Nuclear-retained long noncoding RNAs

描述（由申请人提供）：我们最近发现了新的内含子衍生的长链非编码rna (lncRNAs)，它们在两端由snoRNA机制加工（我们将这些rna命名为sno-lncRNAs）。大多数snorna是由内含子加工而成的。脱支后，外切酶降解内含子而非snoRNAs，因为这些内含子与阻止降解并导致snoRNP组装的特定因子相关。sno - lncrna由含有两个snorna的内含子加工而成。在核外溶剪过程中，snorna之间的序列不会被降解，导致缺乏5‘帽结构或3’聚(A)尾的lncrna积累。这些rna中的一些可以在细胞中积累到非常高的水平，但之前被遗漏了，因为它们很长，它们来自内含子，并且它们缺乏poly(A)尾巴。这些构成了一类全新的核lncrna，本研究建议对它们进行更详细的研究。迄今为止的研究结果表明，只要内含子含有两个而不是一个snoRNA基因，就可以产生sno-lncRNAs。到目前为止，这些rna可以在每一个被检测的细胞中找到，并且似乎在组织中广泛表达。此外，编码这些最丰富的rna （15q11-q13）的基因组区域在一种重要的人类遗传疾病Prader-Willi综合征中被特异性删除。我们将描述sno- lncrna是如何制造的，与它们相关的蛋白质是什么，以及它们有多少。此外，我们将询问它们在细胞中的作用，并开始解决它们在普瑞德-威利综合征中的可能作用。在第一个目标中，我们

DESCRIPTION (provided by applicant): We have recently discovered novel intron-derived long noncoding RNAs (lncRNAs) that are processed on both ends by the snoRNA machinery (we named these sno-lncRNAs). Most snoRNAs are processed from introns. After debranching, exonucleases degrade the introns but not the snoRNAs because these associate with specific factors that prevent degradation and lead to snoRNP assembly. Sno-lncRNAs are processed from introns that contain two snoRNAs. During exonucleolytic trimming, the sequences between the snoRNAs are not degraded, leading to the accumulation of lncRNAs lacking 5' cap structures or 3' poly(A) tails. Some of these RNAs can accumulate to very high levels in cells but were missed before because they are long, they derive from introns, and they lack poly(A) tails. These constitute an entirely new class of nuclear lncRNAs and this proposal is to study them in greater detail. Results so far suggest that whenever introns contain not one but two snoRNA genes, sno-lncRNAs can be produced. Such RNAs can be found in every cell examined so far, and appear to be widely expressed in tissues. Further, the genomic region encoding some of the most abundant of these RNAs (15q11-q13) is specifically deleted in an important human genetic disease, Prader-Willi Syndrome. We will characterize how sno-lncRNAs are made, what proteins associate with them and how many of them there are. In addition, we will ask what they do in cells and begin to address their possible role in Prader-Willi Syndrome. In the first aim, we will characterize the structure and expression of sno-lncRNAs. We will also examine their sub-nuclear localization, and efforts will be made to follow their synthesis and localization dynamically and throughout the cell cycle. Finally in this aim, we will carry out genomewide studies in several different cell types and using several different approaches in order to identify more sno-lncRNAs, some of which will be studied in greater detail. The second aim is to investigate the mechanism of action of sno-lncRNAs. Of particular interest is the connection of the chr15 sno-lncRNAs to Fox1 family splicing regulators. Compelling evidence suggests that these lncRNAs may bind Fox2 and perhaps Fox1 with high affinity. Thus, they may act as molecular "sponges" to titrate splicing factors since in preliminary experiments we have found that they alter splicing patterns. This angle will be examined in detail and could lead directly to new insights into Prader-Willi pathology. We will also ask whether some sno-lncRNAs can alter chromatin organization like a number of other lncRNAs do. Finally, since these new RNAs appear to be relatively stable and strictly retained in the nucleus, we will begin to use our knowledge of their expression to generate a new class of vectors for nuclear expression of a variety of sequences.