PDF电子书：Chromatin Remodeling

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Chromatin Remodeling
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Contents
! T; d: a) {" J. k5 z+ ZPreface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v$ H7 t% w& n+ u4 h4 i& ]7 k5 ^# s
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix2 C. M. T- j4 U
1 Strain Construction and Screening Methods for a Yeast Histone H3/H45 y" W: w- y- h
Mutant Library. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1: v; m' E7 [4 Y
Junbiao Dai and Jef D. Boeke, \+ d! q3 O/ W. _& D9 g# s
2 Measuring Dynamic Changes in Histone Modifications and Nucleosome
) Q/ R! n5 {) @+ YDensity during Activated Transcription in Budding Yeast . . . . . . . . . . . . . . . . . . . . 15
1 |7 ^0 X$ p- lChhabi K. Govind, Daniel Ginsburg, and Alan G. Hinnebusch
: z- o4 D( w6 g6 b4 j1 O8 E3 Monitoring the Effects of Chromatin Remodelers on Long-Range
$ }. \5 G1 Z. ~8 M$ I' v* BInteractions In Vivo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
- c+ g: D! R. t! V8 VChristine M. Kiefer and Ann Dean+ S. ~2 w5 O  X, |
4 Measuring Nucleosome Occupancy In Vivo by Micrococcal Nuclease . . . . . . . . . . . 478 i! A: @' s0 {3 m* M) S2 @+ f
Gene O. Bryant
! _1 \+ x$ w2 a% l" z: ^5 Analysis of Nucleosome Positioning Using a Nucleosome-Scanning Assay. . . . . . . . 63
! F) [0 @6 q+ \. DJuan Jose Infante, G. Lynn Law, and Elton T. Young
; ]5 y9 Y0 T! ]# x* z  Q' ]' s6 Assaying Chromatin Structure and Remodeling by Restriction Enzyme
0 h: ?- c( _1 c% a5 U8 d1 Q. tAccessibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
$ r3 F$ @8 M. _5 ZKevin W. Trotter and Trevor K. Archer1 m  F. C$ h- o$ j) t
7 Generation of DNA Circles in Yeast by Inducible Site-Specific
' x; v9 s  l1 X0 E- m) N1 [+ E* Q- XRecombination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
1 N/ ]3 {! ~2 O, ]Marc R. Gartenberg
: T% t+ {( Z) ~( ~: p+ [8 An Efficient Purification System for Native Minichromosome
1 P2 p" \. v4 n9 }1 |% S- v( Zfrom Saccharomyces cerevisiae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115' |- u6 Q5 W7 K0 _
Ashwin Unnikrishnan, Bungo Akiyoshi, Sue Biggins, and Toshio Tsukiyama$ G% \+ w* H2 [9 P3 j
9 Simultaneous Single-Molecule Detection of Endogenous C-5 DNA
, P" K" s" X( E! `- f% e: ZMethylation and Chromatin Accessibility Using MAPit. . . . . . . . . . . . . . . . . . . . . . 1254 d3 T# r9 ]8 |' x
Russell P. Darst, Carolina E. Pardo, Santhi Pondugula,
2 C* J0 Q! h  z( MVamsi K. Gangaraju, Nancy H. Nabilsi, Blaine Bartholomew,# A  c$ ^1 E% s5 o; {2 o) |7 e
and Michael P. Kladde" _' w  q2 ]4 a& y1 t
10 Analysis of Stable and Transient Protein–Protein Interactions . . . . . . . . . . . . . . . . . 143
# l, D( D) Z, A* T* u1 J+ q) C: IStephanie Byrum, Sherri K. Smart, Signe Larson, and Alan J. Tackett
+ x; y$ T* {# A0 v11 Monitoring Dynamic Binding of Chromatin Proteins In Vivo
* _  N+ `/ F( |" [$ Bby Fluorescence Recovery After Photobleaching . . . . . . . . . . . . . . . . . . . . . . . . . . . 153! s/ e3 m0 n) f
Florian Mueller, Tatiana S. Karpova, Davide Mazza,/ e! m! j! P  L+ K- ^
and James G. McNally
4 s7 l, [- [" N2 B. m& j12 Monitoring Dynamic Binding of Chromatin Proteins In Vivo by Fluorescence# H+ R; X1 Y( ]2 x/ c* g# [: b
Correlation Spectroscopy and Temporal Image Correlation Spectroscopy . . . . . . . . 177, w+ f( _+ y  D9 [$ D
Davide Mazza, Timothy J. Stasevich, Tatiana S. Karpova,3 E% N& w& C1 a
and James G. McNally! M5 H) R- ~7 d
13 Analysis of Chromatin Structure in Plant Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
! n; I7 Y% y+ f) R$ cMala Singh, Amol Ranjan, Krishan Mohan Rai, Sunil Kumar Singh,
; E) \. J' S& c9 b, r$ d9 E% vVerandra Kumar, Ila Trivedi, Niraj Lodhi, and Samir V. Sawant
; |$ G2 ]8 G6 f( d% B& o( g- M* M14 Analysis of Histones and Histone Variants in Plants. . . . . . . . . . . . . . . . . . . . . . . . . 225
% ?1 O$ x( a) V( }0 f7 N- gIla Trivedi, Krishan Mohan Rai, Sunil Kumar Singh,+ h$ e0 e- @) W3 s
Verandra Kumar, Mala Singh, Amol Ranjan, Niraj Lodhi,% ]* I5 K' R% h% q! u! l
and Samir V. Sawant) U* e, R; D) {
15 Reconstitution of Modified Chromatin Templates for In Vitro
4 M* H$ w% F# A# ]0 z2 p8 j* z' IFunctional Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
$ `7 T: q( G! U, W0 x" hMiyong Yun, Chun Ruan, Jae-Wan Huh, and Bing Li9 f' j3 s" D7 j& n
16 A Defined In Vitro System to Study ATP-Dependent Remodeling
% c9 k5 P5 N% P/ Tof Short Chromatin Fibers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2550 q3 {, Z% |9 w: x8 K6 G( [
Verena K. Maier and Peter B. Becker/ d; n% O+ c; E% D; h
17 In Vitro Reconstitution of In Vivo-Like Nucleosome Positioning; q8 T6 {8 @+ g8 S
on Yeast DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271+ t8 z$ B& v5 V
Christian J. Wippo and Philipp Korber, Y* G1 M) N! C: c: o$ w' L% U: n
18 Activator-Dependent Acetylation of Chromatin Model Systems. . . . . . . . . . . . . . . . 289! C% S, v3 k6 F5 m" V8 B6 s/ v
Heather J. Szerlong and Jeffrey C. Hansen
7 l6 H: V* U( S- O; i. ^6 P19 Mapping Assembly Favored and Remodeled Nucleosome Positions' t4 H7 q6 O& B; X5 w$ F+ T
on Polynucleosomal Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3119 j9 H! b8 T! p1 u$ Q) O
Hillel I. Sims, Chuong D. Pham, and Gavin R. Schnitzler# l8 ~* e9 O( D; }) O
20 Analysis of Changes in Nucleosome Conformation Using Fluorescence
1 k$ C9 [5 s/ }0 W% W4 r! V8 CResonance Energy Transfer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337
" P! `) x# x: E5 FTina Shahian and Geeta J. Narlikar" T& g2 t9 w! U/ [7 F
21 Preparation of Nucleosomes Containing a Specific H2A–H2A Cross-Link2 \- X+ [2 P( T/ g; m9 d
Forming a DNA-Constraining Loop Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351  Z5 `  i* T( P8 ~, l
Ning Liu and Jeffrey J. Hayes
7 Y8 b$ G+ s* i4 g$ p22 Sulfyhydryl-Reactive Site-Directed Cross-Linking as a Method for Probing
9 q$ L. S' G  _the Tetrameric Structure of Histones H3 and H4 . . . . . . . . . . . . . . . . . . . . . . . . . . 373
( D# i7 f6 P6 |" U3 J# ^6 \/ pAndrew Bowman and Tom Owen-Hughes. L* m  k' q, O# X/ e' \
23 Genomic Approaches for Determining Nucleosome Occupancy in Yeast . . . . . . . . . 389
6 [4 Q* Y' w5 ?$ R# yKyle Tsui, Tanja Durbic, Marinella Gebbia, and Corey Nislow
, H) l' i  h$ b0 V. J2 \) ]24 Genome-Wide Approaches to Determining Nucleosome Occupancy$ e1 S) ?, Y1 c( f& V
in Metazoans Using MNase-Seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 413
- o5 H/ A/ n4 v2 }Kairong Cui and Keji Zhao7 z& H4 ?8 u5 P( q! ~
25 Salt Fractionation of Nucleosomes for Genome-Wide Profiling . . . . . . . . . . . . . . . . 421
' R! n# }6 d: }Sheila S. Teves and Steven Henikoff8 a; x$ C  S( i  w9 b/ ^
26 Quantitative Analysis of Genome-Wide Chromatin Remodeling . . . . . . . . . . . . . . . 433( L* M4 A; S* g# C3 R$ I/ }
Songjoon Baek, Myong-Hee Sung, and Gordon L. Hager' G  g/ _: {9 ?. U4 s" i& E2 J" w
27 Computational Analysis of Nucleosome Positioning . . . . . . . . . . . . . . . . . . . . . . . . 443
7 t* W* A1 R6 R! o5 f  yItay Tirosh
/ |# ?" k) N  DIndex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451* P- i* B- k  z3 T9 Z+ t