Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing

Liu, Qi; Ding, Changjun; Lang, Xiaoqiang; Guo, Ganggang; Chen, Jiafei; Su, Xiaohua

doi:10.1093/bib/bbz151

Cited by 33 publications

(22 citation statements)

References 83 publications

(89 reference statements)

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“…Importantly, there are currently no Web-based, user-friendly resources that offer comprehensive sncRNA fragment profiling and discovery, functional prediction, and the identification of significant differential expressions among datasets comparable to SURFR. Although two platforms, sRNA toolbox (35) and sRNAtools (36), do offer many of SURFR's features, SURFR distinguishes itself by providing significantly more intuitive, versatile, and user friendly results generated in less than 10% of the time required for data upload and processing by these tools. That said, because SURFR was developed specifically for ncRNA fragment identification, it does not provide expression analysis for full length ncRNAs.…”

Section: Surfr Comparison To Other Existing Toolsmentioning

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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Section: Surfr Comparison To Other Existing Toolsmentioning

confidence: 99%

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

Mv¹,

Houserova²,

Ym³

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…Databases such as MINTmap and tRF2Cancer extract and catalogue raw and normalized tRF levels from published human small RNA-seq data under physiological and pathological conditions ( 62 , 63 ). tRF2Cancer and sRNAtools further provide tRF identification from user uploaded sequencing data ( 64 ).…”

Section: Biogenesis and Profiling Of Pirnas Snornas And Trfsmentioning

confidence: 99%

Emerging Classes of Small Non-Coding RNAs With Potential Implications in Diabetes and Associated Metabolic Disorders

2021

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Most of the sequences in the human genome do not code for proteins but generate thousands of non-coding RNAs (ncRNAs) with regulatory functions. High-throughput sequencing technologies and bioinformatic tools significantly expanded our knowledge about ncRNAs, highlighting their key role in gene regulatory networks, through their capacity to interact with coding and non-coding RNAs, DNAs and proteins. NcRNAs comprise diverse RNA species, including amongst others PIWI-interacting RNAs (piRNAs), involved in transposon silencing, and small nucleolar RNAs (snoRNAs), which participate in the modification of other RNAs such as ribosomal RNAs and transfer RNAs. Recently, a novel class of small ncRNAs generated from the cleavage of tRNAs or pre-tRNAs, called tRNA-derived small RNAs (tRFs) has been identified. tRFs have been suggested to regulate protein translation, RNA silencing and cell survival. While for other ncRNAs an implication in several pathologies is now well established, the potential involvement of piRNAs, snoRNAs and tRFs in human diseases, including diabetes, is only beginning to emerge. In this review, we summarize fundamental aspects of piRNAs, snoRNAs and tRFs biology. We discuss their biogenesis while emphasizing on novel sequencing technologies that allow ncRNA discovery and annotation. Moreover, we give an overview of genomic approaches to decrypt their mechanisms of action and to study their functional relevance. The review will provide a comprehensive landscape of the regulatory roles of these three types of ncRNAs in metabolic disorders by reporting their differential expression in endocrine pancreatic tissue as well as their contribution to diabetes incidence and diabetes-underlying conditions such as inflammation. Based on these discoveries we discuss the potential use of piRNAs, snoRNAs and tRFs as promising therapeutic targets in metabolic disorders.

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“…SncRNAs include but are not limited to microRNAs (miRNAs), endogenous short interfering RNAs (siRNAs), small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), piwi interacting RNAs (piRNAs), ribosomal RNA derived fragments (rRFs), transfer RNAs (tRNAs), and their derived small RNAs (tsRNAs) (Mattick and Makunin, 2006;Kirchner and Ignatova, 2015;Wei et al, 2017;Lambert et al, 2019). With the advance of high-throughput RNA sequencing (Giraldez et al, 2018;Liu et al, 2019), new classes of sncRNAs are being discovered and studied.…”

Section: Introductionmentioning

confidence: 99%

tRNA-Derived Small RNAs and Their Potential Roles in Cardiac Hypertrophy

2020

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Transfer RNAs (tRNAs) are abundantly expressed, small non-coding RNAs that have long been recognized as essential components of the protein translation machinery. The tRNAderived small RNAs (tsRNAs), including tRNA halves (tiRNAs), and tRNA fragments (tRFs), were unexpectedly discovered and have been implicated in a variety of important biological functions such as cell proliferation, cell differentiation, and apoptosis. Mechanistically, tsRNAs regulate mRNA destabilization and translation, as well as retroelement reverse transcriptional and post-transcriptional processes. Emerging evidence has shown that tsRNAs are expressed in the heart, and their expression can be induced by pathological stress, such as hypertrophy. Interestingly, cardiac pathophysiological conditions, such as oxidative stress, aging, and metabolic disorders can be viewed as inducers of tsRNA biogenesis, which further highlights the potential involvement of tsRNAs in these conditions. There is increasing enthusiasm for investigating the molecular and biological functions of tsRNAs in the heart and their role in cardiovascular disease. It is anticipated that this new class of small non-coding RNAs will offer new perspectives in understanding disease mechanisms and may provide new therapeutic targets to treat cardiovascular disease.

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Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing

Cited by 33 publications

References 83 publications

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

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

Emerging Classes of Small Non-Coding RNAs With Potential Implications in Diabetes and Associated Metabolic Disorders

tRNA-Derived Small RNAs and Their Potential Roles in Cardiac Hypertrophy

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