Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning

被引：20

作者：

Buitrago, Diana ^{[1
]}

Codo, Laia ^{[2
]}

Illa, Ricard ^{[1
]}

de Jorge, Pau ^{[1
]}

Battistini, Federica ^{[1
]}

Flores, Oscar ^{[1
]}

Bayarri, Genis ^{[1
]}

Royo, Romina ^{[2
]}

Del Pino, Marc ^{[2
]}

Heath, Simon ^{[3
]}

Hospital, Adam ^{[1
]}

Lluis Gelpi, Josep ^{[2
,4
]}

Brun Heath, Isabelle ^{[1
]}

Orozco, Modesto ^{[1
,4
]}

机构：

[1] Barcelona Inst Sci & Technol, Inst Res Biomed IRB Barcelona, Baldiri Reixac 10, Barcelona 08028, Spain

[2] Barcelona Supercomp Ctr, Jordi Girona 31, Barcelona 08028, Spain

[3] Barcelona Inst Sci & Technol, CRG, Ctr Nacl Anal Gen CNAG CRG, Barcelona, Spain

[4] Univ Barcelona, Dept Bioquim & Biomed, Fac Biol, Avgda Diagonal 647, E-08028 Barcelona, Spain

来源：

NUCLEIC ACIDS RESEARCH | 2019年 / 47卷 / 18期

基金：

欧盟地平线“2020”;

关键词：

GENE-EXPRESSION; ORGANIZATION; YEAST; CHROMATIN; OCCUPANCY; COMPLEXES; STRESS; MAP;

D O I：

10.1093/nar/gkz759

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the definition of nucleosome architectures and the detection of changes in nucleosomal organization due to changes in cellular conditions. Results are displayed in the context of genomic information thanks to different visualizers and browsers, allowing the user a holistic, multidimensional view of the genome/transcriptome. The package shows good performance for both locating equilibrium nucleosome architecture and nucleosome dynamics and provides abundant useful information in several test cases, where experimental data on nucleosome position (and for some cases expression level) have been collected for cells under different external conditions (cell cycle phase, yeast metabolic cycle progression, changes in nutrients or difference in MNase digestion level). Nucleosome Dynamics is a free software and is provided under several distribution models.

引用

页码：9511 / 9523

页数：13

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