Methods in Enzymology

Volume 364

Nuclear Receptors

David W. Russell

David J. Mangelsdorf

CONTRIBUTORS TO VOLUME 364 i x

PREFACE xii i

VOLUMES IN SERIES X V

Section I . Analysis of Nuclear Receptor Ligand s

1 . Identification of Novel Nuclear Hormone Receptor FELIx GRO N

Ligands by Activity-Guided Purification

AND BRUCE BLUMBERG

3

2. Quantitation of Receptor Ligands by Mass ERIK G. LUN D

Spectrometry

AND ULF DICZFALUSY

24

3 . Site-Specific Fluorescent Labeling of Estrogen ANOBEL TAMRAZI

Receptors and Structure-Activity Relationships AND JOHN A .

of Ligands in Terms of Receptor Dimer Stability KATZENELLENBOGEN

3 7

4 . Cell-Free Ligand Binding Assays for Nuclear STACEY A . JONES ,

Receptors

DEREK J. PARKS, AND

STEVEN A. KLIEWER

5 3

5 . Design and Synthesis of Receptor Ligands

HIKARI A. I . YOSHIHARA ,

NGOC-HA NGUYEN, AN D

THOMAS S . SCANLAN

7 1

Section II . Structure/Function Analysis of Nuclear Receptor s

6. Bioinformatics of Nuclear Receptors

MARC ROBINSON-RECHAV I

AND VINCENT LAUDET

9 5

7. Application of Random Peptide Phage Display to CHING-YI CHANG ,

the Study of Nuclear Hormone Receptors

JOHN D . NORRIS ,

MICHELLE JANSEN,

HUEY-DING HUANG, AND

DONALD P . MCDONNELL

11 8

8 . Methods for Detecting Domain Interactions in ELIZABETH M . WILSON ,

Nuclear Receptors

BIN HE, AND

ELIZABETH LANGLEY

142

9 . The Orphan Receptor SHP and the Three-Hybrid YOON-KWANG LEE AND

Interference Assay

DAVID D. MOORE

152

10. Regulation of Glucocorticoid Receptor Ligand- KIMON C . KANELAKIS AND

Binding Activity by the hsp90/hsp70-based WILLIAM B . PRATT

15 9Chaperone Machinery

11 . Analysis of Receptor Phosphorylation

BRIAN G. ROWAN ,

RAMESH NARAYANAN ,

ANI) NANCY L . WEIGEL

17 3

Section III . Analysis of Nuclear Receptor Cofactors an dChromatin Remodeling

12. Acetylation and Methylation in Nuclear Receptor WEI Xu, HELEN CHO, AND

Gene Activation

RONALD M . EVANS

20 5

13. Steroid Receptor Coactivator Peptidomimetics

TIMOTHY R . GEISTLINGER

AND R. KIPLIN Guy

223

14. Biochemical Isolation and Analysis of a Nuclear MATTHEW G . GUENTHER

Receptor Corepressor Complex

AND MITCHELL A. LAZAR

246

15. Isolation and Functional Characterization of the SoHAIL MALIKTRAP/Mediator Complex

AND ROBERT G . ROEDER

257

16. Study of Nuclear Receptor-Induced Transcription HAN MA ,

Complex Assembly and Histone Modification by YONGFENG SHANG ,

Chromatin Immunoprecipitation Assays

DAVID Y. LEE, AND

MICHAEL R . STALLCUP

28 4

Section IV . Identification of Nuclear Receptor Target Genes and Effectors

17. Serial Analysis of Gene Expression and Gene HANA KOUTNIKOVA ,

Trapping to Identify Nuclear Receptor Target ELISABETH FAYARD ,

Genes

JÜRGEN LEHMANN, AND

JOHAN AUWERX

29 9

18. Expression Cloning of Receptor Ligand PAUL A. DAWSON AND

Transporters

ANN L . CRADDOCK

322

19. Nuclear Receptor Target Gene Discovery Using JOSEE LAGANIERE ,

High-Throughput Chromatin Immunoprecipi- GENEVIEVE DEBLOIS, AND

tation

VINCENT GIGUERE

33 9

20. RNA Gel Shift Assays for Analysis of Hormone ROBIN E . DODSON,

Control of mRNA Stability

KATHRYN M . GooLSBY ,

MARIA ACENA-NAGEL ,

CEIENGJIAN MAO, AND

DAVID J . SHAPIRO

35 0

21. Expression Cloning of Ligand Biosynthetic SHIGEAKI KATO AND

Enzymes

KEN-ICHI TAKEYAMA

361

Section V. Use of Animal Models to Study Nuclear Receptor Function

22. Targeted Conditional Somatic Mutagenesis DANIEL METZGER ,

in the Mouse : Temporally-Controlled Knock ARUP KUMAR INDRA, MEI LI,

Out of Retinoid Receptors in Epidermal BENOIT CHAPELLIER,

Keratinocytes

CECILE CALLEJA,

NORBERT B . GHYSELINCK ,

AND PIERRE CHAMBON

379

23. Analysis of Small Molecule Metabolism in SHIU-YING Ho,

Zebrafish

MICHAEL PACK, AND

STEVEN A . FARBER

40 8

24. Analysis of Nuclear Receptor Function in the MATTHEW W. KELLEY ,

Mouse Auditory System

PAMELA J . LANFORD ,

IWAN JONES, LORI AMMA ,

LILY NG, AND

DOUGLAS FORREST

426

25. Analysis of Estrogen Receptor Expression in MARGARET WARNER,

Tissues

LING WANG,

ZHANG WEIHUA ,

GUOJUN CHENG ,

HIDEKI SAKAGUCHI ,

SHIGEHIRA SAJI ,

STEFAN NILSSON ,

THOMAS KIESSELBACH ,

AN D

JAN-AKE GUSTAFSSON

44 8

26. In Vivo and In Vitro Reporter Systems ALEXANDER MATA DE

for Studying Nuclear Receptor and Ligand URQUIZA AND

Activities

THOMAS PERLMANN

463

27. Methods to Characterize Drosophila Nuclear TATIANA KOZLOVA AND

Receptor Activation and Function In Vivo

CARL S . THUMMEL

475

AUTHOR INDEX 49 1

SUBJECT INDEX 525