MicroRNA methods / edited by John J. Rossi, Gregory J. Hannon.

Format:

Book

Contributor:

Rossi, John J.

Hannon, Gregory J., 1964-

Series:

Methods in enzymology ; v. 427.

Methods in enzymology ; v. 427

Language:

English

Subjects (All):

Small interfering RNA.

Physiology.

Physical Description:

1 online resource (302 p.)

Place of Publication:

Amsterdam ; London : Elsevier, c2007.

Language Note:

English

Summary:

MicroRNAs (miRNA) are tiny bits of genetic material that were unknown nearly 10 years ago but now represent an exciting field of study in biology. Upon their discovery, researchers revealed for the first time a new mechanism by which microRNA can stop the function of messenger RNA (mRNA) by literally cutting it in half, interfering with the normal function of specific messenger RNAs in gene expression. This ""expression"" of genes that code for essential proteins is essentially what controls whether a cell turns into a liver, lung, or brain cell, for example. Understanding what activat

Contents:

Cover; Contents; Contributors; Volumes in Series; Section I: Identifying MicroRNAs and their Targets; Chapter 1: Identification of Viral MicroRNAs; 1. Introduction; 2. Computational Prediction of Viral miRNA Candidates; 2.1. Principles of computational miRNA identification; 2.2. Predicting viral miRNA candidates with VMir; 3. Array Confirmation of Viral miRNA Candidates; 3.1. Array design; 3.2. Microarray hybridization; 3.3. Data analysis; 4. Concluding Remarks; References; Chapter 2: Robust Machine Learning Algorithms Predict MicroRNA Genes and Targets; 1. Introduction

2. Appropriate Use of Machine Learning2.1. Data sets; 2.2. Performance estimation; 2.3. Performance measures; 2.4. Machine learning steps; 3. One Deterministic and One Stochastic Algorithm; 3.1. Support vector machines; 3.2. Boosted genetic programming; 4. miRNA Gene Prediction with Support Vector Machines; 4.1. Deciding the input; 4.2. Assembling the training set; 4.3. Training the miRNA gene predictor and estimating its performance; 4.4. Evaluating the miRNA gene predictor's performance; 5. miRNA Target Prediction with Boosted Genetic Programming; 5.1. Deciding the input

5.2. Assembling the training set5.3. Training the miRNA target site predictor and estimating its performance; 5.4. Evaluating the miRNA target site predictor's performance; 6. Summary; Acknowledgments; References; Chapter 3: Identification of Virally Encoded MicroRNAs; 1. Introduction; 2. Purification of Rnl2 (1-249) and Adenylation of 3' Adapter Oligonucleotide; 3. Isolation of the Small RNA Fraction; 4. Ligation of the Purified Small RNA to Adenylated 3' Adapter; 5. Ligation of the Small RNA-3' Adapter to the 5' Adapter; 6. Reverse Transcription of the Final Ligation Product

7. First PCR Amplification of the cDNA8. Pme I Digestion of the PCR Product; 9. Second PCR Amplification; 10. Ban I Digestion of the Second PCR Product; 11. Concatamerization of the Ban I-Digested DNA; 12. End Tailing of Concatamers and Cloning into T/A Vector; 13. Sequencing and Annotation of the Library; 14. Concluding Remarks; References; Chapter 4: Computational Methods for MicroRNA Target Prediction; 1. Introduction; 2. Principles of miRNA Target Recognition; 3. Resources for Analysis of miRNA Target Genes; 4. Software Useful for miRNA Target Prediction

5. Original Strategies for Prediction of miRNA Target Genes6. Validation of Computational Predictions; 7. Concluding Remarks; Acknowledgments; References; Section II: MicroRNA Expression, Maturation, and Functional Analysis; Chapter 5: In Vitro and In Vivo Assays for the Activity of Drosha Complex; 1. Introduction; 2. Assay Methods; 2.1. In vitro analysis of pri-miRNA processing; 2.2. In vivo analysis of pri-miRNA processing; Acknowledgments; References; Chapter 6: Microarray Analysis of miRNA Gene Expression; 1. Introduction; 2. Overview of miRNA Biogenesis and Effector Pathways

3. miRNA Expression Analysis Strategies

Notes:

Description based upon print version of record.

Includes bibliographical references and index.

ISBN:

9786611038281

9781281038289

1281038288

9780080551395

0080551394

OCLC:

476100642