PDF电子书：Chromatin Remodeling

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Chromatin Remodeling
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Contents
' M2 P( u$ r$ _& y- _& z' _1 g; aPreface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
' K, u* x( {; c/ }# x# u: pContributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
% x, O! f6 M4 s4 D; q1 Strain Construction and Screening Methods for a Yeast Histone H3/H4$ |8 M$ ^) w/ \% g
Mutant Library. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
5 O6 ^0 i; i, @! wJunbiao Dai and Jef D. Boeke
5 J2 P7 M, P) ^& a) T2 Measuring Dynamic Changes in Histone Modifications and Nucleosome9 @/ H+ @. e9 }: o; H' ?/ c
Density during Activated Transcription in Budding Yeast . . . . . . . . . . . . . . . . . . . . 159 Y/ C& [6 i+ u* F
Chhabi K. Govind, Daniel Ginsburg, and Alan G. Hinnebusch
5 K5 ~4 M& B7 V8 l( ?  p- T) A) K3 Monitoring the Effects of Chromatin Remodelers on Long-Range6 r# f& f( x  L# v8 p
Interactions In Vivo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29% m+ T( i% ^2 W: u2 y! T  W5 {
Christine M. Kiefer and Ann Dean" Z$ X4 U: F2 R2 ~
4 Measuring Nucleosome Occupancy In Vivo by Micrococcal Nuclease . . . . . . . . . . . 47
+ v: i7 E3 g! \& i4 v$ {Gene O. Bryant' G2 V5 F: J# I; K( m1 T  m
5 Analysis of Nucleosome Positioning Using a Nucleosome-Scanning Assay. . . . . . . . 63
0 \# z* h7 m0 X  m8 OJuan Jose Infante, G. Lynn Law, and Elton T. Young
( U% ^9 l( Z# N5 d, t, |) I0 B6 Assaying Chromatin Structure and Remodeling by Restriction Enzyme
- K$ ?3 w% X: L! l) s, @5 q# c2 MAccessibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 898 V) \: _1 |. e9 O. X
Kevin W. Trotter and Trevor K. Archer0 m; s- b0 {5 Z( W' H9 O
7 Generation of DNA Circles in Yeast by Inducible Site-Specific
" M; m/ p; c  J7 D  Y# \Recombination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
: |. P/ O+ I: I  n' l2 `Marc R. Gartenberg
! k4 ?$ e8 V% j. R8 An Efficient Purification System for Native Minichromosome
+ n' p- s3 Z- i" v. Wfrom Saccharomyces cerevisiae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1159 Z/ j; i( S9 I, v
Ashwin Unnikrishnan, Bungo Akiyoshi, Sue Biggins, and Toshio Tsukiyama
( A- G+ r6 d* H" ~0 e9 Simultaneous Single-Molecule Detection of Endogenous C-5 DNA8 _& W! Y* ?: P+ o- k; H$ `6 Y
Methylation and Chromatin Accessibility Using MAPit. . . . . . . . . . . . . . . . . . . . . . 125$ f- d: l" y. Q3 e
Russell P. Darst, Carolina E. Pardo, Santhi Pondugula,. C  b2 ]0 a6 H+ S# F- m
Vamsi K. Gangaraju, Nancy H. Nabilsi, Blaine Bartholomew,
8 s4 E9 y2 x2 t4 u6 j3 Q- ^/ g6 x+ W$ Iand Michael P. Kladde
# h+ M+ n1 [- n4 s3 Z10 Analysis of Stable and Transient Protein–Protein Interactions . . . . . . . . . . . . . . . . . 143
! N1 v" _6 ]1 u: G8 zStephanie Byrum, Sherri K. Smart, Signe Larson, and Alan J. Tackett
7 ^! M) x( G/ q7 ^11 Monitoring Dynamic Binding of Chromatin Proteins In Vivo3 F% T9 I$ k  g* h9 T
by Fluorescence Recovery After Photobleaching . . . . . . . . . . . . . . . . . . . . . . . . . . . 153" Q5 r0 m4 R0 v; b: c  W5 c
Florian Mueller, Tatiana S. Karpova, Davide Mazza,
2 W0 t6 e% W! @, A* J# Land James G. McNally
/ m) u' U6 {$ W, c12 Monitoring Dynamic Binding of Chromatin Proteins In Vivo by Fluorescence
' N2 _& z+ e2 Q5 tCorrelation Spectroscopy and Temporal Image Correlation Spectroscopy . . . . . . . . 177
6 f* y- f6 _# O, h0 [' z: PDavide Mazza, Timothy J. Stasevich, Tatiana S. Karpova,
, \8 N  ^9 r# k& i: tand James G. McNally& G* B- H# L) P" a* u( _3 _4 I
13 Analysis of Chromatin Structure in Plant Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
; J8 e8 t9 [) j5 b, gMala Singh, Amol Ranjan, Krishan Mohan Rai, Sunil Kumar Singh,
! J) _6 Y- f8 F$ TVerandra Kumar, Ila Trivedi, Niraj Lodhi, and Samir V. Sawant. ^: N; c% K' X
14 Analysis of Histones and Histone Variants in Plants. . . . . . . . . . . . . . . . . . . . . . . . . 2252 N1 E2 b2 L* l
Ila Trivedi, Krishan Mohan Rai, Sunil Kumar Singh,2 p# }' z9 P2 ^1 m8 k3 ]* m
Verandra Kumar, Mala Singh, Amol Ranjan, Niraj Lodhi,
8 X$ A: R  T& ~! s- r( f" x) Nand Samir V. Sawant
$ M& p6 G' s3 u# A- s4 e* p. Y15 Reconstitution of Modified Chromatin Templates for In Vitro
( W0 T, b0 Y, j" T1 Y4 ZFunctional Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
% @8 N% E4 [; {1 O/ W  r- C0 TMiyong Yun, Chun Ruan, Jae-Wan Huh, and Bing Li
5 s( ~4 `$ w# v4 i4 R1 Q) k16 A Defined In Vitro System to Study ATP-Dependent Remodeling
5 V$ y! o; Y% W! J3 nof Short Chromatin Fibers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
* R/ p. |2 I. KVerena K. Maier and Peter B. Becker
$ `; h# ~/ Z# k" ]( w- \7 {3 Q4 u17 In Vitro Reconstitution of In Vivo-Like Nucleosome Positioning/ ]7 J% @9 S9 K3 y# N
on Yeast DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271! Z, Q) ?0 ^& c
Christian J. Wippo and Philipp Korber7 |! a' I0 Y3 b7 Z1 D$ p
18 Activator-Dependent Acetylation of Chromatin Model Systems. . . . . . . . . . . . . . . . 289
' X' o$ o, h7 r8 Z" Q  }Heather J. Szerlong and Jeffrey C. Hansen
- V' S* ^6 i( Q3 g2 X* F, C$ u1 U19 Mapping Assembly Favored and Remodeled Nucleosome Positions% G& s( u: `  K( `6 D2 z1 G- O& c
on Polynucleosomal Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311- q9 S8 T; c, c. ?' t6 @
Hillel I. Sims, Chuong D. Pham, and Gavin R. Schnitzler
) Q& n4 P: u: V$ J20 Analysis of Changes in Nucleosome Conformation Using Fluorescence
! ?. i/ [0 q# x2 `- @' q9 yResonance Energy Transfer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337# K! [( J  h  K8 }/ X6 K8 k
Tina Shahian and Geeta J. Narlikar* g4 p9 D& @4 K5 M) ^, I
21 Preparation of Nucleosomes Containing a Specific H2A–H2A Cross-Link
: q- h7 C" }9 P, @7 h: `Forming a DNA-Constraining Loop Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3516 s* u1 m$ Y7 ]! _; O: X" H
Ning Liu and Jeffrey J. Hayes; y7 y4 V' ~) H; e( N
22 Sulfyhydryl-Reactive Site-Directed Cross-Linking as a Method for Probing
' i' l; C2 |) s3 q2 B# x" Mthe Tetrameric Structure of Histones H3 and H4 . . . . . . . . . . . . . . . . . . . . . . . . . . 373( o( ?( k! C6 o( v
Andrew Bowman and Tom Owen-Hughes
. T0 V9 \7 H) u8 G6 X/ g23 Genomic Approaches for Determining Nucleosome Occupancy in Yeast . . . . . . . . . 389( z: T7 g: ?7 F* g
Kyle Tsui, Tanja Durbic, Marinella Gebbia, and Corey Nislow
, a! M# P5 G+ S, v% P2 P24 Genome-Wide Approaches to Determining Nucleosome Occupancy9 ?9 b' Y9 P( j3 Q4 C
in Metazoans Using MNase-Seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 413# P; ^( ]0 U) o
Kairong Cui and Keji Zhao
* {$ a; n3 k9 o* E25 Salt Fractionation of Nucleosomes for Genome-Wide Profiling . . . . . . . . . . . . . . . . 421
7 h! f) _1 Q4 w/ m4 lSheila S. Teves and Steven Henikoff
# Q8 W) X! k/ a) L1 A5 z; U26 Quantitative Analysis of Genome-Wide Chromatin Remodeling . . . . . . . . . . . . . . . 433
$ p* v* @* a5 T- t& x& N  cSongjoon Baek, Myong-Hee Sung, and Gordon L. Hager( I! l- Z2 y/ B' ?) Q% n
27 Computational Analysis of Nucleosome Positioning . . . . . . . . . . . . . . . . . . . . . . . . 443
5 d+ p3 ^; R, x4 ]3 ZItay Tirosh- j/ `# n" B( N( G* R* M4 G
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451! g  h/ O; J4 u4 K

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