Biomaterial Database

Diverse functions of nuclear non-coding RNAs in eukaryotic gene expression. 2012

Madoka Chinen, and Tokio Tani

Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, 2-39-1, Kurokami, Kumamoto 860-8555, Japan.

Recent genome-wide analyses revealed that eukaryotic genomes are almost entirely transcribed, generating a large number of short or long non-protein coding RNAs (non-coding RNAs; ncRNAs). Rapidly accumulating experimental evidence suggests that ncRNAs are not just transcriptional noise, but have biological roles in gene expression. In this review, we focus on the functions of nuclear-localized ncRNAs including the spliceosomal small nuclear RNAs. These nuclear ncRNAs play diverse regulatory roles in a wide-range of nuclear reactions, such as transcription, precursor-mRNA (pre-mRNA) splicing, nuclear structure formation, nuclear trafficking, and chromatin remodeling. The regulatory functions of ncRNAs in these reactions are reinforced by target-site recognition through base-pairing or formation of an RNA/DNA triple helix. Recent studies revealed an unexpected linkage between the machineries for RNA interference (RNAi)-mediated gene silencing and pre-mRNA splicing. In addition, the biogenesis of some ncRNAs was found to overlap with the pathway of pre-mRNA splicing. Our understanding of the mechanisms of coordinated gene regulation in the nucleus has increased dramatically through studies on nuclear ncRNAs. A new paradigm of "ncRNA regulation" is now emerging.

UI	MeSH Term	Description	Entries
D006570	Heterochromatin	The portion of chromosome material that remains condensed and is transcriptionally inactive during INTERPHASE.	Heterochromatins
D012323	RNA Processing, Post-Transcriptional	Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein.	Post-Transcriptional RNA Modification,RNA Processing,Post-Transcriptional RNA Processing,Posttranscriptional RNA Processing,RNA Processing, Post Transcriptional,RNA Processing, Posttranscriptional,Modification, Post-Transcriptional RNA,Modifications, Post-Transcriptional RNA,Post Transcriptional RNA Modification,Post Transcriptional RNA Processing,Post-Transcriptional RNA Modifications,Processing, Posttranscriptional RNA,Processing, RNA,RNA Modification, Post-Transcriptional,RNA Modifications, Post-Transcriptional
D015870	Gene Expression	The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.	Expression, Gene,Expressions, Gene,Gene Expressions
D044127	Epigenesis, Genetic	A genetic process by which the adult organism is realized via mechanisms that lead to the restriction in the possible fates of cells, eventually leading to their differentiated state. Mechanisms involved cause heritable changes to cells without changes to DNA sequence such as DNA METHYLATION; HISTONE modification; DNA REPLICATION TIMING; NUCLEOSOME positioning; and heterochromatization which result in selective gene expression or repression.	Epigenetic Processes,Epigenetic Process,Epigenetics Processes,Genetic Epigenesis,Process, Epigenetic,Processes, Epigenetic,Processes, Epigenetics
D020868	Gene Silencing	Interruption or suppression of the expression of a gene at transcriptional or translational levels.	Gene Inactivation,Inactivation, Gene,Silencing, Gene
D022661	RNA, Untranslated	RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.	Noncoding RNA,RNA, Non-Coding,RNA, Non-Peptide-Coding,RNA, Non-Protein-Coding,RNA, Noncoding,RNA, Nontranslated,npcRNA,Non-Coding RNA,Non-Peptide-Coding RNA,Non-Protein-Coding RNA,Nontranslated RNA,RNA, Non Coding,RNA, Non Peptide Coding,RNA, Non Protein Coding,Untranslated RNA
D034622	RNA Interference	A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.	Gene Silencing, Post-Transcriptional,Post-Transcriptional Gene Silencing,Co-Suppression,Cosuppression,Posttranscriptional Gene Silencing,RNA Silencing,RNAi,Co Suppression,Gene Silencing, Post Transcriptional,Gene Silencing, Posttranscriptional,Gene Silencings, Posttranscriptional,Interference, RNA,Post Transcriptional Gene Silencing,Post-Transcriptional Gene Silencings,Silencing, Post-Transcriptional Gene