Identification of non-coding transcripts regulated by Rap1 and other transcription factors by RNA-seq analysis

Eukaryotic cells utilize several mechanisms to ensure that expression of aberrant non-coding RNAs is limited. Gene looping, chromatin modification or remodeling, and RNA surveillance contribute to ensure the fidelity of transcription and limit non-coding transcripts. Here we identify that in Saccharomyces cerevisiae, the transcription factor Rap1 is critical for limiting the expression of aberrant RNAs, particularly near the highly expressed ribosomal protein genes, and characterize them in the context of other non-coding RNAs regulated by chromatin and transcription related factors. RNA-seq analysis of Saccharomyces cerevisiae S288C strains. Data include gene deletion strains (spt10Δ, spt21Δ, rlf2Δ), strains transformed with OsTIR1 ligase and auxin-inducible degron (IAA7) tagged proteins (Rap1, Spt6, Spt16), Rap1 auxin-inducible degron strains expressing depletion-insensitive Rap1 mutant proteins, or wild-type control strains. 2 biological replicates for each sample type and condition were analyzed. For each biological replicate, cells were grown overnight in YPD media, diluted, and treated with DMSO or 500 μM 3-indole-acetic acid (3-IAA, auxin). Samples for auxin-inducible degron strains were taken 2 hours after treatment with DMSO or 3-IAA. For wild-type and gene deletion strains, samples were taken in mid-logarithmic growth. RNA was subjected to rRNA depletion to generate TOTAL RNA-seq libraries, respectively.

真核细胞借助多种调控机制，以限制异常非编码RNA的表达。基因成环、染色质修饰或重塑以及RNA监测通路，均有助于保障转录的保真度，并抑制非编码转录本的产生。本研究在酿酒酵母（Saccharomyces cerevisiae）中发现，转录因子Rap1对限制异常RNA的表达至关重要，尤其作用于高表达的核糖体蛋白基因区域；同时结合染色质与转录相关因子调控的其他非编码RNA的研究背景，对该调控过程进行了系统表征。

本数据集包含酿酒酵母S288C菌株的RNA测序（RNA-seq）分析数据，所用样本类型包括：基因敲除菌株（spt10Δ、spt21Δ、rlf2Δ）；转化有OsTIR1连接酶与生长素诱导降解标签（IAA7）融合蛋白的菌株（靶标蛋白为Rap1、Spt6、Spt16）；表达对降解不敏感的Rap1突变蛋白的Rap1生长素诱导降解标签菌株；以及野生型对照菌株。

每个样本类型与实验条件均设置2次生物学重复。对于每一次生物学重复，菌株均在YPD培养基中过夜培养后进行稀释，随后分别用二甲基亚砜（DMSO）或500 μM 3-吲哚乙酸（3-IAA，生长素）处理。生长素诱导降解标签菌株的样本于药物处理后2小时采集；野生型与基因敲除菌株的样本则于对数生长中期采集。所有提取的RNA样本均经核糖体RNA去除处理，以分别构建对应各组的总RNA测序（TOTAL RNA-seq）文库。