
- 积分
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- 威望
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- 包包
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Chromatin Remodeling6 y1 e& u+ [: Z' @3 _
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Contents' ]7 _5 P% u* z8 R5 y# b
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v* l, l- L9 x/ l
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix8 f+ ]' f- d9 k+ Q; y/ e5 d& G
1 Strain Construction and Screening Methods for a Yeast Histone H3/H4
# w! W: W! s: X% rMutant Library. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1% ]' v- D& @# x! i4 F3 b
Junbiao Dai and Jef D. Boeke
' x( B% S6 i; O; t& _( S2 Measuring Dynamic Changes in Histone Modifications and Nucleosome, ?. a9 O% o. ?0 O
Density during Activated Transcription in Budding Yeast . . . . . . . . . . . . . . . . . . . . 15
6 ^" O5 `( i( A: g$ \Chhabi K. Govind, Daniel Ginsburg, and Alan G. Hinnebusch0 g8 o3 u) S% |9 @* }! ~# I
3 Monitoring the Effects of Chromatin Remodelers on Long-Range
0 p) j3 |( G. X. E9 c) rInteractions In Vivo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29- t' u) `0 B; q1 v* B
Christine M. Kiefer and Ann Dean
- c g b2 U" q2 Y' C( o5 U4 Measuring Nucleosome Occupancy In Vivo by Micrococcal Nuclease . . . . . . . . . . . 47
) h' j) D. t! p# VGene O. Bryant
) s* _) Q8 X& V5 Analysis of Nucleosome Positioning Using a Nucleosome-Scanning Assay. . . . . . . . 63
: y+ D3 v$ g2 y1 n/ @4 KJuan Jose Infante, G. Lynn Law, and Elton T. Young
% S& A. e# D4 d6 z! A% @6 c6 f9 }: E6 Assaying Chromatin Structure and Remodeling by Restriction Enzyme
) U( _; ^1 w! W: C( g, ?0 HAccessibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
9 g$ O3 w' q8 D- qKevin W. Trotter and Trevor K. Archer
9 p) y; |% b- [* b5 p F7 Generation of DNA Circles in Yeast by Inducible Site-Specific
, V( c. d3 t6 `Recombination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103! Q2 Z5 F0 W0 H" ~) `1 T2 j: @7 T
Marc R. Gartenberg' h6 ]( n0 U/ N
8 An Efficient Purification System for Native Minichromosome( [( R/ Z) I+ D( J
from Saccharomyces cerevisiae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1152 P5 Q0 \5 j8 f
Ashwin Unnikrishnan, Bungo Akiyoshi, Sue Biggins, and Toshio Tsukiyama+ L* U& N3 L1 w
9 Simultaneous Single-Molecule Detection of Endogenous C-5 DNA/ Q/ {1 H& t" m# S; K+ i
Methylation and Chromatin Accessibility Using MAPit. . . . . . . . . . . . . . . . . . . . . . 125
* y( K- x3 L2 nRussell P. Darst, Carolina E. Pardo, Santhi Pondugula,: D: T' w! j8 G0 j5 d4 }
Vamsi K. Gangaraju, Nancy H. Nabilsi, Blaine Bartholomew,9 y* @* L& A* f* _
and Michael P. Kladde4 e6 C3 E$ G4 C& |: o/ ]0 E# [
10 Analysis of Stable and Transient Protein–Protein Interactions . . . . . . . . . . . . . . . . . 143
4 L' T1 g' x& f4 h3 D1 a' }' A( _Stephanie Byrum, Sherri K. Smart, Signe Larson, and Alan J. Tackett. ]6 L! f! l0 `
11 Monitoring Dynamic Binding of Chromatin Proteins In Vivo
1 Y4 T* ?$ r/ | j& `by Fluorescence Recovery After Photobleaching . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
0 w" e0 @. O4 ?5 j# s0 j% f* iFlorian Mueller, Tatiana S. Karpova, Davide Mazza,5 o& Y5 t- }8 {+ ?3 Q
and James G. McNally
0 m% p& r h6 |12 Monitoring Dynamic Binding of Chromatin Proteins In Vivo by Fluorescence
4 @2 E8 S+ U( E" h; BCorrelation Spectroscopy and Temporal Image Correlation Spectroscopy . . . . . . . . 177
: p' M5 U) V# c2 A" @1 S0 R/ MDavide Mazza, Timothy J. Stasevich, Tatiana S. Karpova,, @2 J7 {% D5 Z6 f% [
and James G. McNally9 P5 N/ R# E( k6 w" Z* q9 f; w/ U
13 Analysis of Chromatin Structure in Plant Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
2 H4 f/ v5 \+ ]7 \( F, t8 yMala Singh, Amol Ranjan, Krishan Mohan Rai, Sunil Kumar Singh,
2 P3 P, Y% k, k. t6 o. VVerandra Kumar, Ila Trivedi, Niraj Lodhi, and Samir V. Sawant0 l2 F, f" q$ N' B5 a
14 Analysis of Histones and Histone Variants in Plants. . . . . . . . . . . . . . . . . . . . . . . . . 225
0 U. ~9 `; P- r+ n: s y, IIla Trivedi, Krishan Mohan Rai, Sunil Kumar Singh,
4 k/ V- f3 x' xVerandra Kumar, Mala Singh, Amol Ranjan, Niraj Lodhi,- W* u# h7 [" E
and Samir V. Sawant8 F3 ?& r, t( v+ Z
15 Reconstitution of Modified Chromatin Templates for In Vitro4 v2 P J7 i+ ?
Functional Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
+ i. x' L! `* D/ {3 AMiyong Yun, Chun Ruan, Jae-Wan Huh, and Bing Li1 x( I4 V" p" d6 O
16 A Defined In Vitro System to Study ATP-Dependent Remodeling+ x+ ^: {) G2 T! E0 ]& Q' S! ^
of Short Chromatin Fibers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2555 t; I6 q! V: Q1 P0 H
Verena K. Maier and Peter B. Becker
& l# Q) L( `5 ]2 `0 m4 O17 In Vitro Reconstitution of In Vivo-Like Nucleosome Positioning
% d1 I [% Z# |. X3 Jon Yeast DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271! h! I2 J( X4 \) c# W5 w- r- S# o
Christian J. Wippo and Philipp Korber" U/ ~/ s& {, }& P0 j9 [
18 Activator-Dependent Acetylation of Chromatin Model Systems. . . . . . . . . . . . . . . . 289- X0 l! ]' n/ N$ k: e
Heather J. Szerlong and Jeffrey C. Hansen) O+ r# |1 M3 v$ X* O( O$ e7 F
19 Mapping Assembly Favored and Remodeled Nucleosome Positions& Y( Q2 i2 k- D' I1 b/ a" {# O
on Polynucleosomal Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311
$ ~- g- X2 O, hHillel I. Sims, Chuong D. Pham, and Gavin R. Schnitzler
/ l9 V7 h1 L) R8 Z$ Y20 Analysis of Changes in Nucleosome Conformation Using Fluorescence3 D7 H: S( o- }, w0 D
Resonance Energy Transfer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337
$ m- g& w' `- F$ O3 a4 h; R9 f0 B/ rTina Shahian and Geeta J. Narlikar# [" }0 n: _/ C+ w3 B
21 Preparation of Nucleosomes Containing a Specific H2A–H2A Cross-Link0 e/ X9 x. [% i9 R
Forming a DNA-Constraining Loop Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3519 \4 C- Q5 Q: O( U: R
Ning Liu and Jeffrey J. Hayes; n2 q- }- {$ I4 F4 E' ]$ V
22 Sulfyhydryl-Reactive Site-Directed Cross-Linking as a Method for Probing6 T- A2 s) j+ |- y: Z3 j
the Tetrameric Structure of Histones H3 and H4 . . . . . . . . . . . . . . . . . . . . . . . . . . 373
1 k& s1 l* C& Q) {Andrew Bowman and Tom Owen-Hughes6 T' k& v3 f; y& P d R# [4 U
23 Genomic Approaches for Determining Nucleosome Occupancy in Yeast . . . . . . . . . 389, r9 r) D) p3 K7 {
Kyle Tsui, Tanja Durbic, Marinella Gebbia, and Corey Nislow
+ q* i. F* _8 g. D# J! M24 Genome-Wide Approaches to Determining Nucleosome Occupancy
; r& E8 N3 F4 W$ L& zin Metazoans Using MNase-Seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 413. L$ L- T% I& }! J4 U; b9 H6 g: Z' _
Kairong Cui and Keji Zhao
1 s- w/ o6 b d2 Y+ f25 Salt Fractionation of Nucleosomes for Genome-Wide Profiling . . . . . . . . . . . . . . . . 421
9 m7 W5 y9 r( j bSheila S. Teves and Steven Henikoff C6 B+ ^" c* P0 L3 B- O7 N
26 Quantitative Analysis of Genome-Wide Chromatin Remodeling . . . . . . . . . . . . . . . 433' M1 E; W8 [( k; D( |6 [+ R* r
Songjoon Baek, Myong-Hee Sung, and Gordon L. Hager
$ l0 [9 _$ V3 t! f. b; }( o27 Computational Analysis of Nucleosome Positioning . . . . . . . . . . . . . . . . . . . . . . . . 4430 `$ E0 Q* M; C: C8 p/ w( n
Itay Tirosh& P" ?: u5 M3 ~; R" p# k+ H
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4512 n5 ~! Y3 ^% a8 g5 d7 |; o
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