PDF电子书：Chromatin Remodeling

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Chromatin Remodeling/ m) F; N5 I* i7 c
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Contents
& H8 L) s2 `# h+ \0 l  i9 PPreface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
* l, t. i9 `4 s( W4 OContributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix' Y6 y+ Y1 J: G$ ]5 _0 H
1 Strain Construction and Screening Methods for a Yeast Histone H3/H4) F( W* y1 @  r( |. `
Mutant Library. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 }$ v1 k' @' P* H* d' B3 l
Junbiao Dai and Jef D. Boeke6 O9 A: i) K& K- N7 `
2 Measuring Dynamic Changes in Histone Modifications and Nucleosome, h. y) F& C3 ~7 z
Density during Activated Transcription in Budding Yeast . . . . . . . . . . . . . . . . . . . . 15+ k! y: O. `- a4 r
Chhabi K. Govind, Daniel Ginsburg, and Alan G. Hinnebusch
' F- M' C1 s3 C! s& i3 Monitoring the Effects of Chromatin Remodelers on Long-Range1 I1 ?0 p9 @! ^1 l0 g& ~
Interactions In Vivo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
( \' r; z3 A' H9 h& p" PChristine M. Kiefer and Ann Dean
" q7 s: g  T& |) P* m% o4 Measuring Nucleosome Occupancy In Vivo by Micrococcal Nuclease . . . . . . . . . . . 47
  C$ ~: ^# `, X9 n9 _" ?Gene O. Bryant4 G6 u. b$ Q- T8 ~# r
5 Analysis of Nucleosome Positioning Using a Nucleosome-Scanning Assay. . . . . . . . 63
! r$ f# p* U' y" ?2 @$ Z5 fJuan Jose Infante, G. Lynn Law, and Elton T. Young
$ J1 Z, D- }5 X# h9 |6 Assaying Chromatin Structure and Remodeling by Restriction Enzyme! k$ n+ Q8 J2 W! R0 @3 V. \* G3 \
Accessibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 899 H! c, a( A. e- |5 d
Kevin W. Trotter and Trevor K. Archer: E6 k6 d# M3 a5 n  }
7 Generation of DNA Circles in Yeast by Inducible Site-Specific/ Y0 U" n! {5 w; T- O
Recombination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1038 K- p8 I/ @  Y$ w. x2 b& }
Marc R. Gartenberg
5 o$ j2 {$ }- `8 An Efficient Purification System for Native Minichromosome+ _( c  i' Q+ t2 o  j) I; s
from Saccharomyces cerevisiae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
  `/ R! B, w: o. j  G1 n$ O- JAshwin Unnikrishnan, Bungo Akiyoshi, Sue Biggins, and Toshio Tsukiyama
1 t9 w3 E# f0 v9 u2 Z9 Simultaneous Single-Molecule Detection of Endogenous C-5 DNA
, y$ _5 r- y/ D  ^Methylation and Chromatin Accessibility Using MAPit. . . . . . . . . . . . . . . . . . . . . . 125$ c* c* l( R5 ^; T, w
Russell P. Darst, Carolina E. Pardo, Santhi Pondugula,
+ J) k+ b7 U+ r2 g: @. b* ?9 ]- n6 |/ OVamsi K. Gangaraju, Nancy H. Nabilsi, Blaine Bartholomew,
/ o- ~  Q* `' D# R  Rand Michael P. Kladde( P0 s0 I( l" b" O1 Z* {% e% y4 `
10 Analysis of Stable and Transient Protein–Protein Interactions . . . . . . . . . . . . . . . . . 143
  z& R& N$ Y" s* R! g* X. EStephanie Byrum, Sherri K. Smart, Signe Larson, and Alan J. Tackett( d$ x7 g6 l+ r. k( @: u/ S
11 Monitoring Dynamic Binding of Chromatin Proteins In Vivo
- j- P  [5 \3 J. Tby Fluorescence Recovery After Photobleaching . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
6 }  \5 o4 f9 k- xFlorian Mueller, Tatiana S. Karpova, Davide Mazza,
+ \/ E9 d, y8 [0 `7 Fand James G. McNally
+ D1 T* w( |- S' o12 Monitoring Dynamic Binding of Chromatin Proteins In Vivo by Fluorescence
- H$ k  `" P3 J8 F$ MCorrelation Spectroscopy and Temporal Image Correlation Spectroscopy . . . . . . . . 177
# e" Q- A  g! X* s& P3 hDavide Mazza, Timothy J. Stasevich, Tatiana S. Karpova,% l! G  b: I- o
and James G. McNally
  d, n# }* _' S( u6 k; F, V13 Analysis of Chromatin Structure in Plant Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201+ f3 G. u: J+ w% A+ {
Mala Singh, Amol Ranjan, Krishan Mohan Rai, Sunil Kumar Singh,
. q2 o) g# K! U7 B+ g: D, DVerandra Kumar, Ila Trivedi, Niraj Lodhi, and Samir V. Sawant
1 N2 R6 j9 n4 m1 F# [14 Analysis of Histones and Histone Variants in Plants. . . . . . . . . . . . . . . . . . . . . . . . . 225
* F3 v; Z. k- i; t6 A1 v/ F  UIla Trivedi, Krishan Mohan Rai, Sunil Kumar Singh,
8 a( U8 a9 n! E0 R+ J* GVerandra Kumar, Mala Singh, Amol Ranjan, Niraj Lodhi,
1 Y4 q& ?9 X4 n" Y2 q. tand Samir V. Sawant
3 [4 A9 ?& H) D15 Reconstitution of Modified Chromatin Templates for In Vitro
! X' n2 K" d7 v6 kFunctional Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
* o& |' P0 [+ Y5 |9 |1 D, _: ?8 m# k% PMiyong Yun, Chun Ruan, Jae-Wan Huh, and Bing Li
& S7 Y2 K4 \& d6 J! b, \1 F8 i16 A Defined In Vitro System to Study ATP-Dependent Remodeling
1 M$ N5 Y) O2 j3 ]% l$ }5 _0 Oof Short Chromatin Fibers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255; s; N6 V- _9 _( D4 Y
Verena K. Maier and Peter B. Becker
% O: E/ C+ q+ d* G! a17 In Vitro Reconstitution of In Vivo-Like Nucleosome Positioning* B* r) \. Q9 b) O% Y
on Yeast DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271
+ a7 r9 x/ x6 B+ E+ o" iChristian J. Wippo and Philipp Korber) W% v5 H, u; b1 n
18 Activator-Dependent Acetylation of Chromatin Model Systems. . . . . . . . . . . . . . . . 289
  n6 M6 J; e, C9 P+ y  J+ f( q; LHeather J. Szerlong and Jeffrey C. Hansen
+ t8 a0 B% A# e( e& k19 Mapping Assembly Favored and Remodeled Nucleosome Positions
6 |" y* U$ \% Y3 i/ y9 Lon Polynucleosomal Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311
) F+ L: e' k! g8 c$ j4 eHillel I. Sims, Chuong D. Pham, and Gavin R. Schnitzler3 q6 ^- n' D* `- U! \. [
20 Analysis of Changes in Nucleosome Conformation Using Fluorescence6 f' F: I5 E1 S- a) r
Resonance Energy Transfer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337
) }0 @) ?! b; xTina Shahian and Geeta J. Narlikar* k% }; G/ I' x+ B8 V
21 Preparation of Nucleosomes Containing a Specific H2A–H2A Cross-Link% H" q2 d8 a* c# X) a8 l5 B! z
Forming a DNA-Constraining Loop Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351
6 p7 X) Y% L9 U0 fNing Liu and Jeffrey J. Hayes. J% S( G& R* J  p, k+ t( v
22 Sulfyhydryl-Reactive Site-Directed Cross-Linking as a Method for Probing9 R! O+ W- m! h
the Tetrameric Structure of Histones H3 and H4 . . . . . . . . . . . . . . . . . . . . . . . . . . 3737 |4 }$ w7 ]  Q/ Z6 X+ v8 |
Andrew Bowman and Tom Owen-Hughes
: P' i/ t  F3 d- r" B, P23 Genomic Approaches for Determining Nucleosome Occupancy in Yeast . . . . . . . . . 389
) D2 s6 G, }* w8 m  W5 XKyle Tsui, Tanja Durbic, Marinella Gebbia, and Corey Nislow. a! G5 B2 V4 z# J  ?
24 Genome-Wide Approaches to Determining Nucleosome Occupancy
, g* h- o! R" e5 xin Metazoans Using MNase-Seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4130 S( m) i& C6 h
Kairong Cui and Keji Zhao
) J' \, A$ @1 R25 Salt Fractionation of Nucleosomes for Genome-Wide Profiling . . . . . . . . . . . . . . . . 421
4 r; d$ f8 ~- u5 u! p: gSheila S. Teves and Steven Henikoff
8 G2 K* _: ~0 v; A! S& f5 X2 L26 Quantitative Analysis of Genome-Wide Chromatin Remodeling . . . . . . . . . . . . . . . 433
/ X. J& f3 j/ kSongjoon Baek, Myong-Hee Sung, and Gordon L. Hager
4 U+ P$ Q, I# @! Z6 O- b27 Computational Analysis of Nucleosome Positioning . . . . . . . . . . . . . . . . . . . . . . . . 443
" [2 E7 d9 t8 aItay Tirosh: x: I. M$ w$ D; J3 J8 n8 P2 F
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451: \. _) `. y% Z4 t( C3 j

daiminzh

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biobio

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bluesuns

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