PDF电子书：Chromatin Remodeling

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Chromatin Remodeling
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Contents
8 x, q& b7 G7 q' w# yPreface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
! E1 k5 v# z# w1 g8 q; V  HContributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
+ V% ]4 K% d! \& i! l9 q6 R1 Strain Construction and Screening Methods for a Yeast Histone H3/H4
7 ]: F1 n1 h- q+ I8 UMutant Library. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
) F! Q" v4 M* z# RJunbiao Dai and Jef D. Boeke/ }* q) k4 n1 D8 H% R1 [- }% I( w8 l
2 Measuring Dynamic Changes in Histone Modifications and Nucleosome4 S- r! ?" X, n% U+ M
Density during Activated Transcription in Budding Yeast . . . . . . . . . . . . . . . . . . . . 15
( t& s: k4 R% ^6 R4 nChhabi K. Govind, Daniel Ginsburg, and Alan G. Hinnebusch
) v7 Z& \0 G9 E. O1 w! `( p3 Monitoring the Effects of Chromatin Remodelers on Long-Range
7 u- T* J5 P, O; H6 nInteractions In Vivo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 298 W) e, _. v* M3 N! Z% Q1 O8 ^
Christine M. Kiefer and Ann Dean
' V$ l# |7 u2 X, s: x  P4 l4 Measuring Nucleosome Occupancy In Vivo by Micrococcal Nuclease . . . . . . . . . . . 474 U0 I6 ^. v7 j. @$ {' v
Gene O. Bryant( A: x4 B+ a& }. R$ Q
5 Analysis of Nucleosome Positioning Using a Nucleosome-Scanning Assay. . . . . . . . 63
+ z' t) T) Q) t2 DJuan Jose Infante, G. Lynn Law, and Elton T. Young
: B7 J  i! ^' p1 T1 T4 D, _6 Assaying Chromatin Structure and Remodeling by Restriction Enzyme' F! A0 q7 B% Y
Accessibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89+ i7 H# Q# ?+ S6 M
Kevin W. Trotter and Trevor K. Archer
6 X8 \& x* ^& V4 k1 k- G7 Generation of DNA Circles in Yeast by Inducible Site-Specific
" m( j' q, j  HRecombination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
) q' [! m' ~, j2 G2 f, qMarc R. Gartenberg) G7 r5 X8 P/ N+ h. D" S
8 An Efficient Purification System for Native Minichromosome6 P7 Q* X' T, S( v
from Saccharomyces cerevisiae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
  `0 _9 a6 h' l! p$ RAshwin Unnikrishnan, Bungo Akiyoshi, Sue Biggins, and Toshio Tsukiyama! c& @2 P( e6 n
9 Simultaneous Single-Molecule Detection of Endogenous C-5 DNA/ C2 U) l$ n( }& w1 ^
Methylation and Chromatin Accessibility Using MAPit. . . . . . . . . . . . . . . . . . . . . . 125
% [  V8 N/ u% L; Q6 f  E7 k  LRussell P. Darst, Carolina E. Pardo, Santhi Pondugula,7 ^# a. V8 [; s
Vamsi K. Gangaraju, Nancy H. Nabilsi, Blaine Bartholomew," M( D9 W6 K' G9 N; E2 v) y9 S+ f
and Michael P. Kladde6 ~4 z. G/ H9 ^( b' D  v. g
10 Analysis of Stable and Transient Protein–Protein Interactions . . . . . . . . . . . . . . . . . 143
# |! Q( u1 }5 H. ?Stephanie Byrum, Sherri K. Smart, Signe Larson, and Alan J. Tackett
% f6 F2 y7 T  x, D" r0 l& T5 h/ ^11 Monitoring Dynamic Binding of Chromatin Proteins In Vivo0 z) u* O7 ^2 E2 e. T" K" L2 D
by Fluorescence Recovery After Photobleaching . . . . . . . . . . . . . . . . . . . . . . . . . . . 153# H; p$ m( K5 ]: _
Florian Mueller, Tatiana S. Karpova, Davide Mazza,
6 f. p0 d  \1 R: [' Eand James G. McNally
& i# h/ k; r: g: ^3 @) R12 Monitoring Dynamic Binding of Chromatin Proteins In Vivo by Fluorescence" f+ G+ H# s+ w1 }, M# j, L
Correlation Spectroscopy and Temporal Image Correlation Spectroscopy . . . . . . . . 177
# _& N# `- Z% x' `  U% LDavide Mazza, Timothy J. Stasevich, Tatiana S. Karpova,& c; z' A) y) t3 K
and James G. McNally
1 C$ f) L3 [, B5 j13 Analysis of Chromatin Structure in Plant Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2013 ?! M7 ?* x- C" w1 o9 l6 t3 ^
Mala Singh, Amol Ranjan, Krishan Mohan Rai, Sunil Kumar Singh,
" ~1 Z; M1 ]0 f4 e3 wVerandra Kumar, Ila Trivedi, Niraj Lodhi, and Samir V. Sawant1 }! o' i- }8 L( n2 q, q' l
14 Analysis of Histones and Histone Variants in Plants. . . . . . . . . . . . . . . . . . . . . . . . . 225$ J) j( d9 Z, I  W5 n; Z* a
Ila Trivedi, Krishan Mohan Rai, Sunil Kumar Singh,
3 v% h3 O; E$ V4 g. n4 |6 U( GVerandra Kumar, Mala Singh, Amol Ranjan, Niraj Lodhi,
6 J/ r. g1 B) J% @9 \/ xand Samir V. Sawant/ L! a" |4 q4 ?* y4 ]
15 Reconstitution of Modified Chromatin Templates for In Vitro
' T3 Y5 b4 J+ v4 x$ z/ s6 pFunctional Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
- t3 N) }+ A# G1 _# lMiyong Yun, Chun Ruan, Jae-Wan Huh, and Bing Li, a  x: `3 G5 h
16 A Defined In Vitro System to Study ATP-Dependent Remodeling
+ p* l, W) o( F- g4 ?* H" V4 Y$ [of Short Chromatin Fibers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
4 U! r6 f8 h% y1 }6 U# E7 zVerena K. Maier and Peter B. Becker2 }4 v: i8 t4 G; {, B2 ]- l4 S
17 In Vitro Reconstitution of In Vivo-Like Nucleosome Positioning, w* e: A* Z1 o0 _! }+ E' C
on Yeast DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271
! Y$ ?) b+ ~. S; N4 Z. }+ J9 l( mChristian J. Wippo and Philipp Korber
+ |. B3 b/ v! n1 v2 ?, t6 t8 y18 Activator-Dependent Acetylation of Chromatin Model Systems. . . . . . . . . . . . . . . . 289+ g1 ?3 G& c, E9 D5 {
Heather J. Szerlong and Jeffrey C. Hansen
/ x6 w  P5 `8 c9 O3 c# l9 d5 v  t19 Mapping Assembly Favored and Remodeled Nucleosome Positions
5 h6 K* b5 C. e& o/ e2 x2 jon Polynucleosomal Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311( c' U6 D/ n/ U. o5 }, x
Hillel I. Sims, Chuong D. Pham, and Gavin R. Schnitzler3 R) G& K% |# |& P7 |
20 Analysis of Changes in Nucleosome Conformation Using Fluorescence
6 g/ ]: a7 L4 j4 b! PResonance Energy Transfer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337
, T6 c5 E% c' r, _+ p& F& ]Tina Shahian and Geeta J. Narlikar% ?# z! J4 p0 d* o4 i1 f+ t' ^
21 Preparation of Nucleosomes Containing a Specific H2A–H2A Cross-Link9 f/ E: I# D" N( Q2 `1 ?! E
Forming a DNA-Constraining Loop Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351. K9 K( ?! u: X7 G1 r
Ning Liu and Jeffrey J. Hayes
4 f4 n, s+ Z1 T; z1 o22 Sulfyhydryl-Reactive Site-Directed Cross-Linking as a Method for Probing
1 _9 x9 ]7 n( r* G- i0 rthe Tetrameric Structure of Histones H3 and H4 . . . . . . . . . . . . . . . . . . . . . . . . . . 373
9 M" K& n" j1 S! FAndrew Bowman and Tom Owen-Hughes) [& b) b- B  V. @
23 Genomic Approaches for Determining Nucleosome Occupancy in Yeast . . . . . . . . . 389
& x* J$ Q3 R' _% U# \; lKyle Tsui, Tanja Durbic, Marinella Gebbia, and Corey Nislow
( k0 k0 U- g. K+ ^24 Genome-Wide Approaches to Determining Nucleosome Occupancy  t  p- g' x+ L& q1 f/ l# Z) F+ z
in Metazoans Using MNase-Seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 413
6 L, l8 K* n7 L1 Y. TKairong Cui and Keji Zhao
8 z2 w$ N% u  y, |* D25 Salt Fractionation of Nucleosomes for Genome-Wide Profiling . . . . . . . . . . . . . . . . 421
1 F2 _+ i' u( V3 f% }! h# USheila S. Teves and Steven Henikoff
/ j0 Z; l0 y: a9 _, K' F26 Quantitative Analysis of Genome-Wide Chromatin Remodeling . . . . . . . . . . . . . . . 433
7 E+ t# q/ q- ?7 p) }! M7 b) {Songjoon Baek, Myong-Hee Sung, and Gordon L. Hager8 Y' b) Q' B* Z1 F( g# D
27 Computational Analysis of Nucleosome Positioning . . . . . . . . . . . . . . . . . . . . . . . . 443
. ^( V7 y- w+ {. e# QItay Tirosh
# n3 E; o; z6 @+ zIndex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451
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biobio

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bluesuns

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