Control of Gene Expression

8 Key excerpts on "Control of Gene Expression"

• 

  eBook - PDF

  Biology Today and Tomorrow Without Physiology

  • Cecie Starr, Christine Evers, Lisa Starr, , Cecie Starr, Cecie Starr, Christine Evers, Lisa Starr(Authors)
  • 2020(Publication Date)
  • Cengage Learning EMEA

    (Publisher)

  Why Cells Control Gene Expression Regulating gene expression is an important part of homeostasis, because it allows control over the kinds and amounts of substances that are present in a cell at any given time. By adjusting expression of particular genes, cells respond appropriately to changes in their internal and external environments. For example, bacteria alter gene expression based on changes in the availability of nutrient carbohydrates in their environment. When a bacterium encounters a preferred nutrient, it begins transcribing genes for enzymes that break it down. When the nutrient is no longer available, transcription of those genes stops. Thus, the cell does not waste energy and resources producing gene products that are not needed. Adjustments to gene expression also affect form and function in multicelled organisms. A typical differentiated body cell uses only about 10 percent of its genes at any given time. Some of the expressed genes affect structural features and metabolic functions common to all cells; others are used only by certain cells. For example, all of your body cells express genes for glycolysis enzymes, but only immature red blood cells express globin genes. Such differences begin early in embryonic development. Master Regulators in Embryonic Development An animal body starts out as a tiny cluster of identical cells, all expressing the same genes. These cells divide repeatedly, and their descendants begin to differentiate as they start expressing different subsets of genes. As the cells diverge in form and function, they give rise to tissues, organs, and other body parts. Embryonic development is orchestrated by transcription factors that are produced in cascades of gene expression. In these cascades, the transcription fac- tor product of one gene affects the expression of other transcription factor genes, whose products in turn affect the expression of others, and so on.

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Karp's Cell and Molecular Biology

  Concepts and Experiments

  • Gerald Karp, Janet Iwasa, Wallace Marshall(Authors)
  • 2016(Publication Date)
  • Wiley

    (Publisher)

  CHAPTER 12 • Control of Gene Expression 488 receptor (ER) or do not. This is important, because treatment protocols differ depending on whether a particular breast cancer expresses the ER. The experimental results shown in Figure 12.36 examined 129 different breast cancer tumors for the expression of 149 genes that segregate between ER− and ER+ tumors. The differ- ences are represented by changes in blue (low expression) or red (high expression) and demonstrate that such analyses can identify the genotype of a breast cancer biopsy, which provides physicians an opportunity to personalize therapy. These technological approaches have many potential uses in addition to providing a visual portrait of gene expression. For example, they can be used to determine the degree of genetic variation in human populations or to identify the alleles for particular genes that a person carries. It is hoped, one day, that this latter information may advise people of the diseases to which they may be susceptible during their life, giving them an opportunity to take early preventive measures. 12.11 The Role of Transcription Factors in Regulating Gene Expression Great progress has been made in elucidating how certain genes can be transcribed in a particular cell, while other genes remain inactive. Transcriptional control is orchestrated by a large number of pro- teins, called transcription factors. As discussed in Chapter 11, these proteins can be divided into two functional classes: general transcription factors that bind at core promoter sites in association with RNA polymerase (page 417) and sequence‐specific transcrip- tion factors that bind to various regulatory sites of particular genes. This latter group of transcription factors can act either as transcrip- tional activators that stimulate transcription of the adjacent gene or as transcriptional repressors that inhibit transcription.

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  Clinical Precision Medicine

  A Primer

  • Judy S. Crabtree(Author)
  • 2019(Publication Date)
  • Academic Press

    (Publisher)

  All of the molecular mechanisms described to this point are necessary for the basic expression of every single gene, which is known as basal gene expression. However, human beings are extremely complex biological machines and require more than simply the basal level of expression. They must be able to turn genes on or off in response to nutrient needs, extracellular signals such as hormones and steroids, organ- or tissue-specific expression, cell type–specific expression, and temporal restrictions such as developmental stage, differentiation stage, and even the different stages of the cell cycle. To do this, the human body, and all biological species, has developed extensive and complex regulatory mechanisms to ensure that the correct genes get turned on or off at the proper time and to the proper extent.

  Pretranscriptional gene regulation

  The most heavily regulated step in gene expression is pretranscriptional and most often affects the process of transcription initiation. Pretranscriptional regulation utilizes regulatory sequences, which are the stretch of DNA that encompasses the complete collection of DNA elements that contribute to altering the expression of any one gene. Regulatory sequences include any or all of the following:

  • 1. The core promoter—the minimal DNA sequence located immediately adjacent to the transcriptional start site that is sufficient to initiate transcription, usually between 60 and 120 bases in length.
  • 2. The proximal promoter—the DNA sequence that contains the core promoter but also contains primary regulatory elements, usually up to several hundred bases in length initiating at the transcriptional start site.
  • 3. The distal promoter—DNA regulatory sequences that are located several hundred, several thousand, or even many kilobases distant from the transcriptional start site. These elements include enhancers, silencers, or insulators.

  In addition to these DNA regulatory sequences, also known as cis-acting factors, regulation requires a host of trans-acting factors. These trans-acting factors are most often proteins known as specific transcription factors, which recognize very specific sequences of DNA located within the regulatory sequences. Binding of the specific transcription factor can either promote or inhibit the expression of a gene, depending on the promoter context in which the transcription factor binds. These factors may have many different functions, which include the ability to recruit or inhibit the binding of general transcription factors to the core promoter element or promote the bending of the DNA to facilitate the interaction of additional proteins that subsequently enhance or repress gene expression.

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  Molecular Pharmacology

  From DNA to Drug Discovery

  • John Dickenson, Fiona Freeman, Chris Lloyd Mills, Christian Thode, Shiva Sivasubramaniam, Christian Thode(Authors)
  • 2012(Publication Date)
  • Wiley

    (Publisher)

  In addition, some lncRNAs are known to control the availability of essential proteins factors for cellular processes (e.g. splicing or transcription). One such example is MALAT-1 (metastasis-associated lung adenocarcinoma transcript-1; Ji et al., 2003), an lncRNA with an interesting biogenesis, subcellular location and function. In mammals, the mature MALAT-1 transcript has a length of ∼6.7 kb and derives from a larger precursor RNA (>7 kb), following RNase P cleavage. This also produces a smaller RNA, which is further processed to mascRNA (MALAT-1-associated RNA), a 61-nt tRNA-like small RNA (Wilusz et al., 2008). While mascRNA is exported to the cytoplasm, MALAT-1 is retained and enriched in nuclear ‘speckles’, that is, subnuclear bodies which play a role in the assembly of the pre-mRNA processing machinery. MALAT-1 is thought to modulate alternative splicing by sequestering inactive SR splicing factors into the speckles and altering their phosphorylation status (Tripathi et al., 2010). Experimentally-induced depletion of MALAT-1, which is normally present at high levels, leads to an increase in mislocalised and unphosphorylated SR proteins, and a higher rate of exon retention in mRNA transcripts. Likewise, trafficking of transcription factor NFAT (nuclear factor of activated T cells) in the cytoplasm can be controlled by NRON (ncRNA repressor of the NFAT; Willingham et al., 2005). Its interaction with the importin proteins in the nuclear envelope prevents NFAT from being transported into the nucleus and from activating genes. Increased NFAT activity, on the other hand, is observed if NRON is knockeddown. Both examples illustrate that important cellular processes can also be regulated indirectly by lncRNAs.

  8.10 Summary

  In this chapter we have seen that gene expression can be controlled at the level of transcription by transcription factors and their accessory proteins/complexes, non-coding RNAs and UTRs. The type of protein expressed is dependent upon splicing sites and the insertion/removal of specific exons. In addition, all of these factors are dependent upon SNP which can alter transcription factor and/or splicesome binding sites to prevent/enhance the expression of certain splice variants from a particular gene. All these elements can interact to produce cell-specific transcripts and hence responses to certain stimuli. This is an exciting area of research for the treatment of many types of disease.

  The human genome project has revealed that there are fewer genes in our chromosomes, than originally thought. This actually means is that different cells are likely to have varying levels of selective expression of the same groups of genes (rather than completely different sets of genes). This is mainly achieved by three processes (i) transcriptional regulation; (ii) post-transcriptional modification such as RNA editing; and (iii) translation/post-translational modifications. However transcriptional regulation is the most important in that it can coordinate the expression of gene products that act antagonistically in physiological processes. The BTFs are essential to initiate the transcription, whereas MTFs help to select, regulate and/or modify the transcriptional events. Thereby cells minimise the energy expenditure.

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  Biochemistry

  An Integrative Approach with Expanded Topics

  • John T. Tansey(Author)
  • 2022(Publication Date)
  • Wiley

    (Publisher)

  techniques such as short interfering RNA (siRNA), short hairpin RNA (shRNA), and morpholinos silence genes by taking advantage of the cell’s native machinery (Dicer, Argonaute, and the RISC complex). These techniques are simple, inexpensive, and readily adaptable to different experimental conditions and to many genes. Solid-phase synthesis and robotic nucleotide synthesizers have made it inexpensive and easy to procure specific DNA, RNA, or modified oligonucleotide analogs. Using these techniques, it has become routine to silence a single gene in a cell or organism or to silence a whole spectrum of genes to see how this affects a pathway of interest. Such techniques are rapidly changing the face of biochemical research.

  Viruses use multiple approaches to regulate gene expression, discussed further in Medical Biochemistry: Viral mechanisms to control gene expression .

  Medical Biochemistry

  Viral mechanisms to control gene expression

  Viruses are parasites that use the host organism’s own expression machinery to replicate. In addition, viruses affect the host’s gene expression, plausibly to prevent the host organism from detecting or having a negative impact on virus propagation. To accomplish these feats, viruses employ a variety of mechanisms to regulate gene expression.

  Viruses infect cells and integrate the viral genome into the host genome. Viral proteins are often coded for by one polycistronic message with a single control element similar to an operon. In the case of most viruses, the virus has a promoter sequence in the 5′ end of the viral genome that recognizes multiple host transcription factors. In the case of human immunodeficiency virus (HIV), the viral promoter region binds strongly to the human transcription factors NF-κB, AP–1, NFAT, and C/EBP, assisted by the viral proteins Vpr and Tat. Following synthesis of viral mRNA, several viruses employ antiterminator loops to further regulate protein synthesis. Both the respiratory syncytial virus (RSV) and the vaccinia virus use antiterminator loops to regulate expression of genes found early in their life cycles. Likewise, viral genomes code for short RNA sequences that also serve in a regulatory capacity (akin to miRNAs in eukaryotic cells). Finally, viruses can mediate epigenetic changes in the host to generate conditions favorable for viral propagation or latency. Kaposi’s sarcoma–associated virus and Epstein-Barr virus both manipulate host genomes to repress host genes involved in inflammation and immunity to remain latent.

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  Gene Transfer and Expression in Mammalian Cells

  • S.C. Makrides(Author)
  • 2003(Publication Date)
  • Elsevier Science

    (Publisher)

  Inducible gene expression in mammalian cells

  Wilfried Weber, Martin Fussenegger Institute of Biotechnology, Swiss Federal Institute of Technology, ETH Hoenggerberg, CH-8093 Zurich, Switzerland, Tel.: +41 1 633 3448; fax: +41 1 633 1051 E-mail address: [email protected]

  Abstract Publisher Summary

  Artificial control systems for adjusting transgene expression in mammalian cells, animals and eventually humans have generated tremendous impact on different areas of modern biomedical engineering ranging from basic gene-function analysis, drug discovery, drug testing in animals, the design of animal-based human disease models and biopharmaceutical manufacturing to gene therapy and tissue engineering strategies. Heterologous gene regulation systems have become an integral part of current spearhead therapeutic technologies focusing on production and delivery of therapeutic proteins where they are needed in the human body. Only a few of these systems have the assets for human therapeutic use including absence of any interference with endogenous regulatory networks, and graded as well as rapid response characteristics showing low basal and high maximum expression levels following administration of a clinically licensed drug (e.g., antibiotics, immunophilins and steroid hormones). The chapter focuses on these human-compatible systems that are currently competing in preclinical studies for optimal performance in adjusting expression of a single therapeutic (model) gene, (e.g., erythropoietin, insulin or human growth hormone). Recent initiatives to combine several compatible heterologous gene regulation systems have exemplified that complex artificial gene control configurations such as regulatory cascades and networks will develop in the next years from concept studies to a therapeutic reality. Such multiregulated multigene metabolic engineering will enable optimal integration of next-generation gene interventions in endogenous proliferation-, differentiation- and apoptosis-regulatory networks to achieve cell phenotypes designed to improve the understanding and therapy of currently untreatable human diseases. This chapter discusses different human-compatible heterologous gene regulation systems, their adaptation to specific expression configurations, and their potential to be integrated into higher order control systems to achieve next-generation gene therapy and tissue engineering strategies.

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  Measuring Gene Expression

  • Matthew Avison(Author)
  • 2008(Publication Date)
  • Taylor & Francis

    (Publisher)

  Escherichia coli, the Mar regulon (Miller and Sulavik, 1996) and how measurements of gene expression have been used to characterize its function.

  Figure 1.1

  Complications in functional genomics illustrated by the Mar regulon. The multiple antimicrobial drug resistance (Mar) regulon consists of two transcriptional regulators, MarR and MarA. The gene ompF and the operon acrAB encode a porin, through which antimicrobial drugs enter the cell, and an efflux pump which exports antimicrobials, respectively. Transcription of acrAB is under repression from the local regulator, AcrR and is activated through MarA binding upstream. Transcription of ompF is repressed when MarA binds upstream. MarR is a repressor for transcription of marA. Thus in (A), MarR binds to the promoter for marA, and represses transcription. AcrR binds to the promoter for acrAB, and represses transcription. There is no MarA to repress ompF transcription. Antimicrobials could flow into the cell through OmpF, and there would be no AcrAB available to pump them out again. In (B) an inducing ligand binds to MarR, reporting the presence of a toxic compound within the cell (e.g. an antimicrobial drug). This causes a conformational change in MarR, and marA transcription becomes derepressed. MarA then blocks transcription of ompF, but cannot significantly activate transcription of acrAB, because AcrR is still bound at the promoter, and its repressive effect is dominant. In this state, further antimicrobial entry would be limited, but the antimicrobial already inside the cell will not be pumped out. In (C) a second regulatory ligand has built up sufficiently to bind to AcrR and de-repress acrAB transcription. However, in the absence of MarA, transcription of acrAB would be low. In this case, however, MarA is available to activate transcription of acrAB, causing active efflux of the antimicrobial present within the cell. This illustrates the idea of multiple signals linking into a regulatory pathway. It also illustrates some of the inherent problems of studying regulation of gene expression. A deletion of marR would cause OmpF production to stop, so it might be concluded that MarR is an activator of ompF expression. Furthermore, mutations lead to activation of MarR, and so production of MarA may not always lead to production of AcrAB, thus it may be missed that MarA regulates acrAB

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  Molecular Genetics of Bacteria

  • Jeremy W. Dale, Simon F. Park(Authors)
  • 2013(Publication Date)
  • Wiley

    (Publisher)

  In addition to controlling gene expression in response to environmental or other stimuli, a bacterial cell needs to be able to produce some proteins (e.g. structural proteins, ribosomal proteins) at very high levels, while other proteins (such as some regulatory proteins) are only produced at a very low level. Although these levels may go up and down in response to environmental changes, or at different stages of growth, the maximum potential expression of genes is fixed at different levels. Fortunately, the mechanisms used for fixed and variable controls are similar, so we can consider them together.

  Looking at the flow of information from the structure of the gene to the activity of the enzyme as the final product (Figure 3.1 ), we can see that control is achieved at three main stages: production of mRNA, translation of that message into protein, and control of the enzymic activity of that protein. Within this framework, there are a number of potential regulatory factors, as follows.

  1 The number of copies of the gene. In general, if there are several copies of a gene the level of product is likely to be higher (although the relationship is not necessarily linear).

  2 The efficiency with which the gene is transcribed, which is mainly determined by the level of initiation of transcription by RNA polymerase (promoter activity). In bacteria this is the major factor influencing the expression of individual genes, whether we are considering fixed or variable controls.

  3 The stability of the mRNA. It is important to recognize that the amount of specific mRNA will be determined by the combined effect of the rate at which it is produced and the length of time each molecule persists in an active state in the cell. Most bacterial mRNA is very short-lived, typically being degraded with a half-life of about 2 minutes. The instability of bacterial mRNA is a key feature in the rapidity with which bacteria can respond to changes in their environment. However, some bacterial mRNA species are more stable than others, in some cases with a half-life as long as 25 minutes. Other forms of RNA (rRNA, tRNA) are also considerably more stable, which can be ascribed to the high degree of secondary structure possessed by these molecules.

  Sign up to read

  Learn more about book