Nuclear Long Noncoding RNAs: Key Regulators of Gene Expression

A significant fraction of lncRNAs is retained in the nucleus, where several of them participate in vital nuclear processes, including chromatin organization, transcriptional and post-transcriptional gene expression, and nuclear structure organization. The advent of new techniques, including chromatin isolation by RNA purification (CHIRP), capture hybridization analysis of RNA targets (CHART), RNA antisense purification (RAP), and mapping RNA genome interactions (MARGI), provides researchers more opportunity to study the chromatin-binding features of nuclear-retained lncRNAs, especially at the genomic level. Many nuclear-retained lncRNAs are biomarkers of diagnosis and/or prognosis and/or therapeutic targets of diseases, including cancer. The development of new computational tools and/or algorithms is required to determine the potential correlation between nuclear-retained lncRNA sequences and/or structures and their functions and/or localization. A significant portion of the human genome encodes genes that transcribe long nonprotein-coding RNAs (lncRNAs). A large number of lncRNAs localize in the nucleus, either enriched on the chromatin or localized to specific subnuclear compartments. Nuclear lncRNAs participate in several biological processes, including chromatin organization, and transcriptional and post-transcriptional gene expression, and also act as structural scaffolds of nuclear domains. Here, we highlight recent studies demonstrating the role of lncRNAs in regulating gene expression and nuclear organization in mammalian cells. In addition, we update current knowledge about the involvement of the most-abundant and conserved lncRNA, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), in gene expression control. A significant portion of the human genome encodes genes that transcribe long nonprotein-coding RNAs (lncRNAs). A large number of lncRNAs localize in the nucleus, either enriched on the chromatin or localized to specific subnuclear compartments. Nuclear lncRNAs participate in several biological processes, including chromatin organization, and transcriptional and post-transcriptional gene expression, and also act as structural scaffolds of nuclear domains. Here, we highlight recent studies demonstrating the role of lncRNAs in regulating gene expression and nuclear organization in mammalian cells. In addition, we update current knowledge about the involvement of the most-abundant and conserved lncRNA, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), in gene expression control. four techniques developed to map the genomic binding sites of RNA. They are often used to discover the roles and mechanisms of lncRNAs on chromatin. Speckles are conserved nuclear domains that are present in the form of 10–30 irregularly shaped nuclear structures. Speckles are enriched with RNAs and proteins involved in pre-mRNA processing and mRNP export. Initial studies suggest that speckles act as storage and/or assembly sites of splicing factors, from where these proteins are recruited to active genes dispersed throughout the nucleoplasm. Recent studies further indicate that nuclear speckles act as a structural domain that controls the efficiency and integration of distinct steps in gene expression, ranging from transcription and splicing to mRNA export. a type of subnuclear domain present in the interchromatin space of mammalian cells. They are nucleated by the lncRNA Neat1. The core paraspeckle proteins include PSF/SFPQ, P54NRB/NONO, and PSPC1. comprises two major types: PRC1 and PRC2. These complexes have important roles in chromatin compaction and transcriptional silencing. a chromatin-remodeling complex. This complex contains multiple subunits, including ATPase, which allows it to remodel nucleosomes from the energy generated through ATP hydrolysis. a phenomenon observed during mammalian female development, whereby most of the genes are inactivated (transcriptional silencing) on one of the two X chromosomes.