Finding The Exosome | p. 1 |
Abstract | p. 1 |
Introduction | p. 1 |
From Northerns to Nucleases | p. 2 |
A Glimpse of the Exosome | p. 3 |
The Complete Complex | p. 5 |
A Broader Perspective | p. 6 |
Conclusion | p. 6 |
Structural Components And Architectures of RNA Exosomes | p. 9 |
Abstract | p. 9 |
Introduction | p. 9 |
Global Structure of the Exosome | p. 11 |
RNase PH-like Domains in Bacterial, Archaeal and Eukaryotic Core Exosomes | p. 15 |
S1 and KH Containing Domains in Bacterial, Archaeal and Eukaryotic Core Exosomes | p. 16 |
Mechanism of Phosphorolytic Activity in Bacterial PNPase and Archaeal Exosomes | p. 17 |
Rrp44, a Eukaryotic Exosome Subunit with Hydrolytic Endoribonuclease and Processive Exoribonuclease Activities | p. 19 |
Rrp44 PIN Domain | p. 19 |
Rrp44 RNB Domain | p. 21 |
Rrp44 and the 10-Component Exosome | p. 22 |
Rrp6, a Eukaryotic Exosome Subunit with Distributive Hydrolytic Activities | p. 23 |
Rrp6 Interactions with the Exosome Core | p. 25 |
Conclusion | p. 25 |
The Archaeal Exosome | p. 29 |
Abstract | p. 29 |
Introduction | p. 29 |
Core Subunits of the Archaeal Exosome | p. 30 |
Structure and Mechanism | p. 31 |
Physiological Functions | p. 35 |
Conclusion | p. 36 |
The Exosomes of Trypanosomes And Other Protists | p. 39 |
Abstract | p. 39 |
Introduction: Why Study the Exosomes of Organisms Other Than Yeast and Animals? | p. 39 |
Trypanosomes as a Model System for RNA Processing and Turnover | p. 40 |
The Structure of the Trypanosome Exosome | p. 41 |
The Position of RRP6 Relative to the Exosome Core | p. 41 |
Functions of the Trypanosome Exosome in the Nucleus | p. 43 |
Functions of the Trypanosome Exosome in the Cytoplasm | p. 44 |
Conservation of the Exosome in Eukaryotic Evolution | p. 46 |
Conclusion | p. 47 |
The Exosome And 3′-5′ RNA Degradation in Plants | p. 50 |
Abstract | p. 50 |
Introduction | p. 50 |
Composition of Plant Exosome Core Complexes | p. 51 |
Functional Specialisation of Individual Subunits? | p. 53 |
Exosome Cofactors and Auxiliary Proteins in Plants | p. 55 |
RNA Substrates of the Plant Exosome Complex | p. 56 |
Impact of 3′-5′ RNA Decay on Plant Genome Expression | p. 57 |
Impact of 3′-5′ Degradation in Organelles | p. 58 |
Conclusion | p. 59 |
Catalytic Properties of the Eukaryotic Exosome | p. 63 |
Abstract | p. 63 |
Introduction | p. 63 |
Exosome Composition | p. 64 |
DIS3 | p. 66 |
Rrp6 | p. 71 |
Holoenzyme Activities | p. 71 |
Noncatalytic Activities of the Exosome Ring | p. 74 |
Conclusion | p. 76 |
Functions of The Cytoplasmic Exosome | p. 79 |
Abstract | p. 79 |
Introduction | p. 79 |
The Cytoplasmic Exosome Requires Four Cofactors | p. 80 |
The Exosome Functions in One of Two General Pathways for Cytoplasmic mRNA Degradation | p. 82 |
The Cytoplasmic Exosome Functions in mRNA Surveillance | p. 83 |
The Antiviral Function of the Cytoplasmic Exosome | p. 85 |
Conclusion and Future Perspectives | p. 86 |
Rrp6, Rrp477 And Cofactors of the Nuclear Exosome | p. 91 |
Abstract | p. 91 |
Introduction | p. 91 |
Structure and Activity of Rrp6 | p. 92 |
The Role of Rrp6 in the Maturation of Noncoding RNAs | p. 93 |
The Role of Rrp6 in mRNA Surveillance | p. 94 |
The Role of Rrp6 in the Regulation of mRNA Levels | p. 94 |
Rrp6 and the TRAMP Complex | p. 95 |
The Exosome Cofactor Rrp47 | p. 96 |
Structure of Rrp47 | p. 96 |
Biochemical Activities of Rrp47 | p. 97 |
The Role of Rrp47 in RNA Processing and Degradation | p. 97 |
The Exosome Cofactor Mpp6 | p. 99 |
Conclusion | p. 100 |
The Exosome And Heterochromatin: Multilevel Regulation of Gene Silencing | p. 105 |
Abstract | p. 105 |
Introduction | p. 105 |
Heterochromatin | p. 106 |
Gene Silencing Pathways: RNAi and the Exosome | p. 108 |
Multilevel Regulation of Gene Expression | p. 112 |
Regulating the Regulators: How the Stability of ncRNAs Determines Their Function in Heterochromatin Formation | p. 114 |
Conclusion | p. 117 |
Control of Cryptic Transcription in Eukaryotes | p. 122 |
Abstract | p. 122 |
Introduction: New Perspectives on the Shape of the Transcriptome | p. 122 |
A Dedicated Pathway of Nuclear RNA Degradation | p. 123 |
Widespread Transcription in Eukaryotic Genomes | p. 124 |
Transcription Termination and the Hallmark of CUTs Instability | p. 125 |
An RNAPII "CTD Code" for the Fate of Nascent Transcripts | p. 126 |
Regulatory Roles of Cryptic Transcription | p. 128 |
Conclusion | p. 129 |
The Human Exosome And Disease | p. 132 |
Abstract | p. 132 |
Introduction | p. 132 |
Identification of the PM/Scl Complex | p. 133 |
Autoantibodies to the Exosome / PM/Scl-Antigen | p. 134 |
Initiation of the Anti-Exosome / PM/Scl Autoimmune Response | p. 137 |
The Human Exosome and Cancer | p. 138 |
Conclusion | p. 139 |
Index | p. 143 |
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