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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

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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

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Co-transcriptional pre-mRNA processing  

This chapter discusses the pre-mRNA processing events that occur co-transcriptionally. It covers the synthesis of the 7-methyl guanosine 5? cap, pre-mRNA splicing, and the formation of the 3? end of an mRNA by cleavage and polyadenylation. It also considers the connections that exist between chromatin structure and pre-mRNA processing, including the special case of metazoan histone mRNA 3? end formation. The chapter reviews the essential elements of the process of transcription, structure, and function of the RNA polymerases. It explores the process of transcription that is required to appreciate the links between transcription and pre-mRNA processing events, as well asthe connection between transcription and post-transcriptional processes that is illustrated by the properties of the C-terminal domain (CTD) of RNA polymerase II.

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

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Messenger RNA localization  

This chapter is focused on the localization of mRNAs1-6, including the localization of microRNAs in neurons. It describes fluorescence in situ hybridization (FISH). Fluorescence uses in situ hybridization wherein a complementary antisense nucleic acid probe is labelled typically with a fluorescent probe. The chapter also highlights how FISH techniques have been greatly improved, to the extent that it is now possible to examine the localization of thousands of mRNAs. The chapter discusses the importance of mRNA localization, which is powerfully illustrated by a genome-wide analysis by Eric Lecuyer and colleagues of mRNA localization during Drosophila embryogenesis. It looks at the machinery of mRNA localization, including the role of the cytoskeleton, RNA zipcodes, and the influence of the nuclear history of a transcript on its localization.

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 Molecular Biology of RNA

Nucleocytoplasmic traffic of messenger RNA  

This chapter focuses on the nuclear export of mRNAs, which are encoded by ~21 000 genes in humans. Each of which is transcribed by RNA polymerase II. It explains that eukaryotic genes are transcribed in the nucleus but mRNAs are translated in the cytoplasm, implying that most mRNAs need to be exported across the nuclear membrane into the cytoplasm in order to be translated. It also shows that passage from the nucleus to the cytoplasm is one directional for mRNAs, prokaryotes have no nuclear membrane, and transcription takes place alongside translation. The chapter also displays that mRNA is exported from the nucleus by a different mechanism to that used for the non-coding, although protein-coding genes are numerous. It talks about the nuclear export of mRNA that starts at the gene and ends in the cytoplasm.

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

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Pre-mRNA splicing defects in development and disease  

This chapter considers the important contribution that RNA splicing defects make to disease, including the NOVA proteins that are important in cancer autoimmunity and splicing regulation in the nervous system. It talks about defective genes in many inherited diseases and the actual mutations within these genes that have been pinpointed by sequencing. It also elaborates how some of the mutations in the genes affect the genetic code by introducing codons for new amino acids and even stop codons that prematurely end open reading frames. The chapter describes mutations that occur in splicing signals and prevent the intron-exon structure of pre-mRNAs from being properly decoded by the spliceosome. It stresses that mutations that affect splicing signals can be particularly severe since they cause changes in the structure of mRNAs.

Chapter

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Regulated alternative splicing  

This chapter highlights alternative splicing, which increases the coding capacity of the genome by challenging the 'one gene-one protein' rule. It defines gene number paradox as the discrepancy between gene copy number and apparent complexity. It also explores how organisms use alternative splicing to expand the information content of their genomes by enabling multiple mRNAs and proteins to be made from each gene. The chapter talks about alternative exons that are variably included into mRNAs and occurs through alternative splicing. It clarifies that only a subset of exons is alternatively spliced, while other exons called constitutive exons are always included in mRNAs.

Chapter

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RNA biology: future perspectives  

This chapter considers the complexities of chromatin modifications and epigenetics, the regulation of transcription, and cotranscriptional and post-transcriptional processes. It reviews some of the topical areas of RNA biology. It begins by describing the explosion of transcriptomics data and the opportunities and challenges that this brings. It also looks at the growing prominence of non-coding RNAs (ncRNAs) and describes the use of CRISPR, an RNA-guided genome editing system that will revolutionize both basic and applied research. The chapter discusses transcriptome sequences that are derived from copying RNA sequences into cDNA using reverse transcriptase, followed by sequencing. It mentions the advent of next-generation sequencing (NGS), which is known as a key technological development.

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RNA can form versatile structures  

This chapter discusses some of the biological functions of RNA structures, including their use as thermosensors in pathogenic bacteria and RNA structures that strongly bind target molecules. It outlines three hierarchical levels of structural organization used by RNA molecules: primary structure, secondary structure, and tertiary structure. The primary structure is the linear sequence of nucleotides in a nucleic acid or nucleotide sequence and the secondary structure is composed of helices that form through base pairing. The tertiary structure is the highest level of organization, in which RNA molecules with secondary structure fold up into very compact and highly organized structures. The chapter explains that DNA molecules are found in long double helices which extend along their full lengths, while RNA molecules form shorter double helices between single-stranded regions.

Chapter

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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

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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

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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

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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.

Chapter

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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

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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.