* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Regulation of Gene Expression
Deoxyribozyme wikipedia , lookup
Protein moonlighting wikipedia , lookup
RNA interference wikipedia , lookup
Secreted frizzled-related protein 1 wikipedia , lookup
Messenger RNA wikipedia , lookup
Polyadenylation wikipedia , lookup
Non-coding DNA wikipedia , lookup
Molecular evolution wikipedia , lookup
RNA silencing wikipedia , lookup
Transcription factor wikipedia , lookup
Biochemistry wikipedia , lookup
Gene expression profiling wikipedia , lookup
List of types of proteins wikipedia , lookup
Expression vector wikipedia , lookup
Non-coding RNA wikipedia , lookup
Histone acetylation and deacetylation wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
Epitranscriptome wikipedia , lookup
Gene regulatory network wikipedia , lookup
Endogenous retrovirus wikipedia , lookup
RNA polymerase II holoenzyme wikipedia , lookup
Eukaryotic transcription wikipedia , lookup
Gene expression wikipedia , lookup
Promoter (genetics) wikipedia , lookup
CHAPTER 28 Regulation of Gene Expression Lehninger Principles of Biochemistry 6th Ed 28.1 Principles of Gene Regulation 28.2 Regulation of Gene Expression in Bacteria 28.3 Regulation of Gene Expression in Eukaryotes Lehninger Principles of Biochemistry 6th Ed 28.1 Principles of Gene Regulation -RNA polymerase binds to DNA at promoters -Transcription initiation is regulated by proteins that bind to or near promoters -Many bacterial genes are clustered and regulated in operons -The lac Operon is subject to negative regulation -Regulatory proteins have discrete DNA-binding domains -Regulatory proteins also have protein-protein interaction domains Lehninger Principles of Biochemistry 6th Ed Seven Processes that Affect the Steady-State Concentration of a Protein How to Control Protein’s Activity in the Cell !!! -How much primary RNA transcript to make -How to process this RNA into mRNA -How rapidly to degrade the mRNA -How much protein to make from this mRNA -How efficiently to target the protein to its location -How to alter the intrinsic activity of this protein -How rapidly to degrade the protein FIGURE 28–1 Seven processes that affect the steady-state concentration of a protein. Each process has several potential points of regulation. Lehninger Principles of Biochemistry 6th Ed Trends in Understanding Gene Regulation • Past focus has been on understanding transcription initiation • There is increasing elucidation of posttranscriptional and translational regulation • Mechanisms can be elaborate and interdependent, especially in development • Regulation relies on precise protein-DNA and protein-protein contacts Lehninger Principles of Biochemistry 6th Ed 28.1 Principles of Gene Regulation Terminology-Gene Regulation Housekeeping gene Under constitutive expression Constantly expressed in ~ all cells Regulated gene Levels of the gene product rise and fall with the needs of the organism Such genes are inducible able to be turned on and repressible able to be turned off Lehninger Principles of Biochemistry 6th Ed RNA polymerase binding to promoters is a major target of regulation • RNA polymerases bind to promoter sequences near starting point of transcription initiation (Fig. 28-2) • The RNA pol-promoter interaction greatly influences the rate of transcription initiation • Regulatory proteins (transcription factors) work to enhance or inhibit this interaction between RNA pol and the promoter DNA Lehninger Principles of Biochemistry 6th Ed Consensus Sequence of Many E. coli Promoters FIGURE 28–2 Consensus sequence for many E. coli promoters. Most base substitutions in the–10 and –35 regions have a negative effect on promoter function. Some promoters also include the UP (upstream promoter) element (see Fig. 26–5). Lehninger Principles of Biochemistry 6th Ed Transcription initiation is regulated by proteins that bind to or near promoters Specificity factors Alter the specificity of RNA pol. For a given promoter or set of promoters ex) subunit of the E. coli RNA pol-> mediates promoter recognition and binding (Fig 28-3) Repressors (Fig 28-4) Impede access of RNA polymerase to the promoter ex) repressors bind to specific sites on the DNA (operator in bacteria) Effectors bind to repressor and induce a conformational change may increase or decrease repressor’s affinity for the operator and thus may increase or decrease transcription Activators (Fig 28-4) Enhance the RNA polymerase-promoter interaction Ex) many eukaryotic activators bind to DNA sites “enhancer” Architectural regulators (Fig 28-5) Lehninger Principles of Biochemistry 6th Ed Many E. coli promoters have a sequence close to a consensus sequence • Most bacterial promoters include the conserved –10 and –35 regions that interact with the factor of RNA polymerase – Substitutions in this –10 to –35 region usually reduce the affinity of RNA Pol for the promoter • Some promoters also include the upstream element that interacts with the subunit of RNA polymerase Lehninger Principles of Biochemistry 6th Ed FIGURE 28-3 Consensus sequence for promoters that regulate expression of the E. coli heat shock genes. This system responds to temperature increases as well as some other environmental stresses, resulting in the induction of a set of proteins. Binding of RNA polymerase to heat shock promoters is mediated by a specialized subunit of the polymerase, 32, which replaces 70 in the RNA polymerase initiation complex. Lehninger Principles of Biochemistry 6th Ed FIGURE 28-5 The interaction between activators/repressors and RNA polymerase in eukaryotes The looping is facilitated in some cases by proteins called architectural regulators that bind to intervening sites and facilitate the looping of the DNA. Most of the eukaryotic systems involve protein activators. The actual interaction between the activators and the RNA polymerase at the promoter is often mediated by intermediary proteins called coactivators. In some instances, protein repressors may take the place of coactivators, binding to the activators and preventing the activating interaction 6th ed only Lehninger Principles of Biochemistry 6th Ed Many bacterial genes are transcribed and regulated together in an operon • An operon is a cluster of genes sharing a promoter and regulatory sequences – Genes are transcribed together so mRNAs are―several genes represented on one mRNA • First example: the lac operon FIGURE 28–6 Representative bacterial operon. Genes A, B, and C are transcribed on one polycistronic mRNA. Typical regulatory sequences include binding sites for proteins that either activate or repress transcription from the promoter. Lehninger Principles of Biochemistry 6th Ed The lac operon reveals many principles of gene regulation • Work of Jacob and Monod • Shows how three genes for metabolism of lactose: – -galactosidase (lacZ) • Cleaves lactose to yield glucose and galactose – Lactose permease (galactoside permease; lacY) • Transports lactose into cell – Thiogalactoside transacetylase (lacA)-unknown • are regulated together as an operon • rely on negative regulation via a repressor Lehninger Principles of Biochemistry 6th Ed Lactose Metabolism in E. coli • Allolactose (an inducer) binds to repressor, causes it to dissociate from operator – -galactosidase not only hydrolyzes lactose; it can also isomerize lactose into allolactose. – [Allolactose] when [Lactose] FIGURE 28–7 Lactose metabolism in E. coli. Uptake and metabolism of lactose require the activities of galactoside (lactose) permease and β-galactosidase. Conversion of lactose to allolactose by transglycosylation is a minor reaction also catalyzed by β-galactosidase. Lehninger Principles of Biochemistry 6th Ed Lactose metabolism in E. coli When glucose is abundant and lactose is lacking, cells make only very low levels of enzymes for lactose metabolism Transcription is repressed If glucose is scarce and cells are fed lactose, the cells can use it as their energy source The cells suddenly express the genes for the enzymes for lactose metabolism Transcription is no longer repressed Lehninger Principles of Biochemistry 6th Ed The lac Operon is subject to negative regulation • A gene called lacI encodes a repressor called the Lac repressor – Has its own promoter PI • So transcription of the repressor is independent of transcription of the enzymes the repressor regulates. – Repressor can bind to three operator sites (O1–O3) • Lac repressor binds primarily to operator O1 – O1 is adjacent to promoter – Binding of repressor helps prevent RNA polymerase from binding to promoter • Repressor also binds to one of two secondary operators, with the DNA looped between this secondary operator and O1 (see Fig. 288b) – Reduces transcription, but transcription occurs at a low, basal rate even with the repressor bound Lehninger Principles of Biochemistry 6th Ed FIGURE 28–8a The lac operon. (a) The lac operon. The lacI gene encodes the Lac repressor. The lac Z, Y, an A genes encode β-galactosidase, galactoside permease, and thiogalactoside transacetylase, respectively. P is the promoter for the lac genes, and PI is the promoter for the I gene. O1 is the main operator for the lac operon; O2 and O3 are secondary operator sites of lesser affinity for the Lac repressor. The inverted repeat to which the Lac repressor binds in O1 is shown in the inset. (b) The Lac repressor binds to the main operator and O2 or O3, apparently forming a loop in the DNA. Lehninger Principles of Biochemistry 6th Ed Regulatory Proteins have discrete DNA-binding domains Binding of proteins to DNA often involves hydrogen bonding • • • • Gln/Asn can form specific H-bond with Adenine’s N-6 and H-7 H’s Arg can form specific H-bonds with Cytosine-Guanine base pair See Fig. 28-10 Major groove is right size for -helix and has exposed H-bonding groups Asn, Gln/ Glu/ Protein Lys, Arg FIGURE 28–10 Specific amino acid residue–base pair interactions. The two examples shown have been observed in DNA-protein binding. DNA Lehninger Principles of Biochemistry 6th Ed Protein-DNA Binding Motifs • A few protein arrangements are used in thousands of different regulatory proteins and are hence called motifs – Helix-turn-helix • Used by Lac repressor – – – – Zinc finger Homeodomain Leucine zipper Basic helix-loop-helix Lehninger Principles of Biochemistry 6th Ed The helix-turn-helix motif is common in DNA-binding proteins • ~ 20 aa – One -helix for recognition for DNA (red in the next slide), then -turn, then another -helix – Sequence-specific binding due to specific contacts between the recognition helix and the major groove • Four DNA-binding helix-turnhelix motifs (gray) in the Lac repressor FIGURE 28–11 Helix-turn-helix. Lehninger Principles of Biochemistry 6th Ed The zinc finger motif is common in eukaryotic transcription factors • ~30 aa • “Finger” portion is a peptide loop cross-linked by Zn2+ – Zn2+ usually coordinated by 4 Cys, or 2 Cys, 2 His • Interact with DNA or RNA – Binding is weak, so several zinc fingers often act in tandem • Binding can range from sequence-specific to random FIGURE 28–12 Zinc fingers. (PDB ID 1ZAA) Three zinc fingers (shades of red) of the regulatory protein Zif268, complexed with DNA (blue). Each Zn2+ coordinates with two His and two Cys residues. Lehninger Principles of Biochemistry 6th Ed The Homeodomain motif - Identified in some proteins that function as transcriptional regulators, especially during eukaryotic development. - Related to the helix-tern-helix motif. - The DNA sequence that encodes this domain is known as the homeobox Lehninger Principles of Biochemistry 6th Ed Regulatory Proteins also have protein-protein interaction domains • Regulatory proteins contain domains not only for DNA binding but also for protein-protein interactions-with RNA polymerase, other regulatory proteins, or other subunits of the same regulatory protein • motif – Helix-turn-helix • Used by Lac repressor – – – – Zinc finger Homeodomain Leucine zipper Basic helix-loop-helix Lehninger Principles of Biochemistry 6th Ed FIGURE 28–14b Leucine zippers. (b) (PDB ID 1YSA) Leucine zipper from the yeast activator protein GCN4. Only the “zippered” α helices (gray), derived from different subunits of the dimeric protein, are shown. The two helices wrap around each other in a gently coiled coil. The interacting Leu side chains and the conserved residues in the DNA-binding region are colored to correspond to the sequence in (a). FIGURE 28–15 Helix-loop-helix Lehninger Principles of Biochemistry 6th Ed The Leucine Zipper Motif • • • • • Dimer of two amphipathic -helices plus a DNA-binding domain Each helix is hydrophobic on one side and hydrophilic on the other – Hydrophobic side is contact between the two monomers ~Every seventh residue in helices is Leu Helices form a coiled coil DNA-binding domain has basic residues (Lys, Arg) to interact with polyanionic DNA FIGURE 28–14a Leucine zippers. (a) Comparison of amino acid sequences of several leucine zipper proteins. Note the Leu (L) residues (red) at every seventh position in the zipper region, and the number of Lys (K) and Arg (R)Lehninger residues in the DNA-binding Principles of Biochemistry region (yellow). 6th Ed Eukaryotic gene regulation relies on combinatorial control • In yeast, only 300 transcription factors for thousands of genes • Transcription factors mix and match • Different combinations regulate different genes • Relies on protein-protein interactions Lehninger Principles of Biochemistry 6th Ed 28.3 Regulation of Gene Expression in Eukaryotes -Transcriptionally activate chromatin is structurally distinct from inactive chromatin -Most eukaryotic promoters are positively regulated -DNA-binding activators and coactivators facilitate assemble of the general transcription factors -The genes of galactose metabolism in yeast are subject to both positive and negative regulation -Transcription activators have a modulator structure -Eukaryotic gene expression can be regulated by intercellular and intercellular signals -Regulation can result from phosphorylation of nuclear transcription factors -Many eukaryotic mRNAs are subject to translational repression -Posttranscriptoinial gene silencing is mediated by RNA interference -RNA-mediated regulation of gene expression takes many forms in Eukaryotes -Development is controlled by cascades of regulatory proteins Summary 28.3 Regulation of Gene expression in Eukaryotes In eukaryotes, positive regulation is more common than negative regulation, and transcription is accompanied by large changes in chromatin structure Promoters for Pol II typically have a TATA box and Inr sequence, as well as multiple binding sites for transcription activators. The latter sites, sometimes located hundreds or thousands of base pairs away from the TATA box, are called upstream activator sequences in yeast and enhancers in higher eukaryotes. Large complexes of proteins are generally required to regulated transcriptional activity. The effects of transcription activators on Pol II are mediated by coactivator protein complexes such as Mediator. The modular structures of the activators have distinct activation and DNA-binding domains. Other protein complexes, including histone acetyltransferases and ATP-dependent complexes such as SWI/SNF and NURF, reversibly remodel and modify chromatin structure. Lehninger Principles of Biochemistry 6th Ed Summary 28.3 Regulation of Gene expression in Eukaryotes Hormones affect the regulation of gene expression in one of two ways. Steroid hormones interact directly with intracellular receptors that are DNA-binding regulatory proteins; binding of the hormone has either positive or negative effects on the transcription of genes targeted by the hormone. Nonsteroidal hormones bind to cell surface receptors, triggering as signaling pathway that can lead to phosphorylation of a regulatory protein, affecting its activity RNA-mediated regulation plays an important role in eukaryotic gene expression, with the range of known mechanisms expanding Development of a multicellular organism presents the most complex regulatory challenge. The fate of cells in the early embryo is determined by establishment of anterior-posterior and dorsal-ventral gradients of proteins that act as transcription activators or translational repressors, regulating the genes required for the development of structures appropriate to a particular part of the organism. Sets of regulatory genes operate in temporal and spatial succession, transforming given areas of an egg cell into predictable The differentiation of stem cells into functional tissues can be controlled by extracellular signals and conditions Transcriptionally activate chromatin is structurally distinct from inactive chromatin Key Features of Eukaryotic Gene Regulation! 1. Access of eukaryotic promoters to RNA polymerase is hindered by chromatin structure – thus requires remodeling chromatin 2. Positive regulation mechanisms predominate and are required for even a basal level of gene expression 3. Eukaryotic gene expression requires a complicated set of proteins!!! Lehninger Principles of Biochemistry 6th Ed • Euchromatin = less-condensed chromatin, distinguished from transcriptionally inactive heterochromatin (~10%) • Transcriptionally active genes have: – Nucleosomes repositioned – Histone variants – Covalent modifications to nucleosomes – These transcription-associated structural changes in chromatin are collectively called “Chromatin remodeling” – The remodeling involves enzymes that promote these changes (Table 28-2) Lehninger Principles of Biochemistry 6th Ed Nucleosomes can be restructured by specific protein complexes • SWI/SNF (SWItch/Sucrose NonFermentable) Complex – Works with proteins of ISWI (imitation switch) family – ATP-dependent alteration of spacing between nucleosomes, etc. – Stimulate transcription factor binding • NURF: a member of ISW1 family, remodels chromatin in ways that complement and overlap the activity of SWI/SNF. • SWR1 Family – Change histone content(lose H1, replace H2 and H3 with variants H3.3 and H2AZ. (Table 28-2) Lehninger Principles of Biochemistry 6th Ed Covalent Modification of Histones • Methylation • Phosphorylation • Acetylation • Ubiquitination • Sumoylation • Occur mostly in the N-terminal domain of the histones found near the exterior of the nucleosome particle Central domain (involved in histone-histone interaction) +Lysine rich N-terminal domain Covalent modification of histones allows recruitment of enzymes and transcription factors • Methylation of Lys-4 and Lys-36 at Histone3 (H3) and Arg of H3 and H4 – Results in transcriptional activation – Recruits histone acetyltransferases (HATs) that then acetylate a particular Lys DNA(-) – Acetylation of Lys results in decreased affinity of histone for DNA – Reversed by histone deacetylases (HDACs) that make chromatin inactive Lehninger Principles of Biochemistry 6th Ed Idea of a “Nucleosome Code” or “Histone Code” • Some speculate that genomes encode directions for nucleosome organization – Nucleosomes seem to occur at specific sequences – Covalent modifications seem to occur at specific regions/sequences • A nucleosome positioning code or histone modification code explains these observations Lehninger Principles of Biochemistry 6th Ed Most eukaryotic promoters are positively regulated • Eukaryotic RNA pol have little or not intrinsic affinity for their promotes; initiation of transcription is almost always dependent on the action of multiple activator proteins. Fig 28-27 The advantages of combinatorial control Lehninger Principles of Biochemistry 6th Ed DNA-binding activators and coactivators facilitate assemble of the general transcription factors In addition to TATA box and Inr (initiator) sequences, PoI II promoters vary greatly in both no. and location of additional sequences required for the regulation of transcription. Additional regulatory sequences: •Enhancer in higher eukaryotes •Upstream activator sequences (UASs) in yeast Lehninger Principles of Biochemistry 6th Ed RNA polymerase II binding to eukaryotic genes requires five types of proteins • Transcription activators – Proteins that bind to Upstream Activator Sequences (UASs), Enhancers • Architectural regulators to facilitate DNA looping • Chromatin modification/remodeling proteins • Coactivators – Act indirectly (with other proteins, not with DNA) • Basal transcription factors (fig 26-9, table 26-2) Lehninger Principles of Biochemistry 6th Ed FIGURE 28–5 The interaction between activators/repressors and RNA polymerase in eukaryotes. Eukaryotic activators and repressors often bind sites thousands of base pairs from the promoters they regulate. DNA looping, often facilitated by architectural regulators, brings the sites together. The interaction between activators and RNA polymerase is often mediated by coactivators, as shown. Repression is sometimes mediated by repressors (described later) that bind to activators, thereby preventing the activating interaction with RNA polymerase. Lehninger Principles of Biochemistry 6th Ed Enhancer proteins are diverse • Can bind thousands of nucleotides away from the TATA box of the promoter • Can have DNA-binding, protein-binding, and/or signal molecule-binding domains – Can bind with multiple proteins • Some regulate a few genes; some regulate many hundreds of genes Lehninger Principles of Biochemistry 6th Ed Architectural regulators regulate looping • Looping of DNA allows distant enhancers to modulate assembly at promoters – Example: High Mobility Group (HMG) proteins • Have multiple functions, including architectural regulation Lehninger Principles of Biochemistry 6th Ed Coactivators such as mediator and TATA-binding protein (TBP) assist RNA polymerase • Mediator complex binds to carboxyl-terminal domain(CTD) of RNA Pol II – Required for both basal and regulated transcription at many promoters – Later provides assembly surface for other complexes • TATA-Binding Protein is first component of preinitiation complex (PIC) at the typical TATA box of a promoter Lehninger Principles of Biochemistry 6th Ed Details of Eukaryotic Regulation that Are Emerging • Binding of activators triggers many promoters to bind RNA Pol II – Binding one activator seems to enable binding of additional activators – Often components bind in a regular order – Histones are displaced as activators bind – Process coordinates with chromatin remodeling (Fig. 28-29) Lehninger Principles of Biochemistry 6th Ed Reversible Transcriptional Activation - Although rarer, some eukaryotic regulatory proteins that bind to PoL II promoters or that interact with transcriptional activators can act as repressors, inhibiting the formation of active PICs Lehninger Principles of Biochemistry 6th Ed The genes of galactose metabolism in yeast are subject to both positive and negative regulation The regulation of genes for importing and metabolizing galactose in yeast illustrates important principles • Genes for galactose metabolism (GAL) are spread over several chromosomes • But all have similar promoters – TATA box, Inr sequences, Upstream Activator Sequence (UASG) recognized by Gal4 protein (Gal4p) Lehninger Principles of Biochemistry 6th Ed All GAL genes are regulated by a common set of proteins • Galactose binds Gal3p, then forms a complex with Gal4p and Gal80p(inhibitor for Gal4p) • Allows Gal4p to be activator • Gal4 also recruits the SWI/NSF and mediator complexes for opening the chromatin Lehninger Principles of Biochemistry 6th Ed Transcription activators have a modulator structure • Three types of structural domains used in activation by transcription activators Gal4p has separate activation domain with many acidic amino acid residues. “acidic activation domain of Gal4p” (acidic nature is critical to its function) Sp1’s DNA binding sites=GCbox (GGGCGG) near TATA box In addition to DNA binding domain with zinc finger, two other domains in Sp1 function in activation are notable in that 25% of their AA residues are Gln (glutamine-rich domain) CTF1 bind CCAAT site. DNA-binding domain of CTF1 contains many basic AA residues, and the binding region is probably arranged as an a helix. This protein has neither a hlix-turn-helix nor a zinc finger motif. It has proline-rich activation domain (proline >20%) Lehninger Principles of Biochemistry 6th Ed Eukaryotic gene expression can be regulated by intercellular and intercellular signals • Steroid hormone: two types of steroid-binding nuclear receptor - The hormone-receptor complex acts by binding to highly specific DNA sequences called hormone response elements (HRE). • Hormone receptors have DNAbinding domain with zinc fingers • Hormone receptors also have ligand-binding region at Cterminus that is highly variable between different receptors Lehninger Principles of Biochemistry 6th Ed Hormones bind to one of two types of receptors Fig. 28-32 • Monomeric Type 1 (NR)―receptors for sex hormones and glucocorticoids – Found in cytoplasm in complex w/Hsp70 – When hormone binds, Hsp70 dissociates • Receptor dimerizes • Exposes nuclear localization region – So hormone-receptor complex travels to nucleus to be transcriptional activator • Type II (includes thyroid hormone receptor; TR) – Found in nucleus bound to DNA and corepressor Retinoid X receptor (RXR) – Hormone binds, corepressor dissociates – Receptor-hormone complex then activates transcription • SRA, an unusual coactivator for some HR(like AR), act as part of a ribonucleoprotin complex. Lehninger Principles of Biochemistry 6th Ed Fig. 28-32 Mechanisms of steroid hormone receptor function Lehninger Principles of Biochemistry 6th Ed Regulation can result from phosphorylation of nuclear transcription factors Eukaryotic gene expression is also regulated by peptide hormones • 2 messengers lead to activation of transcription factors • Example: -adrenergic pathway (ex.epinephrine) – cAMP activates protein kinase A (PKA) – PKA enters nucleus, phosphorylates cAMP response elementbinding protein (CREB) – CREB is a transcription activator of genes leading to fuel use rather than fuel storage Lehninger Principles of Biochemistry 6th Ed Many eukaryotic mRNAs are subject to translational repression Eukaryotes have at least four main mechanisms of translational regulation 1. Translation initiation factors are subject to phosphorylation by protein kinases. The phosphorylated forms are often less active and cause a general depression of translation in the cells. Ex) when reticulocytes become deficient in iron or heme, the translation of globin mRNA is repressed. HCR(hemin-controlled repressor) protein kinase is activated, catalyzing the phosphorylation of eIF2. 2. Some proteines bind directly to mRNA and act as translational repressors. At 3’UTR (Fig 28-34) 3. Binding proteins, present in eukaryotes From yeast to mammals, disrupt the interaction Between dIF4E and eIF4G (fig. 27-28) The mammalian versions are known as 4E-BPs (eIF4E binding proteins) 4. RNA-mediated regulation of gene expression, Lehninger Principles of Biochemistry 6th Ed Posttranscriptoinial gene silencing is mediated by RNA interference Micro-RNAs prevent translation of mRNA • Micro-RNAs (miRNAs) silence genes by binding to mRNAs – Can prevent transcription of the mRNA by cleaving it (via endonucleases Drosha or Dicer) or by blocking it • Some miRNAs are made briefly during development, called small temporal RNAs (stRNAs) Lehninger Principles of Biochemistry 6th Ed Researchers can shut down genes artificially via RNA interference • Any dsRNA that corresponds to an mRNA and is introduced into a cell will be cleaved by Dicer into short segments called small interfering RNAs (siRNAs) • These will bind to the mRNA to silence its translation • Process is called RNA interference Lehninger Principles of Biochemistry 6th Ed RNA-mediated regulation of gene expression takes many forms in Eukaryotes • ncRNA (noncoding RNAs) DO NOT encode proteins, including rRNAs and tRNAs Ex) the special-function RNAs in eukarytoes include miRNAs, snRNA (RNA slicing), snoRNAs (rRNA modification) SRA (coactivator) Lehninger Principles of Biochemistry 6th Ed Stem cells have developmental potential that can be controlled Development is controlled by cascades of regulatory proteins The life cycle of the fruit fly includes complete metamorphosis during its progression from an embryo to an adult (Fig 28-36). Among the most important characteristics of the embryo are its polarity (the anteritor and posterior parts of the animal are readily distinguished, as are its dorsal and ventral parts) and its metamerism (the embryo body is made up of serially repeating segments, each with characteristic features) During the development, these segments become organized into a head, thorax, and abdomen. Each segment of the adult thorax has a different set of appendages (Fig. 28-26). Development of this complex pattern is under genetic control, and a variety of patternregulating genes have been discovered that dramatically affect the organization of the body. Lehninger Principles of Biochemistry 6th Ed Figure 28-26. Life cycle of the fruit fly Drosophila m Lehninger Principles of Biochemistry 6th Ed Proteins that, through changes in local concentration or activity, cause the surrounding tissue to take up a particular shape or structure are sometimes referred to as morphogen; they are the products of pattern-regulating genes. 3 major classes of pattern-regulating genes 1.maternal, 2.segmentation, 3.homeotic genes -function in successive stages of development to specify the basic features of the Drosophila embryo body. 1.Maternal genes are expressed in the unfertilized egg, and the resulting maternal mRNAs remain dormant until fertilization. These provide most of the proteins needed in very early development, until the cellular blastoderm is formed. Some of the proteins encoded by maternal mRNAs direct the spatial organization of the developing embryo at early stages, establishing its polarity. 2.Segmentation genes, transcribed after fertilization, direct the formation of the proper number of body segments. Gap genes(divide the developing embryo into several broad regions, pair-rule gene together with segment polarity genes define 14 strips that become the 14 sements of normal embryo. 3.Homeotic genes are expressed still later, they specify which organs and appendages will develop in particular body segemtns. Lehninger Principles of Biochemistry 6th Ed The key to tissue regeneration lied in stem cells-cells that have retained the capacity to differentiate into various tissues. -In human, after an egg is fertilized, the first few cell divisions create a ball of totipotent cells (the morula), cells that have the capacity to differentiate individually into any tissue or even into a complete organism (Fig 28-43) The inner layers form the germ layers of the developing fetus-the ectoderm, mesoderm, endoderm. These cells are pluripotent: They can give rise to cells of all three germ layers and can differentiate into may types of tissues. However, they can’t differentiated into a complete organism. Some of these cell are unipotent: they can develop into only one type of cell and/or tissue. It is the pluripotent cells of the blastocyst, the embryonic stem cells. In adult organism, adult stem cells, as products of additional differentiation, have a more limited potential for further development than do embryonic stem cells. Ex. hematopoietic stem cells of bone marrow. They are referred to as multipotent.