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Probing the function of long noncoding RNAs in the nucleus

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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Funding

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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Keywords

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