Fundamentals of RNA structure and function / edited by Neena Grover.

Format:

Book

Contributor:

Grover, Neena, editor.

Series:

Learning Materials in Biosciences

Language:

English

Subjects (All):

Life sciences.

Physical Description:

1 online resource (257 pages)

Edition:

1st ed.

Place of Publication:

Cham, Switzerland : Springer, [2022]

Summary:

This highly illustrated textbook provides an essential overview on RNA architecture and function, it offers insights into the RNA basics and also explains novel RNA technologies, such as CRISPR-Cas and their applications.

Contents:

Intro

Preface

Acknowledgments

Contents

Contributors

1: RNA: Composition and Base Pairing

What You Will Learn

Learning Objectives

1.1 Introduction

1.2 Sugar

1.3 Phosphate

1.4 Nucleobase, Nucleoside, and Nucleotide

1.5 Base Pairing: Canonical and Noncanonical

1.6 Base Protonation

1.7 Bifurcated and Water-Mediated Base Pairing

1.8 Isostericity

1.9 Modifications in RNA Bases and Sugars

Take Home Message

References

2: Architecture of RNA

2.1 Introduction

2.2 Secondary Structures in RNA

2.3 Common Tertiary Interactions in RNA

2.4 Examples of RNA Motifs

2.5 Metal Ions and RNA

3: Small Catalytic RNA

3.1 Catalysis by RNA

3.2 Cleavage and Ligation Reactions

3.3 The Role of Metal Ions

3.4 Regulation

3.5 Examples of Four Small Catalytic RNA

3.6 Implication for Health and Medicine

4: The Spliceosome: A Large Catalytic RNA

4.1 Introduction

4.2 The Group I Introns

4.3 Splicing

4.4 The Spliceosome

4.5 The Spliceosome Is a Ribozyme

5: A Genomics Perspective on RNA

5.1 From Transcript to Transcriptome: The Impact of Next-Generation Sequencing Methods on the Study of RNA

5.2 Using mRNA-Seq to Investigate the Protein-Coding Transcriptome

5.2.1 Preparing RNA for Sequencing: Isolation, Fragmentation, and Enrichment

5.2.2 Constructing Sequencing Libraries: Strandedness, Multiplexing, and Amplification

Box 5.1 Polymerase chain reaction

5.2.3 Generating the Transcriptome: Bridge Amplification and Sequencing-by-Synthesis.

5.2.4 Making Sense of the Data: Transcriptome Assembly and Differential Expression

5.3 Beyond mRNA-Seq: Other High-Throughput Sequencing Applications for RNA

5.3.1 Long Noncoding RNA

5.3.2 Small Noncoding RNAs (miRNAs, tRNAs, etc.)

5.3.3 Investigating RNA Biology: Other Applications of RNA Sequencing

5.4 The Present and Future of Transcriptomics

5.4.1 Improving Assembly: The Advent of Long-Read Sequencing Methods

5.4.2 Examining the Epitranscriptome: Direct Detection of RNA Modifications

5.4.3 Deciphering Heterogeneity: Transcriptomes from Individual Cells

6: The mRNA and the New Vaccines

6.1 Introduction

6.2 Key Features in mRNA

6.3 Bacterial Messenger RNA

6.4 Eukaryotic Messenger RNA

6.5 Viral RNA

6.6 Genome Mapping of RNA

6.7 RNA Processing

6.8 Life Cycle of mRNA

6.9 The Development of mRNA Vaccines

7: Riboswitches: Sensors and Regulators

7.1 Introduction

7.2 The Aptamer Domain and the Expression Platform

7.3 Mechanisms of Regulation

7.4 Structural Organization within Riboswitches

7.5 Kinetic and Thermodynamic Control of Riboswitches

7.6 Tandem Glycine Riboswitches

7.7 GlmS Riboswitches Regulate Gene Expression Through Self-Cleavage of mRNA

7.8 Medical Implications

8: Small Noncoding RNA, microRNA in Gene Regulation

8.1 Introduction

8.2 Overview of microRNA (miRNA)

8.3 Canonical Pathway for miRNA Biogenesis

8.4 Pri-miRNA Processing by the Microprocessor Complex

8.5 RNase III Endonucleases Cut dsRNA

8.6 Moving Out of the Nucleus

8.7 Dicer Converts pre-miRNA into miRNA.

8.8 Argonaute Proteins Are Part of the RNA-Induced Silencing Complex (RISC)

8.9 miRNA-Mediated Gene Silencing

8.10 miRNA Regulation

8.11 Circular RNA

8.12 Small Interfering RNA

8.13 Piwi RNA

8.14 Other Small Regulatory RNA

8.15 Long Noncoding RNA (lncRNA)

8.16 Antisense RNA

8.17 ncRNA Research Methods

8.18 Implications in Human Diseases

9: CRISPR-Cas Systems: The Science and Ethics of Gene Manipulation

9.1 Introduction

9.2 Classification of CRISPR-Cas Systems

9.3 Adaptation: Spacer Acquisition

9.4 CRISPR Array

9.5 Creating Mature crRNA

9.6 Cleavage of Pathogenic DNA: Silencing (or Interference)

9.7 CRISPR-Cas Evasion by Viruses

9.8 Gene Manipulation via CRISPR-Cas Systems

9.9 Ethics of Gene Manipulation

10: Transcription

10.1 The Structure and Enzymatic Activity of RNAP

10.1.1 The Basic Structure of the Core Enzyme

10.1.2 Major Differences in Basic Structure of the Core Enzyme

10.1.3 The General Reaction Mechanism of RNAPs

10.1.4 Nucleotide Addition Cycle

10.1.5 The Elongating RNAP Is a Processive Enzyme

10.1.6 Error Rate

10.2 Bacterial Transcription

10.2.1 Transcription Initiation

10.2.1.1 Key Promoter Elements in Bacteria

10.2.2 Sigma Factors Recognizes Promoters as a Part of the Haloenzyme

10.2.3 Recognition of the Promoter by the Haloenzyme

10.2.4 Identity of Sigma Factors Associated with Haloenzyme Determines Gene Expression

10.2.5 The Conserved Protein Domains of Sigma Factor

10.3 Transcription Elongation

10.4 Transcription Termination

10.4.1 Intrinsic Transcription Termination

10.4.2 Rho-Dependent Transcription Termination

10.5 Eukaryotic Transcription.

10.5.1 Major Differences in Eukaryotic and Prokaryotic Transcription

10.5.1.1 Eukaryotic RNAPs Are More Complex Than Bacterial or Archaeal RNAP

10.5.1.2 CTD Domain of RNAPII and the CTD Code

10.5.2 The Core RNAP II Promoter

10.5.3 Recognition of RNAPII Promoter by GTFs

10.5.3.1 General Mechanism of PIC Assembly

10.5.3.2 Promoter Recognition Followed by Closed Complex Formation

10.5.3.3 Formation of the RNAPII Open Complex

10.5.3.4 RNA Polymerase II Promoter Escape

10.6 Transcription Elongation

10.6.1 Proximal Promoter Pausing

10.6.2 Kinetic Coupling of the Rate of Elongation and RNA Processing

10.7 Transcriptional Termination

Index.

Notes:

Includes index.

Description based on print version record.

Description based on publisher supplied metadata and other sources.

Other Format:

Print version: Grover, Neena Fundamentals of RNA Structure and Function

ISBN:

9783030902148

OCLC:

1316697344