Note: Intro -- Preface -- Contents -- About the Editors -- 1 RNA Polymerase II-Dependent Transcription in Fungi and Its Interplay with mRNA Decay -- Abstract -- Transcription Initiation -- PIC Assembly -- Chromatin Remodelling Complexes -- GTFs -- RNA Pol II -- Promoter DNA Melting -- Promoter Escape -- Transcription Elongation -- The CTD Code Through Elongation -- Pausing and Backtracking -- Factors Counteracting and Regulating RNA Pol II Arrest -- Chromatin Dynamics During Transcription Elongation -- Transcription-Coupled Processes and Termination -- 5vprime Capping -- Splicing -- 3vprime End Processing and Termination -- mRNA Transport -- Interplay Between mRNA Synthesis and Decay -- References -- 2 Pre-mRNA Splicing and the Spliceosome: Assembly, Catalysis, and Fidelity -- Abstract -- Gene Architecture -- Pre-mRNA Splicing and the Spliceosome -- Association of U1 snRNP with the pre-mRNA Transcript -- Recognition of the Branchpoint -- Assembly of the U4/U6bulletU5 Triple snRNP -- Spliceosome Activation -- Catalytic Steps -- Spliceosome Remodeling Between Catalytic Steps I and II -- Spliceosome Disassembly -- Splicing Fidelity -- Concluding Remarks -- Acknowledgments -- References -- 3 Fungal Pre-mRNA 3vprime-End Processing -- Abstract -- Pre-mRNA 3vprime-End Processing: An Overview -- Fungal Poly(A) Site Sequence Features -- Fungal mRNA 3vprime Processing Factors -- mRNA 3vprime Processing Factors in S. cerevisiae -- CFIA -- CFIB -- CPF -- Poly(A) Binding Proteins -- S. pombe 3vprime Processing Factors -- Regulators of mRNA 3vprime Processing -- Factors Required for S. cerevisiae Histones mRNA 3vprime Processing -- Release of mRNA 3vprime Processing Factors After Polyadenylation -- Alternative Polyadenylation and its Regulation in Fungi -- APA Regulation and Metabolism -- APA Regulation and DNA Damage Response. , Nab4/Hrp1-Mediated APA Regulation and Copper Stress -- APA Regulation of Meiotic Gene Expression -- Other Examples of Alternative Polyadenylation in Fungi -- Gene Regulation at the 3vprime End -- mRNA 3vprime Processing in the Regulation of S. pombe Meiotic Genes -- mRNA 3vprime Processing Regulates the Expression of Neighboring Genes -- Conclusion /Future Directions -- References -- 4 mRNA Export -- Abstract -- The Early Phase: From Pre-mRNA Transcription and Maturation to Formation of an Export Competent mRNP -- The TREX Complex -- The TREX-2 and the SAGA Complexes -- mRNA Export Receptors -- mRNA Export Adapters -- The Late Phase: The Nuclear Pore Complex and mRNA Translocation -- mRNA Surveillance and Quality Control in the Nucleus -- mRNA Export and its Regulation Via Post-Translational Protein Modifications -- mRNA Export During Cellular Stress -- References -- 5 mRNA Translation: Fungal Variations on a Eukaryotic Theme -- Abstract -- Introduction -- The Molecular Mechanism of Translation -- Translation Initiation -- Translation Elongation -- Translation Termination and Ribosome Recycling -- Round and Round: Translation on Circularised Messages -- Global Regulation of Translational Activity -- mRNA Features that Determine the Efficiency of Protein Synthesis -- 5vprime UTR Length -- 5vprime UTR Structure -- Start Codon Context -- Upstream ORFs -- Codon Usage -- IRESs -- The Cell-Wide Network of Translation -- Acknowledgements -- References -- 6 mRNA Localization -- Abstract -- Introduction to mRNA Localization -- mRNA Localization in Saccharomyces cerevisiae -- Bud-Specific Localization of ASH1 mRNA -- ASH1 -- The Repertoire of the Main Trans-Acting Factors for ASH1 Localization -- Khd1p and Puf6p: Translational Control of ASH1 mRNA during Transport -- The Current Model for ASH1 mRNP Assembly and Localization. , Additional Bud-Localized mRNAs Bound by She2p -- She-Independent mRNA Localization in S. cerevisiae -- mRNA Localization during Shmooing -- Daughter-Cell-Specific Enhancement of Translation by Kap104p -- mRNA Localization to the Yeast Mother Cell: ABP140 -- Localization of mRNAs to Organelles in S. cerevisiae -- mRNA Localization to the Endoplasmic Reticulum -- mRNA Localization to Mitochondria -- mRNA Localization in Other Fungi -- mRNA Localization in Candida albicans -- mRNA Localization in Ustilago maydis -- Outlook -- References -- 7 mRNA Degradation and Decay -- Abstract -- Introduction -- Large-Scale Methods for mRNA Decay Measurements -- RNA Labeling with Modified Nucleotides -- General Transcription Inhibition for Global mRNA Decay Tests -- Linking mRNA Degradation with Global Transcription Changes -- mRNA Stability, Associated Proteins, and the RNA Operon Concept -- Nuclear Degradation of Nascent mRNA -- mRNA Capping and Nuclear Quality-Control of the 5& -- #x2032 -- End -- Nuclear Retention and Transcript Degradation -- Nuclear Degradation from the 3& -- #x2032 -- End: The Exosome -- Mpp6 and Rrp47 -- TRAMP Complexes -- The Nrd1/Nab3/Sen1 Complex (NNS) -- Nuclear mRNA Degradation and Regulation -- Cytoplasmic mRNA Degradation -- Cytoplasmic mRNA Deadenylation -- Poly(A)-Binding Proteins Pab1 and Pub1 -- The Pan2/Pan3 Deadenylase -- The Ccr4/Not Deadenylase -- Cytoplasmic Degradation from the 3& -- #x2032 -- End: The Exosome with Ski -- Cytoplasmic Degradation from the 5& -- #x2032 -- End -- The Cytoplasmic Decapping Enzyme (Dcp1-Dcp2) -- Activators of Decapping: Edc1, Edc2, and Edc3 -- The Lsm Complex: RNA Chaperone and Decapping Activator -- Pat1, Dhh1, and Scd6: Linking Translation and mRNA Decay -- Additional Factors in mRNA Decay: Pbp1, Pbp4, and Lsm12 -- The 5& -- #x2032 -- to 3& -- #x2032. , Degradation of Unprotected RNA: Xrn1 -- Recycling of RNA Degradation Byproducts: Dcs1/Dcs2 -- P Bodies are Large Aggregates of Proteins Involved in RNA Decay -- Mitochondrial mRNA Degradation -- Conclusion -- Acknowledgments -- References -- 8 Cytoplasmic mRNA Surveillance Pathways -- Abstract -- Introduction -- The Nonsense-Mediated mRNA Decay Pathway -- NMD Substrates -- NMD Factors -- Upf1 -- Upf3 -- Upf2 -- Other Yeast NMD Factors -- NMD Mechanism -- PTC Recognition and NMD Activation -- Faulty mRNA Degradation -- Proteasomal Decay of the Truncated Peptide -- NMD Factors in Higher Eukaryotes -- NMD Importance in Human: Involvement in Genetic Diseases and in Some Cancers -- Quality Control Pathways Dealing with Translation Elongation Arrests -- Nonstop mRNA Decay or NSD -- Poly(A)+ NSD Substrates -- Poly(A)-less NSD Substrates -- No-Go Decay or NGD -- Dom34 and Hbs1, Central Factors of these mRNA QC Pathways -- Mechanism of NSD and NGD QC Pathways -- Biological Implications of NSD and NGD QC Pathways -- Conclusion -- Acknowledgments -- References -- 9 Making Ribosomes: Pre-rRNA Transcription and Processing -- Abstract -- Introduction -- Ribosome Assembly has been Extensively Described in S. cerevisiae -- Examination of Ribosome Assembly in Other Yeast Species -- Perspectives -- References -- 10 Biogenesis and Evolution of Functional tRNAs -- Abstract -- Introduction -- tRNA Biogenesis -- tRNA Transcription -- Trimming of the 5vprime Leader and 3vprime Trailer Ends -- Additions to Pre-tRNA Ends: CCA and tRNAHis Gminus1 -- Intron Splicing -- Modifications During tRNA Maturation -- Quality Control and tRNA Decay -- tRNA Transport -- Chemical Modifications on tRNAs -- Modifications Involving tRNA Methyltransferases -- Other tRNA Modifications -- Role of tRNA Modifications in Structure, Function, and Stability of tRNAs. , tRNA Modifications and Evolution -- References -- 11 Small RNA-Mediated Gene Silencing in Neurospora -- Abstract -- The Discovery of RNA Interference -- Neurospora -- Quelling -- qiRNA Biogenesis Pathway -- Convergence of Quelling and qiRNA Pathways -- Meiotic Silencing of Unpaired DNA -- Diverse Biogenesis Pathways of miRNAs in Neurospora -- Dicer-Independent Small Interfering RNAs -- Concluding Remarks -- References -- 12 The RNAi Machinery in Mucorales: The Emerging Role of Endogenous Small RNAs -- Abstract -- Discovery of Gene Silencing in Mucor -- Mucor as a Model Organism to Study Gene Silencing -- Amplification of Silencing -- RNAi Machinery in M. circinelloides -- The Dicer Enzyme -- The Argonaute Protein -- The RNA-Dependent RNA Polymerases -- Evolutionary Conservation of RNAi Machinery in Mucorales -- Dicer Proteins -- Argonaute Proteins -- RdRP Proteins -- Endogenous Small RNAs in M. circinelloides -- ex-siRNAs -- Transcriptional Analysis -- Concluding Remarks -- Acknowledgments -- References -- 13 Regulation of Pericentric Heterochromatin by ncRNA in Schizosaccharomyces pombe -- Abstract -- Introduction -- Heterochromatin: The ''Dark Matter'' of the Genome -- Functions of Constitutive Heterochromatin -- Molecular Determinants of Constitutive Heterochromatin -- The Pericentric Heterochromatin of S. pombe -- Genetic Structure of S. pombe Centromeres -- Chromatin Structure -- Mechanisms of Pericentric Heterochromatin Deposition -- The H3K9me/HP1 Axis -- SHREC -- The RNAi Pathway -- RNAi Processing of Centromeric ncRNA -- The Precursor ncRNA -- RNAi Processing: The Self-reinforcing Loop -- Interaction with Other RNA Degradation Pathways: The Exosome Connection -- Inheritance of Heterochromatin Through Cell Division -- Cell Cycle Regulation of Heterochromatin -- Regulation of Heterochromatic DNA Replication. , Interaction with Homologous Recombination.