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Chromatin dynamics in the gigantic genome of Norway spruce

Research project Norway spruce has a gigantic genome with 20 billion base pairs of DNA. If that DNA were stretched out it would be 12 meters long. Each cell of a tree contains a copy of the genome within the nucleus, so this huge DNA strain must be folded into a dense, compact three dimensional structure. We are interested in how the genome grew to be so large and how the compact structure is reorganised during development to allow access to genes that are expressed at different times.

One PhD student will be recruited.

Head of project

Nathaniel Street
Associate professor
E-mail
Email

Project overview

Project period:

2020-01-01 2023-12-31

Participating departments and units at Umeå University

Department of Plant Physiology

Research subject

Molecular biology and genetics

External funding

Swedish Research Council

Project description

The genome of Norway spruce is about seven times bigger than the human genome but contains a similar number of genes. There are numerous examples of genomes rendered obese by repetitive DNA element expansions, from axolotl to those of gymnosperms. These repeated regions of DNA make copies of themselves that are inserted into the genome, causing it to increase in size.

The underlying reason why these genomes succumbed to runaway repeat expansion remains unresolved as many other genomes have effective defence mechanisms to prevent insertion and to rapidly delete insertions that do occur. Similarly, it remains unknown whether genomic adaptations have evolved to facilitate the rapid and extensive changes in which genes are active during stages development as those genes occupy a tiny fraction of the total genomic space and must be accessible to enable the gene to be active.

There is currently very little known about how the vast non-gene regions of the Norway spruce genome are organised or the dynamics of DNA structure in this, or any, gigantic genome. This project will generate data to profile DNA accessibility, interactions and dynamics to test the hypothesis that sets of genes turned on and off in a coordinated way during development are arranged into physically proximal clusters that are made accessible via dynamic reorganisation of the  three dimensional structure of DNA. This will provide the first insight into the dynamics and structure of DNA in one of the numerous gigantic genomes and will identify the functional subset of the genome, which will inform downstream analyses that aim to link genes to their functional roles.

External funding