RNA, the Epicenter of Genetic Information / John Mattick

By:

Mattick, John

Contributor(s):

Amara, Paulo

Material type: Text

TextLanguage: English Publication details: Florida : CRC Press, 2023.Edition: 1st edDescription: xv, 404 p. : col. ill. ; 24 cmISBN:

9780367567781
9780367623920

Uniform titles:

RNA, the Epicenter of Genetic Information

Subject(s):

DDC classification:

23 572.8 MAT

Contents:

Preface Chapter 1 Overview • The genetic material? • Halcyon days • Worlds apart • Huge genomes, strange genetics • The age of Aquarius • All that junk • The expanding repertoire of RNA • Glimpses of a modern RNA world • Genome sequencing and transposable elements • The human genome • Small RNAs with mighty functions • Large RNAs with many functions • The epigenome • The programming of development • RNA and repeats rule • Plasticity • Beyond the jungle of dogmas Chapter 2 The genetic material? • The nature of matter • Sugars and fats • Proteins: ‘the locus of life’ • Nucleic acids and chromosomes • Chromosomes as the mediators of genetic inheritance • The ‘Modern Synthesis’ • Distinguishing DNA and RNA • One gene-one protein and the ‘nature of mutations’ • DNA is the genetic material • The double helix – icon of the coming age Chapter 3 Halcyon days • The big question • Discovery of the ribosome • The messenger and the adaptor • The ‘genetic code’ • The lac operon and gene regulation • Protein structure • The Central Dogma • It’s all over now Chapter 4 Worlds apart • The origin of cells • Genetic recombination • The emergence of complex organisms • Chromatin • Chromatin-associated RNA • Early models of RNAs in nuclear architecture • Heterogenous nuclear RNA • Heroes or fools? Chapter 5 Strange genomes, strange genetics • Repetitive DNA • Controlling elements • Paramutation, imprinting and transinduction • The bithorax ‘complex locus' • Transvection • Epigenetic modifiers • The Britten and Davidson model • Boolean models of combinatorial control • Processed RNAs as global regulators • Out on a limb Chapter 6 The Age of Aquarius • Recombinant DNA and ‘gene cloning’ • Enabling technologies • DNA sequencing • The gold rushes • Hox genes • Oncogenes and tumor suppressors • Immunology and monoclonal antibodies • Biotechnological exploitation • Cell-free DNA amplification and shotgun cloning • A world of proteins Chapter 7 All that junk • The C-value enigma • Duplication and transposition • Mutational load, nonsense DNA, nonsense RNA • Neutral evolution • Conservation and selection • Junk DNA • Selfish DNA • Genes-in-pieces! • Not junk? Chapter 8 The expanding repertoire of RNA • Spliceosomal RNAs • Small nucleolar RNAs • Other small guide, scaffolding and regulatory RNAs • Catalytic RNAs and the ancient RNA World hypothesis • The catalytic heart of splicing and translation • The digital and analog faces of RNA • Candles in the dark Chapter 9 Glimpses of a modern RNA world • Riboregulators • Riboswitches • Antisense RNAs and complex transcription in eukaryotes • Long untranslated RNAs • UTR derived RNAs • First glimpses of small regulatory RNAs in animals • Curiosities or emissaries? Chapter 10 Genome sequences and transposable elements • Genome mapping • Genetics at genome scale • Whole genome sequencing of bacteria and archaea • Genome sequencing of unicellular eukaryotes • Genome sequencing of model plants and animals • The G-value enigma • Comparative genomics at nucleotide resolution • Pseudogenes and retrogenes • Transposable elements as functional modules • Transposable elements as drivers of phenotypic innovation • The great exploration – the diversity of life • From genome sequence to genome biology Chapter 11 The human genome • The project • Assessment of functionality • The majority of the genome is active • Damaged genes • A plethora of ‘rare’ diseases • Complex traits and disorders • The transformation of medical research and healthcare Chapter 12 Small RNAs with mighty functions • Unusual genetic phenomena involving RNA • The RNA interference pathway • Transcriptional gene silencing: RNA-directed DNA methylation • Research and biotechnology applications • MicroRNAs • Piwi-associated RNAs (piRNAs) • Other classes of small RNAs • RNA communication between species • CRISPR • RNA-directed genome editing Chapter 13 Large RNAs with many functions • Pervasive transcription • The amazing complexity of the transcriptome • Protein-coding or noise? • The restricted expression of long noncoding RNAs • Other indices of functionality of long noncoding RNAs • The genetic signatures of long noncoding RNAs • An avalanche of long noncoding RNAs • A plethora of functions • The Wild West Chapter 14 The epigenome • Chromatin structure • Topological domains • Enhancers • Nucleosomes and histones • Nucleosome remodeling • Histone modifications • The histone code • DNA methylation • The regulation of development Chapter 15 The programming of development • Autopoiesis • The overarching question • Tissue architecture and cell identity • Programmed ontogeny • Lineage specification • How much information is required? • Constraints imposed by the superlinear scaling of regulatory information • How much information is there in the human genome? • Genomes as .zip files of transcriptomes Chapter 16 RNA and repeats rule • RNA is a core component of chromatin • Regulation of chromosome structure • RNA guidance of chromatin remodeling • Guidance of transcription factors • Guidance of DNA methylation • Guidance of histone modifications • Xist as the exemplar • Enhancer RNAs and chromatin structure • RNA scaffolding of phase-separated domains • An addition to the ancient RNA world hypothesis • Structure-function relationships in lncRNAs • A new view of the genome of complex organisms Chapter 17 Plasticity • RNA modifications and the unknown epitranscriptome • The expansion of RNA editing in cognitive evolution • A>I editing • C>U editing • The brain • RNA-directed transgenerational epigenetic inheritance Chapter 18 Beyond the jungle of dogmas • The misunderstanding of molecular biology • The evolution of evolvability References

Summary: The origin story and emergence of molecular biology is muddled. The early triumphs in bacterial genetics and the complexity of animal and plant genomes complicate an intricate history. This book documents the many advances, as well as the prejudices and founder fallacies. It highlights the premature relegation of RNA to simply an intermediate between gene and protein, the underestimation of the amount of information required to program the development of multicellular organisms, and the dawning realization that RNA is the cornerstone of cell biology, development, brain function and probably evolution itself. Key personalities, their hubris as well as prescient predictions are richly illustrated with quotes, archival material, photographs, diagrams and references to bring the people, ideas and discoveries to life, from the conceptual cradles of molecular biology to the current revolution in the understanding of genetic information. Key Features Documents the confused early history of DNA, RNA and proteins - a transformative history of molecular biology like no other. Integrates the influences of biochemistry and genetics on the landscape of molecular biology. Chronicles the important discoveries, preconceptions and misconceptions that retarded or misdirected progress. Highlights major pioneers and contributors to molecular biology, with a focus on RNA and noncoding DNA. Summarizes the mounting evidence for the central roles of non-protein-coding RNA in cell and developmental biology. Provides a thought-provoking retrospective and forward-looking perspective for advanced students and professional researchers. The Open Access version of this book, available at www.taylorfrancis.com, has been made available under a Creative Commons Attribution-Non Commercial-No Derivatives 4.0 license.

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Holdings
Item type	Current library	Collection	Call number	Status	Date due	Barcode
Text Books	CUTN Central Library Sciences	Non-fiction	572.8 MAT (Browse shelf(Opens below))	Available		47691

Preface

Chapter 1 Overview
• The genetic material?
• Halcyon days
• Worlds apart
• Huge genomes, strange genetics
• The age of Aquarius
• All that junk
• The expanding repertoire of RNA
• Glimpses of a modern RNA world
• Genome sequencing and transposable elements
• The human genome
• Small RNAs with mighty functions
• Large RNAs with many functions
• The epigenome
• The programming of development
• RNA and repeats rule
• Plasticity
• Beyond the jungle of dogmas

Chapter 2 The genetic material?
• The nature of matter
• Sugars and fats
• Proteins: ‘the locus of life’
• Nucleic acids and chromosomes
• Chromosomes as the mediators of genetic inheritance
• The ‘Modern Synthesis’
• Distinguishing DNA and RNA
• One gene-one protein and the ‘nature of mutations’
• DNA is the genetic material
• The double helix – icon of the coming age

Chapter 3 Halcyon days
• The big question
• Discovery of the ribosome
• The messenger and the adaptor
• The ‘genetic code’
• The lac operon and gene regulation
• Protein structure
• The Central Dogma
• It’s all over now

Chapter 4 Worlds apart
• The origin of cells
• Genetic recombination
• The emergence of complex organisms
• Chromatin
• Chromatin-associated RNA
• Early models of RNAs in nuclear architecture
• Heterogenous nuclear RNA
• Heroes or fools?

Chapter 5 Strange genomes, strange genetics
• Repetitive DNA
• Controlling elements
• Paramutation, imprinting and transinduction
• The bithorax ‘complex locus'
• Transvection
• Epigenetic modifiers
• The Britten and Davidson model
• Boolean models of combinatorial control
• Processed RNAs as global regulators
• Out on a limb

Chapter 6 The Age of Aquarius
• Recombinant DNA and ‘gene cloning’
• Enabling technologies
• DNA sequencing
• The gold rushes
• Hox genes
• Oncogenes and tumor suppressors
• Immunology and monoclonal antibodies
• Biotechnological exploitation
• Cell-free DNA amplification and shotgun cloning
• A world of proteins

Chapter 7 All that junk
• The C-value enigma
• Duplication and transposition
• Mutational load, nonsense DNA, nonsense RNA
• Neutral evolution
• Conservation and selection
• Junk DNA
• Selfish DNA
• Genes-in-pieces!
• Not junk?

Chapter 8 The expanding repertoire of RNA
• Spliceosomal RNAs
• Small nucleolar RNAs
• Other small guide, scaffolding and regulatory RNAs
• Catalytic RNAs and the ancient RNA World hypothesis
• The catalytic heart of splicing and translation
• The digital and analog faces of RNA
• Candles in the dark

Chapter 9 Glimpses of a modern RNA world
• Riboregulators
• Riboswitches
• Antisense RNAs and complex transcription in eukaryotes
• Long untranslated RNAs
• UTR derived RNAs
• First glimpses of small regulatory RNAs in animals
• Curiosities or emissaries?

Chapter 10 Genome sequences and transposable elements
• Genome mapping
• Genetics at genome scale
• Whole genome sequencing of bacteria and archaea
• Genome sequencing of unicellular eukaryotes
• Genome sequencing of model plants and animals
• The G-value enigma
• Comparative genomics at nucleotide resolution
• Pseudogenes and retrogenes
• Transposable elements as functional modules
• Transposable elements as drivers of phenotypic innovation
• The great exploration – the diversity of life
• From genome sequence to genome biology

Chapter 11 The human genome
• The project
• Assessment of functionality
• The majority of the genome is active
• Damaged genes
• A plethora of ‘rare’ diseases
• Complex traits and disorders
• The transformation of medical research and healthcare

Chapter 12 Small RNAs with mighty functions
• Unusual genetic phenomena involving RNA
• The RNA interference pathway
• Transcriptional gene silencing: RNA-directed DNA methylation
• Research and biotechnology applications
• MicroRNAs
• Piwi-associated RNAs (piRNAs)
• Other classes of small RNAs
• RNA communication between species
• CRISPR
• RNA-directed genome editing

Chapter 13 Large RNAs with many functions
• Pervasive transcription
• The amazing complexity of the transcriptome
• Protein-coding or noise?
• The restricted expression of long noncoding RNAs
• Other indices of functionality of long noncoding RNAs
• The genetic signatures of long noncoding RNAs
• An avalanche of long noncoding RNAs
• A plethora of functions
• The Wild West

Chapter 14 The epigenome
• Chromatin structure
• Topological domains
• Enhancers
• Nucleosomes and histones
• Nucleosome remodeling
• Histone modifications
• The histone code
• DNA methylation
• The regulation of development

Chapter 15 The programming of development
• Autopoiesis
• The overarching question
• Tissue architecture and cell identity
• Programmed ontogeny
• Lineage specification
• How much information is required?
• Constraints imposed by the superlinear scaling of regulatory information
• How much information is there in the human genome?
• Genomes as .zip files of transcriptomes

Chapter 16 RNA and repeats rule
• RNA is a core component of chromatin
• Regulation of chromosome structure
• RNA guidance of chromatin remodeling
• Guidance of transcription factors
• Guidance of DNA methylation
• Guidance of histone modifications
• Xist as the exemplar
• Enhancer RNAs and chromatin structure
• RNA scaffolding of phase-separated domains
• An addition to the ancient RNA world hypothesis
• Structure-function relationships in lncRNAs
• A new view of the genome of complex organisms

Chapter 17 Plasticity
• RNA modifications and the unknown epitranscriptome
• The expansion of RNA editing in cognitive evolution
• A>I editing
• C>U editing
• The brain
• RNA-directed transgenerational epigenetic inheritance

Chapter 18 Beyond the jungle of dogmas
• The misunderstanding of molecular biology
• The evolution of evolvability

References

The origin story and emergence of molecular biology is muddled. The early triumphs in bacterial genetics and the complexity of animal and plant genomes complicate an intricate history. This book documents the many advances, as well as the prejudices and founder fallacies. It highlights the premature relegation of RNA to simply an intermediate between gene and protein, the underestimation of the amount of information required to program the development of multicellular organisms, and the dawning realization that RNA is the cornerstone of cell biology, development, brain function and probably evolution itself. Key personalities, their hubris as well as prescient predictions are richly illustrated with quotes, archival material, photographs, diagrams and references to bring the people, ideas and discoveries to life, from the conceptual cradles of molecular biology to the current revolution in the understanding of genetic information.

Key Features

Documents the confused early history of DNA, RNA and proteins - a transformative history of molecular biology like no other.
Integrates the influences of biochemistry and genetics on the landscape of molecular biology.
Chronicles the important discoveries, preconceptions and misconceptions that retarded or misdirected progress.
Highlights major pioneers and contributors to molecular biology, with a focus on RNA and noncoding DNA.
Summarizes the mounting evidence for the central roles of non-protein-coding RNA in cell and developmental biology.
Provides a thought-provoking retrospective and forward-looking perspective for advanced students and professional researchers.
The Open Access version of this book, available at www.taylorfrancis.com, has been made available under a Creative Commons Attribution-Non Commercial-No Derivatives 4.0 license.

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