PDF电子书：Chromatin Remodeling

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Chromatin Remodeling, O, n- w# V8 ]; N% c7 L

* n2 |7 p) I3 U9 o9 xContents
* E/ i" I# b( c. s* ]$ D8 ^Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v* ?# S6 L+ r) [7 H) i
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
3 v4 B! \% V/ ~: e- ~9 }8 r1 Strain Construction and Screening Methods for a Yeast Histone H3/H4
# j- G9 D1 G" [/ B: ~5 k! HMutant Library. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
3 b7 a# U) O( j8 ^Junbiao Dai and Jef D. Boeke& `# z, f& o0 b% J+ ~
2 Measuring Dynamic Changes in Histone Modifications and Nucleosome
  a4 y6 E- u0 `3 WDensity during Activated Transcription in Budding Yeast . . . . . . . . . . . . . . . . . . . . 15
2 [& l( k2 ?' Z) p8 g  rChhabi K. Govind, Daniel Ginsburg, and Alan G. Hinnebusch
  z. f$ o4 b1 y" P4 U6 k# _3 Monitoring the Effects of Chromatin Remodelers on Long-Range$ x3 d0 K, [  G# x- L
Interactions In Vivo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
% u% o; m* a3 h% F+ u, l+ cChristine M. Kiefer and Ann Dean
. C+ T. p3 b  n5 y7 G! y4 W* G4 Measuring Nucleosome Occupancy In Vivo by Micrococcal Nuclease . . . . . . . . . . . 47
8 J& d0 n) R4 y; pGene O. Bryant3 w. c. w+ i$ e7 ]
5 Analysis of Nucleosome Positioning Using a Nucleosome-Scanning Assay. . . . . . . . 633 Z) U. }: O4 ^
Juan Jose Infante, G. Lynn Law, and Elton T. Young
3 o7 y* ]4 q, s: M0 Z. T. j6 Assaying Chromatin Structure and Remodeling by Restriction Enzyme
0 @+ ]4 A8 O0 sAccessibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
. q4 B- o$ _  g: R0 ?Kevin W. Trotter and Trevor K. Archer
9 m7 r1 @( ^6 {/ w4 G+ {7 Generation of DNA Circles in Yeast by Inducible Site-Specific( q' ]( ~/ |+ |. V5 V6 ^) F  T- k
Recombination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
& C5 s3 W+ _, D% @" M5 x* s- MMarc R. Gartenberg
: p. d+ C1 I2 ?, y8 An Efficient Purification System for Native Minichromosome" s7 z' @5 `5 @
from Saccharomyces cerevisiae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115  J$ h+ F9 y/ Q3 }4 k+ q7 {
Ashwin Unnikrishnan, Bungo Akiyoshi, Sue Biggins, and Toshio Tsukiyama
, R3 H; M! h$ ^' B/ J9 Simultaneous Single-Molecule Detection of Endogenous C-5 DNA  g+ u* j9 S$ x! [( P
Methylation and Chromatin Accessibility Using MAPit. . . . . . . . . . . . . . . . . . . . . . 125
/ v$ k7 J; p  d( l" mRussell P. Darst, Carolina E. Pardo, Santhi Pondugula,5 Z4 O6 r: u# }* {; G
Vamsi K. Gangaraju, Nancy H. Nabilsi, Blaine Bartholomew,) b0 B& b. a: ?3 s( c. S
and Michael P. Kladde; C4 e  }6 ]4 m- |% ~
10 Analysis of Stable and Transient Protein–Protein Interactions . . . . . . . . . . . . . . . . . 143
$ z' w# G% ?: f$ \; HStephanie Byrum, Sherri K. Smart, Signe Larson, and Alan J. Tackett5 b  ~: }6 N' }, V. w6 @! w
11 Monitoring Dynamic Binding of Chromatin Proteins In Vivo
  O1 r+ _, S3 n4 s  Bby Fluorescence Recovery After Photobleaching . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
; u; c) G: {7 hFlorian Mueller, Tatiana S. Karpova, Davide Mazza,
& i' I# Q! ?+ Land James G. McNally& L/ ^/ B; J2 }: N3 z$ M6 p& V
12 Monitoring Dynamic Binding of Chromatin Proteins In Vivo by Fluorescence
" y. w# f  ^7 |; F2 y$ _Correlation Spectroscopy and Temporal Image Correlation Spectroscopy . . . . . . . . 1778 {, J$ Z3 p1 m0 Q# k: d: X& f0 C
Davide Mazza, Timothy J. Stasevich, Tatiana S. Karpova,
, T) s5 B7 G: Q& D* a8 t9 `+ sand James G. McNally  ]+ k& l* V9 q6 Y1 D) n
13 Analysis of Chromatin Structure in Plant Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
) `& i7 e4 s1 ?9 U- V9 AMala Singh, Amol Ranjan, Krishan Mohan Rai, Sunil Kumar Singh,3 D. s; T3 P3 [/ O0 \/ m4 O
Verandra Kumar, Ila Trivedi, Niraj Lodhi, and Samir V. Sawant5 Q7 z! I, s; W8 R2 V  z
14 Analysis of Histones and Histone Variants in Plants. . . . . . . . . . . . . . . . . . . . . . . . . 225
6 f" c. o; G. s- x) c, mIla Trivedi, Krishan Mohan Rai, Sunil Kumar Singh,, h" z# `* f  q! W5 Z( p- S
Verandra Kumar, Mala Singh, Amol Ranjan, Niraj Lodhi,) }" T  J$ o: e. [; O
and Samir V. Sawant% r! y4 M* K: t8 O
15 Reconstitution of Modified Chromatin Templates for In Vitro. Q; [8 k9 a3 P. s* F: e0 A
Functional Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2375 t7 }8 H' Y) B" U4 e" N
Miyong Yun, Chun Ruan, Jae-Wan Huh, and Bing Li+ V" a# a+ u: N) J. J
16 A Defined In Vitro System to Study ATP-Dependent Remodeling( j) l1 _# L& N
of Short Chromatin Fibers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
4 h. J  r9 V  M) b9 vVerena K. Maier and Peter B. Becker
* E+ l, l" E' T) G17 In Vitro Reconstitution of In Vivo-Like Nucleosome Positioning
3 {' l0 `8 c. y8 V" _, _on Yeast DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271: e; u3 o1 `  I1 u7 @% B. @2 _" p
Christian J. Wippo and Philipp Korber: E3 I1 Y$ t, r# z
18 Activator-Dependent Acetylation of Chromatin Model Systems. . . . . . . . . . . . . . . . 289/ `, P% b! O+ k5 ]+ M; p+ Z
Heather J. Szerlong and Jeffrey C. Hansen7 ]8 \+ D4 F  t$ w! M
19 Mapping Assembly Favored and Remodeled Nucleosome Positions% I! p; Y1 g  [# e+ h- m1 i
on Polynucleosomal Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311- F' ]5 N" e& R4 o; W3 y5 m
Hillel I. Sims, Chuong D. Pham, and Gavin R. Schnitzler" J$ B9 e  s( M# D1 |
20 Analysis of Changes in Nucleosome Conformation Using Fluorescence: }% O/ r3 R5 {
Resonance Energy Transfer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3375 }" @6 W: B& l; i$ g
Tina Shahian and Geeta J. Narlikar
7 ~% F) ^7 Z2 }, [* t21 Preparation of Nucleosomes Containing a Specific H2A–H2A Cross-Link% S# w" M8 S& z' _) ^
Forming a DNA-Constraining Loop Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351
8 Q6 r# T6 ^& u( XNing Liu and Jeffrey J. Hayes6 r8 @$ S6 d# t/ H8 G
22 Sulfyhydryl-Reactive Site-Directed Cross-Linking as a Method for Probing
% d  _8 x8 d6 Kthe Tetrameric Structure of Histones H3 and H4 . . . . . . . . . . . . . . . . . . . . . . . . . . 3736 @% p5 i  y' b$ P/ p! b) E
Andrew Bowman and Tom Owen-Hughes3 j. t$ S" K) {. T1 |
23 Genomic Approaches for Determining Nucleosome Occupancy in Yeast . . . . . . . . . 3892 H1 u9 x, i4 `* x
Kyle Tsui, Tanja Durbic, Marinella Gebbia, and Corey Nislow3 f. r5 ^" Q0 B8 o0 l. e7 Q9 j
24 Genome-Wide Approaches to Determining Nucleosome Occupancy- ^1 g1 A* Y8 k0 x) h
in Metazoans Using MNase-Seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 413/ Y- a0 w9 `" ?( c! v* I
Kairong Cui and Keji Zhao
' ^, I* I$ }, Z25 Salt Fractionation of Nucleosomes for Genome-Wide Profiling . . . . . . . . . . . . . . . . 421. w# b) l9 }; L# V  e7 Z" S- }7 }/ w
Sheila S. Teves and Steven Henikoff# |1 M0 Z9 R( @
26 Quantitative Analysis of Genome-Wide Chromatin Remodeling . . . . . . . . . . . . . . . 433
) e6 f6 a- M" }& Q8 F' HSongjoon Baek, Myong-Hee Sung, and Gordon L. Hager
% ^: L' v9 |4 B- U$ S7 x, B+ ]27 Computational Analysis of Nucleosome Positioning . . . . . . . . . . . . . . . . . . . . . . . . 443, D' P2 O* _, A( B% N4 O
Itay Tirosh/ a+ W8 _4 B. }: x
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451
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biobio

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bluesuns

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