The Dynamic Transcriptome of Schizosaccharomyces pombe Revealed by RNA/DNA Hybrid Mapping

We determined the strand-specific transcriptome of the fission yeast S. pombe under multiple growth conditions using a novel RNA/DNA hybridization mapping (HybMap) technique. HybMap uses an antibody against an RNA/DNA hybrid to detect RNA molecules hybridized to a high density DNA oligonucleotide tiling microarray. HybMap exhibited exceptional dynamic range and reproducibility, and clearly revealed coding, non-coding and structural RNAs, as well as new RNAs conserved in distant yeast species. Virtually the entire euchromatic genome (including intergenics) is transcribed, with heterochromatin dampening intergenic transcription. Transcriptomes of alternative growth conditions reveal changes in both coding and non-coding RNAs. Interestingly, our analysis reveals large numbers of non-coding RNAs, extensive antisense transcription, new properties of antisense transcripts, and induced divergent transcription. Furthermore, HybMap informed the efficiency and locations of RNA splicing genome-wide. Finally, a remarkable feature is observed at heterochromatin boundaries inside centromeres; strand-specific transcription islands around tRNAs. These new features are discussed in terms of organism fitness and transcriptome evolution. Keywords: yeast, gene expression, bioinformatics The dynamic transcriptome of S.pombe was determined using a whole genome tiling array hybridized to total RNA. Transcripts were detected using an antibody specific to RNA/DNA hybrids. This technique, called HybMap, was used across three different growth conditions (Heat shock, MMS treatment, and minimal media) in addtion to standard conditions. To further understand the transcriptome, we isolated PolyA RNA from S.pombe grown in standard conditions and used the HybMap method. Finally, the transcriptome was compared to Pol II, histone, and H3K36me3 ChIP occupancy. NOTE: Processed microarray data values listed in this repository represent only those probes that align to unique genomic positions. Probes that align to multiple genomic locations (reported in the Platform description) may not have values. Please refer to the web link above for a complete genomic data set.

本研究采用一种新型RNA/DNA杂交定位（RNA/DNA hybridization mapping, HybMap）技术，解析了多种生长条件下粟酒裂殖酵母（Schizosaccharomyces pombe, S. pombe）的链特异性转录组。HybMap技术利用靶向RNA/DNA杂交体的抗体，对与高密度DNA寡核苷酸平铺微阵列杂交的RNA分子进行检测。该技术展现出优异的动态范围与可重复性，可清晰鉴定编码RNA、非编码RNA、结构RNA，以及在远缘酵母物种中保守的新型RNA。几乎整个常染色质基因组（包含基因间区域）均发生转录，异染色质会抑制基因间区域的转录活动。不同生长条件下的转录组数据显示，编码RNA与非编码RNA的表达均存在显著变化。值得注意的是，本研究分析发现了大量非编码RNA、广泛的反义转录现象、反义转录本的全新特性，以及诱导型双向转录现象。此外，HybMap技术还可在全基因组范围内解析RNA剪接的效率与位点。最后，在着丝粒内部的异染色质边界区域，我们观测到一项显著特征：转运RNA（tRNA）周围存在链特异性转录岛。本研究从生物体适合度与转录组演化的角度，对上述全新特征展开了讨论。关键词：酵母，基因表达，生物信息学
本研究通过将总RNA与全基因组平铺微阵列杂交的方式，解析了粟酒裂殖酵母的动态转录组。通过靶向RNA/DNA杂交体的特异性抗体实现转录本的检测。本研究在标准培养条件之外，还针对三种不同生长条件（热激处理、甲基磺酸甲酯（Methyl methanesulfonate, MMS）处理以及基础培养基培养）应用了这种被命名为HybMap的技术。为进一步解析转录组，我们从标准培养条件下生长的粟酒裂殖酵母中分离出聚腺苷酸（PolyA）RNA，并采用HybMap技术开展检测。最后，本研究将转录组数据与RNA聚合酶II（Pol II）、组蛋白以及H3K36me3染色质免疫沉淀（ChIP）占据谱进行了对比分析
注意：本仓库中列出的已处理微阵列数据值，仅对应比对至唯一基因组位置的探针。比对至多基因组位置的探针（详见平台说明文档）可能未包含数据值。如需获取完整的基因组数据集，请参阅上方的网页链接。