RNA, the Epicenter of Genetic Information

ISBN-13: 9780367567781 / Angielski / Miękka / 2022 / 382 str.

Paulo Amaral

Opis

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.

Spis treści

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
• RNA and repeat regulation of chromosome structure
• RNA guidance of chromatin remodeling
• RNA guidance of sequence specific transcription factors
• RNA guidance of DNA methylation
• RNA guidance of histone modifications
• Xist as the exemplar
• Enhancer RNAs control chromatin structure
• Intrinsically disordered proteins and 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