Modeling the 3D genome of plants

Marco Di Stefano, Hans Wilhelm Nützmann

Research output: Contribution to journalReview articlepeer-review

2 Citations (SciVal)

Abstract

Chromosomes are the carriers of inheritable traits and define cell function and development. This is not only based on the linear DNA sequence of chromosomes but also on the additional molecular information they are associated with, including the transcription machinery, histone modifications, and their three-dimensional folding. The synergistic application of experimental approaches and computer simulations has helped to unveil how these organizational layers of the genome interplay in various organisms. However, such multidisciplinary approaches are still rarely explored in the plant kingdom. Here, we provide an overview of our current knowledge on plant 3D genome organization and review recent efforts to integrate cutting-edge experiments from microscopy and next-generation sequencing approaches with theoretical models. Building on these recent approaches, we propose possible avenues to extend the application of theoretical modeling in the characterization of the 3D genome organization in plants.

Original languageEnglish
Pages (from-to)65-81
Number of pages17
JournalNucleus
Volume12
Issue number1
Early online date21 May 2021
DOIs
Publication statusPublished - 31 Dec 2021

Bibliographical note

Funding Information:
We apologize to the authors whose work could not be discussed due to space limitations. We thank both reviewers for their comments and suggestions to improve the manuscript. This work was supported by a Royal Society University Research Fellowship (UF160138) and a Royal Society Research Fellows Enhancement Award (RGF\EA\201054) to HWN. Furthermore, we would like to acknowledge the networking opportunities provided by the Cost Actions INDEPTH (CA16212) and EUTOPIA (CA17139).

Funding Information:
This work was supported by the The Royal Society [UF160138 and RGF\EA\201054]. We apologize to the authors whose work could not be discussed due to space limitations. We thank both reviewers for their comments and suggestions to improve the manuscript. This work was supported by a Royal Society University Research Fellowship (UF160138) and a Royal Society Research Fellows Enhancement Award (RGF\EA\201054) to HWN. Furthermore, we would like to acknowledge the networking opportunities provided by the Cost Actions INDEPTH (CA16212) and EUTOPIA (CA17139).

Keywords

  • 3D genome
  • chromosome modeling
  • epigenome
  • Hi-C
  • Plants
  • polymer simulations

ASJC Scopus subject areas

  • Cell Biology

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