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Chromatin Remodeling+ w+ Z: ~9 u7 v# r' h( ]
) I7 l2 f" t( q0 s% L8 A3 QContents
- s ?8 f! `' s- n* G( LPreface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
1 ~ G( j3 E7 d3 T: D+ E% g5 EContributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix: ~: T' w5 J$ W
1 Strain Construction and Screening Methods for a Yeast Histone H3/H49 }2 j! t; O# S" i. j
Mutant Library. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
) G, p2 W0 ]. l M, E/ j$ y! TJunbiao Dai and Jef D. Boeke
) a. V& L. x, G3 r" x2 Measuring Dynamic Changes in Histone Modifications and Nucleosome0 Q a) A: q9 h* J* O& S; K4 T$ e1 a
Density during Activated Transcription in Budding Yeast . . . . . . . . . . . . . . . . . . . . 15
9 o! g$ K9 w1 _7 {1 bChhabi K. Govind, Daniel Ginsburg, and Alan G. Hinnebusch$ ?! n; c4 ~1 q. M7 D' {
3 Monitoring the Effects of Chromatin Remodelers on Long-Range
- Y* l; K3 q: {( DInteractions In Vivo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
. ]9 l1 C' T1 a6 L) {$ [Christine M. Kiefer and Ann Dean
- ?9 b, @5 R3 }" B! g4 Measuring Nucleosome Occupancy In Vivo by Micrococcal Nuclease . . . . . . . . . . . 47
- w! @. h* J% i2 ^9 P* SGene O. Bryant
4 @2 z+ m$ ~ r4 U$ D5 Analysis of Nucleosome Positioning Using a Nucleosome-Scanning Assay. . . . . . . . 63
; s$ `4 t) q5 L1 }: ?' iJuan Jose Infante, G. Lynn Law, and Elton T. Young
0 ?0 A5 Q6 D2 M7 ?6 Assaying Chromatin Structure and Remodeling by Restriction Enzyme
/ v2 |: _7 E* a0 b2 V( R3 i! `7 i; |Accessibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 893 H$ T+ N) [. V9 _3 B
Kevin W. Trotter and Trevor K. Archer1 E3 ~" L. j- F. y# H5 g5 D
7 Generation of DNA Circles in Yeast by Inducible Site-Specific$ _% N/ \4 a7 {6 @
Recombination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
9 U$ B4 w$ c, v1 w8 ]3 iMarc R. Gartenberg
# J. R, j l& u4 ]; Z/ V8 An Efficient Purification System for Native Minichromosome; u3 h5 J5 d; h2 g _0 O
from Saccharomyces cerevisiae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
8 M' [) N9 Y: ~' X, c5 j; nAshwin Unnikrishnan, Bungo Akiyoshi, Sue Biggins, and Toshio Tsukiyama8 h" R" O' f. Z( y2 r7 u
9 Simultaneous Single-Molecule Detection of Endogenous C-5 DNA, @% C4 K ~: D; s
Methylation and Chromatin Accessibility Using MAPit. . . . . . . . . . . . . . . . . . . . . . 125
1 u$ q/ v' S. QRussell P. Darst, Carolina E. Pardo, Santhi Pondugula,
0 Q% n7 S2 Z EVamsi K. Gangaraju, Nancy H. Nabilsi, Blaine Bartholomew,% `( G/ ^& p; W5 ~" f
and Michael P. Kladde
P. x' Y! q2 Z* \10 Analysis of Stable and Transient Protein–Protein Interactions . . . . . . . . . . . . . . . . . 143
' F9 m# n2 _: b* D/ K# l. ?0 YStephanie Byrum, Sherri K. Smart, Signe Larson, and Alan J. Tackett* X( ^0 h& u/ V z3 K
11 Monitoring Dynamic Binding of Chromatin Proteins In Vivo
, u7 E$ ~6 b7 _0 {9 Kby Fluorescence Recovery After Photobleaching . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
) r/ A1 R9 C4 EFlorian Mueller, Tatiana S. Karpova, Davide Mazza,
5 g# h4 e- q9 s f/ zand James G. McNally9 Y, B0 S9 i% h( S. c" e3 \
12 Monitoring Dynamic Binding of Chromatin Proteins In Vivo by Fluorescence% Z6 J7 L( z" a% N
Correlation Spectroscopy and Temporal Image Correlation Spectroscopy . . . . . . . . 177; w" o: T( p4 {# |9 v
Davide Mazza, Timothy J. Stasevich, Tatiana S. Karpova,# o5 U9 I" E1 _# e8 c, ^3 @
and James G. McNally) l5 r% l" @1 t8 A" Y
13 Analysis of Chromatin Structure in Plant Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201! s! Q# G! |) A0 Z+ Q8 \' y& a
Mala Singh, Amol Ranjan, Krishan Mohan Rai, Sunil Kumar Singh,8 W; J9 j6 J& l
Verandra Kumar, Ila Trivedi, Niraj Lodhi, and Samir V. Sawant
* m1 K$ V4 o) i( w14 Analysis of Histones and Histone Variants in Plants. . . . . . . . . . . . . . . . . . . . . . . . . 2259 S* c/ o/ _; |; D+ W
Ila Trivedi, Krishan Mohan Rai, Sunil Kumar Singh,, c3 {1 b' O' ~1 I9 P
Verandra Kumar, Mala Singh, Amol Ranjan, Niraj Lodhi,
- m9 b8 n- P8 b. k6 B+ r5 ~and Samir V. Sawant% C% \- f% N5 d6 r! g# f
15 Reconstitution of Modified Chromatin Templates for In Vitro
( r* R3 j3 F( K6 m; L! A3 RFunctional Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2370 w: w" j4 O3 C+ q0 @3 V
Miyong Yun, Chun Ruan, Jae-Wan Huh, and Bing Li
6 `; }: `+ i- J! v$ O% j16 A Defined In Vitro System to Study ATP-Dependent Remodeling
8 B! F, Y# _; Q: ]of Short Chromatin Fibers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
/ g n% h2 L+ @5 e5 LVerena K. Maier and Peter B. Becker
/ O3 `9 {0 h8 S, s# R17 In Vitro Reconstitution of In Vivo-Like Nucleosome Positioning
, N4 ?* c+ Q: c$ G7 U5 mon Yeast DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271) l- c `& M# V# M* }
Christian J. Wippo and Philipp Korber
3 m8 e0 ~9 c$ z18 Activator-Dependent Acetylation of Chromatin Model Systems. . . . . . . . . . . . . . . . 289! V }8 j6 Y! t- X6 V5 L: e
Heather J. Szerlong and Jeffrey C. Hansen) T: g. x% V9 C: t( i# G0 d: f
19 Mapping Assembly Favored and Remodeled Nucleosome Positions
: u" w+ @ p! F& P0 b0 W: C* @on Polynucleosomal Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3113 k7 \3 W2 `9 d+ A
Hillel I. Sims, Chuong D. Pham, and Gavin R. Schnitzler
0 e% D" y$ _3 s: k( \* h! _20 Analysis of Changes in Nucleosome Conformation Using Fluorescence5 j( a6 {" b+ o- l8 f' V
Resonance Energy Transfer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3378 [$ y/ ^! q, Q3 o6 L
Tina Shahian and Geeta J. Narlikar
. X9 P6 j" o3 T2 p. F& H/ [21 Preparation of Nucleosomes Containing a Specific H2A–H2A Cross-Link
$ u/ I, t% {: N+ v+ Z7 M+ n; NForming a DNA-Constraining Loop Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351& V/ N! N: B- O
Ning Liu and Jeffrey J. Hayes* n% z- ?( c4 q" `& J6 f
22 Sulfyhydryl-Reactive Site-Directed Cross-Linking as a Method for Probing
' S2 b, r6 M% i1 X, g+ H- Lthe Tetrameric Structure of Histones H3 and H4 . . . . . . . . . . . . . . . . . . . . . . . . . . 373
, R9 q! ~7 ]2 [$ {/ rAndrew Bowman and Tom Owen-Hughes
) W# y5 u& }5 I2 i23 Genomic Approaches for Determining Nucleosome Occupancy in Yeast . . . . . . . . . 389
6 ]8 {0 B& N( |5 _2 t6 g! TKyle Tsui, Tanja Durbic, Marinella Gebbia, and Corey Nislow/ D: R! Q* k5 E, c# l! D
24 Genome-Wide Approaches to Determining Nucleosome Occupancy
9 i+ ^. H9 b; c$ Win Metazoans Using MNase-Seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4135 \" @4 e+ O3 V' }& u k
Kairong Cui and Keji Zhao2 F2 }5 t b) s# O- `3 L
25 Salt Fractionation of Nucleosomes for Genome-Wide Profiling . . . . . . . . . . . . . . . . 421
+ `: J2 K `0 M) e6 W4 W! ?Sheila S. Teves and Steven Henikoff
/ H3 b3 }, y' Q26 Quantitative Analysis of Genome-Wide Chromatin Remodeling . . . . . . . . . . . . . . . 433% {0 h, M1 q& F8 E8 G) f
Songjoon Baek, Myong-Hee Sung, and Gordon L. Hager
2 \4 ~* g, V3 c3 p6 v$ d+ ^27 Computational Analysis of Nucleosome Positioning . . . . . . . . . . . . . . . . . . . . . . . . 443
. h4 h5 e3 t* n# _, `) OItay Tirosh/ b5 P( t9 Y$ L9 n" ?
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451
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