Long Non-Coding RNA-Ribonucleoprotein Networks in the Post-Transcriptional Control of Gene Expression

Briata, Paola; Gherzi, Roberto

doi:10.3390/ncrna6030040

Cited by 34 publications

(32 citation statements)

References 73 publications

(160 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Studies have shown that lncRNAs can modulate gene expression by interac&ng with chroma&n and changing the genome architecture, sca9olding the regulatory proteins, and facilita&ng the recruitment of the regulatory proteins like RBPs 33 . RBPs are known to bind to chroma&nassociated RNAs and recently emerged as not only transcrip&on regulators but also as playing a role in genome architecture maintenance.…”

Section: Discussionmentioning

confidence: 99%

“…Nostrand et al 32 have shown that knockdown of an RNA binding protein (RBP) results in di9eren&al expression and alterna&ve splicing for genes with DNA binding sites for the RBP, sugges&ng that it mediates pre-and post-transcrip&onal regula&on at the chroma&n level. As lncRNAs have been known to regulate mRNA splicing and post-transla&onal modiFca&ons by interac&ng with the RBPs 33 , lncRNAs may play a role in recrui&ng RBPs to their target sites. Based on eCLIP data for K562 and HepG2 cells 32 we found 6,239 and 6,216 lncRNAs, respec&vely, with at least one RBP binding to it.…”

Section: Regulator Lncrnas Based On Chroma%n Associa%onmentioning

confidence: 99%

See 1 more Smart Citation

Systematic identification of cis-interacting lncRNAs and their targets

Agrawal

Alam

Koido

et al. 2021

Preprint

View full text Add to dashboard Cite

Transcription of the human genome yields mostly long non-coding RNAs (lncRNAs). Systematic functional annotation of lncRNAs is challenging due to their low expression level, cell type-specific occurrence, poor sequence conservation between orthologs, and lack of information about RNA domains. Currently, 95% of human lncRNAs have no functional characterization. Using chromatin conformation and Cap Analysis of Gene Expression (CAGE) data in 18 human cell types, we systematically located genomic regions in spatial proximity to lncRNA genes and identified functional clusters of interacting protein-coding genes, lncRNAs and enhancers. Using these clusters we provide a cell type-specific functional annotation for 7,651 out of 14,198 (53.88%) lncRNAs. LncRNAs tend to have specialized roles in the cell type in which it is first expressed, and to incorporate more general functions as its expression is acquired by multiple cell types during evolution. By analyzing RNA-binding protein and RNA-chromatin interaction data in the context of the spatial genomic interaction map, we explored mechanisms by which these lncRNAs can act.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Regulator Lncrnas Based On Chroma%n Associa%onmentioning

confidence: 99%

Systematic identification of cis-interacting lncRNAs and their targets

Agrawal

Alam

Koido

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…One of the best studied lncRNAs, Xist , can form ribonucleoprotein complexes (RNPs) in the nucleus to affect target gene transcription regulation [ 70 ]. It has been shown that lncRNAs can also be cytoplasmic and bind RBPs to affect other mRNA metabolism processes such as mRNA stability and turnover [ 71 , 72 , 73 ]. Depending on which factors interact with a given lncRNA, this could increase or decrease the targeted mRNA.…”

Section: Interaction Between Lncrnas and Rbps In Mrna Stabilizatiomentioning

confidence: 99%

The Role of lncRNAs in Gene Expression Regulation through mRNA Stabilization

Sebastian-delaCruz

González-Moro

Olazagoitia-Garmendia

et al. 2021

ncRNA

View full text Add to dashboard Cite

mRNA stability influences gene expression and translation in almost all living organisms, and the levels of mRNA molecules in the cell are determined by a balance between production and decay. Maintaining an accurate balance is crucial for the correct function of a wide variety of biological processes and to maintain an appropriate cellular homeostasis. Long non-coding RNAs (lncRNAs) have been shown to participate in the regulation of gene expression through different molecular mechanisms, including mRNA stabilization. In this review we provide an overview on the molecular mechanisms by which lncRNAs modulate mRNA stability and decay. We focus on how lncRNAs interact with RNA binding proteins and microRNAs to avoid mRNA degradation, and also on how lncRNAs modulate epitranscriptomic marks that directly impact on mRNA stability.

show abstract

“…Both in the nucleus and in the cytoplasm, lncRNAs may also act post-transcriptionally to modulate mRNA splicing (Figure 2D ), turnover or translation (Figure 2E ) by titrating RNA binding proteins (e.g. splicing factors, proteins involved in mRNA degradation) or by forming RNA-RNA hybrids with target pre-mRNAs ( 58 , 59 ). Some cytoplasmic lncRNAs act as ‘sponges’ of miRNAs: in light of the presence of miRNA binding sites in their sequence, such lncRNAs can physically sequester miRNAs, thus reducing their availability (Figure 2F ).…”

Section: Noncoding Rna Biology and Functionmentioning

confidence: 99%

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

Tassinari

Richter

Gandellini

2021

Nucleic Acids Research

View full text Add to dashboard Cite

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.

show abstract

Long Non-Coding RNA-Ribonucleoprotein Networks in the Post-Transcriptional Control of Gene Expression

Cited by 34 publications

References 73 publications

Systematic identification of cis-interacting lncRNAs and their targets

Systematic identification of cis-interacting lncRNAs and their targets

The Role of lncRNAs in Gene Expression Regulation through mRNA Stabilization

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

Contact Info

Product

Resources

About