment around the cell, especially signals from nearby embryonic cells In the process called induction, signal molecules from embryonic cells cause transcriptional changes in nearby target cells Thus, interactions between cells induce differentiation of specialized cell types Animation: Cell Signaling © 2011 Pearson Education, Inc.

(b) Induction by nearby cells Figure 18.17b (b) Induction by nearby cells Early embryo (32 cells) NUCLEUS Signal transduction pathway Figure 18.17 Sources of developmental information for the early embryo. Signal receptor Signaling molecule (inducer)

© 2011 Pearson Education, Inc. Sequential Regulation of Gene Expression During Cellular Differentiation Determination commits a cell to its final fate Determination precedes differentiation Cell differentiation is marked by the production of tissue-specific proteins © 2011 Pearson Education, Inc.

© 2011 Pearson Education, Inc. Myoblasts produce muscle-specific proteins and form skeletal muscle cells MyoD is one of several “master regulatory genes” that produce proteins that commit the cell to becoming skeletal muscle The MyoD protein is a transcription factor that binds to enhancers of various target genes © 2011 Pearson Education, Inc.

Master regulatory gene myoD Figure 18.18-1 Nucleus Master regulatory gene myoD Other muscle-specific genes DNA Embryonic precursor cell OFF OFF Figure 18.18 Determination and differentiation of muscle cells.

Master regulatory gene myoD Figure 18.18-2 Nucleus Master regulatory gene myoD Other muscle-specific genes DNA Embryonic precursor cell OFF OFF mRNA OFF MyoD protein (transcription factor) Myoblast (determined) Figure 18.18 Determination and differentiation of muscle cells.

Master regulatory gene myoD Figure 18.18-3 Nucleus Master regulatory gene myoD Other muscle-specific genes DNA Embryonic precursor cell OFF OFF mRNA OFF MyoD protein (transcription factor) Myoblast (determined) Figure 18.18 Determination and differentiation of muscle cells. mRNA mRNA mRNA mRNA Myosin, other muscle proteins, and cell cycle– blocking proteins MyoD Another transcription factor Part of a muscle fiber (fully differentiated cell)

Pattern Formation: Setting Up the Body Plan Pattern formation is the development of a spatial organization of tissues and organs In animals, pattern formation begins with the establishment of the major axes Positional information, the molecular cues that control pattern formation, tells a cell its location relative to the body axes and to neighboring cells © 2011 Pearson Education, Inc.

© 2011 Pearson Education, Inc. Pattern formation has been extensively studied in the fruit fly Drosophila melanogaster Combining anatomical, genetic, and biochemical approaches, researchers have discovered developmental principles common to many other species, including humans © 2011 Pearson Education, Inc.

The Life Cycle of Drosophila In Drosophila, cytoplasmic determinants in the unfertilized egg determine the axes before fertilization After fertilization, the embryo develops into a segmented larva with three larval stages © 2011 Pearson Education, Inc.

Egg developing within ovarian follicle Nucleus Figure 18.19 Head Thorax Abdomen Follicle cell 1 Egg developing within ovarian follicle Nucleus Egg 0.5 mm Nurse cell Dorsal Right 2 Unfertilized egg Egg shell BODY AXES Anterior Posterior Depleted nurse cells Left Ventral Fertilization (a) Adult Laying of egg 3 Fertilized egg Embryonic development Figure 18.19 Key developmental events in the life cycle of Drosophila. 4 Segmented embryo 0.1 mm Body segments Hatching 5 Larval stage (b) Development from egg to larva

Head Thorax Abdomen 0.5 mm Dorsal Right BODY AXES Anterior Posterior Figure 18.19a Head Thorax Abdomen 0.5 mm Dorsal Right BODY AXES Anterior Posterior Figure 18.19 Key developmental events in the life cycle of Drosophila. Left Ventral (a) Adult

1 2 3 4 5 Follicle cell Egg developing within ovarian follicle Nucleus Figure 18.19b Follicle cell 1 Egg developing within ovarian follicle Nucleus Egg Nurse cell 2 Unfertilized egg Egg shell Depleted nurse cells Fertilization Laying of egg 3 Fertilized egg Embryonic development Figure 18.19 Key developmental events in the life cycle of Drosophila. 4 Segmented embryo 0.1 mm Body segments Hatching 5 Larval stage (b) Development from egg to larva

Genetic Analysis of Early Development: Scientific Inquiry Edward B. Lewis, Christiane Nüsslein-Volhard, and Eric Wieschaus won a Nobel 1995 Prize for decoding pattern formation in Drosophila Lewis discovered the homeotic genes, which control pattern formation in late embryo, larva, and adult stages © 2011 Pearson Education, Inc.

Eye Leg Antenna Wild type Mutant Figure 18.20 Figure 18.20 Abnormal pattern formation in Drosophila. Wild type Mutant

Eye Antenna Wild type Figure 18.20a Figure 18.20 Abnormal pattern formation in Drosophila. Antenna Wild type

Figure 18.20b Leg Figure 18.20 Abnormal pattern formation in Drosophila. Mutant

© 2011 Pearson Education, Inc. Nüsslein-Volhard and Wieschaus studied segment formation They created mutants, conducted breeding experiments, and looked for corresponding genes Many of the identified mutations were embryonic lethals, causing death during embryogenesis They found 120 genes essential for normal segmentation © 2011 Pearson Education, Inc.

© 2011 Pearson Education, Inc. Axis Establishment Maternal effect genes encode for cytoplasmic determinants that initially establish the axes of the body of Drosophila These maternal effect genes are also called egg-polarity genes because they control orientation of the egg and consequently the fly Animation: Development of Head-Tail Axis in Fruit Flies © 2011 Pearson Education, Inc.

© 2011 Pearson Education, Inc. Bicoid: A Morphogen Determining Head Structures One maternal effect gene, the bicoid gene, affects the front half of the body An embryo whose mother has no functional bicoid gene lacks the front half of its body and has duplicate posterior structures at both ends © 2011 Pearson Education, Inc.

Head Tail Wild-type larva 250 m Tail Tail Mutant larva (bicoid) A8 T1 Figure 18.21 Head Tail A8 T1 T2 T3 A7 A6 A1 A5 A2 A4 A3 Wild-type larva 250 m Tail Tail Figure 18.21 Effect of the bicoid gene on Drosophila development. A8 A8 A7 A6 A7 Mutant larva (bicoid)

Head Tail Wild-type larva 250 m A8 T1 T2 A7 T3 A6 A1 A5 A2 A4 A3 Figure 18.21a Head Tail A8 T1 T2 T3 A7 A6 A1 A5 A2 A4 A3 Figure 18.21 Effect of the bicoid gene on Drosophila development. Wild-type larva 250 m

Tail Tail Mutant larva (bicoid) A8 A8 A7 A7 A6 Figure 18.21b Figure 18.21 Effect of the bicoid gene on Drosophila development. Mutant larva (bicoid)

© 2011 Pearson Education, Inc. This phenotype suggests that the product of the mother’s bicoid gene is concentrated at the future anterior end This hypothesis is an example of the morphogen gradient hypothesis, in which gradients of substances called morphogens establish an embryo’s axes and other features © 2011 Pearson Education, Inc.

Fertilization, translation of bicoid mRNA Figure 18.22 RESULTS 100 m Anterior end Fertilization, translation of bicoid mRNA Bicoid mRNA in mature unfertilized egg Bicoid protein in early embryo Figure 18.22 Inquiry: Is Bicoid a morphogen that determines the anterior end of a fruit fly? Bicoid mRNA in mature unfertilized egg Bicoid protein in early embryo

Bicoid mRNA in mature unfertilized egg Figure 18.22a Bicoid mRNA in mature unfertilized egg Figure 18.22 Inquiry: Is Bicoid a morphogen that determines the anterior end of a fruit fly?

Bicoid protein in early embryo Figure 18.22b 100 m Anterior end Bicoid protein in early embryo Figure 18.22 Inquiry: Is Bicoid a morphogen that determines the anterior end of a fruit fly?

© 2011 Pearson Education, Inc. The bicoid research is important for three reasons – It identified a specific protein required for some early steps in pattern formation – It increased understanding of the mother’s role in embryo development – It demonstrated a key developmental principle that a gradient of molecules can determine polarity and position in the embryo © 2011 Pearson Education, Inc.

© 2011 Pearson Education, Inc. Concept 18.5: Cancer results from genetic changes that affect cell cycle control The gene regulation systems that go wrong during cancer are the very same systems involved in embryonic development © 2011 Pearson Education, Inc.

Types of Genes Associated with Cancer Cancer can be caused by mutations to genes that regulate cell growth and division Tumor viruses can cause cancer in animals including humans © 2011 Pearson Education, Inc.

© 2011 Pearson Education, Inc. Oncogenes are cancer-causing genes Proto-oncogenes are the corresponding normal cellular genes that are responsible for normal cell growth and division Conversion of a proto-oncogene to an oncogene can lead to abnormal stimulation of the cell cycle © 2011 Pearson Education, Inc.

within a control element Figure 18.23 Proto-oncogene DNA Translocation or transposition: gene moved to new locus, under new controls Gene amplification: multiple copies of the gene Point mutation: within a control element within the gene New promoter Oncogene Oncogene Figure 18.23 Genetic changes that can turn proto-oncogenes into oncogenes. Normal growth- stimulating protein in excess Normal growth-stimulating protein in excess Normal growth- stimulating protein in excess Hyperactive or degradation- resistant protein

© 2011 Pearson Education, Inc. Proto-oncogenes can be converted to oncogenes by Movement of DNA within the 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: cause an increase in gene expression © 2011 Pearson Education, Inc.

Tumor-Suppressor Genes Tumor-suppressor genes help prevent uncontrolled cell growth Mutations that decrease protein products of tumor-suppressor genes may contribute to cancer onset Tumor-suppressor proteins Repair damaged DNA Control cell adhesion Inhibit the cell cycle in the cell-signaling pathway © 2011 Pearson Education, Inc.

Interference with Normal Cell-Signaling Pathways Mutations in the ras proto-oncogene and p53 tumor-suppressor gene are common in human cancers Mutations in the ras gene can lead to production of a hyperactive Ras protein and increased cell division © 2011 Pearson Education, Inc.

Figure 18.24 Signaling pathways that regulate cell division. Growth factor MUTATION 2 Protein kinases Ras Hyperactive Ras protein (product of oncogene) issues signals on its own. MUTATION 3 G protein GTP Defective or missing transcription factor, such as p53, cannot activate transcription. Ras P P P P GTP UV light 3 Active form of p53 P P 2 4 Receptor Protein kinases (phosphorylation cascade) 1 DNA damage in genome DNA NUCLEUS 5 Transcription factor (activator) Protein that inhibits the cell cycle DNA Gene expression (b) Cell cycle–inhibiting pathway Protein that stimulates the cell cycle EFFECTS OF MUTATIONS Figure 18.24 Signaling pathways that regulate cell division. Protein overexpressed Protein absent (a) Cell cycle–stimulating pathway Cell cycle overstimulated Increased cell division Cell cycle not inhibited (c) Effects of mutations

Protein kinases (phosphorylation cascade) Receptor Figure 18.24a 1 Growth factor MUTATION Ras Hyperactive Ras protein (product of oncogene) issues signals on its own. 3 G protein GTP Ras P P P P GTP P P 4 2 Protein kinases (phosphorylation cascade) Receptor NUCLEUS 5 Transcription factor (activator) DNA Figure 18.24 Signaling pathways that regulate cell division. Gene expression Protein that stimulates the cell cycle (a) Cell cycle–stimulating pathway

Protein that inhibits the cell cycle Figure 18.24b 2 Protein kinases MUTATION Defective or missing transcription factor, such as p53, cannot activate transcription. 3 UV light Active form of p53 1 DNA damage in genome DNA Figure 18.24 Signaling pathways that regulate cell division. Protein that inhibits the cell cycle (b) Cell cycle–inhibiting pathway

© 2011 Pearson Education, Inc. Suppression of the cell cycle can be important in the case of damage to a cell’s DNA; p53 prevents a cell from passing on mutations due to DNA damage Mutations in the p53 gene prevent suppression of the cell cycle © 2011 Pearson Education, Inc.

Protein overexpressed Protein absent Figure 18.24c EFFECTS OF MUTATIONS Protein overexpressed Protein absent Cell cycle overstimulated Increased cell division Cell cycle not inhibited Figure 18.24 Signaling pathways that regulate cell division. (c) Effects of mutations

The Multistep Model of Cancer Development Multiple mutations are generally needed for full-fledged cancer; thus the incidence increases with age At the DNA level, a cancerous cell is usually characterized by at least one active oncogene and the mutation of several tumor-suppressor genes © 2011 Pearson Education, Inc.

Loss of tumor- suppressor gene APC (or other) 4 Figure 18.25 Colon 1 Loss of tumor- suppressor gene APC (or other) 4 Loss of tumor- suppressor gene p53 2 Activation of ras oncogene 3 Loss of tumor- suppressor gene DCC Additional mutations 5 Colon wall Figure 18.25 A multistep model for the development of colorectal cancer. Normal colon epithelial cells Small benign growth (polyp) Larger benign growth (adenoma) Malignant tumor (carcinoma)

Normal colon epithelial cells Figure 18.25a Colon Colon wall Figure 18.25 A multistep model for the development of colorectal cancer. Normal colon epithelial cells

Loss of tumor- suppressor gene APC (or other) Figure 18.25b 1 Loss of tumor- suppressor gene APC (or other) Small benign growth (polyp) Figure 18.25 A multistep model for the development of colorectal cancer.

Activation of ras oncogene Figure 18.25c 2 Activation of ras oncogene 3 Loss of tumor-suppressor gene DCC Larger benign growth (adenoma) Figure 18.25 A multistep model for the development of colorectal cancer.

Loss of tumor-suppressor gene p53 Figure 18.25d 4 Loss of tumor-suppressor gene p53 5 Additional mutations Malignant tumor (carcinoma) Figure 18.25 A multistep model for the development of colorectal cancer.

Inherited Predisposition and Other Factors Contributing to Cancer Individuals can inherit oncogenes or mutant alleles of tumor-suppressor genes Inherited mutations in the tumor-suppressor gene adenomatous polyposis coli are common in individuals with colorectal cancer Mutations in the BRCA1 or BRCA2 gene are found in at least half of inherited breast cancers, and tests using DNA sequencing can detect these mutations © 2011 Pearson Education, Inc.

Figure 18.26 Figure 18.26 Testing for mutations in BRCA1 and BRCA2.

Operon Promoter Genes A B C Operator RNA polymerase A B C Polypeptides Figure 18.UN01 Operon Promoter Genes A B C Operator RNA polymerase Figure 18.UN01 Summary figure, Concept 18.1 A B C Polypeptides

Active repressor: corepressor bound Figure 18.UN02 Genes expressed Genes not expressed Promoter Genes Operator Active repressor: corepressor bound Inactive repressor: no corepressor present Corepressor Figure 18.UN02 Summary figure, Concept 18.1

Active repressor: no inducer present Inactive repressor: inducer bound Figure 18.UN03 Genes not expressed Genes expressed Promoter Operator Genes Active repressor: no inducer present Inactive repressor: inducer bound Figure 18.UN03 Summary figure, Concept 18.1

Figure 18.UN04 Summary figure, Concept 18.2 Chromatin modification Transcription • Genes in highly compacted chromatin are generally not transcribed. • Regulation of transcription initiation: DNA control elements in enhancers bind specific transcription factors. • Histone acetylation seems to loosen chromatin structure, enhancing transcription. Bending of the DNA enables activators to contact proteins at the promoter, initiating transcription. • DNA methylation generally reduces transcription. • Coordinate regulation: Enhancer for liver-specific genes Enhancer for lens-specific genes Chromatin modification Transcription RNA processing • Alternative RNA splicing: RNA processing Primary RNA transcript mRNA degradation Translation mRNA or Figure 18.UN04 Summary figure, Concept 18.2 Protein processing and degradation Translation • Initiation of translation can be controlled via regulation of initiation factors. mRNA degradation • Each mRNA has a characteristic life span, determined in part by sequences in the 5 and 3 UTRs. Protein processing and degradation • Protein processing and degradation by proteasomes are subject to regulation.

Enhancer for liver-specific genes Enhancer for lens-specific genes Figure 18.UN04a Chromatin modification Transcription • Genes in highly compacted chromatin are generally not transcribed. • Regulation of transcription initiation: DNA control elements in enhancers bind specific transcription factors. • Histone acetylation seems to loosen chromatin structure, enhancing transcription. Bending of the DNA enables activators to contact proteins at the promoter, initiating transcription. • DNA methylation generally reduces transcription. • Coordinate regulation: Enhancer for liver-specific genes Enhancer for lens-specific genes Chromatin modification Figure 18.UN04a Summary figure, Concept 18.2 (part 1) Transcription RNA processing • Alternative RNA splicing: RNA processing Primary RNA transcript mRNA degradation Translation mRNA or Protein processing and degradation

Protein processing and degradation Figure 18.UN04b Chromatin modification Transcription RNA processing mRNA degradation Translation Protein processing and degradation Translation • Initiation of translation can be controlled via regulation of initiation factors. Figure 18.UN04b Summary figure, Concept 18.2 (part 2) mRNA degradation • Each mRNA has a characteristic life span, determined in part by sequences in the 5 and 3 UTRs. Protein processing and degradation • Protein processing and degradation by proteasomes are subject to regulation.

Protein processing and degradation Figure 18.UN05 Chromatin modification • Small or large noncoding RNAs can promote the formation of heterochromatin in certain regions, blocking transcription. Chromatin modification Transcription Translation RNA processing • miRNA or siRNA can block the translation of specific mRNAs. mRNA degradation Translation Protein processing and degradation Figure 18.UN05 Summary figure, Concept 18.3 mRNA degradation • miRNA or siRNA can target specific mRNAs for destruction.

Enhancer Promoter Gene 1 Gene 2 Gene 3 Gene 4 Gene 5 Figure 18.UN06 Figure 18.UN06 Test Your Understanding, question 11 Gene 4 Gene 5

Enhancer Promoter Gene 1 Gene 2 Gene 3 Gene 4 Gene 5 Figure 18.UN07 Figure 18.UN07 Appendix A: answer to Test Your Understanding, question 11 Gene 5

Enhancer Promoter Gene 1 Gene 2 Gene 3 Gene 4 Gene 5 Figure 18.UN08 Figure 18.UN08 Appendix A: answer to Test Your Understanding, question 11 Gene 5