RNA, the Epicenter of Genetic Information: A new understanding of molecular biology

Cover
Half Title
Title Page
Copyright Page
Table of Contents
Preface
Acknowledgments
Authors
Chapter 1 Overview
	The Genetic Material?
	Halcyon Days
	Worlds Apart
	Strange 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 Rules
	Plasticity
	Beyond the Jungle of Dogmas
Chapter 2 The Genetic Material?
	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
	Further Reading
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
	Further Reading
Chapter 4 Worlds Apart
	The Origin of Cells
	Genetic Recombination
	The Emergence of Complex Organisms
	Chromatin
	Chromatin-Associated RNAs
	Early Models of RNAs in Nuclear Architecture
	Heterogeneous Nuclear RNA
	Heroes or Fools?
	Further Reading
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
	Further Reading
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 Amplicat fi ion and Shotgun Cloning
	A World of Proteins
	Further Reading
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?
	Further Reading
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
	Further Reading
Chapter 9 Glimpses of a Modern RNA World
	Riboregulators
	Riboswitches
	Antisense RNAs and Complex Transcription in Eukaryotes
	Long Untranslated RNAs
	UTR-Derived RNAs
	First Examples of Small Regulatory RNAs in Animals
	Curiosities or Emissaries?
	Further Reading
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
	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
	Further Reading
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
	Further Reading
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
	Other Classes of Small RNAs
	RNA Communication between Species
	CRISPR
	RNA-Directed Genome Editing
	Further Reading
Chapter 13 Large RNAs with Many Functions
	Pervasive Transcription
	The Amazing Complexity of the Transcriptome
	Protein-Coding or Noise?
	The Restricted Expression of Long Non-coding RNAs
	Other Indices of Functionality
	Genetic Signatures
	An Avalanche of Long Non-coding RNAs
	A Plethora of Functions
	The Wild West
	Further Reading
Chapter 14 The Epigenome
	Chromatin Structure
	Topological Domains
	Enhancers
	Nucleosomes and Histones
	Nucleosome Remodeling
	Histone Modicat fi ions
	The Histone Code
	DNA Methylation
	The Regulation of Development
	Further Reading
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
	Further Reading
Chapter 16 RNA Rules
	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
	Further Reading
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
	Further Reading
Chapter 18 Beyond the Jungle of Dogmas
	The Misunderstanding of Molecular Biology
	The Evolution of Evolvability
	Further Reading
References