Gene Control: Unlocking Genetic Secrets

Gene Control

Unlocking Genetic Secrets

Gene Control Unlocking Genetic Secrets

Deevakar Asan

Gene Control

Unlocking Genetic Secrets

Deevakar Asan

ISBN - 9789361520785

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Preface

Gene regulation is a key process in the development and maintenance of a healthy body and, as such, is central to both basic science and medical research. Epigenetic changes such as DNA methylation and histone methylation have added layers of complexity in recent years, as they also regulate gene expression. Long-range DNA looping can also greatly affect gene expression by bringing proximal promoters and enhancers to genes. With the application of high throughput sequencing, gene expression profiling in different tissues and diseases is now a very popular field of research. What has become a significant obstacle is to draw a coherent picture from a large volume of data of what are key regulators of gene expression. The basic mechanisms for gene regulation in prokaryotic and eukaryotic systems are identical. However, a significant difference is that transcription and translation of eukaryotes are carried out in different compartments. The transcription is done in the nucleus, while the translation is performed by ribosomes in the cytoplasm. As a result, many elements of genomic complexity remain unique to eukaryotes. Because eukaryotic gene regulation includes much more complicated mechanisms and specialized techniques of prokaryotic gene regulation are shared with eukaryotic systems, this book will primarily focus on how genes are regulated in eukaryotes. One benefit of multicellularity is that cells can be programmed to play various biological roles. However, in addition to determining cells to a specific function or fate, genes within certain tissues need to be triggered at a specific time throughout development. This process, known as spatiotemporal regulation, is regulated by various regulatory genes, particularly transcription factors and cell signaling molecules. Complex interactions between genes and their products in the cellular system can be studied via genetic regulatory networks (GRNs). Gene expression and how it is regulated is a fundamental question in biology and therefore, its complexity is not surprising. Initially, the major focus of the research was on transcription factors as the major modulators of gene expression. Then enhancers and enhancer-binding proteins were found to be critical for gene expression.

The current book deals with the role of genetic regulation in particular biological processes. The chapters in this book deal with the role of gene control in cell signaling processes and in the normal development of the embryo. With the advent of microarray and late-generation sequencing techniques, transcriptional profiling of biological samples, such as tumor samples and samples from other model organisms, has been performed to study molecular level or transcriptional control of sample subtypes during biological processes. Although popular data analysis methods use hierarchical clustering algorithms or pattern classification to explore associated genes and their functions, approaches to the Genetic Regulatory Network (GRN) have been used to track for deregulation between different tumor groups or biological processes. The emphasis of this book, therefore, is the explanation of the post-genome understanding of gene regulation.

Table of Contents

1 Gene Control and Expression 1

1.1 Gene Control 2

1.1.1 Non-coding RNAs (ncRNAs) 3

1.1.2 Modification of Chromatin Structure 4

1.1.3 Control of Gene Expression 5

1.1.4 Control of Gene Expression in Eukaryotes 7

1.1.5 Eukaryotes Require Complex Controls Over Gene Expression 10

1.1.6 Transcriptional Regulation in Eukaryotes 11

1.1.7 Transcription Factors and Combinatorial Control 11

1.1.8 Rnai 14

1.1.9 Gene Regulation 14

1.2 Gene Expression System 18

1.2.1 RNA Processing 18

1.2.2 Gene Networks 19

1.2.3 Expression of the Genetic Code: Transcription

and Translation 20

1.2.4 Gene Expression and Regulation 24

1.3 Gene Expression Control Model 27

1.3.1 The Chromosome Of E. Coli 28

1.3.2 The Operon Model 29

1.3.3 Viruses 33

1.3.4 The Eukaryotic Chromosome 36

1.3.5 Replication of the Eukaryotic Chromosome 38

1.3.6 Regulation of Eukaryotic Gene Expression 38

1.3.7 Types of Chromatin 39

1.3.8 The Eukaryotic Genome 39

1.3.9 Transcription and Processing of mRNA 41

1.3.10 Antibody-coding Genes 42

1.3.11 Viruses and Eukaryotes 43

1.3.12 Eukaryotic Transposons 43

1.3.13 Genes, Viruses and Cancer 43

1.4 Self-Assessment 44

2 Gene Transfer 45

2.1 Fundamental of Gene Transfer 45

2.1.1 History of Gene Transfer 45

2.1.2 Horizontal Gene Transfer 47

2.1.3 Vertical Gene Transfer 49

2.1.4 Process of Gene Transfer 50

2.1.5 Transfection 53

2.1.6 Transposition 53

2.2 Gene Transfer Techniques 53

2.2.1 Different Gene Transfection Techniques 54

2.2.2 Chemical Transfection 56

2.2.3 Calcium phosphate Transfection 57

2.2.4 Transfection with DEAE-dextran 57

2.2.5 Lipofection 58

2.2.6 Physical Transfection 58

2.2.7 Electroporation 59

2.2.8 Microinjection 60

2.2.9 Transfection by Particle Bombardment 60

2.2.10 Transfection by Ultrasound 61

2.2.11 Virus-mediated Transduction 61

2.3 Gene Transfer Methods and Treatment 64

2.3.1 General Considerations 65

2.3.2 Direct DNA Uptake 66

2.3.3 Chemical Treatments 67

2.3.4 DNA Microinjection 68

2.4 DNA Transfer 69

2.4.1 Transformation Techniques 70

2.4.2 Natural Competence and Transformation 73

2.4.3 Selection and Screening in Plasmid Transformation 77

2.5 Self-Assessment 78

3 Genetic and Genome Analysis 79

3.1 The Phenomena of Genetics 80

3.1.1 Curriculum of Geneticist 82

3.1.2 Genetic Analysis 84

3.2 Human Genetic Variation 85

3.2.1 Alteration in Human Genetic Variation 86

3.2.2 Existence of Genetic Variation among Humans 89

3.2.3 Significance of Human Genetic Variation 91

3.2.4 Human Genetic Variation and Medicine 92

3.2.5 Genetics, Ethics, and Society 98

3.3 Genome Analysis 100

3.3.1 Genome Map 102

3.3.2 Genome Anatomy 103

3.3.3 Eukaryotic Genome 108

3.4 Human Genome Analysis 113

3.4.1 Role of the Human Genome in Research 114

3.4.2 Origins of the Human Genome 115

3.4.3 Social Impacts of Human Genome Research 116

3.4.4 Whole-genome Sequencing 117

3.4.5 Sequencing Methods: From Genes to Genomes 118

3.4.6 Next-Generation Technologies 119

3.5 Genomics and Process of Bioinformatics System 120

3.5.1 Sequencing and Bioinformatics Analysis of Genomes 122

3.5.2 Analysis of Bioinformatics 123

3.5.3 The Data of Bioinformatics 124

3.5.4 Goals of Bioinformatics 125

3.5.5 Applications of Bioinformatics in Crop Improvement 127

3.6 Self-Assessment 128

4 Gene Regulation and Sequencing 129

4.1 Gene: Structure and Regulation 130

4.1.1 Chemical Structure of Genes 130

4.1.2 Gene Transcription and Translation 131

4.1.3 Role of Gene Regulation 131

4.1.4 Gene Mutations 133

4.1.5 Operon Regulatory System 135

4.1.6 Genetic Regulation of Cell Cycle 136

4.2 System of Gene Regulation 141

4.2.1 Transcriptional Regulation 142

4.2.2 Gene Mapping 143

4.2.3 Gene Interaction 144

4.2.4 Gene Dosage 145

4.2.5 Gene Silencing 146

4.3 Gene Sequencing 147

4.3.1 Whole-genome Sequencing 148

4.3.2 Sequencing Methods: From Genes to Genomes 148

4.3.3 Next-Generation Technologies 150

4.3.4 Hierarchical Shotgun Sequencing vs. Whole-genome Shotgun Sequencing 151

4.3.5 Pyrosequencing of Genomes in Picolitre Reactors 155

4.4 Self-Assessment 158

5 Gene Cloning and DNA analysis 159

5.1 Basics of DNA Cloning 159

5.1.1 Choice Of Vector For Dependent On Insert Size

And Application 162

5.1.2 Cutting And Joining Dna Molecules 163

5.1.3 Gene Libraries in Cloning 166

5.1.4 Steps Involved in Gene Cloning 169

5.2 DNA into Living Cells 171

5.2.1 Transformation—The Uptake Of Dna By Bacterial Cells 173

5.2.2 Identification Of Recombinants 176

5.2.3 Introduction Of Phage Dna Into Bacterial Cells 181

5.2.4 Identification Of Recombinant Phages 185

5.2.5 DNA into non-Bacterial Cells 187

5.3 Self-Assessment 189

6 Mitosis and Meiosis 190

6.1 Gene Transmission in Mitosis 191

6.1.1 Phases of Mitosis 193

6.1.2 Stages 198

6.1.3 Mitotic Abnormalities 201

6.2 Gene Transmission in Meiosis 203

6.2.1 Transmission System 205

6.2.2 Aberrations That Alter Chromosome Number 207

6.2.3 Meiosis and Sexual Reproduction 209

6.2.4 Sexual Reproduction 220

6.3 Self-Assessment 229

7 Genetic Control of Protein Synthesis 230

7.1 Genetic Control of Protein Synthesis, Cell Function, and

Cell Reproduction 231

7.1.1 Genes in the Cell Nucleus 232

7.1.2 Basic Building Blocks of DNA 233

7.1.3 Nucleotides 234

7.1.4 Genetic Code 236

7.1.5 Synthesis of RNA 237

7.1.6 Chemical Steps in Protein Synthesis 239

7.2 Protein Structure and Functionality 245

7.2.1 Primary Structure of Proteins 247

7.2.2 Protein Functionality 254

7.2.3 Biochemistry of Protein 261

7.2.4 Recombinant Protein Production 262

7.3 Protein Purification and Characterization 263

7.3.1 Methods for Protein Purification 264

7.3.2 Types of Protein 267

7.3.3 Proteins and Biological Membranes 268

7.4 Self-Assessment 274

Glossary 275

References 278

Index 286

Chapter

1 Gene Control and Expression

Genes are functional units of heredity as they are made of DNA. The chromosome is made of DNA containing many genes. Every gene comprises a particular set of instructions for a particular function or protein-coding. Speaking in usual terms, genes are responsible for heredity.

There are about 30000 genes in each cell of the human body. DNA present in the gene comprises only 2 percent of the genome. Many studies have been made on the same that found the location of nearly 13000 genes on each of the chromosomes.

William Bateson introduced the term genetics in the year 1905. Later, Wilhelm Johannes was the first one who coined the term GENE in 1909. He was a Danish botanist. He named it Gene to symbolize hereditary.

The human cell contains 23 pairs of chromosomes. The trait is one of the characteristics determined by one or more genes. Abnormal genes and genes that are formed due to new mutations also result in certain traits. Genes vary in size depending on the code or the protein they produce. All cells in the human body contain the same DNA. The difference between the cells occurs due to the different types of genes that are turned on and therefore produce a variety of proteins.

Genes come in pairs in the same way as the chromosomes. Each parent of a human being carries two copies of their genes and each parent passes one copy of genes to their child. This is the reason why the child has many characteristics of both the parents like hair color, same eyes etc.

1. Genes control the functions of DNA and RNA.

2. Proteins are the most important materials in the human body, which not only help by being the building blocks for muscles, connecting tissue and skin but also takes care of the production of the enzyme.

3. These enzymes play an important role in conducting various chemical processes and reactions within the body. Therefore, protein synthesis is responsible for all activities carried on by the body and is mainly controlled by genes.

4. Genes consist of a particular set of instructions or specific functions. For example, the globin gene was instructed to produce hemoglobin. Hemoglobin is a protein that helps to carry oxygen in the blood.

1.1 Gene Control

Genes are the basic unit of heredity and continuous stretch of DNA, which are linearly arranged on chromosomes. Replication of DNA copies the genetic information present in it, which is transcribed into RNA by an RNA polymerase enzyme. The RNA sequence of ribonucleotides is translated into the amino acid sequence of polypeptides (proteins) by the process of translation and proteins determine the physical and mental traits of organisms. Thus, genes control protein synthesis. As we know that heredity is the transmission of genetic traits from one generation to the next and genetic traits are determined by different types of proteins, the genetic information for the synthesis of which is present in genes. Thus, genes control protein synthesis and heredity through DNA replication, transcription and translation (the central dogma). An enzyme is a protein that accelerates the biological reactions and genes control enzyme synthesis through the central dogma, not their reactivity.

The process of protein synthesis does not constantly occur in the cell. Rather, it occurs at intervals followed by periods of genetic silence. Thus, the cell regulates and controls the gene expression process.

The control of gene expression may occur at several levels in the cell. For example, genes rarely operate during mitosis, when the DNA fibers shorten and thicken to form chromatin. The inactive chromatin is compacted and tightly coiled, and this coiling regulates access to the genes.

Other levels of gene control can occur during and after transcription. In transcription, certain segments of DNA can increase and accelerate the activity of nearby genes. After transcription has taken place, the mRNA molecule can be altered to regulate gene activity. For example, researchers have found that an mRNA molecule contains many useless bits of RNA that are removed in the production of the final mRNA molecule. These useless bits of nucleic acid are called introns. The remaining pieces of mRNA, called exons, are then spliced to form the final mRNA molecule. Thus, through the removal of introns and the retention of exons, the cell can alter the message received from the DNA and control gene expression.

The concept of gene control has been researched thoroughly in bacteria. In these microorganisms, genes have been identified as structural genes, regulator genes, and control genes (or control regions). The three units form a functional unit called the operon.

The operon has been examined in close detail in certain bacteria. Scientists have found, for example, that certain carbohydrates can induce the presence of the enzymes needed to digest those carbohydrates. When lactose is present, bacteria synthesize the enzyme needed to break down the lactose. Lactose acts as the inducer molecule in the following way: In the absence of lactose, a regulator gene produces a repressor, and the repressor binds to a control region called the operator. This binding prevents the structural genes from encoding the enzyme for lactose digestion. When lactose is present, however, it binds to the repressor and thereby removes the repressor at the operator site. With the operator site free, the structural genes are free to produce their lactose-digesting enzyme.

The operon system in bacteria shows how gene expression can occur in relatively simple cells. The gene is inactive until it is needed and is active when it becomes necessary to produce an enzyme. Other methods of gene control are more complex and are currently being researched.

1.1.1 Non-coding RNAs (ncRNAs)

Protein-encoding mRNA is clearly an important molecule, but the other non-coding RNAs (ncRNAs) that control mRNA transcription are increasingly becoming the focus of attention. Two such ncRNA molecules are microRNA and small interfering RNA.

MicroRNAs (miRNAs) are small, single-stranded RNA molecules that, along with associated proteins, bind to complementary sequences in certain mRNA molecules. Once bound, these miRNAs block the translation of the mRNA by either physically preventing the ribosome from binding or by causing the mRNA to degrade. The result—either blocked translation or mRNA degradation— depends on the extent of the base pairing between the miRNA and the target mRNA. Possibly half of the human genes are regulated by miRNA.

Small interfering RNAs (siRNAs) are similar in structure and function to miRNAs. RNA interference (RNAi) is a means of disabling a gene by introducing siRNAs into a cell. Researchers employ RNAi to knock out specific genes in order to study their function.

1.1.2 Modification of Chromatin Structure

Recall that DNA is condensed and packaged with histone proteins into a complex known as chromatin. This compact structure helps DNA to fit into the nucleus and also provides an opportunity for gene regulation. In order for a gene to be accessed by the transcriptional machinery, it must be unwound from the histone proteins. This is facilitated by certain enzymes adding acetyl groups (–COCH3) to the histones (histone acetylation). Alternatively, if a segment of DNA needs to remain unexpressed (such as the inactivated mammalian X chromosomes), a different set of enzymes will add methyl groups (–CH3) to certain bases, thus maintaining DNA’s tightly wound and inaccessible form.

How a cell controls the expression of its genes is almost as important as the genes themselves. Modification of DNA and its associated histone proteins have a profound effect on that gene’s expression. Furthermore, these modifications can be passed on to future generations and thus affect gene expression in progeny. This is called epigenetic inheritance. Alterations in normal modification have also been linked to some cancers due to inappropriate gene expression.

Can genes be turned on and off in cells?

Each cell expresses or turns on only a fraction of its genes. The rest of the genes are repressed or turned off. The process of turning genes on and off is known as gene regulation. Gene regulation is an important part of normal development. Genes are turned on and off in different patterns during development to make a brain cell look and act different from a liver cell or a muscle cell, for example. Gene regulation also allows cells to react quickly to changes in their environments. Although we know that the regulation of genes is critical for life, this complex process is not yet fully understood.

Gene regulation can occur at any point during gene expression but most commonly occurs at the level of transcription (when the information in a gene’s DNA is transferred to mRNA). Signals from the environment or from other cells activate proteins called transcription factors. These proteins bind to regulatory regions of a gene and increase or decrease the level of transcription. By controlling the level of transcription, this process can determine the amount of protein product that is made by a gene at any given time.

1.1.3 Control of Gene Expression

By gene expression, we mean the transcription of a gene into mRNA and its subsequent translation into protein. Gene expression is primarily controlled at the level of transcription, largely as a result of the binding of proteins to specific sites on DNA. In 1965 Francois Jacob, Jacques Monod, and Andre Lwoff shared the Nobel prize in medicine for their work supporting the idea that control of enzyme levels in cells is regulated by transcription of DNA occurs through regulation of transcription, which can be either induced or repressed. These researchers proposed that the production of the enzyme is controlled by an operon, which consists of a series of related genes on the chromosome consisting of an operator, a promoter, a regulator gene, and structural genes.

• The structural genes contain the code for the protein products that are to be produced. Regulation of protein production is largely achieved by modulating access of RNA polymerase to the structural gene being transcribed.

• The promoter gene doesn›t encode anything; it is simply a DNA sequence that is the initial binding site for RNA polymerase.

• The operator gene is also non-coding; it is just a DNA sequence that is the binding site for the repressor.

• The regulator gene codes for the synthesis of a repressor molecule that binds to the operator and blocks RNA polymerase from transcribing the structural genes.

The operator gene is the sequence of non-transcribable DNA that is the repressor binding site. There is also a regulator gene, which codes for the synthesis of a repressor molecule that binds to the operator

• Example of Inducible Transcription: The bacterium E. coli has three genes that encode for enzymes that enable it to split and metabolize lactose (a sugar in milk). The promoter is the site on DNA where RNA polymerase binds in order to initiate transcription. However, the enzymes are usually present in very low concentrations because their transcription is inhibited by a repressor protein produced by a regulator gene (see the top portion of the figure below). The repressor protein binds to the operator site and inhibits transcription. However, if lactose is present in the environment, it can bind to the repressor protein and inactivate it, effectively removing the blockade and enabling transcription of the messenger RNA needed for the synthesis of these genes (lower portion of the figure below).

• Example of Repressible Transcription: E. coli need the amino acid tryptophan, and the DNA in E. coli also has genes for synthesizing it. These genes generally transcribe continuously since the bacterium needs tryptophan. However, if tryptophan concentrations are high, transcription is repressed (turned off) by binding to a repressor protein and activating it, as illustrated below.

1.1.4 Control of Gene Expression in Eukaryotes

Eukaryotic cells have similar mechanisms for the control of gene expression, but they are more complex. Consider, for example, that prokaryotic cells of a given species are all the same, but most eukaryotes are multicellular organisms with many cell types, so control of gene expression is much more complicated. Not surprisingly, gene expression in eukaryotic cells is controlled by a number of complex processes, which are summarized by the following list.

• After fertilization, the cells in the developing embryo become increasingly specialized, largely by turning on some genes and turning off many others. Some cells in the pancreas, for example, are specialized to synthesize and secrete digestive enzymes, while other pancreatic cells (β-cells in the islets of Langerhans) are specialized to synthesize and secrete insulin. Each type of cell has a particular pattern of expressed genes. This differentiation into specialized cells occurs largely as a result of turning off the expression of most genes in the cell; mature cells may only use ٣-٥٪ of the genes present in the cell›s nucleus.

• Gene expression in eukaryotes may also be regulated through by alterations in the packing of DNA, which modulates the access of the cell’s transcription enzymes (e.g., RNA polymerase) to DNA. The illustration below shows that chromosomes have a complex structure. The DNA helix is wrapped around special proteins called histones, and these are wrapped into tight helical fibers. These fibers are then looped and folded into increasingly compact structures, which, when fully coiled and condensed, give the chromosomes their characteristic appearance in metaphase.

• Similar to the operons described above for prokaryotes, eukaryotes also use regulatory proteins to control transcription, but each eukaryotic gene has its own set of controls. In addition, there are many more regulatory proteins in eukaryotes and the interactions are much more complex.

• In eukaryotes, transcription takes place within the membrane-bound nucleus, and the initial transcript is modified before it is transported from the nucleus to the cytoplasm for translation at the ribosome s. The initial transcript in eukaryotes has coding segments (exons) alternating with non-coding segments (introns). Before the mRNA leaves the nucleus, the introns are removed from the transcript by a process called RNA splicing (see graphic & video below), and extra nucleotides are added to the ends of the transcript; these non-coding caps and tails protect the mRNA from attack by cellular enzymes and aid in recognition by the ribosomes.

• Variation in the longevity of mRNA provides yet another opportunity for control of gene expression. Prokaryotic mRNA is very short-lived, but eukaryotic transcripts can last hours, or sometimes even weeks (e.g., mRNA for hemoglobin in the red blood cells of birds).

• The process of translation offers additional opportunities for regulation by many proteins. For example, the translation of hemoglobin mRNA is inhibited unless iron-containing heme is present in the cell.

• There are also opportunities for post-translational controls of gene expression in eukaryotes. Some translated polypeptides (proteins) are cut by enzymes into smaller, active final products. as illustrated in the figure below, which depicts post-translational processing of the hormone insulin. Insulin is initially translated as a large, inactive precursor; a signal sequence is removed from the head of the precursor, and a large central portion (the C-chain) is cut away, leaving two smaller peptide chains which are then linked to each other by disulfide bridges. The smaller final form is the active form of insulin.

• Gene expression can also be modified by the breakdown of the proteins that are produced. For example, some of the enzymes involved in cell metabolism are broken down shortly after they are produced; this provides a mechanism for rapidly responding to changing metabolic demands.

• Gene expression can also be influenced by signals from other cells. There are many examples in which a signal molecule (e.g., a hormone) from one cell binds to a receptor protein on a target cell and initiates a sequence of biochemical changes (a signal transduction pathway) that result in changes within the target cell. These changes can include increased or decreased transcription, as illustrated in the figure below.

• The RNA Interference system (RNAi) is yet another mechanism by which cells control gene expression by shutting off the translation of mRNA. RNAi can also be used to shut down the translation of viral proteins when a cell is infected by a virus. The RNAi system also has the potential to be exploited therapeutically.

It is estimated that the human genome encodes approximately 25,000 genes, about the same number as that for corn and nearly twice as many as that for the common fruit fly. Even more interesting is the fact that those 25,000 genes are encoded in about 1.5% of the genome. So, what exactly does the other 98.5% of our DNA do? While many mysteries remain about what all of that extra sequence is for, we know that it does contain complex instructions that direct the intricate turning on and off of gene transcription.

1.1.5 Eukaryotes Require Complex Controls Over Gene Expression

While basic similarities in gene transcription exist between prokaryotes and eukaryotes—including the fact that RNA polymerase binds upstream of the gene on its promoter to initiate the process of transcription—multicellular eukaryotes control cell differentiation through more complex and precise temporal and spatial regulation of gene expression.

Multicellular eukaryotes have a much larger genome than prokaryotes, which are organized into multiple chromosomes with greater sequence complexity. Many eukaryotic species carry genes with the same sequences as other plants and animals. In addition, the same DNA sequences (though not the same proteins) are found within all of an organism’s diploid, nucleated cells, even though these cells form tissues with drastically different appearances, properties, and functions. Why, then, is there such great variation among and within such organisms? Quite simply, the way in which different genes are turned on and off in specific cells generates the variety we observe in nature. In other words, specific functions of different cell types are generated through differential gene regulation.

Of course, higher eukaryotes still respond to environmental signals by regulating their genes. But there is an additional