Noncoding RNAs : molecular biology and molecular medicine / Jan Barciszewski, Volker A. Erdmann.

Format:

Book

Author/Creator:

Barciszewski, Jan.

Contributor:

Erdmann, V. A. (Volker A.), 1941-2015.

Series:

Molecular biology intelligence unit (Unnumbered)

Molecular biology intelligence unit

Language:

English

Subjects (All):

RNA.

Catalytic RNA.

Introns.

RNA, Untranslated--genetics.

RNA, Untranslated--physiology.

Molecular Biology.

Medical Subjects:

RNA, Untranslated--genetics.

RNA, Untranslated--physiology.

Molecular Biology.

Physical Description:

274 pages : illustrations ; 24 cm.

Place of Publication:

Georgetown, Tex. : Landes Bioscience/Eurekah.com ; New York : Kluwer Academic/Plenum Publishers, [2003]

Contents:

1. Riboregulators: An Overview / Maciej Szymanski, Volker A. Erdmann, Jan Barciszewski 1

Properties of Ribonucleic Acids 1

Coding vs. Noncoding Transcripts 2

Functions of RNA Regulators 4

Perspectives 6

2. Introns and Noncoding RNAs: The Hidden Layer of Eukaryotic Complexity / John S. Mattick 11

Noncoding RNAs Represent the Majority of Genomic Output in Mammals and Probably All Complex Organisms 13

Do Introns and ncRNAs Represent a Second Tier of Gene Expression 14

Introns 15

Noncoding RNAs 16

Origin and Nomenclature of Noncoding RNAs 19

A New Definition of a Gene

A Transcription Cluster with cis-Acting Regulatory Elements 19

Complex Genetic Phenomena Involving RNA 20

RNA Binding and Signaling Proteins 21

Possible Functions of ncRNAs 22

A New Genetics 23

3. Computational Gene-Finding for Noncoding RNAs / Peter Schattner 33

Gene-Finding for Protein-Coding Genes and ncRNAs 34

Custom-Designed ncRNA Gene-Finders 36

Reconfigurable ncRNA Gene-Finders 38

De novo ncRNA Gene-Finding

Searching for Genes without a priori Knowledge of Sequence or Structure 40

Current Status and Future Prospects for Computational ncRNA Gene-Finding 44

4. Xist RNA Associates with Chromatin and Causes Gene Silencing / Anton Wutz 49

The Xist Gene 51

Initiation of Xist-Mediated Silencing in the Embryo 53

Regulation of Xist Expression

Counting and Choosing the Xs 55

The Mechanism of Xist Function 57

A Model for Xist Function 60

Evolutionary Considerations 62

5. Dosage Compensation in Drosophila: A Ribonucleoprotein Complex Mediates Transcriptional Up-Regulation / Dianne Kindel, Hubert Amrein 66

Different Mechanisms of Dosage Compensation 67

Male-Specific Hyper-Transcription Through Chromatin Modification 67

Male-Specific Implementation of Dosage Compensation Is Dependent on the Absence of SXL Repressor 68

The Components of the DCC 69

The roX RNAs Are Chromatin Entry Sites 74

Ordered Assembly of the DCC 74

Specific Functions of and Interactions Among MSL Proteins 76

The roX RNAs Are Essential for Dosage Compensation 77

Models and Outlook 78

6. The Structure, Regulation and Function of the Imprinted H19 RNA / Raluca I. Verona, Marisa S. Bartolomei 84

Riboregulatory RNAs 85

Imprinting of H19 87

Tissue-Specific Expression of H19 89

Sequence Conservation of H19 91

H19 and Growth Control 91

Is the H19 RNA Functional? 91

7. MicroRNAs / Eric G. Moss 99

Discovery and Isolation of miRNAs 100

Characteristics of miRNAs 105

The Mechanism of Action of lin-4 107

Proteins Involved in miRNA Biogenesis and Function 110

Identifying miRNA Targets 111

Artificial miRNAs 112

8. Short Interfering and MicroRNAs: Tiny but Mighty / Martin Tabler, Alexandra Boutla, Kriton Kalantidis, Mina Tsagris 117

MicroRNAs (miRNAs) 118

Short Interfering RNA (siRNA) 120

Application of siRNAs to Trigger RNAi 123

9. Post-Transcriptional Gene Silencing in Plants / Matthew A. Escobar, Abhaya M. Dandekar 129

Initiation of PTGS in Plants Many Roads to dsRNA 130

From dsRNA to Silencing Models of the RNA Degradation Pathway 133

Roles of PTGS in Plants 137

10. RNA-Directed DNA Methylation and Chromatin Modifications / Marjori A. Matzke, M. Florian Mette, Tatsuo Kanno, Istvan Papp, Werner Aufsatz, Antonius J.M. Matzke 141

Homology-Dependent Gene Silencing 142

Discovery and Characteristics of RNA-Directed DNA Methylation 143

Mechanism of RdDM 144

RNA Guiding Chromatin Modifications 150

Evolution of RNA Silencing Mechanisms 152

11. Brain-Specific Nonmessenger RNAs / Jurgen Brosius, Alexander Huttenhofer, Henri Tiedge 159

Large nmRNAs in the Brain 160

snmRNAs in the Brain 160

12. New Frontiers for the snoRNA World / Jean-Pierre Bachellerie, Jerome Cavaille 170

Two Large Families of Modification Guide snoRNAs 171

snoRNP Biogenesis 173

Novel Guides for snRNA Modifications 176

Orphan Guides snoRNAs in Search of RNA Targets 177

Brain-Specific Imprinted snoRNAs 178

Archaeal Homologs of Modification Guide snoRNAs 181

Archaeal tRNAs Are Targeted Too 182

13. New Perspectives on Noncoding or Short ORF-Encoding RNAs in Plants / Martin Crespi, Anna Campalans, Claude Thermes, Adam Kondorosi 192

mRNAs without Long ORFs Exist in Plants and Animals 193

mRNAs Only Containing sORFs Are Involved in Plant Growth and Development 194

Potential Mechanisms of Action 197

Perspectives: Small Regulatory RNAs and sORF-Encoded Oligopeptides as Novel Regulators of Gene Expression 199

14. The Noncoding Developmentally Active and Stress Inducible hsrw Gene of Drosophila melanogaster Integrates Post-Transcriptional Processing of Other Nuclear Transcripts / Subhash C. Lakhotia 202

The 93D or the hsrw Gene in Drosophila Displays Unique and Conserved Inducibility but Apparently Does Not Produce a Protein 203

The hsrw Gene Shows a Unique Conserved Architecture but with Little Conservation of Base Sequence in Drosophila Species 206

The hsrw Gene Produces Multiple Noncoding Transcripts 207

The hsrw Gene Shows Widespread Developmental Expression 208

Promoter Region of the hsrw Gene Is Complex 208

The hsrw Gene Is Functional in Spite of Its Noncoding Transcripts 208

Functions of hsrw Transcripts 210

Future Prospects 214

15. Adapt Gene RNA Transcripts as Riboregulators / Dana R. Crawford, Kelvin J. A. Davies 220

Identification of adapt15 and adapt33 221

Mechanism of Action of adapt15 and adapt33 225

16. RNA Pathogenesis in Dominant Noncoding Microsatellite Expansion Disorders / Laura P. W. Ranum, John W. Day 230

Myotonic Dystrophy Type 1: Gene Discovery and Proposed Pathogenic Models 231

Spinocerebellar Ataxia Type 8 233

Spinocerebellar Ataxia Type 10 234

Clinical and Molecular Distinctions Between DM1 SCA8 and SCA10 234

Myotonic Dystrophy Type 2 234

RNA Pathogenesis in the Myotonic Dystrophies 235

Other Noncoding Expansion Disorders 237

17. Noncoding RNAs Encoded by Bacterial Chromosomes / E. Gerhart H. Wagner, Jorg Vogel 242

Housekeeping sRNAs 243

Regulatory Antisense RNAs Come in Two Flavors 244

The Trans-Encoded Antisense RNA MicF Is a Stress Response Regulator 244

sRNAs Can Regulate Multiple Genes 246

One Regulatory RNA

Two (or More) Target RNAs 248

More Than One RNA Acting on the Same Target 249

Discoordinate Expression of Genes within Operons

Another Role for sRNAs 250

Some sRNAs Require Helper Proteins 250

The Exception (?): cis-Encoded Antisense RNAs in the E. coli Chromosome 252

Regulation of Gene Expression by Interaction between sRNAs and Proteins 252

Structures of sRNAs 252

Stable or Unstable in Cells? 253

Primary or Processed Transcripts 253

What Is the Job of the New sRNAs? 254

And by What Mechanisms? 254

How Many Are There? 254

18. We Are Legion: Noncoding Regulatory RNAs and Hfq / Cristin C. Brescia, Darren D. Sledjeski 259

Noncoding RNAs 259

Functions of Noncoding RNAs in Gram Negatives 260

Noncoding RNAs in Gram-Positive Bacteria 261

Regulating the Regulators. How Are ncRNAs Regulated? 261

The RNA-Binding Protein Hfq and ncRNAs 262

What Is the Function of Hfq? 262

How Is Hfq Interacting with RNAs? 264.

Notes:

Includes bibliographical references and index.

ISBN:

0306478358

OCLC:

52380937