Functions and properties of nuclear lncRNAs—from systematically mapping the interactomes of lncRNAs

Guh, Chia-Yu; Hsieh, Yu-Hung; Chu, Hao-Hua

doi:10.1186/s12929-020-00640-3

Cited by 61 publications

(39 citation statements)

References 110 publications

(152 reference statements)

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“…Many molecular processes, such as transcription, splicing, replication, histone modification, and DNA repair, occur in the nucleus and are regulated combinatorially by various protein factors. Only until recent 20 years, lncRNAs have been considered important regulators in the processes mentioned above [ 19 , [178] , [179] , [180] ]. Although some of lncRNAs ( e.g.…”

Section: Discussionmentioning

confidence: 99%

The nuclear functions of long noncoding RNAs come into focus

Song

Lin

et al. 2021

Non-coding RNA Research

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Long noncoding RNAs (lncRNAs), defined as untranslated and tightly-regulated transcripts with a length exceeding 200 nt, are common outputs of the eukaryotic genome. It is becoming increasingly apparent that many lncRNAs likely serve as important regulators in a variety of biological processes. In particular, some of them accumulate in the nucleus and function in diverse nuclear events, including chromatin remodeling, transcriptional regulation, RNA processing, DNA damage repair, etc. Here, we unite recent progresses on the functions of nuclear lncRNAs and provide insights into the future research directions of this field.

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Section: Discussionmentioning

confidence: 99%

The nuclear functions of long noncoding RNAs come into focus

Song

Lin

et al. 2021

Non-coding RNA Research

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“…Importantly, coupling of these methods to next-generation sequencing is starting to provide hints on RNA structure at the transcriptome-wide scale, the so called ‘RNA structurome’ ( 73 , 74 ). In addition, methods to assess RNA–RNA, RNA–DNA and RNA–protein interactions are increasingly developed, as reviewed in ( 75 , 76 ).…”

Section: The Rna Structuromementioning

confidence: 99%

Biological relevance and therapeutic potential of G-quadruplex structures in the human noncoding transcriptome

Tassinari

Richter

Gandellini

2021

Nucleic Acids Research

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Noncoding RNAs are functional transcripts that are not translated into proteins. They represent the largest portion of the human transcriptome and have been shown to regulate gene expression networks in both physiological and pathological cell conditions. Research in this field has made remarkable progress in the comprehension of how aberrations in noncoding RNA drive relevant disease-associated phenotypes; however, the biological role and mechanism of action of several noncoding RNAs still need full understanding. Besides fulfilling its function through sequence-based mechanisms, RNA can form complex secondary and tertiary structures which allow non-canonical interactions with proteins and/or other nucleic acids. In this context, the presence of G-quadruplexes in microRNAs and long noncoding RNAs is increasingly being reported. This evidence suggests a role for RNA G-quadruplexes in controlling microRNA biogenesis and mediating noncoding RNA interaction with biological partners, thus ultimately regulating gene expression. Here, we review the state of the art of G-quadruplexes in the noncoding transcriptome, with their structural and functional characterization. In light of the existence and further possible development of G-quadruplex binders that modulate G-quadruplex conformation and protein interactions, we also discuss the therapeutic potential of G-quadruplexes as targets to interfere with disease-associated noncoding RNAs.

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“…These structural elements can form through intramolecular interactions within the same RNA molecule or intermolecular interactions with other molecules such as other RNA, DNA, and proteins. Identifying RNA motifs, structures, and interactions with binding partners is critical for understanding gene regulation and function [ 50 , 51 , 52 , 53 ].…”

Section: Lncrna Structure and Its Link To Functionsmentioning

confidence: 99%

Challenges and Strategies in Ascribing Functions to Long Noncoding RNAs

Zhao

Teng

Yao

et al. 2020

Cancers

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Long noncoding RNAs (lncRNAs) are involved in many physiological and pathological processes, such as development, aging, immunity, and cancer. Mechanistically, lncRNAs exert their functions through interaction with proteins, genomic DNA, and other RNA, leading to transcriptional and post-transcriptional regulation of gene expression, either in cis or in trans; it is often difficult to distinguish between these two regulatory mechanisms. A variety of approaches, including RNA interference, antisense oligonucleotides, CRISPR-based methods, and genetically engineered mouse models, have yielded abundant information about lncRNA functions and underlying mechanisms, albeit with many discrepancies. In this review, we elaborate on the challenges in ascribing functions to lncRNAs based on the features of lncRNAs, including the genomic location, copy number, domain structure, subcellular localization, stability, evolution, and expression pattern. We also describe a framework for the investigation of lncRNA functions and mechanisms of action. Rigorous characterization of cancer-implicated lncRNAs is critical for the identification of bona fide anticancer targets.

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Functions and properties of nuclear lncRNAs—from systematically mapping the interactomes of lncRNAs

Cited by 61 publications

References 110 publications

The nuclear functions of long noncoding RNAs come into focus

The nuclear functions of long noncoding RNAs come into focus

Biological relevance and therapeutic potential of G-quadruplex structures in the human noncoding transcriptome

Challenges and Strategies in Ascribing Functions to Long Noncoding RNAs

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