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2006). was suppressed inMEN /-depleted cells. Our findings indicate that theMEN /non-coding RNAs are essential structural/organizational components of paraspeckles. Sequencing of the human and other mammalian genomes has revealed the number of protein-coding genes to be in the range of 20,00025,000 (Waterston et al. 2002;International Human Genome Sequencing Consortium 2004), representing <2% of the total genomic sequence. However, recent studies of the mammalian transcriptome have shown that the majority of the genome is transcribed and that many transcripts lack protein-coding capacity (Carninci et al. 2005;Birney et al. 2007;Kapranov et al. 2007). Such analyses have prompted considerable discussion as to whether these non-coding RNAs (ncRNAs) simply represent transcriptional noise or are involved in cellular functions (for review, seeMattick and Makunin 2006). Interestingly, large-scale studies of ncRNAs have shown that many are dynamically regulated during differentiation and exhibit cell- and tissue-specific expression patterns (Ravasi et al. 2006;Dinger et al. 2008;Mercer et al. 2008). These observations support the contention that ncRNAs are likely to have functional roles in the cell, some of which may serve in regulatory and/or structural paradigms (for review, seeMattick 2004). Although the number of ncRNAs identified has increased exponentially, very few ncRNAs have thus far been assigned a cellular function Montelukast sodium (for review, seeCosta 2005;Prasanth and Spector 2007). Interestingly, several ncRNAs have been shown to be involved in the regulation of the transcriptional state of a locus or at the level of a single chromosome. For example, expression of the long (>100 kb) ncRNAAirn(AntisenseIgf2rRNA, also known asAir) is associated with silencing of theIgf2r,Slc22a2, andSlc22a3genes in mice (Sleutels et al. 2002). In another case, it was suggested that the translocation of nuclear factor of activated T cells (NFAT) into the nucleus is repressed by non-coding repressor of NFAT (NRON) ncRNAs, a series of transcripts ranging in size between 0.8 and 3.7 kb (Willingham et al. 2005). In fission yeast, a recent report argued that transcription of ncRNAs at the promoter region can induce chromatin remodeling at thefbp1+locus (Hirota et al. 2008). Perhaps the best studied ncRNAs areXist(X-inactive specific transcript) andTsix(X inactive-specific transcript, antisense), key players in dosage compensation of the mammalian X chromosome. In females,Tsixis an antisense transcript ofXist, and its expression determines which X chromosome will be inactivated for dosage compensation (for review, seeHeard and Disteche 2006;Erwin and Lee 2008). At the stage of X inactivation in mammalian development,Xist/XISTRNA, 1517 kb in mouse and 19 kb in human, is transcribed from one of the two X chromosomes. This ncRNA subsequently coats the chromosome from which it is transcribed and represents part of the mechanism by which transcriptional inactivation of the coated chromosome is achieved (for review, Montelukast sodium seePlath et al. 2002;Heard and Disteche 2006). In addition, several ncRNAs have been shown to be misregulated in various cancers (for review, seeCosta 2005;Prasanth and Spector 2007). For example, elevated levels of the ncRNAMALAT1(metastasis associated in lung adenocarcinoma transcript 1) were Montelukast sodium originally identified in individuals exhibiting a high risk for metastasis of non-small cell lung tumor (Ji et al. 2003). More recently,MALAT1ncRNA was also shown to be present at higher levels in many other cancers, including uterine endometrial stromal carcinoma and hepatocellular carcinoma (Yamada et al. 2006;Lin et al. 2007). Increased expression of another ncRNA,PCA3(prostate cancer antigen 3, also known asDD3), has been observed in individuals with prostate cancer (Bussemakers et al. 1999). Although the functions of these ncRNAs are not yet known, they may represent useful diagnostic markers in a large number of different cancers (for review, seeCosta 2005;Prasanth and Spector 2007). Determining the subcellular localization of ncRNAs is important for Rabbit Polyclonal to Chk2 (phospho-Thr383) providing insights into their potential partners and the functional pathways with which they interact. The mammalian nucleus is a highly organized organelle with several membraneless subcompartments such as Cajal bodies, nucleoli, paraspeckles, PML bodies, and speckles, to name just a few (for review, seeSpector 2001,2006). Among them, paraspeckles were initially discovered via the identification and characterization of a paraspeckle-associated protein in a proteomic analysis of human nucleoli (Fox et al. 2002). Paraspeckles generally appear in clusters and are frequently localized in the nucleoplasm close to nuclear speckles, where pre-mRNA splicing factors are stored, assembled, and/or modified. Inhibition of RNA polymerase II transcription results in its protein components relocating to the periphery of nucleoli. As paraspeckles.