The Effect of Micrococcal Nuclease Digestion on Nucleosome Positioning Data

被引:90
作者
Chung, Ho-Ryun [1 ]
Dunkel, Ilona [2 ]
Heise, Franziska [3 ]
Linke, Christian [4 ]
Krobitsch, Sylvia [4 ]
Ehrenhofer-Murray, Ann E. [3 ]
Sperling, Silke R. [2 ]
Vingron, Martin [1 ]
机构
[1] MPI Mol Genet, Dept Computat Mol Biol, Berlin, Germany
[2] MPI Mol Genet, Grp Cardiovasc Genet, Dept Vertebrate Genom, Berlin, Germany
[3] Univ Duisburg Essen, Genet Abt, ZMB, Essen, Germany
[4] MPI Mol Genet, Neurodegenerat Disorder Grp, Otto Warburg Lab, Berlin, Germany
来源
PLOS ONE | 2010年 / 5卷 / 12期
关键词
HISTONE-DNA INTERACTIONS; CHROMATIN-STRUCTURE; SACCHAROMYCES-CEREVISIAE; IN-VIVO; EUKARYOTIC GENOME; HIGH-RESOLUTION; YEAST; ORGANIZATION; CLEAVAGE; REVEALS;
D O I
10.1371/journal.pone.0015754
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Eukaryotic genomes are packed into chromatin, whose basic repeating unit is the nucleosome. Nucleosome positioning is a widely researched area. A common experimental procedure to determine nucleosome positions involves the use of micrococcal nuclease (MNase). Here, we show that the cutting preference of MNase in combination with size selection generates a sequence-dependent bias in the resulting fragments. This strongly affects nucleosome positioning data and especially sequence-dependent models for nucleosome positioning. As a consequence we see a need to re-evaluate whether the DNA sequence is a major determinant of nucleosome positioning in vivo. More generally, our results show that data generated after MNase digestion of chromatin requires a matched control experiment in order to determine nucleosome positions.
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页数:8
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共 50 条
[1]   Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome [J].
Albert, Istvan ;
Mavrich, Travis N. ;
Tomsho, Lynn P. ;
Qi, Ji ;
Zanton, Sara J. ;
Schuster, Stephan C. ;
Pugh, B. Franklin .
NATURE, 2007, 446 (7135) :572-576
[2]  
[Anonymous], NUCL ACIDS RES
[3]   CLEAVAGE OF DNA IN NUCLEI AND CHROMATIN WITH STAPHYLOCOCCAL NUCLEASE [J].
AXEL, R .
BIOCHEMISTRY, 1975, 14 (13) :2921-2925
[4]  
Cartwright IL, 1999, METHOD ENZYMOL, V304, P462
[5]   Sequence-dependent Nucleosome Positioning [J].
Chung, Ho-Ryun ;
Vingron, Martin .
JOURNAL OF MOLECULAR BIOLOGY, 2009, 386 (05) :1411-1422
[6]   STRUCTURE OF CHROMATIN [J].
CLARK, RJ ;
FELSENFELD, G .
NATURE-NEW BIOLOGY, 1971, 229 (04) :101-+
[7]   LOCATION OF THE PRIMARY SITES OF MICROCOCCAL NUCLEASE CLEAVAGE ON THE NUCLEOSOME CORE [J].
COCKELL, M ;
RHODES, D ;
KLUG, A .
JOURNAL OF MOLECULAR BIOLOGY, 1983, 170 (02) :423-446
[8]   HIGH SEQUENCE SPECIFICITY OF MICROCOCCAL NUCLEASE [J].
DINGWALL, C ;
LOMONOSSOFF, GP ;
LASKEY, RA .
NUCLEIC ACIDS RESEARCH, 1981, 9 (12) :2659-2673
[9]   Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3′-end formation [J].
Fan, Xiaochun ;
Moqtaderi, Zarmik ;
Jin, Yi ;
Zhang, Yong ;
Liu, X. Shirley ;
Struhl, Kevin .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (42) :17945-17950
[10]   UPSTREAM ACTIVATION SEQUENCE-DEPENDENT ALTERATION OF CHROMATIN STRUCTURE AND TRANSCRIPTION ACTIVATION OF THE YEAST GAL1-GAL10 GENES [J].
FEDOR, MJ ;
KORNBERG, RD .
MOLECULAR AND CELLULAR BIOLOGY, 1989, 9 (04) :1721-1732