Department of Cell Biology and NCCR "Frontiers in Genetics", iGE3, University of Geneva, 1211 Geneva, Switzerland, EBI-EMBL Hinxton, Cambridge CB101SD, England, European Molecular Biology Laboratory, 69117 Heidelberg, Germany, Department of Genetics, Stanford University, Stanford, CA 94395 USA and Stanford Genome Technology Center, Palo Alto, CA 94303, USA.
Nucleic Acids Res. 2014 Apr;42(7):4348-62. doi: 10.1093/nar/gku100. Epub 2014 Feb 4.
Most genomes, including yeast Saccharomyces cerevisiae, are pervasively transcribed producing numerous non-coding RNAs, many of which are unstable and eliminated by nuclear or cytoplasmic surveillance pathways. We previously showed that accumulation of PHO84 antisense RNA (asRNA), in cells lacking the nuclear exosome component Rrp6, is paralleled by repression of sense transcription in a process dependent on the Hda1 histone deacetylase (HDAC) and the H3K4 histone methyl transferase Set1. Here we investigate this process genome-wide and measure the whole transcriptome of various histone modification mutants in a Δrrp6 strain using tiling arrays. We confirm widespread occurrence of potentially antisense-dependent gene regulation and identify three functionally distinct classes of genes that accumulate asRNAs in the absence of Rrp6. These classes differ in whether the genes are silenced by the asRNA and whether the silencing is HDACs and histone methyl transferase-dependent. Among the distinguishing features of asRNAs with regulatory potential, we identify weak early termination by Nrd1/Nab3/Sen1, extension of the asRNA into the open reading frame promoter and dependence of the silencing capacity on Set1 and the HDACs Hda1 and Rpd3 particularly at promoters undergoing extensive chromatin remodelling. Finally, depending on the efficiency of Nrd1/Nab3/Sen1 early termination, asRNA levels are modulated and their capability of silencing is changed.
大多数基因组，包括酵母酿酒酵母，都广泛转录产生许多非编码 RNA，其中许多不稳定，会被核或细胞质监控途径所消除。我们之前曾表明，在缺乏核外切体成分 Rrp6 的细胞中，PHO84 反义 RNA（asRNA）的积累伴随着 sense 转录的抑制，这个过程依赖于 Hda1 组蛋白去乙酰化酶（HDAC）和 H3K4 组蛋白甲基转移酶 Set1。在这里，我们在全基因组范围内研究了这一过程，并使用平铺阵列测量了各种组蛋白修饰突变体在 Δrrp6 菌株中的整个转录组。我们证实了广泛存在的潜在反义依赖性基因调控，并鉴定了三种功能不同的基因类别，这些基因在没有 Rrp6 的情况下积累 asRNA。这些类别在基因是否被 asRNA 沉默以及沉默是否依赖于 HDACs 和组蛋白甲基转移酶方面存在差异。在具有潜在调节功能的 asRNA 的区别特征中，我们发现 Nrd1/Nab3/Sen1 存在较弱的早期终止，asRNA 延伸到开放阅读框启动子，并且沉默能力依赖于 Set1 和 HDACs Hda1 和 Rpd3，特别是在经历广泛染色质重塑的启动子上。最后，根据 Nrd1/Nab3/Sen1 早期终止的效率，asRNA 水平会发生变化，其沉默能力也会发生变化。
