5-氟尿嘧啶 RNA 表达查看器(5-FUR)有助于解读药物治疗和 RRP6 缺失对酵母转录景观的影响。

IF 2.2 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY
Yeast Pub Date : 2024-10-01 Epub Date: 2024-09-30 DOI:10.1002/yea.3982
Ugo Szachnowski, Oliver Sallou, Mateo Boudet, Anthony Bretaudeau, Maxime Wery, Antonin Morillon, Michael Primig
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引用次数: 0

摘要

酿酒酵母是研究外界因素对细胞分裂和应激反应影响的极佳模型。几十年来,5-氟尿嘧啶(5-FU)一直被用于治疗实体瘤。这种药物最初是用来干扰 DNA 复制的,但后来发现它也能通过 RNA 依赖过程发挥抗增殖作用。由于 5-FU 可抑制酵母和哺乳动物体内 3'-5'- 外切核酸酶 Rrp6 的活性,因此早先的研究比较了二倍体同步酵母细胞中 5-FU 处理和 RRP6 缺失在转录组水平上的效果。为了便于解读表达数据,我们开发了一个改进的 5-FUR RNA 表达查看器。用户可以通过基因组坐标、mRNA 的系统或标准名称以及 Xrn1 依赖性、稳定、隐性和减数分裂未注释转录本(XUT、SUT、CUT 和 MUT)来获取信息。归一化对数 2 转换或线性数据可以填充图、线图或彩色热图的形式显示。这些表达数据对研究细胞周期调控、减数分裂基因的有丝分裂抑制、5-FU 处理和 Rrp6 缺乏对转录组的影响以及编码重叠转录本的有义/无义位点的表达谱等过程很有帮助。查看器可从 http://5fur.genouest.org 上获取。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
The 5-Fluorouracil RNA Expression Viewer (5-FUR) Facilitates Interpreting the Effects of Drug Treatment and RRP6 Deletion on the Transcriptional Landscape in Yeast.

Saccharomyces cerevisiae is an excellent model to study the effect of external cues on cell division and stress response. 5-Fluorocuracil (5-FU) has been used to treat solid tumors since several decades. The drug was initially designed to interfere with DNA replication but was later found to exert its antiproliferative effect also via RNA-dependent processes. Since 5-FU inhibits the activity of the 3'-5'-exoribonuclease Rrp6 in yeast and mammals, earlier work has compared the effect of 5-FU treatment and RRP6 deletion at the transcriptome level in diploid synchronized yeast cells. To facilitate interpreting the expression data we have developed an improved 5-Fluorouracil RNA (5-FUR) expression viewer. Users can access information via genome coordinates and systematic or standard names for mRNAs and Xrn1-dependent-, stable-, cryptic-, and meiotic unannotated transcripts (XUTs, SUTs, CUTs, and MUTs). Normalized log2-transformed or linear data can be displayed as filled diagrams, line graphs or color-coded heatmaps. The expression data are useful for researchers interested in processes such as cell cycle regulation, mitotic repression of meiotic genes, the effect of 5-FU treatment and Rrp6 deficiency on the transcriptome and expression profiles of sense/antisense loci that encode overlapping transcripts. The viewer is accessible at http://5fur.genouest.org.

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来源期刊
Yeast
Yeast 生物-生化与分子生物学
CiteScore
5.30
自引率
3.80%
发文量
55
审稿时长
3 months
期刊介绍: Yeast publishes original articles and reviews on the most significant developments of research with unicellular fungi, including innovative methods of broad applicability. It is essential reading for those wishing to keep up to date with this rapidly moving field of yeast biology. Topics covered include: biochemistry and molecular biology; biodiversity and taxonomy; biotechnology; cell and developmental biology; ecology and evolution; genetics and genomics; metabolism and physiology; pathobiology; synthetic and systems biology; tools and resources
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