Nucleosomes, histones & chromatin: 1
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Amsterdam [u.a.]
Elsevier, Acad. Press
2012
|
| Ausgabe: | 1. ed. |
| Schriftenreihe: | Methods in enzymology
512 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | LI, 337 S. Ill., graph. Darst. |
| ISBN: | 9780123919403 |
Internformat
MARC
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Datensatz im Suchindex
| _version_ | 1804149511796293632 |
|---|---|
| adam_text | CONTENTS
Contributors
xi
Preface
xv
Volumes in Series
xvii
Section
1
Histone and
DNA
Modifications, Enzymes,
Chromatin Effectors
1.
Examining Histone Posttranslational Modification Patterns
by High-Resolution Mass Spectrometry
3
Shu Lin and Benjamin A. Garcia
1.
Introduction
4
2.
Materials
5
3.
Nuclei Isolation
6
4.
Acid Extraction
8
5.
Offline Reverse-Phase High-Performance Liquid Chromatography
for Histone Variant Purification (Optional)
9
6.
Chemical Derivatization of Histones
11
7.
Stage-Tip Cleanup of
Peptide
Samples Prior to MS Analysis
15
8.
Enrichment for Phosphorylated Peptides Using Titanium
Dioxide (TiO2) Beads (Optional)
і б
9.
Online RP-HPLC and MS
19
Acknowledgments
27
References
28
2.
Investigating the Cell Cycle-Associated Dynamics of Histone
Modifications Using Quantitative Mass Spectrometry
29
Mo Xu, She Chen, and
Bing
Zhu
1.
Introduction
30
2.
Experimental Design
31
3.
Cell Culture
39
4.
Extraction and Separation of Histones
43
5.
Preparation of Propionic Anhydride-Derivatized Tryptic
Histone Peptides
46
Contents
6.
Mass
Spectrometric
Analysis
and Quantification
of Histone PTMs
51
Acknowledgments
53
References
53
3.
A Method to Site-Specifically Incorporate Methyl-Lysine
Analogues into
Recombinant
Proteins
57
Matthew D. Simon and Kevan M. Shokat
1.
Introduction
58
2.
Protocol to Install MLA into
Recombinant
Proteins
59
References
68
4.
Methods Applied to the Study of Protein
Arginine
Methylation
71
Donghang Cheng, Vidyasiri Vemulapalli, and Mark T. Bedford
1.
Introduction
72
2.
In Vitro Arginine-Methylation Assays
73
3.
Enzyme Sources for In Vitro Methylation Reactions
74
4.
Substrate Sources for In Vitro Methylation Assays
81
5.
Cell-Based Methylation Assays
81
6.
Methyl-Specific Antibodies
84
7.
Using Global-Methylation Inhibitors
87
8.
Using Cell-Based Reporter Systems to Screen for PRMT Inhibitors
88
9.
Summary
89
Acknowledgments
89
References
89
5.
Enzymatic Analysis of
Tet
Proteins: Key Enzymes in the
Metabolism of
DNA
Methylation
93
Li Shen and Yi Zhang
1.
Introduction
94
2.
Expression and Purification of
Tet
Proteins
95
3.
Tet
Activity Assays
97
4.
Analysis of the Cytosine Derivatives by 2D-TLC
99
5.
Analysis of the Cytosine Derivatives by Mass Spectrometry
100
6.
Analysis of the Endogenous Level of Cytosine Derivatives
by Mass Spectrometry
103
Acknowledgments
104
References
104
Contents
vii
6.
Peptide Microarrays
to Interrogate the
Historie Code 107
Scott
В.
Rothbart,
Krzysztof Krajewski,
Brian
D.
Strahl,
and
Stephen
M.
Fuchs
1.
Introduction
108
2. Histone
Peptide
Library
ПО
3.
Microarray Printing
120
4.
Analysis of Antibodies, Effector Proteins, and Enzymes
125
5.
Data Analysis
129
6.
Summary and Perspectives
130
Acknowledgments
133
References
133
7.
Identifying Chromatin Readers Using a SILAC-Based Histone
Peptide Pull-Down
Approach
137
Michiel
Vermeulen
1.
Introduction
137
2.
Histone
Peptide
Synthesis
138
3.
SILAC Labeling
139
4.
Incorporation Check
143
5.
Preparation of Nuclear Extract
146
6.
Histone
Peptide Pull-Down
148
7.
In-gel Digestion
151
8.
Mass Spectrometry
154
9.
Data Analysis
155
10.
Outlook
157
Acknowledgments
159
References
159
8.
High-Throughput Strategy to Identify Inhibitors of
Histone-Binding Domains
161
Elise K.
Wagner, Brittany
N.
Albaugh, and John M. Denu
1.
Introduction
162
2.
AlphaScreen Assay Principles
164
3.
Materials and Instrumentation
166
4.
Design and Preparation of Histone Peptides and Histidine
Tag Fusion Proteins
166
5. Initial Optimization of an AlphaScreen-Based Histone-Binding Assay
170
6.
Primary Screening
176
viii Contents
7.
Hit Selection and Secondary Screening
178
8.
Concentration-Dependence Validation Studies
179
9.
Assay-Specific Compound Interference
180
10.
Additional Assays for Validation
182
11.
Summary
184
Acknowledgments
184
References
184
9.
Validation of Histone-Binding Partners by
Peptide
Pull-Downs and Isothermal
Titration Calorimetry 187
Kathryn Malecek and Alexander
Ruthenburg
1.
Introduction
188
2.
Initial Screening: Discovering Putative Interactions Between
Histone Peptides and Potential Binding Partners
191
3.
Peptide Pull-downs:
Establishing Candidates for Quantitative
Assessment
195
4.
Isothermal
Titration
Calorimetry
(ITC):
Defining Histone PTM Binding
Affinities
200
5.
Reagent Considerations
212
6.
Summary:
Peptide Pull-Downs
and
ITC in
the Chromatin Field
216
Acknowledgments
218
References
218
Section
2
Nucleosome and Histone Dynamics
10.
Analysis of Histone Chaperone Antisilencing Function
1
Interactions
223
Jean K. Scorgie, Douglas
С
Donham
III, and Mair EA Churchill
1.
Introduction
224
2.
Preparation of Asf1
225
3.
Preparation of Histone Components
228
4.
Fluorescence Spectroscopy Analysis of Asfl Binding Interactions
with Histones
230
5.
Eiectrophoretic Mobility Shift Analysis of Asfl Binding Interactions
with Histones
232
6.
Summary and Implications
238
Acknowledgments
239
References
239
Contents
¡χ
11.
Quantifying Chromatin-Associated Interactions: The HI-FI System
243
Duane D.
Winkler,
Karolin
Luger,
and Aaron
R.
Hieb
1.
Introduction to Chromatin and the HI-FI System
244
2.
Fluorescent Labeling and Preparation of Nucleosome Components
246
3.
Imaging Requirements and Reaction Conditions
251
4.
HI-FI Binding Affinity Assay Setup and Execution
255
5.
HI-FI Stoichiometric Assays Setup and Execution
266
6.
HI-FI Competition Assays with FRET
267
7.
Summary
272
Acknowledgments
272
References
272
12.
Biochemical Assay for Histone H2A.Z Replacement
by the Yeast SWR1 Chromatin Remodeling Complex
275
Gaku
Mizuguchi, Wei-Hua Wu,
Samar Alami,
and Ed
Luk
1.
Introduction
276
2.
Preparation of Reagents
277
3.
In Vitro Htzi Replacement Assay by Chromatin Remodeling
Complex SWR1
285
4.
Special Notes
287
5.
Concluding Remarks
289
Acknowledgments
289
References
290
13.
Experimental Analysis of the Mechanism of Chromatin
Remodeling by
RNA Polymerase
II
293
Daria
A. Gaykalova,
Olga
I. Kulaeva, Nikolai A. Pestov, Fu-Kai Hsieh,
and Vasily M. Studitsky
1.
Introduction
294
2.
Materials and Methods
296
3.
DNase I Footprinting of ECs Formed by
E. coli RNAP
During
Transcription Through a Nucleosome
296
4.
Mapping of ECs Formed by Pol II During Transcription Through a
Nucleosome Using Restriction Endonucleases
305
Acknowledgments
311
References
311
Author Index
315
Subject Index
329
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| id | DE-604.BV040450835 |
| illustrated | Illustrated |
| indexdate | 2024-07-10T00:24:12Z |
| institution | BVB |
| isbn | 9780123919403 |
| language | English |
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| physical | LI, 337 S. Ill., graph. Darst. |
| publishDate | 2012 |
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| publisher | Elsevier, Acad. Press |
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| series | Methods in enzymology |
| series2 | Methods in enzymology |
| spelling | Nucleosomes, histones & chromatin 1 ed. by Carl Wu ... 1. ed. Amsterdam [u.a.] Elsevier, Acad. Press 2012 LI, 337 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 512 Methods in enzymology ... Nucleosom (DE-588)4172154-8 gnd rswk-swf Histone (DE-588)4159992-5 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 1 Methods in enzymology 512 (DE-604)BV000000938 512 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025298496&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Nucleosomes, histones & chromatin Methods in enzymology Nucleosom (DE-588)4172154-8 gnd Histone (DE-588)4159992-5 gnd Methode (DE-588)4038971-6 gnd |
| subject_GND | (DE-588)4172154-8 (DE-588)4159992-5 (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 1 ed. by Carl Wu ... |
| title_fullStr | Nucleosomes, histones & chromatin 1 ed. by Carl Wu ... |
| title_full_unstemmed | Nucleosomes, histones & chromatin 1 ed. by Carl Wu ... |
| title_short | Nucleosomes, histones & chromatin |
| title_sort | nucleosomes histones chromatin |
| topic | Nucleosom (DE-588)4172154-8 gnd Histone (DE-588)4159992-5 gnd Methode (DE-588)4038971-6 gnd |
| topic_facet | Nucleosom Histone Methode Aufsatzsammlung |
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