PDF电子书：Epigenetics Protocols

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Preface .................................................................................................. v
& W# m' P* I4 _0 Q7 bContributors ......................................................................................... ix4 ]) t* y, U9 j+ q* S& {& l. K
1 Methods of Epigenetic Analysis$ R+ z  ^) R0 N! F! L) C
Trygve O. Tollefsbol ................................................................... 1- J4 U; t( S" ]4 g6 D1 |) h1 X5 ~
2 Chromatin Immunoprecipitation Assays
/ {4 ^$ @5 H  {: `7 [; G. mYan Yan, Haobin Chen, and Max Costa ..................................... 9
1 ?% Q, y8 j' O* ?3 p+ H% V3 Native Chromatin Immunoprecipitation
2 v8 ~, b  M; L- Z5 @* y( }Alan W. Thorne, Fiona A. Myers, and Tim R. Hebbes.............. 217 R. O( H# s9 b
4 Q-PCR in Combination With ChIP Assays to Detect Changes( L. w' q; c* v1 L6 I* U- c. [! c$ X* O
in Chromatin Acetylation0 l( u/ X) g7 {. E( C, P
Ryan A. Irvine and Chih-Lin Hsieh ........................................... 45; y1 V+ V- \- D0 T
5 Restriction Endonuclease Accessibility as a Determinant: R- x8 X) M0 ?8 g
of Altered Chromatin Structure; X+ t. x" N, v& U
William M. Hempel and Pierre Ferrier ..................................... 53- p# E7 \, @- p: _5 M# w
6 Measuring Changes in Chromatin Using Micrococcal Nuclease( y6 M" v3 U6 V8 i3 l
Nicolas Steward and Hiroshi Sano ........................................... 658 h& @! H- z0 M4 r9 n$ J! Z
7 DNaseI Hypersensitivity Analysis of Chromatin Structure
% q8 d, s! m5 ~3 b) o- l& S8 mQianjin Lu and Bruce Richardson............................................. 77' S0 P$ t3 z6 l- ?* [* V4 R
8 Inhibition of Histone Deacetylases
% L- }, F, @- ]: _) G$ ^/ w7 u4 bCheng Liu and Dawei Xu .......................................................... 872 Y* x# X1 s* e4 s8 H6 k& {2 g" _
9 Site-Specific Analysis of Histone Methylation and Acetylation
! k! H9 ^5 n0 c5 P0 TDavid Umlauf, Yuji Goto, and Robert Feil ............................... 99( B# A9 ^2 W9 E7 K" l
10 Analysis of Mammalian Telomere Position Effect
3 [( K+ J6 n$ xJoseph A. Baur, Woodring E. Wright, and Jerry W. Shay....... 121. ], X: W. p' y# r. E
11 Activity Assays for Poly-ADP Ribose Polymerase 19 S6 `- @& ~! [8 a4 C: d
Eva Kirsten, Ernest Kun, Jerome Mendeleyev,
* K, w! S& o1 t( \4 yand Charles P. Ordahl ......................................................... 1372 a0 O5 o: R  m- q
12 Multigenerational Selection and Detection of Altered Histone
2 {* t* O# U$ m2 L) r5 FAcetylation and Methylation Patterns:2 o8 a  K6 s/ V
Toward a Quantitative Epigenetics in Drosophila( ~0 N" k3 _0 w: ^% m( u# q
Mark D. Garfinkel, Vincent E. Sollars, Xiangyi Lu,/ a* s# P2 l2 H" P' B9 O9 v
and Douglas M. Ruden ........................................................ 151; I3 N- p" |9 N. ~1 u* p- r
13 Profiling DNA Methylation by Bisulfite Genomic Sequencing:* s* k: V% c8 q
Problems and Solutions
- u) l  V- [2 P0 X" }" `. d6 vLiang Liu, Rebecca C. Wylie, Nathaniel J. Hansen,
7 w  A) j% I$ g# B2 H* L9 bLucy G. Andrews, and Trygve O. Tollefsbol ....................... 169, U  ^# e" q. _) i% @- C
14 Methylation-Sensitive Single-Strand Conformation Analysis:: ]" r4 w7 W3 G1 Z9 F8 b
A Rapid Method to Screen for$ [- j' n- _2 _  v7 j) n& q8 y% G0 e
and Analyze DNA Methylation
4 J# c" g! s+ q. s0 }8 [$ SJean Benhattar and Geneviève Clément ................................. 1811 b& E" C) a1 L5 V
15 SIRPH Analysis: SNuPE With IP-RP-HPLC+ j% j& q! Q6 ]3 e: f6 H
for Quantitative Measurements of DNA Methylation
6 C8 W/ o, W( P) ~. vat Specific CpG Sites
, K. |; N7 l% |Osman El-Maarri ..................................................................... 195: |9 b5 `9 ~+ i( o
16 Real-Time PCR-Based Assay for Quantitative Determination
" y( p- q9 |3 B7 y2 c7 \of Methylation Status
/ |$ t* W/ O0 U7 N( kUlrich Lehmann and Hans Kreipe........................................... 207' \0 C- M8 A! k; ?( @
17 Denaturing Gradient Gel Electrophoresis
9 w' d; `1 j, Q' A3 O0 G- ^to Detect Methylation Changes in DNA2 o+ W2 q& p, `# I
Masahiko Shiraishi .................................................................. 219: S) t6 b( p1 G% ?: j
18 Photocrosslinking Oligonucleotide Hybridization Assay for
, A% ^" N$ Y4 Y( Q& uConcurrent Gene Dosage and CpG Methylation Analysis! f- }( g* x8 Y4 T5 |" [: D% V- T
Risa Peoples, Michael Wood, and Reuel Van Atta ................. 233
, \& @  y$ V8 _3 B2 x# W* b0 u19 Methylation-Specific Oligonucleotide Microarray
0 P* G( i/ }# b* EPearlly S. Yan, Susan H. Wei, and Tim Hui-Ming Huang ....... 251  U, p% \5 d3 \" C9 Q. R
20 Methylation-Specific PCR In Situ Hybridization
" m0 c. x) S2 ^( w- PGerard J. Nuovo ...................................................................... 261
+ G/ x1 s9 u5 K21 Relative Quantitation of DNA Methyltransferase mRNA
/ g) v8 _0 v/ B+ o" kby Real-Time RT-PCR Assay, O& l& H* L9 `8 u. e2 b+ h* t
John Attwood and Bruce Richardson ..................................... 273
/ b* r! o8 V- D/ x. C/ M22 DMB (DNMT-Magnetic Beads) Assay: Measuring DNA7 ?5 s# P0 R6 L5 a+ p) ^6 x+ {
Methyltransferase Activity In Vitro6 w) C  u! h$ B2 q! T* Z. F
Tomoki Yokochi and Keith D. Robertson ............................... 285
" l% O; w/ x: G8 `Index ................................................................................................. 297

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