Nucleosomes, histones & chromatin: 2
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Amsterdam [u.a.]
Elsevier, Acad. Press
2012
|
| Edition: | 1. ed. |
| Series: | Methods in enzymology
513 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | LI, 356, [10] Bl. Ill., graph. Darst. |
| ISBN: | 9780123919380 |
Staff View
MARC
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Record in the Search Index
| _version_ | 1804149602860924928 |
|---|---|
| adam_text | CONTENTS
Contributors
xi
Preface
xv
Volumes in Series
xvii
Section
1
Single Molecule Studies of Nucleosomes
1. DNA
Translocation
of ATP-Dependent Chromatin Remodeling
Factors Revealed by High-Resolution Optical Tweezers
3
Yongli Zhang, George Sirinakis, Greg Gundersen, Zhiqun
Xi,
and Ying
Gao
1.
Introduction
4
2.
Instrument
6
3.
Remodeler Translocation
on Bare
DNA 13
4.
Nucleosome-Dependent
Remodeler Translocation
18
5.
Data Analysis
25
Acknowledgments
26
References
26
2.
Unzipping Single
DNA
Molecules to Study Nucleosome
Structure and Dynamics
29
Ming
U
and Michelle D. Wang
1.
Introduction
30
2.
Sample Preparation
33
3.
Instrumentation and Data Collection
39
4.
Data Processing
43
5.
Determination of Unzipping Accuracy and Precision
46
6.
Unzipping in Nucleosome Studies
48
7.
Conclusions
56
Acknowledgments
56
References
56
Contents
3. Monitoring Conformational Dynamics
with
Single-Molecule
Fluorescence
Energy Transfer: Applications in Nucleosome
Remodeling
59
Sebastian Deindl and Xiaowei Zhuang
1.
Introduction
60
2.
Preparation of Fluorescently Labeled
Sample
for
Single-Molecule
FRET
Imaging
62
3.
Preparing PEG-Coated Slides with Sample Chamber
69
4.
Optical Setup and Single-Molecule FRET Data Acquisition
71
5.
Data Analysis
77
6.
Summary
83
Acknowledgments
83
References
83
Section
2
Higher Order Chromatin Interactions
4.
4C Technology: Protocols and Data Analysis
89
Härmen
J.G. van
de Werken,
Paula J.P.
de Vree,
Erik Splinter,
Sjoerd J.B.
Holwerda, Petra Klous, Elzo de Wit, and Wouter de Laat
1.
Introduction
90
2.
4C
Template Preparation
92
3.
4C-Seq
Primer Design and PCR
100
4.
High-Throughput Sequencing of
4C PCR Products
103
5.
Data
Analysis
103
Acknowledgments
110
References
110
5.
A Torrent
of Data: Mapping
Chromatin
Organization Using
5C
and High-Throughput Sequencing
113
James
Fraser, Sylvain
D.
Ethier, Hisashi Miura, and
Josée Dostie
1.
Introduction
Π
4
2.
Preparing Torrent 5C Libraries
121
3.
Overview of the Ion Torrent Sequencing Protocol
129
4.
Torrent 5C Data Processing
131
5.
Conclusion
138
Acknowledgments
138
References
138
Contents______________________________________________________________
vii
Section
З
Genome wide Analyses of Chromatin and Transcripts
6.
Genome-Wide Mapping of Nucleosomes in Yeast Using
Paired-End Sequencing
145
Hope A. Cole, Bruce H. Howard, and David J. Clark
1.
Introduction
146
2.
Preparation of Nucleosome Core Particles from Yeast
148
3.
Preparation of Core Particle
DNA
for Sequencing
152
4.
Paired-End Sequencing
158
5.
Bioinformatic Analysis of Nucleosome Sequences
159
6.
Some General Experimental Considerations
165
Acknowledgments
166
References
167
7.
Measuring Genome-Wide Nucleosome Turnover Using CATCH-IT
169
Sheila S.
Teves,
Roger B. Deal, and Steven Henikoff
1.
Introduction
170
2.
Covalent Attachment of Tagged Histones to Capture and
Identify Turnover
171
3.
Modified Solexa Library Preparation
178
References
184
8. DNA Methyltransferase
Accessibility Protocol for Individual
Templates by Deep Sequencing
185
Russell P. Darst, Nancy H. Nabilsi, Carolina
E. Pardo,
Alberto
Riva,
and Michael P.
Kladde
1.
Introduction
186
2.
Materials
188
3.
Protocols
190
Acknowledgments
202
References
202
9.
Genome-Wide In Vitro
Reconstitution
of Yeast Chromatin with
In V/vo-Like Nucleosome Positioning
205
Nils Krietenstein, Christian J. Wippo,
Corinna Lieleg,
and
Philipp Korber
1.
Introduction
206
2.
Preparation of Yeast WCE
207
viii Contents
3.
Preparation of Histories
211
4.
Expansion of Genomic
Plasmici
Library
214
5.
Chromatin
Reconstitution
by Salt Gradient Dialysis
217
6.
Incubation of Salt Gradient Dialysis Chromatin with WCE or
Purified Factors
227
7.
Generation of Mononucleosomes by Limited MNase Digestion
228
8.
Summary
229
Acknowledgments
230
References
230
10.
Genome-Wide Mapping of Nucleosome Positions in Yeast
Using High-Resolution MNase ChlP-Seq
233
Megha Wai and B. Franklin Pugh
1.
Introduction
233
2.
Methodology
235
Acknowledgments
249
References
249
11.
Preparation of
Drosophila
Tissue Culture Cells from Different
Stages of the Cell Cycle for Chromatin Immunoprecipitation
Using Centrifugal Counterflow Elutriation and
Fluorescence-Activated Cell Sorting
251
Nicole E. Follmer and Nicole J. Francis
1.
Introduction
252
2.
Centrifugal Elutriation of
Drosophila
Cells to Obtain G1, S,
and G2 Populations
253
3.
FACS Sorting of
Drosophila
Cells to Obtain Mitotic Cell Populations
261
4.
Summary
268
Acknowledgments
268
References
268
12.
Genome-Wide Polyadenylation Site Mapping
271
Vicent Pelechano, Stefan Wilkening,
Aino
Inkeri
Järvelin,
Manu M. Tekkedil,
and Lars M.
Steinmetz
1.
Introduction
272
2.
General Recommendations
275
3.
Sample Preparation
276
4.
Library Construction
282
5.
Bioinformatic Analysis of Polyadenylation Site Sequencing Reads
289
Contents__________________________________________________________________ix
6.
Quality Control
291
7.
Preparation of Double-Stranded Linkers
293
8.
Summary
294
Acknowledgments
294
References
294
13.
Genome-Wide Mapping of Nucleosome Occupancy, Histone
Modifications, and Gene Expression Using Next-Generation
Sequencing Technology
297
Gang Wei, Gangqing Hu, Kairong
Cui,
and Keji Zhao
1.
Introduction
298
2.
Mapping Genome-Wide Nucleosome Occupancy and Positions by
High-Throughput Next-Generation Sequencing
299
3.
Mapping Histone Modifications Using ChlP-Seq
302
4.
Mapping Genome-Wide mRNA Profiles Using RNA-Seq
304
5.
RNA-Seq Analysis with a Small Number of Cells
307
Acknowledgment
311
References
311
14.
A Chemical Approach to Mapping Nucleosomes at Base Pair
Resolution in Yeast
315
Kristin R. Brogaard, Liqun
Xi,
Ji-Ping Wang, and Jonathan
Widom
1.
Introduction
316
2.
Construction of H4S47C S. cerevisiae Strain
317
3.
Chemical Cleavage of Nucleosome Center Positions
318
4.
Statistical Analysis of Chemical Mapping Data
324
5.
Summary
332
Acknowledgments
333
References
333
Author Index
335
Subject Index
349
|
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| series | Methods in enzymology |
| series2 | Methods in enzymology |
| spelling | Nucleosomes, histones & chromatin 2 ed. by Carl Wu ... 1. ed. Amsterdam [u.a.] Elsevier, Acad. Press 2012 LI, 356, [10] Bl. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 513 Methods in enzymology ... Histone (DE-588)4159992-5 gnd rswk-swf Nucleosom (DE-588)4172154-8 gnd rswk-swf Methode (DE-588)4038971-6 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Nucleosom (DE-588)4172154-8 s Methode (DE-588)4038971-6 s DE-604 Histone (DE-588)4159992-5 s b DE-604 Wu, Carl Sonstige oth (DE-604)BV040450823 2 Methods in enzymology 513 (DE-604)BV000000938 513 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025367399&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Nucleosomes, histones & chromatin Methods in enzymology Histone (DE-588)4159992-5 gnd Nucleosom (DE-588)4172154-8 gnd Methode (DE-588)4038971-6 gnd |
| subject_GND | (DE-588)4159992-5 (DE-588)4172154-8 (DE-588)4038971-6 (DE-588)4143413-4 |
| title | Nucleosomes, histones & chromatin |
| title_auth | Nucleosomes, histones & chromatin |
| title_exact_search | Nucleosomes, histones & chromatin |
| title_full | Nucleosomes, histones & chromatin 2 ed. by Carl Wu ... |
| title_fullStr | Nucleosomes, histones & chromatin 2 ed. by Carl Wu ... |
| title_full_unstemmed | Nucleosomes, histones & chromatin 2 ed. by Carl Wu ... |
| title_short | Nucleosomes, histones & chromatin |
| title_sort | nucleosomes histones chromatin |
| topic | Histone (DE-588)4159992-5 gnd Nucleosom (DE-588)4172154-8 gnd Methode (DE-588)4038971-6 gnd |
| topic_facet | Histone Nucleosom Methode Aufsatzsammlung |
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