Nuclear Long Noncoding RNAs: Key Regulators of Gene Expression

• Published in: Trends in genetics Vol. 34; no. 2; pp. 142 - 157
• Main Authors: Sun, Qinyu, Hao, Qinyu, Prasanth, Kannanganattu V.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.02.2018
• Subjects: Animals; Cell Nucleus - genetics; Cell Nucleus - metabolism; Chromatin - chemistry; Chromatin - metabolism; Chromosomal Proteins, Non-Histone - genetics; Chromosomal Proteins, Non-Histone - metabolism; Humans; Neoplasms - genetics; Neoplasms - metabolism; Neoplasms - pathology; Polycomb-Group Proteins - genetics; Polycomb-Group Proteins - metabolism; RNA Processing, Post-Transcriptional; RNA, Long Noncoding - classification; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; Transcription Factors - genetics; Transcription Factors - metabolism; Transcription, Genetic; X Chromosome Inactivation
• ISSN: 0168-9525
• DOI: 10.1016/j.tig.2017.11.005

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 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.