Progress in Nucleic Acid Research and Molecular Biology (eBook)

Cover 1
Contents 6
Abbreviations and Symbols 10
Some Articles Planned for Future Volumes 12
Chapter 1. Ribosome-catalyzed Peptide-bond Formation 14
I. The Enzyme 18
II. The Substrates 20
III. Reactions with UnnaturalŽ Substrates 22
IV. Implication of 23-S rRNA in Peptide-bond Formation 23
V. Prospective 30
References 33
Chapter 2. Promotion and Regulation of Ribosomal Transcription in Eukaryotes by RNA Polymerase I 38
I. General Aspects of Ribosomal Gene Regulation 40
II. Ribosomal Gene Organization and Evolution 41
III. RNA Polymerase I Promoters 46
IV. The Basal Transcription Factors 49
V. Activation at the Ribosomal Promoter 57
VI. Enhancement 62
VII. Mechanisms of Regulation 67
VIII. In Conclusion 70
References 71
Chapter 3. Targeting and Regulation of Immunoglobulin Gene Somatic Hypermutation and lsotype Switch Recombination 80
I. Somatic Hypermutation 82
II. Isotype Switch Recombination 96
III. Conclusions and Future Directions 108
References 109
Chapter 4. Capping Enzyme in Eukaryotic mRNA Synthesis 114
I. Domain Structure of Vaccinia Virus Capping Enzyme 116
II. What Is the Rate-limiting Step in Cap Formation? 122
III. Cotranscriptional Capping of Nascent mRNA 124
IV. Direct Role for Capping Enzyme in Vaccinia Virus Transcription 125
V. Yeast mRNA Capping Enzyme 127
VI. Capping Enzyme from Schizosaccharomyces pombe 130
VII. Sequence Conservation among Capping Enzymes and Polynucleotide Ligases 132
VIII. Capping Enzyme and mRNA Identity 135
IX. Genetic Link between Capping Enzyme and Pre-mKNA Splicing 137
X. Perspective 138
References 140
Chapter 5. Rearrangement of snRNA Structure during Assembly and Function of the Spliceosome 144
I. General Features of Splicing 145
II. Dynamic RNA: Technical Considerations 149
III. RNA–RNA Interactions Early in Spliceosome Assembly 152
IV. RNA–RNA Interactions in the Assembling Spliceosome Prior to the First Chemical Step 156
V. Rearrangement of Spliceosomal RNA Structure during the Catalytic Steps of Splicing 159
VI. Conserved Residues in the Core of the Assembled Spliceosome 163
VII. Interactions during the Second Catalytic Step 164
VIII. Modified Nucleotides in Splicing 167
IX. Release of Spliced mRNA and Regeneration of snRNA Structures 169
X. Conclusions and Perspectives 170
References 170
Chapter 6. Transcriptional Control of the Human Apolipoprotein B Gene in Cell Culture and in Transgenic Animals 174
I. Boundaries and Chromatin Organization of the Human apo-B Gene 175
II. Identification of apo-B Regulatory Elements, Using Cell-Culture Models 176
III. Probing the in Vivo Function of the apo-B Gene Regulatory Elements 185
IV. Concluding Remarks 197
References 202
Chapter 7. Early Growth Response Protein 1 (Egr-1): Prototype of a Zinc-finger Family of Transcription Factors 204
I. Overview of Immediate-early Genes 204
II. Identification of Egr-l cDNA by Differential Screening 205
III. Egr-l Is Expressed in Response to Diverse Stimuli 206
IV. Proximal Events 212
V. Distal Events 214
VI. In Vivo Role of Egr-1 232
VII. Egr-1 Is Part of a Gene Family, Including the Wilms Tumor Suppressor Gene WTl 232
VIII. Conclusion and Future Perspectives 233
References 234
Chapter 8. Two New Collagen Subgroups: Membrane- associated Collagens and Types XV and XVIII 238
I. The Collagen Superfamily 239
II. Membrane-associated Collagenous Proteins 243
III. Collagen Types XV and XVIII 261
IV. Conclusions and Perspectives 270
References 272
Chapter 9. Genetic Dissection of Synthesis and Function of Modified Nucleosides in Bacterial Transfer RNA 276
I. Mutants (hisT) Defective in the Synthesis of . in Positions 38, 39, and 40 280
II. Mutants ( trmA) Defective in the Synthesis of m5U in Position 54 292
III. Mutants (trmC, trmE, asuE) Defective in the Synthesis of mnm5s2U34 300
IV. Mutants (nuvA, nuvC) Defective in the Synthesis of s4U in Position 8 306
V. Mutants (miaA, miaB, miaE) Defective in the Synthesis of ms2i6A or msz2io6A37 in Position 37 309
VI. Mutants (trmD) Defective in the Synthesis of mlG in Position 37 323
VII. Mutants (gueA, queB, tgt) Defective in the Synthesis of Queuosine in Position 34 331
VIII. Mutants (aro) Defective in the Synthesis of cmo5U (V-Nucleoside) and Its Methyl Ester in Position 34 335
IX. Conclusions and Perspectives 337
References 342
Chapter 10. Corrigendum 352
Index 354