Identification of functional genomic elements in Schizosaccharomyces Pombe using high-density transposon mutagenesis

The non-protein coding 'dark matter' of eukaryotic genomes remains poorly understood. Diversity studies, comparative genomics and biochemical outputs of genomic sites can be indicators of functional elements, but none of them produces fine-scale genome-wide descriptions of all the functional elements in a genome. As a step towards a comprehensive fine-scale description of functional elements in the fission yeast genome, we generated high-density transposon mutagenesis libraries to a density of one insertion/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. We infer that transposon insertions lead to fitness consequences in 90% of the genome, including 80% of the non-protein coding regions, revealing numerous non-coding functional elements in this compact genome.