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Probing the function of long noncoding RNAs in the nucleus


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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Fig. 1
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Fig. 3



Long non-coding RNA




Piwi-interacting RNA


Centromere repeat-associated small interacting RNA


Fluorescence in situ hybridization


Structured illumination microscopy


Stimulated emission depletion


Stochastic optical reconstruction microscopy


Photo-activated localization microscopy


Nuclear-enriched abundant transcript 1


X-inactive specific transcript


Human satellite


Long interspersed nuclear element


Cancer-associated satellite transcript


Ribonuclear protein


RNA binding protein


Stable isotope labeling by amino acids in cell culture


Comprehensive identification of RNA-binding proteins


RNA antisense purification


Mass spectrometry


Capture hybridization analysis of RNA targets


RNA recognition motif


RNA binding domain


RNA binding region


Intrinsically disordered region


Selective 2′-hydroxyl acylation and primer extension


Psoralen analysis of RNA structures and interactions


Cross-linking and immunoprecipitation


Targets of RNA-binding proteins identified by editing


Ligation of interacting RNA


Antisense oligonucleotide


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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SMKA, AV, and DMC conceived and wrote the manuscript.

Correspondence to Dawn M. Carone.

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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 (2020). https://doi.org/10.1007/s10577-019-09625-x

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  • Noncoding RNA
  • Nuclear organization
  • Genome regulation
  • Molecular cytology
  • Microscopy
  • Biochemical methods