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bioRxiv · 10.1101/398024

Fitness Landscape of the Fission Yeast Genome

Grech, L.·Jeffares, D. C.·Sadee, C. Y.·Rodriguez-Lopez, M.·Bitton, D. A.·Hoti, M.·Biagosch, C.·Aravani, D.·Speekenbrink, M.·Illingworth, C. J. R.·Schiffer, P. H.·Pidoux, A. L.·Tong, P.·Tallada, V. A.·Allshire, R.·Levin, H. L.·Bahler, J.
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Abstract

BackgroundNon-protein-coding regions of eukaryotic genomes remain poorly understood. Diversity studies, comparative genomics and biochemical outputs of genomic sites can be indicators of functional elements, but none produce fine-scale genome-wide descriptions of all functional elements.\n\nResultsTowards the generation of a comprehensive description of functional elements in the haploid Schizosaccharomyces pombe genome, we generated transposon mutagenesis libraries to a density of one insertion per 13 nucleotides of the genome. We applied a five-state hidden Markov model (HMM) to characterise insertion-depleted regions at nucleotide-level resolution. HMM-defined functional constraint was consistent with genetic diversity, comparative genomics, gene-expression data and genome annotation.\n\nConclusionsWe infer that transposon insertions lead to fitness consequences in 90% of the genome, including 80% of the non-protein-coding regions, reflecting the presence of numerous non-coding elements in this compact genome that have functional roles. Display of this data in genome browsers provides fine-scale views of structure-function relationships within specific genes.

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Grech, L., Jeffares, D. C., Sadee, C. Y., Rodriguez-Lopez, M., Bitton, D. A., Hoti, M., Biagosch, C., Aravani, D., Speekenbrink, M., Illingworth, C. J. R., Schiffer, P. H., Pidoux, A. L., Tong, P., Tallada, V. A., Allshire, R., Levin, H. L., Bahler, J.. 2018-08-22. Fitness Landscape of the Fission Yeast Genome. https://doi.org/10.1101/398024

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