PDF电子书：Chromatin Remodeling

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Chromatin Remodeling/ u: K8 t; ^# Q! u

; ~$ e2 D2 ]4 o, F8 F% q* u+ ?Contents
% w4 @+ Z8 R; G3 z  {& nPreface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
4 V& j* G% x1 j, W( ]) K5 ^Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix/ F% W, Y  Q8 B# v" a
1 Strain Construction and Screening Methods for a Yeast Histone H3/H4/ s# R( x0 S' l9 Q: Q7 {' ^
Mutant Library. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 {, [5 j6 L8 k! n6 q
Junbiao Dai and Jef D. Boeke) G4 ?6 f' i6 g# p9 G
2 Measuring Dynamic Changes in Histone Modifications and Nucleosome2 ~! W' H5 \4 y: c9 t6 b- b
Density during Activated Transcription in Budding Yeast . . . . . . . . . . . . . . . . . . . . 15$ {8 H1 I/ Z0 U: T. u% E' f+ ?  o
Chhabi K. Govind, Daniel Ginsburg, and Alan G. Hinnebusch/ h3 m3 b7 O3 B- n) b
3 Monitoring the Effects of Chromatin Remodelers on Long-Range$ l8 ~/ B3 S- T* S, U: D
Interactions In Vivo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29" f: N  [4 }. y* C& T2 D8 x
Christine M. Kiefer and Ann Dean, V7 V# {0 O3 R9 c- Z  p  r
4 Measuring Nucleosome Occupancy In Vivo by Micrococcal Nuclease . . . . . . . . . . . 47
3 z$ r/ Q. s, FGene O. Bryant6 X# C9 Z( o5 f5 g1 V7 p
5 Analysis of Nucleosome Positioning Using a Nucleosome-Scanning Assay. . . . . . . . 63) f. s' O/ V( I0 C5 ]
Juan Jose Infante, G. Lynn Law, and Elton T. Young- ^8 _# S, `  B) H8 e( e7 a, Z
6 Assaying Chromatin Structure and Remodeling by Restriction Enzyme' \8 K! w2 `! s* H& k: K9 p9 W
Accessibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
7 [) W" H. ]. g1 LKevin W. Trotter and Trevor K. Archer- i8 f/ E6 x' m2 ]1 a+ U3 V
7 Generation of DNA Circles in Yeast by Inducible Site-Specific
% K3 {1 s: o( G1 P% d8 {/ GRecombination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103; F0 K$ c' F, u" L# }; {0 @; I
Marc R. Gartenberg
% v4 o4 l3 A7 U3 y6 S8 An Efficient Purification System for Native Minichromosome
4 X: l' ^& M1 \5 afrom Saccharomyces cerevisiae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
8 u# J8 H$ X0 B' d% L" yAshwin Unnikrishnan, Bungo Akiyoshi, Sue Biggins, and Toshio Tsukiyama
7 J; q, }3 ]6 f1 w2 ~" E  k$ P) x9 Simultaneous Single-Molecule Detection of Endogenous C-5 DNA
4 l/ I% B' T7 D+ NMethylation and Chromatin Accessibility Using MAPit. . . . . . . . . . . . . . . . . . . . . . 125
) y/ E) G5 c- o) IRussell P. Darst, Carolina E. Pardo, Santhi Pondugula,3 x$ K. k( N; O0 i2 ^) I
Vamsi K. Gangaraju, Nancy H. Nabilsi, Blaine Bartholomew,
( Q( `& i$ R1 l/ W: i( }5 I- ^and Michael P. Kladde
$ j# K3 X5 N; z  B+ ^+ X10 Analysis of Stable and Transient Protein–Protein Interactions . . . . . . . . . . . . . . . . . 143( d  {3 [" n+ S# T. j& A2 N
Stephanie Byrum, Sherri K. Smart, Signe Larson, and Alan J. Tackett& g# V% T$ t% j9 x' X% K2 R
11 Monitoring Dynamic Binding of Chromatin Proteins In Vivo
1 z$ G7 n% L2 I% N2 sby Fluorescence Recovery After Photobleaching . . . . . . . . . . . . . . . . . . . . . . . . . . . 153( d; n8 k' }1 c, a! ]' T, S3 [0 v
Florian Mueller, Tatiana S. Karpova, Davide Mazza,$ n  Z) E4 `/ i( F
and James G. McNally
( K0 p1 o( O% N! P2 ^3 E" Y/ W# B; I4 z12 Monitoring Dynamic Binding of Chromatin Proteins In Vivo by Fluorescence
9 F6 V7 I0 e) a& i0 `5 `2 j3 NCorrelation Spectroscopy and Temporal Image Correlation Spectroscopy . . . . . . . . 177; z) S4 K/ K, ~
Davide Mazza, Timothy J. Stasevich, Tatiana S. Karpova,/ h* I$ A9 t9 w7 h  f! r" x
and James G. McNally) U" s, E5 P" E9 R
13 Analysis of Chromatin Structure in Plant Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201$ Y  q9 M& E# t* U
Mala Singh, Amol Ranjan, Krishan Mohan Rai, Sunil Kumar Singh,7 v; a8 d4 [' l$ Y' k) p# J5 s
Verandra Kumar, Ila Trivedi, Niraj Lodhi, and Samir V. Sawant% z! o, k$ {; s1 l
14 Analysis of Histones and Histone Variants in Plants. . . . . . . . . . . . . . . . . . . . . . . . . 225# F4 e+ O  z* F" y2 I
Ila Trivedi, Krishan Mohan Rai, Sunil Kumar Singh,
2 T+ X4 O! h# `7 q' TVerandra Kumar, Mala Singh, Amol Ranjan, Niraj Lodhi,
% a# F3 u2 M7 q* {4 s- i0 _$ r3 Iand Samir V. Sawant
) H, r! f; d, j6 P* p15 Reconstitution of Modified Chromatin Templates for In Vitro5 h1 s; Q( o0 G7 W" N: }+ Z
Functional Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
& K1 V) P9 `! c: h+ K2 `Miyong Yun, Chun Ruan, Jae-Wan Huh, and Bing Li  P, N" J+ f1 Q7 \( [
16 A Defined In Vitro System to Study ATP-Dependent Remodeling
7 l7 Z2 g6 Q6 S+ S% H: a2 Lof Short Chromatin Fibers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
8 n5 o0 Q3 b* i# |, o& d) o: R6 G9 Y/ oVerena K. Maier and Peter B. Becker6 u# I9 v* g; m! m3 b% ?3 ]
17 In Vitro Reconstitution of In Vivo-Like Nucleosome Positioning
/ d3 }' A+ m7 _: ]on Yeast DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271
. k* J  R0 p+ W- E# L' dChristian J. Wippo and Philipp Korber
# t- s; j6 K& u/ p0 u9 n" f. @18 Activator-Dependent Acetylation of Chromatin Model Systems. . . . . . . . . . . . . . . . 289
: y0 Z" p# J$ u4 \! Q- j$ UHeather J. Szerlong and Jeffrey C. Hansen
* S/ [+ \+ B0 A+ l1 x. ?+ E! V19 Mapping Assembly Favored and Remodeled Nucleosome Positions+ b) }3 l- C/ N  S6 h
on Polynucleosomal Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311
& }$ o7 ?& X5 f) j1 ~% ^9 @Hillel I. Sims, Chuong D. Pham, and Gavin R. Schnitzler
& |. g9 {& c$ f7 x/ D& n6 a20 Analysis of Changes in Nucleosome Conformation Using Fluorescence5 X0 e; M1 a- I" X
Resonance Energy Transfer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337
4 M6 f( a& \6 N; o4 S$ }Tina Shahian and Geeta J. Narlikar8 R2 D( O: B. d
21 Preparation of Nucleosomes Containing a Specific H2A–H2A Cross-Link
! w; {3 y) N9 V+ F4 I. }/ y! CForming a DNA-Constraining Loop Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351
, F/ [- b. T1 j# ?9 KNing Liu and Jeffrey J. Hayes
% J# M4 C3 B( f- z& O22 Sulfyhydryl-Reactive Site-Directed Cross-Linking as a Method for Probing
3 j9 w' {% O" O& m" Vthe Tetrameric Structure of Histones H3 and H4 . . . . . . . . . . . . . . . . . . . . . . . . . . 373
7 R3 X$ U6 _4 z$ }5 B) U; VAndrew Bowman and Tom Owen-Hughes/ K+ Q/ `# A, k' ]; A# e; |% `
23 Genomic Approaches for Determining Nucleosome Occupancy in Yeast . . . . . . . . . 3899 m5 P- W# v2 x
Kyle Tsui, Tanja Durbic, Marinella Gebbia, and Corey Nislow2 f$ [+ O. Y$ t. k2 p
24 Genome-Wide Approaches to Determining Nucleosome Occupancy! z. j9 m0 M5 i; C; G
in Metazoans Using MNase-Seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4137 ]7 m4 R( t/ i. y% A
Kairong Cui and Keji Zhao
* B" L# H& M8 v; _5 W( `25 Salt Fractionation of Nucleosomes for Genome-Wide Profiling . . . . . . . . . . . . . . . . 421. |# k( e4 |, H2 S
Sheila S. Teves and Steven Henikoff, N2 i  \" g" W6 u9 x8 ?; ]8 O
26 Quantitative Analysis of Genome-Wide Chromatin Remodeling . . . . . . . . . . . . . . . 433+ ]$ G- e( i  q: X3 P: o0 H% f
Songjoon Baek, Myong-Hee Sung, and Gordon L. Hager2 q2 Q3 t( K/ v9 O. R" [
27 Computational Analysis of Nucleosome Positioning . . . . . . . . . . . . . . . . . . . . . . . . 443/ Z) |! i9 F& }" I
Itay Tirosh
3 Y6 d/ B$ w3 x" N: P; SIndex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451) J* a2 w6 i9 _& c) G) ?

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