A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains.
A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains.
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DOI：
10.1186/1471-2164-8-39
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发表时间：
2007-02-01
期刊：
影响因子：
4.4
通讯作者：
Chess, Andrew
中科院分区：
文献类型：
--
作者：
Hutchinson, John N;Ensminger, Alexander W;Clemson, Christine M;Lynch, Christopher R;Lawrence, Jeanne B;Chess, Andrew
非编码RNA物种在真核细胞中扮演着不同的角色。虽然最近的注意力主要集中在较小的RNA物种上，但较大的非编码转录本也被认为在哺乳动物细胞中高度丰富。为了寻找可能控制基因表达或mRNA代谢的大的非编码RNA，我们使用Affymetrix表达阵列来鉴定显示核浓缩的多腺苷RNA转录本。这一筛选只发现了三个转录本；XIST和两个独特的非编码核丰富转录(NET)RNA，它们位于人类11号染色体上，相距不到70kb：NEAT1，一个来自TncRNA编码基因的非编码RNA，以及NEAT2(也称为Malat-1)。虽然这两个整齐的转录本彼此没有显著的同源性，但每个转录本在哺乳动物谱系中都是保守的，这表明这些非编码RNA具有重要的功能。NEAT2对于非编码RNA来说非常保守，甚至比XIST都要保守。对公开可用的小鼠转录组数据进行的生物信息学分析支持了我们在人类细胞中的发现，因为它们证实了这些非编码RNA的小鼠同源物也是核浓缩的。RNA FISH分析表明，这些非编码RNA在mRNA新陈代谢中发挥作用，因为它们表明这些RNA物种与人和小鼠细胞中的SC35核斑点密切相关。这些研究表明，其中一个转录本NEAT1定位于这些结构域的外围，而邻近的转录本NEAT2是长期寻找的核斑点多腺化成分的一部分。我们对两个哺乳动物物种的全基因组筛选显示，细胞核中不超过三个丰富的大型非编码多腺苷化RNA；规范的大型非编码RNA XIST和NEAT1和NEAT2。这些非编码RNA在mRNA代谢中的功能表明，它们在多种哺乳动物中具有高度的保守性，并与SC35剪接域密切相关。
Noncoding RNA species play a diverse set of roles in the eukaryotic cell. While much recent attention has focused on smaller RNA species, larger noncoding transcripts are also thought to be highly abundant in mammalian cells. To search for large noncoding RNAs that might control gene expression or mRNA metabolism, we used Affymetrix expression arrays to identify polyadenylated RNA transcripts displaying nuclear enrichment. This screen identified no more than three transcripts; XIST, and two unique noncoding nuclear enriched abundant transcripts (NEAT) RNAs strikingly located less than 70 kb apart on human chromosome 11: NEAT1, a noncoding RNA from the locus encoding for TncRNA, and NEAT2 (also known as MALAT-1). While the two NEAT transcripts share no significant homology with each other, each is conserved within the mammalian lineage, suggesting significant function for these noncoding RNAs. NEAT2 is extraordinarily well conserved for a noncoding RNA, more so than even XIST. Bioinformatic analyses of publicly available mouse transcriptome data support our findings from human cells as they confirm that the murine homologs of these noncoding RNAs are also nuclear enriched. RNA FISH analyses suggest that these noncoding RNAs function in mRNA metabolism as they demonstrate an intimate association of these RNA species with SC35 nuclear speckles in both human and mouse cells. These studies show that one of these transcripts, NEAT1 localizes to the periphery of such domains, whereas the neighboring transcript, NEAT2, is part of the long-sought polyadenylated component of nuclear speckles. Our genome-wide screens in two mammalian species reveal no more than three abundant large non-coding polyadenylated RNAs in the nucleus; the canonical large noncoding RNA XIST and NEAT1 and NEAT2. The function of these noncoding RNAs in mRNA metabolism is suggested by their high levels of conservation and their intimate association with SC35 splicing domains in multiple mammalian species.