Platforms for Investigating LncRNA Functions

Richard, John Lalith Charles; Eichhorn, Pieter J.A.

doi:10.1177/2472630318780639

Cited by 144 publications

(100 citation statements)

References 139 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Antisense lncRNAs can affect biogenesis or mobilization of target RNA on multiple levels, such as transcription, splicing, and translation (14). To elucidate the exact mechanism of P3H2‐AS1 regulating P3H2 , complementary functional studies employing clustered regularly interspaced short palindromic repeat/Cas9, RNA fluorescence in situ hybridization, or crosslinked immunoprecipitation are necessary to investigate whether P3H2‐AS1 can be used as a potential preclinical target by modulating P3H2 expression levels via P3H2‐AS1 (33).…”

Section: Discussionmentioning

confidence: 99%

Elucidating Epigenetic Regulation by Identifying Functional cis‐Acting Long Noncoding RNAs and Their Targets in Osteoarthritic Articular Cartilage

Hoolwerff

Metselaar

Tuerlings

et al. 2020

Arthritis & Rheumatology

View full text Add to dashboard Cite

Objective To identify robustly differentially expressed long noncoding RNAs (lncRNAs) with osteoarthritis (OA) pathophysiology in cartilage and to explore potential target messenger RNA (mRNA) by establishing coexpression networks, followed by functional validation. Methods RNA sequencing was performed on macroscopically lesioned and preserved OA cartilage from patients who underwent joint replacement surgery due to OA (n = 98). Differential expression analysis was performed on lncRNAs that were annotated in GENCODE and Ensembl databases. To identify potential interactions, correlations were calculated between the identified differentially expressed lncRNAs and the previously reported differentially expressed protein‐coding genes in the same samples. Modulation of chondrocyte lncRNA expression was achieved using locked nucleic acid GapmeRs. Results By applying our in‐house pipeline, we identified 5,053 lncRNAs that were robustly expressed, of which 191 were significantly differentially expressed (according to false discovery rate) between lesioned and preserved OA cartilage. Upon integrating mRNA sequencing data, we showed that intergenic and antisense differentially expressed lncRNAs demonstrate high, positive correlations with their respective flanking sense genes. To functionally validate this observation, we selected P3H2‐AS1, which was down‐regulated in primary chondrocytes, resulting in the down‐regulation of P3H2 gene expression levels. As such, we can confirm that P3H2‐AS1 regulates its sense gene P3H2. Conclusion By applying an improved detection strategy, robustly differentially expressed lncRNAs in OA cartilage were detected. Integration of these lncRNAs with differential mRNA expression levels in the same samples provided insight into their regulatory networks. Our data indicates that intergenic and antisense lncRNAs play an important role in regulating the pathophysiology of OA.

show abstract

Section: Discussionmentioning

confidence: 99%

Elucidating Epigenetic Regulation by Identifying Functional cis‐Acting Long Noncoding RNAs and Their Targets in Osteoarthritic Articular Cartilage

Hoolwerff

Metselaar

Tuerlings

et al. 2020

Arthritis & Rheumatology

View full text Add to dashboard Cite

show abstract

“…Analysis of lncRNAs is technically challenging due to their relatively low expression level and their tissue-specific expression[62], therefore, the following methods are optimized for studying lncRNAs with high sensitivity and resolution.…”

Section: Lncrna Expression Analysis Methodsmentioning

confidence: 99%

“…The higher resolution and reproducibility of RNA-Seq compared to microarrays[65] resulted in broad use of this approach. RNA-Seq supports the annotation of novel lncRNAs, RNA editing sites, and alternative splicing sites, as well[62]. Cap analysis of gene expression (CAGE) is an NGS-based approach to map and quantify the expression of 5’ capped RNAs[66] and also to identify tran-scriptionally active promoter regions and Pol II-driven TSSs[64].…”

Section: Lncrna Expression Analysis Methodsmentioning

confidence: 99%

“…The downstream analysis can be performed by combining with the previously discussed methods, including RIP-Chip and RIP-Seq[68]. Native RIP is suitable for the exploration of strong and direct RNA-protein interactions, whereas the crosslinked immunoprecipitation method (CLIP) is used to study weak or indirect binding[62]. Crosslinking is achieved by ultraviolet light (UV) followed by RNase treatment and stringent washes which increases the specificity of the interaction detection[69].…”

Section: Lncrna Expression Analysis Methodsmentioning

confidence: 99%

“…Crosslinking is achieved by ultraviolet light (UV) followed by RNase treatment and stringent washes which increases the specificity of the interaction detection[69]. In order to minimize the disadvantages of CLIP, modified methods, such as individual nucleotide resolution CLIP (iCLIP)[70], and photoactivable ribonucleoside-enhanced CLIP (PAR-CLIP) are also available for the identification of the exact crosslinking sites with single nucleotide resolution[62,69].…”

Section: Lncrna Expression Analysis Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Diagnostic and prognostic potential of tissue and circulating long non-coding RNAs in colorectal tumors

Galamb¹,

Barták²,

Kalmár³

et al. 2019

WJG

View full text Add to dashboard Cite

Long non-coding RNAs (lncRNAs) are members of the non-protein coding RNA family longer than 200 nucleotides. They participate in the regulation of gene and protein expression influencing apoptosis, cell proliferation and immune responses, thereby playing a critical role in the development and progression of various cancers, including colorectal cancer (CRC). As CRC is one of the most frequently diagnosed malignancies worldwide with high mortality, its screening and early detection are crucial, so the identification of disease-specific biomarkers is necessary. LncRNAs are promising candidates as they are involved in carcinogenesis, and certain lncRNAs (e.g., CCAT1, CRNDE, CRCAL1-4) show altered expression in adenomas, making them potential early diagnostic markers. In addition to being useful as tissue-specific markers, analysis of circulating lncRNAs (e.g., CCAT1, CCAT2, BLACAT1, CRNDE, NEAT1, UCA1) in peripheral blood offers the possibility to establish minimally invasive, liquid biopsy-based diagnostic tests. This review article aims to describe the origin, structure, and functions of lncRNAs and to discuss their contribution to CRC development. Moreover, our purpose is to summarise lncRNAs showing altered expression levels during tumor formation in both colon tissue and plasma/serum samples and to demonstrate their clinical implications as diagnostic or prognostic biomarkers for CRC.

show abstract

An overview of long noncoding RNAs: Biology, functions, therapeutics, analysis methods, and bioinformatics tools

Jafari-Raddani

Davoodi-Moghaddam

Yousefi

et al. 2022

Cell Biochemistry & Function

View full text Add to dashboard Cite

Long noncoding RNAs (lncRNAs) are a diverse class of RNAs whose functions are widespread in all branches of life and have been the focus of attention in the last decade. While a huge number of lncRNAs have been identified, there is still much work to be done and plenty to be learned. In the current review, we begin with the biogenesis and function of lncRNAs as they are involved in the different cellular processes from regulating the architecture of chromosomes to controlling translation and post‐translation modifications. Questions on how overexpression, mutations, or deficiency of lncRNAs can affect the cellular status and result in the pathogenesis of various human diseases are responded to. Besides, we allocate an overview of several studies, concerning the application of lncRNAs either as diagnostic and prognostic biomarkers or novel therapeutics. We also introduce the currently available techniques to explore details of lncRNAs such as their function, cellular localization, and structure. In the last section, as exponentially growing data in this area need to be gathered and organized in comprehensive databases, we have a particular focus on presenting general and specialized databases. Taken together, with this review, we aim to provide the latest information on different aspects of lncRNAs to highlight their importance in physiopathologic states and take a step towards helping future studies.

show abstract

Platforms for Investigating LncRNA Functions

Cited by 144 publications

References 139 publications

Elucidating Epigenetic Regulation by Identifying Functional cis‐Acting Long Noncoding RNAs and Their Targets in Osteoarthritic Articular Cartilage

Elucidating Epigenetic Regulation by Identifying Functional cis‐Acting Long Noncoding RNAs and Their Targets in Osteoarthritic Articular Cartilage

Diagnostic and prognostic potential of tissue and circulating long non-coding RNAs in colorectal tumors

An overview of long noncoding RNAs: Biology, functions, therapeutics, analysis methods, and bioinformatics tools

Contact Info

Product

Resources

About