Preface ..v
Contributors ..xi
1. The MicroRNA: Overview of the RNA Gene That Modulates
Gene Functions
Shao-Yao Ying, Donald C. Chang, Joseph D. Miller,
and Shi-Lung Lin 1
2. Structure Analysis of MicroRNA Precursors
Jacek Krol and Wlodzimierz J. Krzyzosiak .. 19
3. MicroRNA Biogenesis: Isolation and Characterization
of the Microprocessor Complex
Richard I. Gregory, Thimmaiah P. Chendrimada,
and Ramin Shiekhattar . 33
4. Recognition and Cleavage of Primary MicroRNA Transcripts
Yan Zeng and Bryan R. Cullen  49
5. Mouse Embryonic Stem Cells as a Model Genetic System
to Dissect and Exploit the RNA Interference Machinery
Stefan A. Muljo and Chryssa Kanellopoulou .. 57
6. MicroRNAs and Messenger RNA Turnover
Julia A. Chekanova and Dmitry A. Belostotsky . 73
7. Prediction of MicroRNA Targets
Marc Rehmsmeier . 87
8. Prediction of Human MicroRNA Targets
Bino John, Chris Sander, and Debora S. Marks .. 101
9. Complications in Mammalian MicroRNA Target Prediction
Neil R. Smalheiser and Vetle I. Torvik  115
10. miRBase:The MicroRNA Sequence Database
Sam Griffiths-Jones  129
11. Methodologies for High-Throughput Expression Profiling
of MicroRNAs
Paz Einat.. 139
12. In Situ Hybridization as a Tool to Study the Role of MicroRNAs
in Plant Development
Catherine Kidner and Marja Timmermans  159
13. Usefulness of the Luciferase Reporter System to Test
the Efficacy of siRNA
Fengfeng Zhuang and Yi-Hsin Liu .. 181
14. Cloning MicroRNAs From Mammalian Tissues
Michael Z. Michael  189
15. Methods for Analyzing MicroRNA Expression and Function
During Hematopoietic Lineage Differentiation
Hyeyoung Min and Chang-Zheng Chen.. 209
16. Identifying MicroRNA Regulators of Cell Death in Drosophila
Chun-Hong Chen, Ming Guo, and Bruce A. Hay .. 229
17. MicroRNAs in Human Immunodeficiency Virus-1 Infection
Yamina Bennasser, Shu-Yun Le, Man Lung Yeung,
and Kuan-Teh Jeang . 241
18. Cloning and Detection of HIV-1-Encoded MicroRNA
Shinya Omoto and Yoichi R. Fujii . 255
19. Identification of Messenger RNAs and MicroRNAs Associated
With Fragile X Mental Retardation Protein
Ranhui Duan and Peng Jin . 267
20. In Vitro Precursor MicroRNA Processing Assays Using Drosophila
Schneider-2 Cell Lysates
Akira Ishizuka, Kuniaki Saito, Mikiko C. Siomi,
and Haruhiko Siomi . 277
21. Downregulation of Human Cdc6 Protein Using a Lentivirus RNA
Interference Expression Vector
Feng Luo, Jiing-Kuan Yee, Sheng-He Huang, Ling-Tao Wu,
and Ambrose Y. Jong .. 287
22. Gene Silencing In Vitro and In Vivo Using Intronic MicroRNAs
Shi-Lung Lin and Shao-Yao Ying . 295
23. Isolation and Identification of Gene-Specific MicroRNAs
Shi-Lung Lin, Donald C. Chang, and Shao-Yao Ying  313
24. Transgene-Like Animal Models Using Intronic MicroRNAs
Shi-Lung Lin, Shin-Ju E. Chang, and Shao-Yao Ying . 321
25. Evolution of MicroRNAs
Andrea Tanzer and Peter F. Stadler .. 335
26. Perspectives
Shao-Yao Ying, Donald C. Chang, Joseph D. Miller,
and Shi-Lung Lin  351
Index  359