Telomeres and Telomerase: Methods and Protocols

190 Pages·2011·3.799 MB·English

by  Zhou Songyang (auth.), Zhou Songyang (eds.)

M M B ™
ethods in olecular iology
Series Editor
John M. Walker
School of Life Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB, UK
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Telomeres and Telomerase
Methods and Protocols
Edited by
Zhou Songyang
Department of Biochemistry and Molecular Biology, Baylor College of Medicine,
Houston, TX, USA
Editor
Zhou Songyang, Ph.D.
Department of Biochemistry and Molecular Biology
Baylor College of Medicine
Houston, TX
USA
[email protected]
ISSN 1064-3745 e-ISSN 1940-6029
ISBN 978-1-61779-091-1 e-ISBN 978-1-61779-092-8
DOI 10.1007/978-1-61779-092-8
Springer New York Dordrecht Heidelberg London
Library of Congress Control Number: 2011924473
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Preface
A gap of 40 years separates the first identification of telomeres and the discovery of the
telomerase. Our knowledge of the telomerase and how telomeres are maintained, how-
ever, has undergone exponential growth since then. The telomeres are coming into sharper
focus as we look deeper and wider at how telomere maintenance is critically linked to cell
growth, proliferation, aging, and diseases such as cancer. For example, in the majority of
human cancers, normal telomere maintenance is often bypassed. And in many human cell
types, telomere erosion is thought to limit the proliferative capacity of transformed cells.
This book has come at an exciting time when the 2009 Nobel Prize in Physiology or
Medicine was just awarded to Drs. Elizabeth H. Blackburn, Carol W. Greider, and Jack W.
Szostak for their pioneer work on telomeres and telomerase.
New and rapid advances in technology have equipped us with a variety of tools and
platforms to ask fundamental questions of telomere regulation and have allowed investiga-
tors to carry out experiments using diverse model systems. For example, proteomic,
genomic, and molecular approaches have afforded us unprecedented insight into the com-
plex protein interaction networks at work on the telomere chromatin and the detailed
information regarding telomere dynamics in response to stress or stimuli.
While the first volume of Telomeres and Telomerase: Methods and Protocols (MiMB
Vol. 191) focused mostly on telomerase assays, this volume expands the scope to encompass
many different assays that allow investigators to query the function of telomere proteins and
the responses of the telomere DNA. Biochemical, molecular, and proteomic approaches
are detailed so that investigators may easily follow these protocols. It is our belief that this
work will prove useful and informative.
Houston, TX Zhou Songyang
v
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Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
1 Introduction to Telomeres and Telomerase.............................. 1
Zhou Songyang
2 Analysis of Average Telomere Length in Cultured Human Cells .............. 13
Dan Liu
3 Telomere Length Analysis by Quantitative Fluorescent
In situ Hybridization (Q-FISH) ...................................... 21
Isabelle Ourliac-Garnier and Arturo Londoño-Vallejo
4 Telomere Strand-Specific Length Analysis by Fluorescent
In Situ Hybridization (Q-CO-FISH) .................................. 33
Isabelle Ourliac-Garnier and Arturo Londoño-Vallejo
5 Telomere G-Overhang Length Measurement Method 1:
The DSN Method ................................................ 47
Yong Zhao, Jerry W. Shay, and Woodring E. Wright
6 Telomere G-Overhang Length Measurement Method 2:
G-Tail Telomere HPA.............................................. 55
Hidetoshi Tahara
7 Telomere Terminal G/C Strand Synthesis: Measuring Telomerase
Action and C-Rich Fill-In........................................... 63
Yong Zhao, Jerry W. Shay, and Woodring E. Wright
8 G-Quadruplex Structures and G-Quadruplex-Interactive Compounds.......... 77
Raveendra I. Mathad and Danzhou Yang
9 Analysis of Yeast Telomerase by Primer Extension Assays.................... 97
Min Hsu and Neal F. Lue
10 Telomeric Repeat Amplification Protocol: Measuring the Activity
of the Telomerase................................................. 107
Huawei Xin
11 CO-FISH, COD-FISH, ReD-FISH, SKY-FISH .......................... 113
Eli S. Williams, Michael N. Cornforth, Edwin H. Goodwin,
and Susan M. Bailey
12 Visualization of Human Telomerase Localization by Fluorescence
Microscopy Techniques ............................................ 125
Eladio Abreu, Rebecca M. Terns, and Michael P. Terns
13 Cytogenetic Analysis of Telomere Dysfunction ........................... 139
Asha S. Multani and Sandy Chang
14 Probing the Telomere Damage Response ............................... 145
Rekha Rai and Sandy Chang
vii
viii Contents
15 Analysis of Telomere Proteins by Chromatin Immunoprecipitation (ChIP)...... 151
Wenbin Ma
16 Studying of Telomeric Protein–Protein Interactions by Bi-Molecular
Fluorescence Complementation (BiFC) and Peptide
Array-Based Assays................................................ 161
Wenbin Ma, Hyeung Kim, and Zhou Songyang
17 Human Telomere POT1-TPP1 Complex and Its Role in Telomerase
Activity Regulation................................................ 173
Feng Wang and Ming Lei
Index.............................................................. 189
Contributors
Eladio abrEu • Department of Biochemistry and Molecular Biology,
University of Georgia, Athens, GA, USA;
Department of Genetics, University of Georgia, Athens, GA, USA
SuSan M. bailEy • Department of Environmental & Radiological Health Sciences,
Colorado State University, Fort Collins, CO, USA
Sandy Chang • Department of Genetics, The University of Texas
M .D . Anderson Cancer Center, Houston, TX, USA
MiChaEl n. Cornforth • Department of Radiation Oncology,
University Texas Medical Branch, Galveston, TX, USA
Edwin h. goodwin • KromaTiD Inc ., Fort Collins, CO, USA
Min hSu • Department of Microbiology & Immunology, W .R . Hearst Microbiology
Research Center, Weill Medical College of Cornell University, New York, NY, USA
hyEung KiM • Department of Biochemistry and Molecular Biology,
Baylor College of Medicine, Houston, TX, USA
Ming lEi • Department of Biological Chemistry, Howard Hughes Medical Institute,
University of Michigan Medical School, Ann Arbor, MI, USA
dan liu • Department of Biochemistry and Molecular Biology, Cell-based Assay
Screening Service Core, Baylor College of Medicine, Houston, TX, USA
arturo londoño-VallEjo • Telomeres & Cancer Laboratory, Institut Curie,
Paris, France;
UPMC University Paris 06, Paris, France
nEal f. luE • Department of Microbiology & Immunology, W .R . Hearst Microbiology
Research Center, Weill Medical College of Cornell University, New York, NY, USA
wEnbin Ma • Department of Biochemistry, State Key Laboratory of Biocontrol,
College of Life Sciences, Sun Yat-sen University, Guangzhou, China
and
Department of Biochemistry and Molecular Biology,
Baylor College of Medicine, Houston, TX, USA
raVEEndra i. Mathad • College of Pharmacy, The University of Arizona,
Tucson, AZ, USA
aSha S. Multani • Department of Genetics, The University of Texas
M .D . Anderson Cancer Center, Houston, TX, USA
iSabEllE ourliaC-garniEr • Telomeres & Cancer Laboratory,
Institut Curie, Paris, France;
UPMC University Paris 06, Paris, France
rEKha rai • Department of Laboratory Medicine,
Yale University School of Medicine, New Haven, CT, USA
jErry w. Shay • Department of Cell Biology, University of Texas
Southwestern Medical Center, Dallas, TX, USA
ix
x Contributors
Zhou Songyang • Department of Biochemistry and Molecular Biology,
Baylor College of Medicine, Houston, TX, USA
hidEtoShi tahara • Department of Cellular and Molecular Biology,
Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
MiChaEl P. tErnS • Department of Biochemistry and Molecular Biology,
University of Georgia, Athens, GA, USA;
Department of Genetics, University of Georgia, Athens, GA, USA
rEbECCa M. tErnS • Department of Biochemistry and Molecular Biology,
University of Georgia, Athens, GA, USA;
Department of Genetics, University of Georgia, Athens, GA, USA
fEng wang • Department of Biological Chemistry, Howard Hughes Medical Institute,
University of Michigan Medical School, Ann Arbor, MI, USA
Eli S. williaMS • Department of Human Genetics, Emory University School
of Medicine, Atlanta, GA, USA
woodring E. wright • Department of Cell Biology, University of Texas
Southwestern Medical Center, Dallas, TX, USA
huawEi Xin • Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, USA
danZhou yang • Department of Chemistry, BIO5 Institute, College of Pharmacy,
The University of Arizona, Tucson, AZ, USA;
Arizona Cancer Center, Tucson, AZ, USA
yong Zhao • Department of Cell Biology, University of Texas
Southwestern Medical Center, Dallas, TX, USA