PDF电子书：Chromatin Remodeling

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Chromatin Remodeling. d. A4 l( U7 W! @- U6 R% s
8 Q# S& @2 G3 x. y- G+ z) S
Contents7 p% o' [9 W! r2 z  }2 }- B% W
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
7 g$ V# P- L( C& s8 f. sContributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
& Z) ?3 Z: Q( I1 Strain Construction and Screening Methods for a Yeast Histone H3/H46 q5 o  G) I4 y6 u+ Q
Mutant Library. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
  A6 w( O- w9 A! aJunbiao Dai and Jef D. Boeke& e9 g0 Z$ G8 G6 `/ a9 [
2 Measuring Dynamic Changes in Histone Modifications and Nucleosome7 t0 Y  a2 G4 Q3 V5 m. y7 O8 G6 [
Density during Activated Transcription in Budding Yeast . . . . . . . . . . . . . . . . . . . . 15( n0 h7 S  {* z- Q
Chhabi K. Govind, Daniel Ginsburg, and Alan G. Hinnebusch  F, P& }% X8 f% E7 \; E
3 Monitoring the Effects of Chromatin Remodelers on Long-Range
8 a. _  Q& b" j( p7 ~% ?Interactions In Vivo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
# {1 N5 q) o1 [2 d/ H% s) \Christine M. Kiefer and Ann Dean7 M( |' N$ ^- n: L9 V
4 Measuring Nucleosome Occupancy In Vivo by Micrococcal Nuclease . . . . . . . . . . . 47
* r4 o; j& F- x' H% O1 ]% ~1 L  ZGene O. Bryant* |& @! U  a3 [5 Y6 u1 y
5 Analysis of Nucleosome Positioning Using a Nucleosome-Scanning Assay. . . . . . . . 635 k) C; k8 ~8 F1 N' U/ U: }: ~* x
Juan Jose Infante, G. Lynn Law, and Elton T. Young
! k) u# A* G/ Z# ?/ K6 _6 Assaying Chromatin Structure and Remodeling by Restriction Enzyme2 ]4 ~5 M, ]% _- [; h, b9 M
Accessibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89$ N- p) h3 |9 r2 e& e6 P
Kevin W. Trotter and Trevor K. Archer  K5 u: w0 [, w0 j6 _( S2 C
7 Generation of DNA Circles in Yeast by Inducible Site-Specific  E0 J3 u5 [" L
Recombination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103  v! }: G& E% u! j. ?) l7 D
Marc R. Gartenberg
+ }4 M! H1 @* i/ v' E8 An Efficient Purification System for Native Minichromosome
# l' Z; r2 j( H: P$ R* h0 U7 g+ Wfrom Saccharomyces cerevisiae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
) N9 T, r) K5 G7 u  _3 C- sAshwin Unnikrishnan, Bungo Akiyoshi, Sue Biggins, and Toshio Tsukiyama
  l; f+ J9 G6 b. O, V% w2 ?8 M9 Simultaneous Single-Molecule Detection of Endogenous C-5 DNA1 Q1 X' u4 |$ }4 l; ]5 l8 Z
Methylation and Chromatin Accessibility Using MAPit. . . . . . . . . . . . . . . . . . . . . . 125
5 @0 o& G7 ?, B- oRussell P. Darst, Carolina E. Pardo, Santhi Pondugula,
( u0 O# B& A$ A9 C! GVamsi K. Gangaraju, Nancy H. Nabilsi, Blaine Bartholomew,2 R. h5 c' ^2 q8 P  ?
and Michael P. Kladde
5 Y" ^4 Q+ C# w) w( C" E) O10 Analysis of Stable and Transient Protein–Protein Interactions . . . . . . . . . . . . . . . . . 143  G2 n# e2 a4 I" p
Stephanie Byrum, Sherri K. Smart, Signe Larson, and Alan J. Tackett
9 i5 W  v& m9 Y, `2 A" h* ^6 T11 Monitoring Dynamic Binding of Chromatin Proteins In Vivo
  f) [3 ]8 O4 n. E0 m5 h- g3 C3 S: Fby Fluorescence Recovery After Photobleaching . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
7 U, ]) K7 a( C0 u- |Florian Mueller, Tatiana S. Karpova, Davide Mazza,
5 r7 o, ]* Q# Pand James G. McNally
' w' h0 Y2 L4 a2 D5 |/ {12 Monitoring Dynamic Binding of Chromatin Proteins In Vivo by Fluorescence' z1 S- H: \' Y% n& {; ^
Correlation Spectroscopy and Temporal Image Correlation Spectroscopy . . . . . . . . 177# w+ m0 t. e# n2 R
Davide Mazza, Timothy J. Stasevich, Tatiana S. Karpova,
/ a! K6 \2 w5 pand James G. McNally' J/ {3 Q7 x6 T
13 Analysis of Chromatin Structure in Plant Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201( _7 V. `, H) Y$ o
Mala Singh, Amol Ranjan, Krishan Mohan Rai, Sunil Kumar Singh,
! j; [$ U7 I) n; u' A. YVerandra Kumar, Ila Trivedi, Niraj Lodhi, and Samir V. Sawant
: z8 _2 @) t3 M+ Y" U$ c14 Analysis of Histones and Histone Variants in Plants. . . . . . . . . . . . . . . . . . . . . . . . . 225
3 [+ O. q  O* h$ q- J: z- _' O; AIla Trivedi, Krishan Mohan Rai, Sunil Kumar Singh,4 D$ p/ E4 L* }2 ?5 Q
Verandra Kumar, Mala Singh, Amol Ranjan, Niraj Lodhi,
9 D( Q7 I/ P9 m+ w6 |7 C8 Hand Samir V. Sawant
% v' w% X, [. n$ ~  K. s15 Reconstitution of Modified Chromatin Templates for In Vitro
3 q5 s4 s# J4 \Functional Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
2 r$ k# w% g# e+ |: h. hMiyong Yun, Chun Ruan, Jae-Wan Huh, and Bing Li: h, M- @7 z7 [
16 A Defined In Vitro System to Study ATP-Dependent Remodeling
8 V0 Y: o$ q7 Oof Short Chromatin Fibers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255# Z  y- M) c. J
Verena K. Maier and Peter B. Becker$ {* @& {$ Q/ k6 J1 \' N: }9 X
17 In Vitro Reconstitution of In Vivo-Like Nucleosome Positioning' w' I4 O) f- j9 U: v
on Yeast DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271, m5 M6 z% N/ h; h! R  D! j
Christian J. Wippo and Philipp Korber1 g# t2 Z; _4 K% d
18 Activator-Dependent Acetylation of Chromatin Model Systems. . . . . . . . . . . . . . . . 289
5 w* f, B3 b! Z- x* O4 O) aHeather J. Szerlong and Jeffrey C. Hansen
. ~; u# [& U' Q( y. i: X19 Mapping Assembly Favored and Remodeled Nucleosome Positions
3 f% x  A# P0 x" \on Polynucleosomal Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3116 G, @- j% P, R6 j* W; k. ^
Hillel I. Sims, Chuong D. Pham, and Gavin R. Schnitzler, ^% f8 E) R& I* c. v, V
20 Analysis of Changes in Nucleosome Conformation Using Fluorescence# n1 ]* Z( O/ C, t' C1 W; n! b  N
Resonance Energy Transfer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337; b% M  E' x- S/ u, @. |( ]
Tina Shahian and Geeta J. Narlikar  j/ Y" q' D1 k
21 Preparation of Nucleosomes Containing a Specific H2A–H2A Cross-Link
8 y- w8 ~# X5 A% E+ T0 I! b8 F5 NForming a DNA-Constraining Loop Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351$ l$ n& B0 x2 `; ?  N  P" f, U
Ning Liu and Jeffrey J. Hayes% l; K: I9 X) s# k. t
22 Sulfyhydryl-Reactive Site-Directed Cross-Linking as a Method for Probing
: G4 E4 g: E) o* b, ]& ]2 G- rthe Tetrameric Structure of Histones H3 and H4 . . . . . . . . . . . . . . . . . . . . . . . . . . 373
, U6 z! V9 X) i2 E5 H! u6 zAndrew Bowman and Tom Owen-Hughes7 W. J( n' a" V- e8 ~( Y  x
23 Genomic Approaches for Determining Nucleosome Occupancy in Yeast . . . . . . . . . 3894 |% K% a. y; N$ @0 q1 L
Kyle Tsui, Tanja Durbic, Marinella Gebbia, and Corey Nislow
5 n8 U' o4 S9 s' U9 F4 W0 o3 [24 Genome-Wide Approaches to Determining Nucleosome Occupancy
1 B( W! U/ S7 {4 Pin Metazoans Using MNase-Seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 413/ T* ]& G; _5 m% m+ u
Kairong Cui and Keji Zhao
' o7 h/ p, r) q4 g: b25 Salt Fractionation of Nucleosomes for Genome-Wide Profiling . . . . . . . . . . . . . . . . 421
6 b8 L5 d- [* n8 PSheila S. Teves and Steven Henikoff2 O9 u: l1 @8 e. w; |- S
26 Quantitative Analysis of Genome-Wide Chromatin Remodeling . . . . . . . . . . . . . . . 433
4 n4 X5 B+ j' z; G2 w$ tSongjoon Baek, Myong-Hee Sung, and Gordon L. Hager
$ D; A+ E: F% J7 f27 Computational Analysis of Nucleosome Positioning . . . . . . . . . . . . . . . . . . . . . . . . 443
% c, t9 A1 C* n& ^" a/ {; gItay Tirosh: Z* ?. a" {. t; N1 ^( Q3 z+ N
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451
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