Genome regulation by long noncoding RNAs

By Johannes Rinn, Howard Y. Chang. Annual Review of Biochemistry, 2012

3,959 citations recorded by the source corpus.

The central dogma of gene expression is that DNA is transcribed into messenger RNAs, which in turn serves as the template for protein synthesis. The discovery of extensive transcription of large RNA transcripts that do not code for proteins, termed long noncoding RNAs (lncRNAs) provide an important new perspective on the centrality of RNA in gene regulation. Here we discuss genome-scale strategies to discover and characterize lncRNAs. An emerging theme from multiple model systems is that lncRNAs form extensive networks of ribonucleoprotein (RNP) complexes with numerous chromatin regulators, and target these enzymatic activities to appropriate locations in the genome. Consistent with this notion, long noncoding RNAs can function as modular scaffolds to specify higher order organization in RNP complexes and in chromatin states. The importance of these modes of regulation is underscored by the newly recognized roles of long RNAs for proper gene control across all kingdoms of life.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/db8f976d3d49b74ce586bf40652f9875563adfe9

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Citations in the corpus

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution (2015, background): “While a number of studies have implicated functional roles lncRNAs [1-3] the vast majority remain uncharacterized [4,5].”
The Landscape of long non-coding RNA classification (2015, positive): “These long RNAs are involved in linking the dynamics of nuclear architecture, chromatin signalling plasticity, and transcriptional regulation [69].”
CRISPRi-based genome-scale identification of functional long non-coding RNA loci in human cells (2016, positive): “By catalyzing repressive chromatin modifications around the TSS and serving as a transcriptional roadblock, CRISPRi tests a broad range of lncRNA gene functions including the production of cis- and trans-acting RNA transcripts (4), cis-mediated regulation related to lncRNA transcription itself (26–2”
lincRNAs: Genomics, Evolution, and Mechanisms (2013, positive): “, 1996), clearly are functional, and the roster of biological processes in which long noncoding RNAs are reported to play key roles is rapidly growing and now includes cell-cycle regulation, apoptosis, and establishment of cell identity (reviewed in Ponting et al., 2009; Pauli et al., 2011; Rinn and”
3D RNA and Functional Interactions from Evolutionary Couplings. (2015, positive): “For instance, transcriptional profiling has revealed large numbers of non-coding RNA genes, with unknown functions beyond context-specific expression (Eddy, 2014; Rinn and Chang, 2012).”
Nanotoxicology in Caenorhabditis elegans (2018, background): “Additionally, although the PEG-modified GO (GO-PEG) are relatively safe under normal conditions, GO-PEG could still significantly reduce the lifespan under juglone-induced oxidative stress [49].”
Long Noncoding RNA MALAT1 Controls Cell Cycle Progression by Regulating the Expression of Oncogenic Transcription Factor B-MYB (2013, background): “LncRNAs are involved in several crucial functions: they can act as a scaffold to keep several proteins tethered to a specific cellular compartment, act as a guide to recruit proteins to a specific chromatin site or influence local chromatin architecture [3,4,13,14,15].”
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Xist nucleates local protein gradients to propagate silencing across the X chromosome (2021, background): “Mammalian genomes encode thousands of long non-coding (lnc) RNAs, many of which play key roles in regulating gene expression by localizing effector proteins to genomic targets (Engreitz et al., 2016; Rinn and Chang, 2012; Statello et al., 2021).”
CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features (2017, background): “As many important biological roles of long ncRNAs (lncRNAs) have been revealed by recent studies performed in this decade (7), CPC2 adopted a more balanced calling of protein-coding and non-coding transcripts, which is more suitable for current transcriptome studies.”