Abstract
The nucleus is a highly organized and dynamic environment where regulation and coordination of processes such as gene expression and DNA replication are paramount. In recent years, noncoding RNAs have emerged as key participants in the regulation of nuclear processes. There are a multitude of functional roles for long noncoding RNA (lncRNA), mediated through their ability to act as molecular scaffolds bridging interactions with proteins, chromatin, and other RNA molecules within the nuclear environment. In this review, we discuss the diversity of techniques that have been developed to probe the function of nuclear lncRNAs, along with the ways in which those techniques have revealed insights into their mechanisms of action. Foundational observations into lncRNA function have been gleaned from molecular cytology-based, single-cell approaches to illuminate both the localization and abundance of lncRNAs in addition to their potential binding partners. Biochemical, extraction-based approaches have revealed the molecular contacts between lncRNAs and other molecules within the nuclear environment and how those interactions may contribute to nuclear organization and regulation. Using examples of well-studied nuclear lncRNAs, we demonstrate that the emerging functions of individual lncRNAs have been most clearly deduced from combined cytology and biochemical approaches tailored to study specific lncRNAs. As more functional nuclear lncRNAs continue to emerge, the development of additional technologies to study their interactions and mechanisms of action promise to continually expand our understanding of nuclear organization, chromosome architecture, genome regulation, and disease states.
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Abbreviations
- lncRNA:
-
Long non-coding RNA
- miRNA:
-
MicroRNA
- piRNA:
-
Piwi-interacting RNA
- crasiRNA:
-
Centromere repeat-associated small interacting RNA
- FISH:
-
Fluorescence in situ hybridization
- SIM:
-
Structured illumination microscopy
- STED:
-
Stimulated emission depletion
- STORM:
-
Stochastic optical reconstruction microscopy
- PALM:
-
Photo-activated localization microscopy
- NEAT1:
-
Nuclear-enriched abundant transcript 1
- XIST:
-
X-inactive specific transcript
- HSAT:
-
Human satellite
- LINE:
-
Long interspersed nuclear element
- CAST:
-
Cancer-associated satellite transcript
- RNP:
-
Ribonuclear protein
- RBP:
-
RNA binding protein
- SILAC:
-
Stable isotope labeling by amino acids in cell culture
- CHIRP:
-
Comprehensive identification of RNA-binding proteins
- RAP:
-
RNA antisense purification
- MS:
-
Mass spectrometry
- CHART:
-
Capture hybridization analysis of RNA targets
- RRM:
-
RNA recognition motif
- RBD:
-
RNA binding domain
- RBR:
-
RNA binding region
- IDR:
-
Intrinsically disordered region
- SHAPE:
-
Selective 2′-hydroxyl acylation and primer extension
- PARIS:
-
Psoralen analysis of RNA structures and interactions
- CLIP:
-
Cross-linking and immunoprecipitation
- TRIBE:
-
Targets of RNA-binding proteins identified by editing
- LIGR:
-
Ligation of interacting RNA
- ASO:
-
Antisense oligonucleotide
- LNA:
-
Locked nucleic acid
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This work was supported by funding to DMC from the Charles E. Kaufman Foundation of the Pittsburgh Foundation.
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Akkipeddi, S.M.K., Velleca, A.J. & Carone, D.M. Probing the function of long noncoding RNAs in the nucleus. Chromosome Res 28, 87–110 (2020). https://doi.org/10.1007/s10577-019-09625-x
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DOI: https://doi.org/10.1007/s10577-019-09625-x