PDF电子书：Chromatin Remodeling

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Chromatin Remodeling
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9 Y8 }) s- n7 E5 U! \/ DContents) o3 M2 _* E- `9 Q
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
; c$ X3 v8 }" u3 {4 w! f8 ?Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
) k) p5 Y1 m9 o: L$ q1 Strain Construction and Screening Methods for a Yeast Histone H3/H4- m" p+ \4 Y1 D1 h* x" ~6 G
Mutant Library. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 F2 f  W/ A0 Z& n
Junbiao Dai and Jef D. Boeke
$ n/ @0 R8 m% {3 H1 U2 Measuring Dynamic Changes in Histone Modifications and Nucleosome
# v6 ~& }# |% N0 ^Density during Activated Transcription in Budding Yeast . . . . . . . . . . . . . . . . . . . . 15" p. h8 z# c8 [" V  S3 }$ H
Chhabi K. Govind, Daniel Ginsburg, and Alan G. Hinnebusch. I0 e; M  {- ?2 q2 l
3 Monitoring the Effects of Chromatin Remodelers on Long-Range% U6 Q) G( h* y! ?" O
Interactions In Vivo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29& G3 m) h5 u2 A( P6 v
Christine M. Kiefer and Ann Dean5 {. ~# g5 j8 Y  Y( l. [1 i) V( D
4 Measuring Nucleosome Occupancy In Vivo by Micrococcal Nuclease . . . . . . . . . . . 47: j' u1 ^, W9 l7 L; }" K" W! Z
Gene O. Bryant
3 X% m4 ~9 q$ q1 w: L- Q3 o% o5 Analysis of Nucleosome Positioning Using a Nucleosome-Scanning Assay. . . . . . . . 63) W0 s- p7 H; B( Q# c4 |: n
Juan Jose Infante, G. Lynn Law, and Elton T. Young. }4 j: h+ D! ~) K# N
6 Assaying Chromatin Structure and Remodeling by Restriction Enzyme" G1 @8 u  h# P) Q0 a* _; D+ H1 Q
Accessibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
- r% d( t+ i: Y& O5 ]Kevin W. Trotter and Trevor K. Archer
( z' S5 S& }5 U  b% i  c7 Generation of DNA Circles in Yeast by Inducible Site-Specific( N9 v1 a$ i/ x8 A. ]+ E; q+ B; Q) C
Recombination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
) Z9 W" I2 J# Z6 H& iMarc R. Gartenberg0 K" \% _: C( y& }
8 An Efficient Purification System for Native Minichromosome
1 H" _4 H. {  @; P5 y! J6 X0 yfrom Saccharomyces cerevisiae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115) W2 H+ E; S# D/ u  E
Ashwin Unnikrishnan, Bungo Akiyoshi, Sue Biggins, and Toshio Tsukiyama
  `+ [" M" B9 P+ e# C9 Simultaneous Single-Molecule Detection of Endogenous C-5 DNA
' n# N& x, f; F% BMethylation and Chromatin Accessibility Using MAPit. . . . . . . . . . . . . . . . . . . . . . 125
, @/ [  Z7 G! D) X- w6 yRussell P. Darst, Carolina E. Pardo, Santhi Pondugula,  x3 n/ w7 u+ S
Vamsi K. Gangaraju, Nancy H. Nabilsi, Blaine Bartholomew,
4 S8 \% L  L& U( T% wand Michael P. Kladde! p" T, s2 f2 g) s
10 Analysis of Stable and Transient Protein–Protein Interactions . . . . . . . . . . . . . . . . . 143# X$ ^) V( o$ Z8 Y7 V% r1 I& b8 V" t
Stephanie Byrum, Sherri K. Smart, Signe Larson, and Alan J. Tackett
2 i) U; b2 X) Q3 L. S11 Monitoring Dynamic Binding of Chromatin Proteins In Vivo
2 y1 Y# s2 \$ c# v7 w* W- Yby Fluorescence Recovery After Photobleaching . . . . . . . . . . . . . . . . . . . . . . . . . . . 153- m7 y. k% N2 g% C# M
Florian Mueller, Tatiana S. Karpova, Davide Mazza,. U. g& s1 k) i7 b
and James G. McNally; V& `. [: }4 |+ K" c# s: K
12 Monitoring Dynamic Binding of Chromatin Proteins In Vivo by Fluorescence
& `3 d0 C0 f0 g$ ICorrelation Spectroscopy and Temporal Image Correlation Spectroscopy . . . . . . . . 177- \$ Q* ]# a4 X6 X2 G
Davide Mazza, Timothy J. Stasevich, Tatiana S. Karpova,
2 J0 B: H  d& Q, V9 _8 q3 }- Tand James G. McNally
; Y6 `$ B5 s2 d9 j13 Analysis of Chromatin Structure in Plant Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
  {: S$ {8 c6 _/ l4 bMala Singh, Amol Ranjan, Krishan Mohan Rai, Sunil Kumar Singh,
$ m, W9 m6 l8 l% b# p0 o  s5 DVerandra Kumar, Ila Trivedi, Niraj Lodhi, and Samir V. Sawant" t  c; F0 T, n7 t* V5 W, f/ C$ r5 q
14 Analysis of Histones and Histone Variants in Plants. . . . . . . . . . . . . . . . . . . . . . . . . 2256 @% j  n- ^& s# c- U
Ila Trivedi, Krishan Mohan Rai, Sunil Kumar Singh,5 K* g* \, n. V) C1 a, M3 V
Verandra Kumar, Mala Singh, Amol Ranjan, Niraj Lodhi,( b. z; S0 Q& j
and Samir V. Sawant
: c! x/ i$ ~" ~" ~' m6 p15 Reconstitution of Modified Chromatin Templates for In Vitro
2 m2 g1 @6 O- v/ u% R# c/ [Functional Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237( A- `1 r: B6 x/ R4 [4 u
Miyong Yun, Chun Ruan, Jae-Wan Huh, and Bing Li
, o  q9 H9 W. g7 c16 A Defined In Vitro System to Study ATP-Dependent Remodeling# v( G1 w6 S2 w6 P4 C- Q
of Short Chromatin Fibers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
7 ]0 i! T! u9 Q9 L$ ?9 F1 RVerena K. Maier and Peter B. Becker- K. y8 w. b3 h/ @( L
17 In Vitro Reconstitution of In Vivo-Like Nucleosome Positioning$ q, s& r$ V. g( C
on Yeast DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2716 a- v: X- _, z) z8 Z! Q* C
Christian J. Wippo and Philipp Korber
# p( m3 z  }8 z: ]  N18 Activator-Dependent Acetylation of Chromatin Model Systems. . . . . . . . . . . . . . . . 2893 l2 l6 R, I9 n8 V7 S, a1 N1 E* ~
Heather J. Szerlong and Jeffrey C. Hansen
& Y1 P: K  T/ c, y3 y( M4 Q19 Mapping Assembly Favored and Remodeled Nucleosome Positions
6 D9 y4 R4 ?- F2 |on Polynucleosomal Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311
: j; ~3 O5 ^% m# nHillel I. Sims, Chuong D. Pham, and Gavin R. Schnitzler1 t6 R3 K- A# j2 _% u
20 Analysis of Changes in Nucleosome Conformation Using Fluorescence2 O; [# i9 e! M/ V) x
Resonance Energy Transfer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337
, z3 X: a5 c9 T+ Y5 o$ ^$ n" uTina Shahian and Geeta J. Narlikar
, ~1 _. j# a8 t4 D2 S6 l) }, g21 Preparation of Nucleosomes Containing a Specific H2A–H2A Cross-Link$ X# k) G# X3 A: q, P6 y
Forming a DNA-Constraining Loop Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351
5 k+ ?) H. R# i% P7 [Ning Liu and Jeffrey J. Hayes
+ I6 r3 r' X5 q/ u  P  @4 {" y22 Sulfyhydryl-Reactive Site-Directed Cross-Linking as a Method for Probing
! v8 Z" p7 T1 O9 h# J$ Ethe Tetrameric Structure of Histones H3 and H4 . . . . . . . . . . . . . . . . . . . . . . . . . . 373
* v# s" U- m6 P5 J% N$ FAndrew Bowman and Tom Owen-Hughes8 g  @  G5 J$ a: E  v3 v7 z2 ]
23 Genomic Approaches for Determining Nucleosome Occupancy in Yeast . . . . . . . . . 3890 w; @/ U6 y- Q8 P
Kyle Tsui, Tanja Durbic, Marinella Gebbia, and Corey Nislow
3 ~; i+ [* Y; B6 i5 q* ?5 J24 Genome-Wide Approaches to Determining Nucleosome Occupancy
& ]% p! a+ d9 j! }3 u8 C* O) pin Metazoans Using MNase-Seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4134 k1 T# L2 t3 ~% L3 `+ x
Kairong Cui and Keji Zhao
. J7 d4 [. ^4 ?: M25 Salt Fractionation of Nucleosomes for Genome-Wide Profiling . . . . . . . . . . . . . . . . 421/ j' Y- t+ J1 A8 o/ C* h
Sheila S. Teves and Steven Henikoff
$ m4 f8 N1 i: H7 Q% a26 Quantitative Analysis of Genome-Wide Chromatin Remodeling . . . . . . . . . . . . . . . 433! K/ |( z1 d2 S
Songjoon Baek, Myong-Hee Sung, and Gordon L. Hager
) V' n. d0 z" U; e27 Computational Analysis of Nucleosome Positioning . . . . . . . . . . . . . . . . . . . . . . . . 443
% {4 x: }# k) \, O. `Itay Tirosh
. \9 |% g5 I0 ~( b% {' rIndex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451  H( J! Y, ]7 K* U' h7 k" p2 R

aakkaa

说的真有道理啊！

mk990

谢谢分享了!  

Diary

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yunshu

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Kuo

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HongHong

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netlover

越办越好~~~~~~~~~`  

tian2006

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