Data formats for modelling the spatial structure of chromatin based on experimental positions of nucleosomes

Michael-Christian Mörl; Tilo Zülske; Robert Schöpflin; Gero Wedemann; Michael-Christian Mörl; Tilo Zülske; Robert Schöpflin; Gero Wedemann

doi:10.3934/biophy.2019.3.83

AIMS Biophysics

2019, Volume 6, Issue 3: 83-98. doi: 10.3934/biophy.2019.3.83

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Data formats for modelling the spatial structure of chromatin based on experimental positions of nucleosomes

Competence Center Bioinformatics, Institute for Applied Computer Science, University of Applied Sciences Stralsund, Zur Schwedenschanze 15, 18435 Stralsund, Germany

Received: 31 May 2019 Accepted: 16 July 2019 Published: 15 August 2019

In the nucleus of eukaryotic cells, DNA is wrapped around histone proteins, forming units termed nucleosomes. Nucleosome chains fold into chromatin. Despite extensive experimental advancement, many fundamental features of chromatin remain uncertain. Since all cell types and states cannot be profiled experimentally, especially in solution and in vivo, computer simulations are valuable tools for research. Most computer simulation models of chromatin are coarse-grained and describe the main characteristics of 3D chromatin packing. Newer models include experimentally derived positions of nucleosomes. While it is common practice in other disciplines, such as systems biology, to make experimental data publicly available, data from computer simulations of chromatin models are not usually published. Thus, data standard exchange formats are lacking, and we address this issue in the present work. We analysed the workflow, from experimental determination of the positions of nucleosomes through to analysis of outputs from simulated computer models. We defined standardized formats based on Extensible Markup Language (XML) for artefacts generated by steps in this workflow. We found that XML is useful since it is easy to transform XML-based-files by applying Extensible Stylesheet Language Transformations (XSLT) to other formats. We demonstrate the viability of this approach and the associated file formats using a complete example of computer simulation of chromatin domains based on experimentally determined nucleosome positions. The XML schemas and examples are published in an open source repository.
- exchange format,
- xml,
- chromatin,
- computer simulation
Citation: Michael-Christian Mörl, Tilo Zülske, Robert Schöpflin, Gero Wedemann. Data formats for modelling the spatial structure of chromatin based on experimental positions of nucleosomes[J]. AIMS Biophysics, 2019, 6(3): 83-98. doi: 10.3934/biophy.2019.3.83

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Abstract

In the nucleus of eukaryotic cells, DNA is wrapped around histone proteins, forming units termed nucleosomes. Nucleosome chains fold into chromatin. Despite extensive experimental advancement, many fundamental features of chromatin remain uncertain. Since all cell types and states cannot be profiled experimentally, especially in solution and in vivo, computer simulations are valuable tools for research. Most computer simulation models of chromatin are coarse-grained and describe the main characteristics of 3D chromatin packing. Newer models include experimentally derived positions of nucleosomes. While it is common practice in other disciplines, such as systems biology, to make experimental data publicly available, data from computer simulations of chromatin models are not usually published. Thus, data standard exchange formats are lacking, and we address this issue in the present work. We analysed the workflow, from experimental determination of the positions of nucleosomes through to analysis of outputs from simulated computer models. We defined standardized formats based on Extensible Markup Language (XML) for artefacts generated by steps in this workflow. We found that XML is useful since it is easy to transform XML-based-files by applying Extensible Stylesheet Language Transformations (XSLT) to other formats. We demonstrate the viability of this approach and the associated file formats using a complete example of computer simulation of chromatin domains based on experimentally determined nucleosome positions. The XML schemas and examples are published in an open source repository.

Acknowledgments

We thank Antonio Tilocca for critical reading and copyediting of the manuscript.

Conflict of interest

The authors declare no conflicts of interest.

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