Long noncoding RNAs as Organizers of Nuclear Architecture

Cheng, Lü; Ming, Hui; Zhu, Minzhe; Wen, Bo

doi:10.1007/s11427-016-5012-y

Cited by 9 publications

(5 citation statements)

References 80 publications

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“…The mammalian genome is organized in higher order chromatin structures, forming intra- and inter-chromosomal loops and membrane-less nuclear compartments, such as speckles and paraspeckles. LncRNAs are increasingly being recognized as essential organizers of this architecture [ 136 , 137 ]. WiNTRLINC1 (WNT-regulated lincRNA1) is a direct WNT/β-catenin target gene that is located in the vicinity of the ASCL2 gene locus and participates in the formation of an intra-chromosomal loop ( Fig.…”

Section: Crosstalk Mechanisms Of Wnt/β-catenin Signaling and Lncrnasmentioning

confidence: 99%

Crosstalk mechanisms between the WNT signaling pathway and long non-coding RNAs

Zarkou

Galaras

Giakountis

et al. 2018

Non-coding RNA Research

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The WNT/β-catenin signaling pathway controls a plethora of biological processes throughout animal development and adult life. Because of its fundamental role during animal lifespan, the WNT pathway is subject to strict positive and negative multi-layered regulation, while its aberrant activity causes a wide range of pathologies, including cancer. At present, despite the inroads into the molecules involved in WNT-mediated transcriptional responses, the fine-tuning of WNT pathway activity and the totality of its target genes have not been fully elucidated. Over the past few years, long non-coding RNAs (lncRNAs), RNA transcripts longer that 200nt that do not code for proteins, have emerged as significant transcriptional regulators. Recent studies show that lncRNAs can modulate WNT pathway outcome by affecting gene expression through diversified mechanisms, from the transcriptional to post-translational level. In this review, we selectively discuss those lncRNA-mediated mechanisms we believe the most important to WNT pathway modulation.

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Section: Crosstalk Mechanisms Of Wnt/β-catenin Signaling and Lncrnasmentioning

confidence: 99%

Crosstalk mechanisms between the WNT signaling pathway and long non-coding RNAs

Zarkou

Galaras

Giakountis

et al. 2018

Non-coding RNA Research

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“…The genome is in fact a packaged 3D structure that forms higher-order chromatin structures, such as intra- and inter-chromosomal loops and nuclear compartmentalization [ 102 ]. This is nowadays known to be the result of specific and regulated interactions between DNA, proteins and RNAs, and lncRNAs are increasingly being recognized as important organizers of this architecture [ 9 , 103 , 104 ]. Moreover, emerging evidence supports the notion that nuclear compartmentalization could be based on liquid-phase separation dependent on the biophysical properties of the molecules that constitute the distinct chromatin domains [ 105 ].…”

Section: Lncrnas and Higher-order Structuresmentioning

confidence: 99%

The multidimensional mechanisms of long noncoding RNA function

Marchese¹,

Raimondi²,

Huarte³

2017

Genome Biol

822

652

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A major shift in our understanding of genome regulation has emerged recently. It is now apparent that the majority of cellular transcripts do not code for proteins, and many of them are long noncoding RNAs (lncRNAs). Increasingly, studies suggest that lncRNAs regulate gene expression through diverse mechanisms. We review emerging mechanistic views of lncRNAs in gene regulation in the cell nucleus. We discuss the functional interactions that lncRNAs establish with other molecules as well as the relationship between lncRNA transcription and function. While some of these mechanisms are specific to lncRNAs, others might be shared with other types of genes.

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“…RNA-FISH experiments led to our current understanding that many lncRNAs are fundamental constituents of subnuclear compartments (Quinodoz and Guttman 2014;Rinn and Guttman 2014;Vance and Ponting 2014;Cheng et al 2016;Engreitz et al 2016;Melé and Rinn 2016). Consistent with this notion, a similar and contemporary study of the lncRNA Gomafu (MIAT/Rncr2) showed a stunning nuclear localization pattern (Sone et al 2007).…”

Section: The Basics: Complementary Probe Preparation For Rna-fishmentioning

confidence: 78%

Illuminating Genomic Dark Matter with RNA Imaging

Raj

Rinn

2019

Cold Spring Harb Perspect Biol

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In the postgenomic era, it is clear that the human genome encodes thousands of long noncoding RNAs (lncRNAs). Along the way, RNA imaging (e.g., RNA fluorescence in situ hybridization [RNA-FISH]) has been instrumental in identifying powerful roles for lncRNAs based on their subcellular localization patterns. Here, we explore how RNA imaging technologies have shed new light on how, when, and where lncRNAs may play functional roles. Specifically, we will synthesize the underlying principles of RNA imaging techniques by exploring several landmark lncRNA imaging studies that have illuminated key insights into lncRNA biology. Outline 1 Introduction 2 The basics: Complementary probe preparation for RNA-FISH 3 Neat RNA-FISH: cDNA and cRNA pattern recognition of lncRNAs 4 Single-molecule RNA-FISH approaches 5 Location-tracking lncRNAs: One molecule at a time 6 Entering the fourth dimension: Live-cell RNA imaging 7 CRISPR-based visualization of lncRNA loci 8 Concluding remarks References 3 Authorship was listed alphabetically.

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Long noncoding RNAs as Organizers of Nuclear Architecture

Cited by 9 publications

References 80 publications

Crosstalk mechanisms between the WNT signaling pathway and long non-coding RNAs

Crosstalk mechanisms between the WNT signaling pathway and long non-coding RNAs

The multidimensional mechanisms of long noncoding RNA function

Illuminating Genomic Dark Matter with RNA Imaging

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