Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains
Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains
复制标题
DOI：
10.1016/j.dib.2019.103701
复制
发表时间：
2019-04-01
期刊：
影响因子：
1.2
通讯作者：
Dmitriev, Sergey E.
中科院分区：
文献类型：
--
作者：
Makeeva, Desislava S.;Lando, Andrey S.;Dmitriev, Sergey E.
TMA20 (MCT-1)、TMA22 (DENR) 和 TMA64 (eIF2D) 是参与核糖体回收和重新启动的真核翻译因子。它们在终止后或（重新）起始翻译复合物中与 P 位点结合的 tRNA 一起作用，从而参与终止后从 mRNA 终止密码子中去除 40S 核糖体亚基，并控制具有上游开放阅读框 (uORF) 的 mRNA 上的翻译重新起始，以及某些特定 mRNA 上的从头起始。在这里，我们报告了单独删除 TMA20、TMA64 或同时删除 TMA20 和 TMA64 基因的酿酒酵母菌株的核糖体分析数据。我们提供在丰富的 YPD 或基本 SD 培养基中生长的酵母菌株的 RNA-Seq 和 Ribo-Seq 数据。我们通过绘制 GCN4 mRNA 5'-非翻译区 (5' UTR) 中 uORF 中核糖体结合 mRNA 片段的差异分布以及突变型和野生型菌株 MAT 基因座中编码的 mRNA 转录物的差异分布来说明我们的数据，从而为研究这些因素在应激反应、交配和孢子形成中的作用提供基础。我们还记录了 APC4 基因转录起始位点的变化，当邻近的 TMA64 基因被用于创建酵母删除文库的标准 G418 抗性盒替换时，就会发生这种变化。正如我们的 Ribo-Seq 数据所揭示的，这种转变导致 APC4 基因表达的急剧失调，这可能可以用来解释 TMA64 与参与细胞周期和有丝分裂检查点的基因之间的强烈遗传相互作用。原始 RNA-Seq 和 Ribo-Seq 数据以及所有基因计数可在 NCBI 基因表达综合 (GEO) 存储库中获取，GEO 登录号为 GSE122039 (htips://wwvv.ncbLnim.nih.gov/geo/guery/acc.cgi?acc=GSE122039)。 (C) 2019 年作者。由爱思唯尔公司出版
TMA20 (MCT-1), TMA22 (DENR) and TMA64 (eIF2D) are eukaryotic translation factors involved in ribosome recycling and re-initiation. They operate with P-site bound tRNA in post-termination or (re-) initiation translation complexes, thus participating in the removal of 40S ribosomal subunit from mRNA stop codons after termination and controlling translation re-initiation on mRNAs with upstream open reading frames (uORFs), as well as de novo initiation on some specific mRNAs. Here we report ribosomal profiling data of S.cerevisiae strains with individual deletions of TMA20, TMA64 or both TMA20 and TMA64 genes. We provide RNA-Seq and Ribo-Seq data from yeast strains grown in the rich YPD or minimal SD medium. We illustrate our data by plotting differential distribution of ribosomal-bound mRNA fragments throughout uORFs in 5'-untranslated region (5' UTR) of GCN4 mRNA and on mRNA transcripts encoded in MAT locus in the mutant and wild-type strains, thus providing a basis for investigation of the role of these factors in the stress response, mating and sporulation. We also document a shift of transcription start site of the APC4 gene which occurs when the neighboring TMA64 gene is replaced by the standard G418-resistance cassette used for the creation of the Yeast Deletion Library. This shift results in dramatic deregulation of the APC4 gene expression, as revealed by our Ribo-Seq data, which can be probably used to explain strong genetic interactions of TMA64 with genes involved in the cell cycle and mitotic checkpoints. Raw RNA-Seq and Ribo-Seq data as well as all gene counts are available in NCBI Gene Expression Omnibus (GEO) repository under GEO accession GSE122039 (htips://wwvv.ncbLnim.nih.gov/geo/guery/acc.cgi?acc=GSE122039). (C) 2019 The Authors. Published by Elsevier Inc.