Challenges and Strategies in Ascribing Functions to Long Noncoding RNAs

Zhao, Yang; Teng, Hongqi; Yao, Fan; Yap, Shannon; Sun, Yutong; Ma, Li

doi:10.3390/cancers12061458

Cited by 39 publications

(32 citation statements)

References 165 publications

(218 reference statements)

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“…Among the regulatory molecules in the interaction between CAFs and cancer cells, lncRNAs are relatively novel biomolecules and are receiving more and more attention from cancer researchers. However, because they have lower expression levels, lower stability, less accurate annotation, and more complicated functional mechanisms compared with protein-coding mRNAs and miRNAs, more difficult and higher barriers lie ahead of lncRNA research [ 90 ]. Recently, the development of novel methodologies, such as RNA IP followed by sequencing, high-throughput sequencing cross-linking IP, and chromatin isolation by RNA purification sequencing, has enabled broader and more detailed studies to elucidate the functional molecular mechanisms of lncRNAs [ 91 ].…”

Section: Discussionmentioning

confidence: 99%

Long Non-Coding RNAs as Regulators of Interactions between Cancer-Associated Fibroblasts and Cancer Cells in the Tumor Microenvironment

Ahn

Kim²

2020

IJMS

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Long non-coding RNAs (lncRNAs) regulate diverse physiological and pathological processes via post-transcriptional, post-translational, and epigenetic mechanisms. They are also involved in tumor initiation, progression, and metastasis by functioning as key players in the tumor microenvironment. Cancer-associated fibroblasts (CAFs) promote tumor initiation, progression, metastasis, drug resistance, and immunosuppression, which can be modulated by lncRNAs. LncRNAs regulate the intrinsic properties of CAFs or cancer cells intracellularly or function extracellularly through exosomal secretion. In-depth studies on the mechanisms of lncRNA functions will enable their clinical use as diagnosis/prognosis markers and therapeutic targets in cancer treatment.

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Section: Discussionmentioning

confidence: 99%

Long Non-Coding RNAs as Regulators of Interactions between Cancer-Associated Fibroblasts and Cancer Cells in the Tumor Microenvironment

Ahn

Kim²

2020

IJMS

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“…Less trivial is understanding how RNA may interact with double stranded DNA or proteins, as it occurs, for example, when RNA binds to RNA-binding proteins, including the interaction of pre- and pri-miRNAs with the processing enzymes Drosha or Dicer, and in all the above mentioned reported modes of action of lncRNAs ( 62 ). In fact, if decoding of mRNA primary sequence into aminoacids can be used to identify known functional protein domains and ultimately predict the function of a still unknown protein-coding gene, prediction of lncRNA function is still challenging.…”

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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“…Long non-coding RNAs (lncRNAs), of which some were identified in platelets [ 52 ], constitute yet an additional group of regulatory non-protein-coding RNAs. LncRNAs can be subdivided into sense-, antisense-, intronic-, bidirectional-, and long intergenic ncRNAs and are characterized by a minimum length of >200 nt [ 87 , 88 , 89 ]. Importantly, lncRNAs have been shown to play important roles in several human diseases, especially in cancer [ 90 , 91 , 92 , 93 ].…”

Section: Composition and Sources Of Rna Species In Plateletsmentioning

confidence: 99%

Post-Transcriptional Expression Control in Platelet Biogenesis and Function

Neu

Gutschner

Haemmerle

2020

IJMS

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Platelets are highly abundant cell fragments of the peripheral blood that originate from megakaryocytes. Beside their well-known role in wound healing and hemostasis, they are emerging mediators of the immune response and implicated in a variety of pathophysiological conditions including cancer. Despite their anucleate nature, they harbor a diverse set of RNAs, which are subject to an active sorting mechanism from megakaryocytes into proplatelets and affect platelet biogenesis and function. However, sorting mechanisms are poorly understood, but RNA-binding proteins (RBPs) have been suggested to play a crucial role. Moreover, RBPs may regulate RNA translation and decay following platelet activation. In concert with other regulators, including microRNAs, long non-coding and circular RNAs, RBPs control multiple steps of the platelet life cycle. In this review, we will highlight the different RNA species within platelets and their impact on megakaryopoiesis, platelet biogenesis and platelet function. Additionally, we will focus on the currently known concepts of post-transcriptional control mechanisms important for RNA fate within platelets with a special emphasis on RBPs.

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Challenges and Strategies in Ascribing Functions to Long Noncoding RNAs

Cited by 39 publications

References 165 publications

Long Non-Coding RNAs as Regulators of Interactions between Cancer-Associated Fibroblasts and Cancer Cells in the Tumor Microenvironment

Long Non-Coding RNAs as Regulators of Interactions between Cancer-Associated Fibroblasts and Cancer Cells in the Tumor Microenvironment

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

Post-Transcriptional Expression Control in Platelet Biogenesis and Function

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