Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

Genome expression: A hive of activity Until recently, it was thought that much of a genome sequence is silent for much of the time. Now a study in the fission yeast Schizosaccharomyces pombe , using recently developed DNA sequencing technologies, shows that almost all of the yeast genome is genetically active. More than 90% of the genome is transcribed into RNA, including more than 450 newly discovered transcripts, many of them non-coding, with regulatory or other unknown roles. Using recently developed DNA sequencing technologies, nucleic acid transcripts are characterized in unprecedented detail from the yeast Schizosaccharomyces pombe . The sequences definitively demonstrate that 90% of more of the genome is transcribed into RNA, and show a previously unseen link between transcription and splicing efficiency at different points in the cell's growth. Recent data from several organisms indicate that the transcribed portions of genomes are larger and more complex than expected, and that many functional properties of transcripts are based not on coding sequences but on regulatory sequences in untranslated regions or non-coding RNAs 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 . Alternative start and polyadenylation sites and regulation of intron splicing add additional dimensions to the rich transcriptional output 10 , 11 . This transcriptional complexity has been sampled mainly using hybridization-based methods under one or few experimental conditions. Here we applied direct high-throughput sequencing of complementary DNAs (RNA-Seq), supplemented with data from high-density tiling arrays, to globally sample transcripts of the fission yeast Schizosaccharomyces pombe , independently from available gene annotations. We interrogated transcriptomes under multiple conditions, including rapid proliferation, meiotic differentiation and environmental stress, as well as in RNA processing mutants to reveal the dynamic plasticity of the transcriptional landscape as a function of environmental, developmental and genetic factors. High-throughput sequencing proved to be a powerful and quantitative method to sample transcriptomes deeply at maximal resolution. In contrast to hybridization, sequencing showed little, if any, background noise and was sensitive enough to detect widespread transcription in >90% of the genome, including traces of RNAs that were not robustly transcribed or rapidly degraded. The combined sequencing and strand-specific array data provide rich condition-specif