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A huge number of non-protein-coding (noncoding) transcripts have recently been identified by a series of large-scale transcriptome studies, and "long noncoding RNA (lncRNA)" has been arbitrarily defined as transcripts longer than 200 nt lacking protein-coding capacity. The lncRNAs constitute at least one-third of the genes in the human genome and exhibit more tissue- and temporal-specific expression patterns compared with protein-coding genes. Interestingly, many lncRNAs are mammalian-specific and are exclusively expressed in the brain, and a large fraction of lncRNAs associate with chromatin-modifying complexes and regulate epigenetic gene expression. Aside from the transcriptional regulators, another group of lncRNAs is abundantly expressed and accumulates in the nucleus, forming distinct structures or "nuclear bodies" in the nucleus. We are especially interested in the function of abundant nuclear lncRNAs, such as Nuclear paraspeckle assembly transcript 1 (Neat1), Metastasis-associated lung adenocarcinoma transcript 1 (Malat1), and Gomafu (Gomafu means speckled pattern in Japanese), all of which are specific to higher vertebrate species.