Condition-specific 3' mRNA isoform half-lives and stability elements in yeast.
Condition-specific 3' mRNA isoform half-lives and stability elements in yeast.
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DOI：
10.1073/pnas.2301117120
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发表时间：
2023-05-02
影响因子：
11.1
通讯作者：
Struhl, Kevin
中科院分区：
文献类型：
--
作者：
V. Geisberg, Joseph;Moqtaderi, Zarmik;Struhl, Kevin
选择性多聚腺苷酸化可产生许多在稳定性、结构和功能上可能不同的3‘端信使核糖核酸异构体，其差异性异构体稳定性由3’非翻译区内的序列元件介导。我们确定了>；1,000酵母的稳定和不稳定因子，它们只在测试的四种生长条件中的一种中起作用。与这些条件特定的稳定性元件中的某些类别相关的基因在特定的功能类别中被丰富。令人惊讶的是，各个3‘端亚型在不同的条件下具有相似的结构。条件特定的稳定元件不会在稳态的mRNA亚型水平上产生相应的条件特定的变化。这些观察结果表明，在酵母中，受调控的mRNA稳定性可能有助于适应不同的生长环境，条件特异性的mRNA稳定性元件可能反映了条件特异性的mRNA 3‘末端形成的调控。选择性多聚腺苷酸化可产生许多在稳定性、结构和功能上不同的3‘m RNA异构体。这些异构体可用于定位3‘非翻译区(3’UTRs)内的mRNA稳定和不稳定元件。在这里，我们研究了环境条件如何在转录组规模上影响酵母细胞中3‘mRNA异构体的周转和结构。当细胞生长较慢时，异构体的稳定性普遍增加，大多数异构体的相对半衰期在多种条件下都有很好的相关性。令人惊讶的是，硫酸二甲酯探测表明，在不同的条件下，各个3‘异构体具有相似的结构，而在单个条件下，密切相关的异构体之间可能存在广泛的结构差异。出乎意料的是，大多数稳定和不稳定mRNA的元件只在单一的生长条件下发挥作用。与某些条件特异性稳定元件相关的基因在不同的功能类别中都得到了丰富，这表明受调控的mRNA稳定性可能有助于适应不同的生长环境。条件特定的稳定元件不会导致稳态mRNA亚型水平的相应条件特定的变化。这一观察结果与多聚腺苷化与稳定性之间的补偿机制是一致的，这表明条件特异性的mRNA稳定元件可能在很大程度上反映了条件特异性的mRNA3‘末端形成的调节。
Alternative polyadenylation generates numerous 3′ mRNA isoforms that can differ in stability, structure, and function, with differential isoform stability mediated by sequence elements within 3′ untranslated regions. We identify >1,000 yeast mRNA stabilizing and destabilizing elements that function in only one of four growth conditions tested. Genes associated with some classes of these condition-specific stability elements are enriched for specific functional categories. Surprisingly, individual 3′ isoforms have similar structures across different conditions. Condition-specific stability elements do not yield corresponding condition-specific changes in steady-state mRNA isoform levels. These observations suggest that, in yeast, regulated mRNA stability might facilitate adaptation to different growth environments and that condition-specific mRNA stability elements might reflect condition-specific regulation of mRNA 3′ end formation. Alternative polyadenylation generates numerous 3′ mRNA isoforms that can differ in their stability, structure, and function. These isoforms can be used to map mRNA stabilizing and destabilizing elements within 3′ untranslated regions (3′UTRs). Here, we examine how environmental conditions affect 3′ mRNA isoform turnover and structure in yeast cells on a transcriptome scale. Isoform stability broadly increases when cells grow more slowly, with relative half-lives of most isoforms being well correlated across multiple conditions. Surprisingly, dimethyl sulfate probing reveals that individual 3′ isoforms have similar structures across different conditions, in contrast to the extensive structural differences that can exist between closely related isoforms in an individual condition. Unexpectedly, most mRNA stabilizing and destabilizing elements function only in a single growth condition. The genes associated with some classes of condition-specific stability elements are enriched for different functional categories, suggesting that regulated mRNA stability might contribute to adaptation to different growth environments. Condition-specific stability elements do not result in corresponding condition-specific changes in steady-state mRNA isoform levels. This observation is consistent with a compensatory mechanism between polyadenylation and stability, and it suggests that condition-specific mRNA stability elements might largely reflect condition-specific regulation of mRNA 3′ end formation.
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影响因子：
7.7
作者：
Geisberg JV;Moqtaderi Z;Struhl K
通讯作者：
Struhl K
DOI：
10.1073/pnas.2121488119
发表时间：
2022-01-25
影响因子：
11.1
作者：
Moqtaderi Z;Geisberg JV;Struhl K
通讯作者：
Struhl K
影响因子：
48
作者：
Molinie B;Wang J;Lim KS;Hillebrand R;Lu ZX;Van Wittenberghe N;Howard BD;Daneshvar K;Mullen AC;Dedon P;Xing Y;Giallourakis CC
通讯作者：
Giallourakis CC
影响因子：
64.5
作者：
Geisberg JV;Moqtaderi Z;Fan X;Ozsolak F;Struhl K
通讯作者：
Struhl K
DOI：
10.1073/pnas.93.11.5208
发表时间：
1996-05-28
影响因子：
11.1
作者：
Iyer, V;Struhl, K
通讯作者：
Struhl, K