Ellahi Aisha, Thurtle Deborah M, Rine Jasper
Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720.
Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720
Genetics. 2015 Jun;200(2):505-21. doi: 10.1534/genetics.115.175711. Epub 2015 Mar 30.
Saccharomyces cerevisiae telomeres have been a paradigm for studying telomere position effects on gene expression. Telomere position effect was first described in yeast by its effect on the expression of reporter genes inserted adjacent to truncated telomeres. The reporter genes showed variable silencing that depended on the Sir2/3/4 complex. Later studies examining subtelomeric reporter genes inserted at natural telomeres hinted that telomere position effects were less pervasive than previously thought. Additionally, more recent data using the sensitive technology of chromatin immunoprecipitation and massively parallel sequencing (ChIP-Seq) revealed a discrete and noncontinuous pattern of coenrichment for all three Sir proteins at a few telomeres, calling the generality of these conclusions into question. Here we combined the ChIP-Seq of the Sir proteins with RNA sequencing (RNA-Seq) of messenger RNAs (mRNAs) in wild-type and in SIR2, SIR3, and SIR4 deletion mutants to characterize the chromatin and transcriptional landscape of all native S. cerevisiae telomeres at the highest achievable resolution. Most S. cerevisiae chromosomes had subtelomeric genes that were expressed, with only ∼6% of subtelomeric genes silenced in a SIR-dependent manner. In addition, we uncovered 29 genes with previously unknown cell-type-specific patterns of expression. These detailed data provided a comprehensive assessment of the chromatin and transcriptional landscape of the subtelomeric domains of a eukaryotic genome.
酿酒酵母端粒一直是研究端粒位置效应如何影响基因表达的范例。端粒位置效应最初是在酵母中被描述的，它通过对插入截短端粒附近的报告基因的表达产生影响来体现。报告基因表现出可变的沉默现象，这种沉默依赖于Sir2/3/4复合物。后来对插入天然端粒的亚端粒报告基因进行的研究暗示，端粒位置效应并不像之前认为的那样普遍。此外，最近使用染色质免疫沉淀和大规模平行测序（ChIP-Seq）的敏感技术的数据显示，在少数端粒处，所有三种Sir蛋白的共富集呈现离散且不连续的模式，这使得这些结论的普遍性受到质疑。在这里，我们将Sir蛋白的ChIP-Seq与野生型以及SIR2、SIR3和SIR4缺失突变体中信使RNA（mRNA）的RNA测序（RNA-Seq）相结合，以最高分辨率描绘所有天然酿酒酵母端粒的染色质和转录图谱。大多数酿酒酵母染色体都有表达的亚端粒基因，只有约6%的亚端粒基因以依赖Sir的方式沉默。此外，我们还发现了29个具有以前未知的细胞类型特异性表达模式的基因。这些详细数据为真核基因组亚端粒区域的染色质和转录图谱提供了全面评估。
