Ribosome-omics of the human ribosome.
Ribosome-omics of the human ribosome.
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DOI：
10.1261/rna.043653.113
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发表时间：
2014-07
期刊：
影响因子：
--
通讯作者：
Warner JR
中科院分区：
文献类型：
--
作者：
Gupta V;Warner JR
本文描述了与编码核糖体蛋白的mrna水平相关的RNA-seq数据的信息学分析。主要发现是这些mrna的绝大多数摩尔比在彼此的三倍之内。此外，其中一些mrna，显然是从“假基因”转录而来，以组织特异性的方式表达。大量的RNA-seq数据不仅提供了整个转录组的概述，而且还提供了关注特定领域的工具。我们对核糖体合成的关注是，编码核糖体蛋白（RPs）的mrna的丰度是否与核糖体组装中RPs的等摩尔需求相匹配。起初，我们惊讶地发现，在ENCODE和其他来源的图谱数据中，编码不同rp的mrna的水平相差近100倍。然而，在纠正了由RP mrna衍生的2000多个假基因的存在所引入的定位歧义之后，我们表明，对于80%-90%的RP基因，mrna的摩尔比变化小于三倍，几乎没有组织特异性。然而，由于需要等量的RP，因此一定存在更丰富的RP mrna的缓慢或受调节的翻译和/或未使用的RP的大量周转。此外，7个RPs有附属基因，其中3个是通过引入启动子和/或上游内含子“拯救”的假基因。其中一些以组织特异性的方式转录，例如睾丸中的RPL10L和肌肉中的RPL3L，导致核糖体结构从一个组织到另一个组织的潜在差异。在RP基因的376个内含子中，单个内含子以组织特异性方式选择性剪接。
This paper describes an informatic analysis of RNA-seq data relevant to levels of mRNAs encoding ribosomal proteins. Major findings are that the vast majority of molar ratios of these mRNAs are within threefold of one another. In addition, some of these mRNAs, apparently transcribed from “pseudogenes,” are expressed in a tissue-specific manner. The torrent of RNA-seq data becoming available not only furnishes an overview of the entire transcriptome but also provides tools to focus on specific areas of interest. Our focus on the synthesis of ribosomes asked whether the abundance of mRNAs encoding ribosomal proteins (RPs) matched the equimolar need for the RPs in the assembly of ribosomes. We were at first surprised to find, in the mapping data of ENCODE and other sources, that there were nearly 100-fold differences in the level of the mRNAs encoding the different RPs. However, after correcting for the mapping ambiguities introduced by the presence of more than 2000 pseudogenes derived from RP mRNAs, we show that for 80%–90% of the RP genes, the molar ratio of mRNAs varies less than threefold, with little tissue specificity. Nevertheless, since the RPs are needed in equimolar amounts, there must be sluggish or regulated translation of the more abundant RP mRNAs and/or substantial turnover of unused RPs. In addition, seven of the RPs have subsidiary genes, three of which are pseudogenes that have been “rescued” by the introduction of promoters and/or upstream introns. Several of these are transcribed in a tissue-specific manner, e.g., RPL10L in testis and RPL3L in muscle, leading to potential variation in ribosome structure from one tissue to another. Of the 376 introns in the RP genes, a single one is alternatively spliced in a tissue-specific manner.
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