An RNA structure-mediated, posttranscriptional model of human α-1-antitrypsin expression.
An RNA structure-mediated, posttranscriptional model of human α-1-antitrypsin expression.
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DOI：
10.1073/pnas.1706539114
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发表时间：
2017-11-21
影响因子：
11.1
通讯作者：
Laederach A
中科院分区：
文献类型：
--
作者：
Corley M;Solem A;Phillips G;Lackey L;Ziehr B;Vincent HA;Mustoe AM;Ramos SBV;Weeks KM;Moorman NJ;Laederach A
蛋白质和mRNA的表达在大多数情况下是不相关的，这表明细胞的转录后调控程序是基因表达的重要组成部分。这个调控网络仍然知之甚少，包括RNA结构如何定量地促进翻译控制。我们在这里提出了一系列的结构和功能实验，这些实验共同使我们能够得出一个定量的，结构依赖的翻译模型，该模型可以准确地预测报告分析和初级人体组织中复杂且医学上重要的蛋白质α-1-抗胰蛋白酶的翻译效率。我们的模型证明了精确的，实验推导的RNA结构模型与Kozak序列信息合作的重要性，以解释蛋白质表达，并提出了一种α-1-抗胰蛋白酶表达可能在患病个体中增加的策略。慢性阻塞性肺疾病（COPD）影响全球超过6500万人，其中α-1-抗胰蛋白酶缺乏是该疾病的主要遗传原因。α-1抗胰蛋白酶基因SERPINA1表达了大量完全由5 ' -非翻译区（5 ' -UTR）的选择性剪接产生的mRNA异构体。尽管所有SERPINA1 mrna编码完全相同的蛋白质，但个体mrna的表达水平在不同的人体组织中存在很大差异。我们假设这些转录物的表现不平等是由于转录后调控程序由它们不同的5 ' - utr控制，并且这种调控最终决定α-1-抗胰蛋白酶的表达。通过引物延伸（SHAPE）化学探针，我们发现剪接在SERPINA1转录本中产生了不同的局部5 ' -UTR二级结构。5 ' -UTR中的剪接也改变了上游长orf （uorf）的包含。我们证明，在荧光素酶报告基因检测中，破坏uorf可显著提高翻译效率。这些uorf依赖性的变化表明α-1-抗胰蛋白酶蛋白的表达水平在转录后水平受到控制。仅基于Kozak翻译起始序列的翻译泄漏扫描模型不能充分解释我们的定量表达数据。然而，当我们结合实验获得的RNA结构数据时，该模型准确地预测了报告基因分析的翻译效率，并提高了α-1-抗胰蛋白酶在原代人体组织中的表达预测。我们的研究结果表明，RNA结构控制着α-1-抗胰蛋白酶表达的复杂转录后调控程序。至关重要的是，这些发现描述了非编码基因区域的遗传改变可能导致α-1抗胰蛋白酶缺乏的机制。
Protein and mRNA expression are in most cases poorly correlated, which suggests that the posttranscriptional regulatory program of a cell is an important component of gene expression. This regulatory network is still poorly understood, including how RNA structure quantitatively contributes to translational control. We present here a series of structural and functional experiments that together allow us to derive a quantitative, structure-dependent model of translation that accurately predicts translation efficiency in reporter assays and primary human tissue for a complex and medically important protein, α-1-antitrypsin. Our model demonstrates the importance of accurate, experimentally derived RNA structural models partnered with Kozak sequence information to explain protein expression and suggests a strategy by which α-1-antitrypsin expression may be increased in diseased individuals. Chronic obstructive pulmonary disease (COPD) affects over 65 million individuals worldwide, where α-1-antitrypsin deficiency is a major genetic cause of the disease. The α-1-antitrypsin gene, SERPINA1, expresses an exceptional number of mRNA isoforms generated entirely by alternative splicing in the 5′-untranslated region (5′-UTR). Although all SERPINA1 mRNAs encode exactly the same protein, expression levels of the individual mRNAs vary substantially in different human tissues. We hypothesize that these transcripts behave unequally due to a posttranscriptional regulatory program governed by their distinct 5′-UTRs and that this regulation ultimately determines α-1-antitrypsin expression. Using whole-transcript selective 2′-hydroxyl acylation by primer extension (SHAPE) chemical probing, we show that splicing yields distinct local 5′-UTR secondary structures in SERPINA1 transcripts. Splicing in the 5′-UTR also changes the inclusion of long upstream ORFs (uORFs). We demonstrate that disrupting the uORFs results in markedly increased translation efficiencies in luciferase reporter assays. These uORF-dependent changes suggest that α-1-antitrypsin protein expression levels are controlled at the posttranscriptional level. A leaky-scanning model of translation based on Kozak translation initiation sequences alone does not adequately explain our quantitative expression data. However, when we incorporate the experimentally derived RNA structure data, the model accurately predicts translation efficiencies in reporter assays and improves α-1-antitrypsin expression prediction in primary human tissues. Our results reveal that RNA structure governs a complex posttranscriptional regulatory program of α-1-antitrypsin expression. Crucially, these findings describe a mechanism by which genetic alterations in noncoding gene regions may result in α-1-antitrypsin deficiency.
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影响因子：
64.8
作者：
Kim, Min-Sik;Pinto, Sneha M.;Getnet, Derese;Nirujogi, Raja Sekhar;Manda, Srikanth S.;Chaerkady, Raghothama;Madugundu, Anil K.;Kelkar, Dhanashree S.;Isserlin, Ruth;Jain, Shobhit;Thomas, Joji K.;Muthusamy, Babylakshmi;Leal-Rojas, Pamela;Kumar, Praveen;Sahasrabuddhe, Nandini A.;Balakrishnan, Lavanya;Advani, Jayshree;George, Bijesh;Renuse, Santosh;Selvan, Lakshmi Dhevi N.;Patil, Arun H.;Nanjappa, Vishalakshi;Radhakrishnan, Aneesha;Prasad, Samarjeet;Subbannayya, Tejaswini;Raju, Rajesh;Kumar, Manish;Sreenivasamurthy, Sreelakshmi K.;Marimuthu, Arivusudar;Sathe, Gajanan J.;Chavan, Sandip;Datta, Keshava K.;Subbannayya, Yashwanth;Sahu, Apeksha;Yelamanchi, Soujanya D.;Jayaram, Savita;Rajagopalan, Pavithra;Sharma, Jyoti;Murthy, Krishna R.;Syed, Nazia;Goel, Renu;Khan, Aafaque A.;Ahmad, Sartaj;Dey, Gourav;Mudgal, Keshav;Chatterjee, Aditi;Huang, Tai-Chung;Zhong, Jun;Wu, Xinyan;Shaw, Patrick G.;Freed, Donald;Zahari, Muhammad S.;Mukherjee, Kanchan K.;Shankar, Subramanian;Mahadevan, Anita;Lam, Henry;Mitchell, Christopher J.;Shankar, Susarla Krishna;Satishchandra, Parthasarathy;Schroeder, John T.;Sirdeshmukh, Ravi;Maitra, Anirban;Leach, Steven D.;Drake, Charles G.;Halushka, Marc K.;Prasad, T. S. Keshava;Hruban, Ralph H.;Kerr, Candace L.;Bader, Gary D.;Iacobuzio-Donahue, Christine A.;Gowda, Harsha;Pandey, Akhilesh
通讯作者：
Pandey, Akhilesh
影响因子：
--
作者：
Araujo PR;Yoon K;Ko D;Smith AD;Qiao M;Suresh U;Burns SC;Penalva LO
通讯作者：
Penalva LO
影响因子：
3.7
作者：
Elfakess, Rofa;Dikstein, Rivka
通讯作者：
Dikstein, Rivka
原核生物和真核生物翻译起始位点附近 mRNA 稳定性降低的普遍趋势
影响因子：
4.3
作者：
Gu W;Zhou T;Wilke CO
通讯作者：
Wilke CO
影响因子：
14.9
作者：
Grillo G;Turi A;Licciulli F;Mignone F;Liuni S;Banfi S;Gennarino VA;Horner DS;Pavesi G;Picardi E;Pesole G
通讯作者：
Pesole G