PDF电子书：Chromatin Remodeling

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Chromatin Remodeling
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Contents, o! D& V0 K  ^8 G
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v( v  b2 n! t7 y# L8 ?  t; J# B$ ~. \
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
' Q# F7 |+ ?2 p1 Strain Construction and Screening Methods for a Yeast Histone H3/H4# Y1 R3 Z( W, t
Mutant Library. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 ~6 Y; D- a+ j; I( z
Junbiao Dai and Jef D. Boeke
2 T/ f6 ]& y; D; s7 M2 Measuring Dynamic Changes in Histone Modifications and Nucleosome
, @; {2 n7 A: m6 h" V* S7 BDensity during Activated Transcription in Budding Yeast . . . . . . . . . . . . . . . . . . . . 15
1 ^% o& R7 Z6 B( sChhabi K. Govind, Daniel Ginsburg, and Alan G. Hinnebusch" q# a: @2 q- E7 ?. ?/ A; u
3 Monitoring the Effects of Chromatin Remodelers on Long-Range
8 }& T) [8 n9 E; k% aInteractions In Vivo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
/ N2 n: }% U3 {' y/ hChristine M. Kiefer and Ann Dean
$ t( h9 q- ?, H  N. E& R& G, k4 Measuring Nucleosome Occupancy In Vivo by Micrococcal Nuclease . . . . . . . . . . . 47% T8 ~$ v+ Q, N! X  m
Gene O. Bryant. U6 y! @$ K+ w7 a* [/ c
5 Analysis of Nucleosome Positioning Using a Nucleosome-Scanning Assay. . . . . . . . 63# R  a7 ?: L& a, \. n
Juan Jose Infante, G. Lynn Law, and Elton T. Young! A$ A2 y- c7 n3 M& Z  Z& u
6 Assaying Chromatin Structure and Remodeling by Restriction Enzyme# C; c5 U/ p. ?9 q/ ~$ Q1 ~
Accessibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
5 X9 [# k, S, i/ n1 CKevin W. Trotter and Trevor K. Archer
/ B: v. ^) u/ w" K% c% |& Z7 Generation of DNA Circles in Yeast by Inducible Site-Specific
7 l. I" G/ @* c5 n8 e0 N+ iRecombination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103+ a6 r+ n* ?) H6 w
Marc R. Gartenberg
3 |/ f9 `9 [3 J2 K) N) \' \, _# n/ G8 An Efficient Purification System for Native Minichromosome
9 [# Q% o" z5 k; Z1 L. _, Sfrom Saccharomyces cerevisiae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1155 a( Y' ]% c% E, ~. _3 J- @0 F* c
Ashwin Unnikrishnan, Bungo Akiyoshi, Sue Biggins, and Toshio Tsukiyama) w) k& j+ {5 {
9 Simultaneous Single-Molecule Detection of Endogenous C-5 DNA. w! k; i5 j3 r" H) v2 b' {8 b3 a
Methylation and Chromatin Accessibility Using MAPit. . . . . . . . . . . . . . . . . . . . . . 125
+ @. D$ {& p* {, h$ PRussell P. Darst, Carolina E. Pardo, Santhi Pondugula,9 B% O2 w3 N- p* f, ^7 n- i7 k
Vamsi K. Gangaraju, Nancy H. Nabilsi, Blaine Bartholomew,
' x1 {9 i$ M& Q( F9 c# ?and Michael P. Kladde
, c: r- ^( k( k' O10 Analysis of Stable and Transient Protein–Protein Interactions . . . . . . . . . . . . . . . . . 143( U6 b1 f7 F; h1 p; m
Stephanie Byrum, Sherri K. Smart, Signe Larson, and Alan J. Tackett
4 O* S: Z8 s& v1 [9 U. a, A11 Monitoring Dynamic Binding of Chromatin Proteins In Vivo: n3 y6 \+ J- @7 E/ @$ {( Q9 F
by Fluorescence Recovery After Photobleaching . . . . . . . . . . . . . . . . . . . . . . . . . . . 1530 R' q& m; n  K! m
Florian Mueller, Tatiana S. Karpova, Davide Mazza,2 \" Q$ H3 `  b  Z/ v: D
and James G. McNally& D7 p+ x5 s1 A% f- \7 }
12 Monitoring Dynamic Binding of Chromatin Proteins In Vivo by Fluorescence  K0 y. S" t. @* u
Correlation Spectroscopy and Temporal Image Correlation Spectroscopy . . . . . . . . 177! I0 n: P. I( A% R8 h
Davide Mazza, Timothy J. Stasevich, Tatiana S. Karpova,
6 R4 q& }# E# pand James G. McNally
2 i4 t& {. d  o2 `, {13 Analysis of Chromatin Structure in Plant Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2019 x; A4 g+ A2 }& k$ G
Mala Singh, Amol Ranjan, Krishan Mohan Rai, Sunil Kumar Singh,; i1 w5 P& p) [
Verandra Kumar, Ila Trivedi, Niraj Lodhi, and Samir V. Sawant. D2 x! [) f# o1 Y, E" O5 d
14 Analysis of Histones and Histone Variants in Plants. . . . . . . . . . . . . . . . . . . . . . . . . 225
. h) t1 ~% F. |6 l! }, F" HIla Trivedi, Krishan Mohan Rai, Sunil Kumar Singh,; Z+ M( Y5 j- D9 K/ {
Verandra Kumar, Mala Singh, Amol Ranjan, Niraj Lodhi,
3 b+ L* j" t! P+ n: o9 iand Samir V. Sawant, [$ U: `7 U7 c8 w
15 Reconstitution of Modified Chromatin Templates for In Vitro
+ W# j  C- h! |5 aFunctional Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
. Z: k) L4 x8 V- @; n1 l* p% _Miyong Yun, Chun Ruan, Jae-Wan Huh, and Bing Li
1 E7 v) A& |- q6 G6 Y16 A Defined In Vitro System to Study ATP-Dependent Remodeling
* u: _  }! a' n, ]5 L4 s# F6 P! Dof Short Chromatin Fibers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255; N/ ]* |& l  n
Verena K. Maier and Peter B. Becker  s7 h7 T" ]$ l/ i& Q
17 In Vitro Reconstitution of In Vivo-Like Nucleosome Positioning
  k" `1 l+ Z: `7 P4 m( l1 }on Yeast DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271
; O' b) q& _# s1 M' ~2 mChristian J. Wippo and Philipp Korber
) D) B$ a( S* M7 l18 Activator-Dependent Acetylation of Chromatin Model Systems. . . . . . . . . . . . . . . . 2893 q' `9 @7 {% X& T
Heather J. Szerlong and Jeffrey C. Hansen
- c. I' w5 e( N19 Mapping Assembly Favored and Remodeled Nucleosome Positions0 _' y4 J: u" A* L0 Q: V6 t
on Polynucleosomal Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3110 V( G' [! ^/ {0 {/ @
Hillel I. Sims, Chuong D. Pham, and Gavin R. Schnitzler3 [% u5 f* z' [7 R
20 Analysis of Changes in Nucleosome Conformation Using Fluorescence
) t% H, p# Z+ A, o. S4 B. M- }: B5 OResonance Energy Transfer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337
& [5 b$ u$ n5 N8 ?: {Tina Shahian and Geeta J. Narlikar
( s" f" R! ~' E) C$ w  [21 Preparation of Nucleosomes Containing a Specific H2A–H2A Cross-Link( }# d+ c+ O9 b
Forming a DNA-Constraining Loop Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351
, P' a) l( v  ^3 LNing Liu and Jeffrey J. Hayes6 z: B5 j1 k( [, S  n4 l
22 Sulfyhydryl-Reactive Site-Directed Cross-Linking as a Method for Probing
8 R3 V7 u' W8 {3 V) K; f. athe Tetrameric Structure of Histones H3 and H4 . . . . . . . . . . . . . . . . . . . . . . . . . . 373
) u; Q5 U" ^, X) Z: zAndrew Bowman and Tom Owen-Hughes0 W6 @( C$ |1 v! @  f4 L% x
23 Genomic Approaches for Determining Nucleosome Occupancy in Yeast . . . . . . . . . 389
/ @7 X/ T8 o" B+ J0 o$ bKyle Tsui, Tanja Durbic, Marinella Gebbia, and Corey Nislow! ^9 l# u0 C% n
24 Genome-Wide Approaches to Determining Nucleosome Occupancy8 ?7 ]0 E# W9 A' q* K
in Metazoans Using MNase-Seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 413
. T. o6 H" c: `+ P# hKairong Cui and Keji Zhao9 y" A) ~) K" @* j' b
25 Salt Fractionation of Nucleosomes for Genome-Wide Profiling . . . . . . . . . . . . . . . . 421
  p, y% X+ h$ O- V; {Sheila S. Teves and Steven Henikoff% W7 }+ J; R' o2 m8 V
26 Quantitative Analysis of Genome-Wide Chromatin Remodeling . . . . . . . . . . . . . . . 433
# w3 X- ?0 X4 d- CSongjoon Baek, Myong-Hee Sung, and Gordon L. Hager1 u3 R% G4 N# {$ e0 o% E
27 Computational Analysis of Nucleosome Positioning . . . . . . . . . . . . . . . . . . . . . . . . 443* B0 v, c. u3 I4 t( X
Itay Tirosh' U+ j  U) {! A" q$ f
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451  Z* E8 \* j. y/ c5 e7 U) o

daiminzh

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biobio

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bluesuns

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