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Chapter

Cover Molecular Biology

RNA processing  

This chapter explores RNA processing events, which are points for regulation and quality control, and are sources of diversity. Many RNA processing reactions are directed by RNA components. Transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs) are processed out of longer precursor transcripts, and the nucleotides are post-transcriptionally modified. Meanwhile, the maturation of eukaryotic messenger RNAs (mRNAs) requires the addition of a 5' cap and a poly(A) tail—processes that are closely tied to transcription, splicing, transport out of the nucleus, and ultimately translation. The chapter then explains RNA splicing, RNA editing, and RNA degradation. RNA splicing allows the generation of great diversity in RNA products and can be catalysed by the RNA itself (self-splicing) or by a large protein and RNA-containing complex called the spliceosome. The chapter also looks at RNA-binding domains in proteins.

Chapter

Cover Thrive in Genetics

From Genotype to Phenotype II: RNA to Protein  

This chapter explores translation, which is the mechanism by which amino acids are assembled into proteins according to information encoded in messenger RNA (mRNA). It takes place on ribosomes, which attach near the 5′ end of mRNA and move towards its 3′ end, positioning and linking amino acids according to the codons they encounter. Translation involves a number of RNA–RNA interactions: between mRNA and ribosomal RNA (rRNA), which holds the mRNA for translation; mRNA codon and transfer RNA (tRNA) anticodon; and tRNA and the rRNA of ribosomes. Translation in both prokaryotes and eukaryotes involves three main stages: initiation, elongation, and termination. The chapter then considers the post-translational modification of polypeptides.

Chapter

Cover Molecular Biology

Regulatory RNAs  

This chapter highlights regulatory RNAs. RNA molecules can act as regulators by base-pairing with target RNAs or even DNA, or by binding metabolites or proteins, to block or facilitate the binding of other RNAs or proteins and bring molecules into proximity. Most base-pairing RNAs in bacteria are expressed in response to specific environmental conditions. The chapter then looks at microRNAs (miRNAs), small interfering RNAs (siRNAs), and Piwi-interacting RNAs (piRNAs). miRNAs are encoded by distinct genes and modulate translation and mRNA destabilization. siRNAs are generated through excision along the length of a double-stranded RNA of either external origin or endogenous origin and direct RNA interference and transcriptional silencing. Meanwhile, piRNAs are derived from repetitive regions of the genome, are associated with Piwi family Argonaute proteins, and repress the expression of diverse repeat sequences in the nucleus. The chapter also considers the viral defense role of CRISPR systems.

Chapter

Cover Molecular Biology of RNA

The biogenesis and nucleocytoplasmic traffic of non-coding RNAs  

This chapter explores non-coding RNAs (ncRNAs) that are processed during their biogenesis. It covers the processing and maturation of ribosomal RNA (rRNA), small nuclear RNA (snRNA), transfer RNA (tRNA), mitochondrial transcripts, and telomerase. It also gives an overview of the important aspects of RNA processing, including the RNA processing machinery that involves the action of other RNA molecules. The chapter reviews the main features of the biogenesis of ribosomal RNA, which is a process that is facilitated by a family of small RNA molecules known as the small nucleolar RNAs (snoRNAs). It describes the organization of rRNA processing in an important multifunctional nuclear organelle, the nucleolus.

Chapter

Cover Molecular Biology of RNA

Translation of messenger RNA  

This chapter covers the process of mRNA translation. Itbegins by reviewing the structure and function of the essential machinery of translation, namely the ribosome and transfer RNA. The chapter outlines the three phases of translation: initiation, elongation, and termination. It also discusses several ways in which mRNA translation can be regulated. The chapter details how ribosomes catalyse the synthesis of polypeptide chains that form when amino acids are covalently linked through peptide bonds. The chapter explains that ribosomes are made up of large and small subunits that contain ribosomal RNA (rRNA) and a multitude of ribosomal proteins. The chapter then looks at the different components of the ribosomal subunits that are distinguished according to the rate at which they sediment, as measured in Svedberg units.

Chapter

Cover Molecular Biology of RNA

Catalytic RNAs  

This chapter looks at how RNA molecules catalyse chemical reactions, a domain which was previously thought to be reserved only for proteins. It clarifies that RNA has a more limited set of functional groups for building catalysts, which are confined to just four different nucleotides: A, C, G, and U. It also highlights the ability of RNA molecules to form structures which also enables the assembly of RNA active sites. The chapter outlines the important function of metal ions in ribozymes, which includes helping RNA structures form and balance the strong negative charge in ribozyme active sites that result from high densities of RNA strands. It also mentions that the purine and pyrimidine bases of RNA have NH groups that can potentially act as hydrogen donors or acceptors in acid-base catalysis.

Chapter

Cover The Cell

RNA Synthesis and Processing  

This chapter discusses the initial level at which gene expression is regulated in both prokaryotic and eukaryotic cells, which is the first step in expression of a gene and transcription of DNA into RNA. It highlights different types of RNA that play distinct roles in cells, such as messenger RNAs (mRNAs) that serve as templates for protein synthesis. It also considers other noncoding RNAs function in gene regulation, mRNA splicing, rRNA processing, and protein sorting in eukaryotes. The chapter examines the roles of noncoding RNAs as regulators of gene expression in eukaryotic cells. It describes mRNA processing and the roles of snRNAs and patterns of alternative splicing, including RNA editing.

Book

Cover Molecular Biology of RNA

David Elliott and Michael Ladomery

Molecular Biology of RNA provides an overview of a cutting-edge field of biology. It starts with an introduction to the subject. It looks at how RNA can form versatile structures. It moves on to consider catalytic RNAs. Other topics covered include pre-mRNA splicing by the spliceosome, the RNA-binding proteins, pre-mRNA splicing defects found in development and disease, and co-transcriptional pre-mRNA processing. The text also looks at nucleocytoplasmic traffic of messenger RNA, messenger RNA localization, and translation of messenger RNA. It also examines stability and degradation of mRNA and RNA editing. Finally, the text provides an analysis on biogenesis and nucleocytoplasmic traffic of non-coding RNAs; the 'macro' RNAs, which include long non-coding RNAs and epigenetics; and the short non-coding RNAs and gene silencing. The text ends with a quick look at future perspectives.

Chapter

Cover Biochemistry and Molecular Biology

Gene transcription  

This chapter discusses how a gene is expressed by one strand of DNA, a template strand. It is then copied into single-stranded RNA and protein-coding genes, wherein the mRNA is translated to form protein. The chapter refers to transcription and notes that this is catalysed by RNA polymerase using ATP, CTP, GTP, and UTP as building blocks. Prokaryotes have a single RNA polymerase, while eukaryotes have three: Pol I, Pol II, and Pol III. The chapter explains Pol II and shows that it transcribes protein-coding genes to make mRNA, while Pol I transcribes a large rRNA precursor, and Pol III transcribes small RNAs. The coding region of a prokaryotic gene is a continuous stretch of DNA, so that the primary transcript is a messenger RNA (mRNA) and can be translated immediately, while in eukaryotes the primary transcript.

Chapter

Cover Molecular Biology of RNA

The ‘macro’ RNAs: long non-coding RNAs and epigenetics  

This chapter deals with long non-coding RNAs (ncRNAs) which are transcribed from separate genes and are between 5,000 and 15,000 individuals. It explains that long ncRNAs are transcribed by RNA polymerase II and are spliced to give the final ncRNA, but do not have any open reading frames to encode proteins. It also focuses on the long class of ncRNAs. These are referred to as macroRNAs, which are involved in the epigenetic regulation of gene expression. The chapter mentions important groups of shorter ncRNAs that have partially overlapping functional roles in directing epigenetics, including the siRNAs and rasiRNA. It discusses the specific roles of RNA molecules in controlling gene expression through epigenetic mechanisms.

Chapter

Cover Molecular Biology of RNA

The RNA-binding proteins  

This chapter details how RNA-binding proteins package RNA, protect RNA, organize RNA, and prepare RNA for post-transcriptional processes. It describes different kinds of RNA-binding and auxiliary domains that enable RNA-binding proteins to bind RNA in a versatile way. It also mentions hnRNP proteins, which are the first RNA-binding proteins to be studied in some detail. The chapter discusses the hnRNP proteins that package premRNA. These are involved in multiple post-transcriptional processes. Also, hnRNP proteins remain bound to messenger RNA in the cytoplasm in mRNP particles. The chapter covers the RNA recognition motif, which is a sequence of amino acids or a specific arrangement of secondary structure.

Chapter

Cover Molecular Biology of RNA

The short non-coding RNAs and gene silencing  

This chapter concentrates on a group of very important RNAs with critical roles in regulating gene expression, noting that the RNA molecules involved are much shorter. It explains why short RNA molecules have been co-opted into gene expression pathways, implying that they can be hybridized very selectively to target RNA sequences and act as an efficient targeting mechanism for directing protein components to nucleic acids. It also refers to protein components that carry out catalytic reactions that include the targeted destruction of RNA and the modification of chromatin. The chapter covers important and diverse roles in cells carried out by short ncRNAs, such as the siRNAs that generally target RNA for destruction and the microRNAs that generally regulate protein translation from mRNAs. The chapter describes the siRNAs that work like an intracellular immune system with the aim of incapacitating double-stranded (ds) RNAs that have invaded the cell.

Chapter

Cover Concepts in Bioinformatics and Genomics

Transcript and Protein Expression Analysis  

This chapter highlights the history of gene expression regulation and analysis. It illustrates the methods to measure transcript levels with an emphasis on microarrays and RNA-sequencing, then explicates the nature of proteomics. The chapter further considers the fundamentals of microarray technique, its power, and its limitations as well as the principle of RNA-seq analysis. It also analyses the concept of heatmaps and their use in analysis of microarray expression data. The chapter then moves to highlight the theoretical basis of two-dimensional gel electrophoresis in the separation of proteins. It describes how mass spectrometry is used to identify proteins isolated from 2D-gels. Next, the chapter concludes by examining the peptide mass spectrometry data and software to identify proteins. It then considers the power and limitations of current techniques used for proteome analysis.

Chapter

Cover Genetics

Translation: From Nucleic Acids to Amino Acids  

This chapter reviews RNA transcripts made from the DNA sequence of a gene which are translated into the amino acid sequence of polypeptides. It explains that the process of translation is highly similar in all living organisms and arose only once with relatively small modifications during evolution. It also highlights genome-based analysis of transcription that has led to the realization that the genomes of nearly all organisms are pervasively transcribed. The chapter reviews the Central Dogma that originally did not include non-coding RNA but posits that the functional molecules in the cell are polypeptides and that a gene encodes the capacity to make a polypeptide. It details the process of translating information from the string of nucleotides in nucleic acids into the string of amino acids in polypeptides.

Chapter

Cover Biological Science

Reading the Genome  

Gene Expression and Protein Synthesis

This chapter provides an overview of gene expression and protein synthesis, which have two main phases: transcription and translation. It explains how cells utilize the information stored in their genome. Most genes encode proteins are synthesized via the expression of an intermediate RNA molecule called a messenger RNA (mRNA). However, some genes encode other types of RNA not destined to be translated into protein. Thus, gene expression is regulated mainly at the level of transcription, by DNA-binding proteins that bind regulatory sequences in gene promoters. The chapter details the process of RNA synthesis through transcription and protein synthesis through translation.

Chapter

Cover Biological Science

Reading the Genome  

Gene Expression and Protein Synthesis

This chapter provides an overview of gene expression and protein synthesis, which have two main phases: transcription and translation. It explains how cells utilize the information stored in their genome. Most genes encode proteins are synthesized via the expression of an intermediate RNA molecule called a messenger RNA (mRNA). However, some genes encode other types of RNA not destined to be translated into protein. Thus, gene expression is regulated mainly at the level of transcription, by DNA-binding proteins that bind regulatory sequences in gene promoters. The chapter details the process of RNA synthesis through transcription and protein synthesis through translation.

Chapter

Cover Molecular Biology of RNA

Pre-mRNA splicing by the spliceosome  

This chapter focuses on an important development in eukaryotic RNA processing, which is pre-mRNA splicing catalysed by the spliceosome. It explains that spliceosomal splicing is needed as a large proportion of eukaryotic genes are split between segments called introns and exons. The chapter also points out that splicing occurs in the nucleus during transcription and both the introns and exons of split genes are transcribed within the nucleus into long pre-mRNAs. The chapter mentions the origin of the name exon, which derives from the fact that exon sequences are EXpressed, while introns are removed by splicing and so are not expressed in the mature mRNA. It considers the biology of splicing.

Chapter

Cover Molecular Biology of RNA

RNA editing  

This chapter discusses how open reading frames (ORFs) of some RNAs can be altered after transcription by RNA editing. The chapter highlights the important role RNA editing plays in keeping selfish DNA elements in the genome in check. It also mentions the significant role RNA editing plays in enabling tRNAs to translate mRNAs efficiently, which is a process that is conserved between bacteria and eukaryotes. The chapter explains how RNA editing changes the sequence of RNAs once they have already been transcribed. It analyses RNA editing through base modification that changes the chemical identity of nucleotides already present within the transcript.

Chapter

Cover Molecular Biology of RNA

Introduction to Molecular Biology of RNA  

This chapter provides an overview of the biochemical properties of RNA, including the versatility of its structure that enables a multitude of RNA molecules and functions in cells. It describes different types of RNA-binding domains that have evolved, and the co-transcriptional processes of capping and pre-mRNA splicing, cleavage, and polyadenylation. It also discusses the process of alternative splicing, which is a major generator of proteomic diversity. The chapter covers the processes of RNA editing, nucleocytoplasmic traffic, mRNA localization, translation, stability, decay, and rRNA and tRNA processing. It also gives a historical perspective in explaining the roles of pioneering scientists in some of the key discoveries in molecular biology.

Chapter

Cover Molecular Biology of RNA

Stability and degradation of mRNA  

This chapter focuses on the stability and degradation of mRNA, highlighting other classes of RNA molecules that have regulated half-lives. It talks about regulating the stability of mRNA which provides another means of controlling gene expression. The chapter also clarifies that protein molecules can be synthesized if an mRNA is more stable. It also describes a classical way to demonstrate the stability of mRNA, which is to block transcription with the poison α-amanitin, a cyclic eight amino acid peptide found in the Amanita genus of mushrooms. The chapter covers the main issues connected with mRNA decay, which includes regulating the amount of protein produced and eliminating faulty mRNAs which could potentially produce toxic proteins. It presents special aspects of mRNA decay, such as the connection between extracellular stimuli and mRNA decay and the role of P-bodies as cytoplasmic zones of concentrated mRNA degradation.