Principles and innovative technologies for decrypting noncoding RNAs: from discovery and functional prediction to clinical application

Sun, Yu-Meng; Chen, Yue‐Qin

doi:10.1186/s13045-020-00945-8

Cited by 75 publications

(56 citation statements)

References 235 publications

(434 reference statements)

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“…There have been many efforts in the development of computational tools and high-throughput sequencing technologies, such as RNA capture sequencing (RNA CaptureSeq), whole-genome tiling arrays, the lncRNA microarray technique, serial expression of gene expression (SAGE), the expressed sequence tag (EST) method, and RNA-sequencing (RNA-seq). More than half a million lncRNA transcripts have been predicted in silico to understand their biological mechanisms [ 49 ]. Accumulating evidence suggests that lncRNAs are emerging regulators of diverse biological processes.…”

Section: Introductionmentioning

confidence: 99%

Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants

Waseem

Liu

Xia

2020

IJMS

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Long non-coding RNAs (lncRNAs) are pervasive transcripts of longer than 200 nucleotides and indiscernible coding potential. lncRNAs are implicated as key regulatory molecules in various fundamental biological processes at transcriptional, post-transcriptional, and epigenetic levels. Advances in computational and experimental approaches have identified numerous lncRNAs in plants. lncRNAs have been found to act as prime mediators in plant growth, development, and tolerance to stresses. This review summarizes the current research status of lncRNAs in planta, their classification based on genomic context, their mechanism of action, and specific bioinformatics tools and resources for their identification and characterization. Our overarching goal is to summarize recent progress on understanding the regulatory role of lncRNAs in plant developmental processes such as flowering time, reproductive growth, and abiotic stresses. We also review the role of lncRNA in nutrient stress and the ability to improve biotic stress tolerance in plants. Given the pivotal role of lncRNAs in various biological processes, their functional characterization in agriculturally essential crop plants is crucial for bridging the gap between phenotype and genotype.

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Section: Introductionmentioning

confidence: 99%

Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants

Waseem

Liu

Xia

2020

IJMS

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“…Despite a mounting body of evidence supporting the physiological relevance of ncRNAs, most studies performed to date have focused primarily on proteins themselves or deciphering the pathways associated with annotated ncRNAs. Moreover, due to the perceived insurmountability of the sheer amount of data generated by NGS/TGS analyses, the full extent of regulatory networks created by ncRNAs often gets overlooked (68). In addition, whereas the cost of RNA-seq is now reasonable for most active research programs, tools necessary for the interpretation of these sequencing datasets typically require significant computational expertise and resources markedly hindering widespread utilization of these tools.…”

Section: Discussionmentioning

confidence: 99%

SALTS – SURFR (sncRNA) And LAGOOn (lncRNA) Transcriptomics Suite

Mv¹,

Houserova²,

Ym³

et al. 2021

Preprint

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The widespread utilization of high-throughput sequencing technologies has unequivocally demonstrated that eukaryotic transcriptomes consist primarily (>98%) of non-coding RNA (ncRNA) transcripts significantly more diverse than their protein-coding counterparts. ncRNAs are typically divided into two categories based on their length. (1) ncRNAs less than 200 nucleotides (nt) long are referred as small non-coding RNAs (sncRNAs) and include microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), transfer ribonucleic RNAs (tRNAs), etc., and the majority of these are thought to function primarily in controlling gene expression. That said, the full repertoire of sncRNAs remains fairly poorly defined as evidenced by two entirely new classes of sncRNAs only recently being reported, i.e., snoRNA-derived RNAs (sdRNAs) and tRNA-derived fragments (tRFs). (2) ncRNAs longer than 200 nt long are known as long ncRNAs (lncRNAs). lncRNAs represent the 2nd largest transcriptional output of the cell (behind only ribosomal RNAs), and although functional roles for several lncRNAs have been reported, most lncRNAs remain largely uncharacterized due to a lack of predictive tools aimed at guiding functional characterizations. Importantly, whereas the cost of high-throughput transcriptome sequencing is now feasible for most active research programs, tools necessary for the interpretation of these sequencings typically require significant computational expertise and resources markedly hindering widespread utilization of these datasets. In light of this, we have developed a powerful new ncRNA transcriptomics suite, SALTS, which is highly accurate, markedly efficient, and extremely user-friendly. SALTS stands for SURFR (sncRNA) And LAGOOn (lncRNA) Transcriptomics Suite and offers platforms for comprehensive sncRNA and lncRNA profiling and discovery, ncRNA functional prediction, and the identification of significant differential expressions among datasets. Notably, SALTS is accessed through an intuitive Web-based interface, can be used to analyze either user-generated, standard next-generation sequencing (NGS) output file uploads (e.g., FASTQ) or existing NCBI Sequence Read Archive (SRA) data, and requires absolutely no dataset pre-processing or knowledge of library adapters/oligonucleotides. SALTS constitutes the first publically available, Web-based, comprehensive ncRNA transcriptomic NGS analysis platform designed specifically for users with no computational background, providing a much needed, powerful new resource capable of enabling more widespread ncRNA transcriptomic analyses. The SALTS WebServer is freely available online at http://salts.soc.southalabama.edu.

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“…miRNAs constitute a class of noncoding RNA molecules with powerful gene regulation potential. They bind to complementary target mRNAs, resulting in mRNA translational inhibition or degradation [ 137 ]. Notably, seven miRNAs have been found that directly target m6A methyltransferases in diseases (Fig.…”

Section: Targeting M6a Methyltransferase By Ncrnamentioning

confidence: 99%

N6-methyladenosine methyltransferases: functions, regulation, and clinical potential

et al. 2021

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N6-methyladenosine (m6A) has emerged as an abundant modification throughout the transcriptome with widespread functions in protein-coding and noncoding RNAs. It affects the fates of modified RNAs, including their stability, splicing, and/or translation, and thus plays important roles in posttranscriptional regulation. To date, m6A methyltransferases have been reported to execute m6A deposition on distinct RNAs by their own or forming different complexes with additional partner proteins. In this review, we summarize the function of these m6A methyltransferases or complexes in regulating the key genes and pathways of cancer biology. We also highlight the progress in the use of m6A methyltransferases in mediating therapy resistance, including chemotherapy, targeted therapy, immunotherapy and radiotherapy. Finally, we discuss the current approaches and clinical potential of m6A methyltransferase-targeting strategies.

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Principles and innovative technologies for decrypting noncoding RNAs: from discovery and functional prediction to clinical application

Cited by 75 publications

References 235 publications

Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants

Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants

SALTS – SURFR (sncRNA) And LAGOOn (lncRNA) Transcriptomics Suite

N6-methyladenosine methyltransferases: functions, regulation, and clinical potential

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