Visualization of the small RNA transcriptome using seqclusterViz

The study of small RNAs provides us with a deeper understanding of the complexity of gene regulation within cells. Of the different types of small RNAs, the most important in mammals are miRNA, tRNA fragments and piRNAs. Using small RNA-seq analysis, we can study all small RNA types simultaneously, with the potential to detect novel small RNA types. We describe SeqclusterViz, an interactive HTML-javascript webpage for visualizing small noncoding RNAs (small RNAs) detected by Seqcluster. The SeqclusterViz tool allows users to visualize known and novel small RNA types in model or non-model organisms, and to select small RNA candidates for further validation. SeqclusterViz is divided into three panels: i) query-ready tables showing detected small RNA clusters and their genomic locations, ii) the expression profile over the precursor for all the samples together with RNA secondary structures, and iii) the mostly highly expressed sequences. Here, we show the capabilities of the visualization tool and its validation using human brain samples from patients with Parkinson’s disease .

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DANSR: A Tool for the Detection of Annotated and Novel Small RNAs

Non-Coding RNA ◽

10.3390/ncrna8010009 ◽

2022 ◽

Vol 8 (1) ◽

pp. 9

Author(s):

Jin Zhang ◽

Abdallah M. Eteleeb ◽

Emily B. Rozycki ◽

Matthew J. Inkman ◽

Amy Ly ◽

...

Keyword(s):

Colorectal Cancer ◽

Small Rna ◽

Small Rnas ◽

Noncoding Rna ◽

Noncoding Rnas ◽

Biologically Relevant ◽

Small Noncoding Rna ◽

Small Noncoding Rnas ◽

Rna Analysis ◽

Length Range

Existing small noncoding RNA analysis tools are optimized for processing short sequencing reads (17–35 nucleotides) to monitor microRNA expression. However, these strategies under-represent many biologically relevant classes of small noncoding RNAs in the 36–200 nucleotides length range (tRNAs, snoRNAs, etc.). To address this, we developed DANSR, a tool for the detection of annotated and novel small RNAs using sequencing reads with variable lengths (ranging from 17–200 nt). While DANSR is broadly applicable to any small RNA dataset, we applied it to a cohort of matched normal, primary, and distant metastatic colorectal cancer specimens to demonstrate its ability to quantify annotated small RNAs, discover novel genes, and calculate differential expression. DANSR is available as an open source tool.

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Abstract 4447: Analysis of small RNA-seq data for differential expression of small noncoding RNAs in human colorectal cancer

10.1158/1538-7445.am2017-4447 ◽

2017 ◽

Author(s):

Srinivas V. Koduru ◽

Amit K. Tiwari ◽

Sprague W. Hazard ◽

Milind K. Mahajan ◽

Dino J. Ravnic

Keyword(s):

Colorectal Cancer ◽

Differential Expression ◽

Small Rna ◽

Noncoding Rnas ◽

Rna Seq ◽

Human Colorectal Cancer ◽

Small Noncoding Rnas

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Analysis of RDR1/RDR2/RDR6-independent small RNAs in Arabidopsis thaliana improves MIRNA annotations and reveals novel siRNA loci

10.1101/238691 ◽

2017 ◽

Cited By ~ 1

Author(s):

Seth Polydore ◽

Michael J. Axtell

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Small Rna ◽

Small Rnas ◽

Rna Seq ◽

Triple Mutant ◽

Physiological Mechanisms ◽

Protein Coding ◽

Regulate Gene Expression ◽

Rna Biogenesis

SummaryPlant small RNAs regulate key physiological mechanisms through post-transcriptional and transcriptional silencing of gene expression. sRNAs fall into two major categories: those that are reliant on RNA Dependent RNA Polymerases (RDRs) for biogenesis and those that aren’t. Known RDR-dependent sRNAs include phased and repeat-associated short interfering RNAs, while known RDR-independent sRNAs are primarily microRNAs and other hairpin-derived sRNAs. In this study, we produced and analyzed small RNA-seq libraries from rdr1/rdr2/rdr6 triple mutant plants. Only a small fraction of all sRNA loci were RDR1/RDR2/RDR6-independent; most of these were microRNA loci or associated with predicted hairpin precursors. We found 58 previously annotated microRNA loci that were reliant on RDR1, −2, or −6 function, casting doubt on their classification. We also found 38 RDR1/2/6-independent small RNA loci that are not MIRNAs or otherwise hairpin-derived, and did not fit into other known paradigms for small RNA biogenesis. These 38 small RNA-producing loci have novel biogenesis mechanisms, and are frequently located in the vicinity of protein-coding genes. Altogether, our analysis suggest that these 38 loci represent one or more new types of small RNAs in Arabidopsis thaliana.Significance StatementSmall RNAs regulate gene expression in plants and are produced through a variety of previously-described mechanisms. Here, we examine a set of previously undiscovered small RNA-producing loci that are produced by novel mechanisms.

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Salient Genetic Notes on Small-RNAs and their Applications in Agricultural Biotechnology

Journal of Advances in Biology & Biotechnology ◽

10.9734/jabb/2019/v22i430131 ◽

2020 ◽

pp. 1-17

Author(s):

Samuel Amiteye

Keyword(s):

Gene Regulation ◽

Small Rna ◽

Small Rnas ◽

Small Interfering Rna ◽

Crop Improvement ◽

Regulation Of Gene Expression ◽

Healthy Plant ◽

Biological Processes ◽

Protein Coding ◽

Interfering Rna

Small-RNAs are 20 to 27 nucleotides long non-protein-coding RNAs that act on either DNA or RNA to effect the regulation of gene expression. Small-RNAs are key in genetic and epigenetic regulation of diverse biological processes and pathways in response to biotic and abiotic environmental stresses. The gene regulatory functions of small-RNA molecules enhance healthy plant growth and normal development by controlling biological processes such as flowering programming, fruit development, disease and pests resistance. Small-RNAs comprise mainly microRNA and small interfering RNA species. MicroRNAs have been proven to primarily engage in posttranscriptional gene regulation while small interfering RNA have been implicated mainly in transcriptional gene regulation. This review covers the recent advancements in small-RNA research in plants, with emphasis on particularly microRNAs and small interfering RNA biogenesis, biological functions and their relevance in the regulation of traits of agronomic importance in plants. Also discussed extensively is the potential biotechnological applications of these small-RNAs for crop improvement.

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Removing bias against short sequences enables northern blotting to better complement RNA-seq for the study of small RNAs

10.1101/068031 ◽

2016 ◽

Author(s):

Yun S. Choi ◽

Lanelle O. Edwards ◽

Aubrey DiBello ◽

Antony M. Jose

Keyword(s):

Small Rna ◽

Small Rnas ◽

Degradation Products ◽

Northern Blotting ◽

Rna Seq ◽

Single Nucleotide ◽

Rna Integrity ◽

C Elegans ◽

Micro Rnas ◽

Functional Rnas

ABSTRACTChanges in small non-coding RNAs such as micro RNAs (miRNAs) can serve as indicators of disease and can be measured using next-generation sequencing of RNA (RNA-seq). Here, we highlight the need for approaches that complement RNA-seq, discover that northern blotting of small RNAs is biased against short sequences, and develop a protocol that removes this bias. We found that multiple small RNA-seq datasets from the worm C. elegans had shorter forms of miRNAs that appear to be degradation products that arose during the preparatory steps required for RNA-seq. When using northern blotting during these studies, we discovered that miRNA-length probes can have a ~360-fold bias against detecting even synthetic sequences that are 8 nt shorter. By using shorter probes and by performing hybridization and washes at low temperatures, we greatly reduced this bias to enable equivalent detection of 24 nt to 14 nt RNAs. Our protocol can better discriminate RNAs that differ by a single nucleotide and can detect specific miRNAs present in total RNA from C. elegans. This improved northern blotting is particularly useful to obtain a measure of small RNA integrity, analyze products of RNA processing or turnover, and analyze functional RNAs that are shorter than typical miRNAs.

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MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data

International Journal of Molecular Sciences ◽

10.3390/ijms21051754 ◽

2020 ◽

Vol 21 (5) ◽

pp. 1754 ◽

Cited By ~ 3

Author(s):

Enrico Gaffo ◽

Michele Bortolomeazzi ◽

Andrea Bisognin ◽

Piero Di Battista ◽

Federica Lovisa ◽

...

Keyword(s):

Small Rna ◽

Small Rnas ◽

Cell Types ◽

Small Rna Sequencing ◽

Rna Seq ◽

Sequencing Data ◽

Research Findings ◽

Human Blood Cell ◽

And Function ◽

Comprehensive Study

MicroRNA-offset RNAs (moRNAs) are microRNA-like small RNAs generated by microRNA precursors. To date, little is known about moRNAs and bioinformatics tools to inspect their expression are still missing. We developed miR&moRe2, the first bioinformatics method to consistently characterize microRNAs, moRNAs, and their isoforms from small RNA sequencing data. To illustrate miR&moRe2 discovery power, we applied it to several published datasets. MoRNAs identified by miR&moRe2 were in agreement with previous research findings. Moreover, we observed that moRNAs and new microRNAs predicted by miR&moRe2 were downregulated upon the silencing of the microRNA-biogenesis pathway. Further, in a sizeable dataset of human blood cell populations, tens of novel miRNAs and moRNAs were discovered, some of them with significantly varied expression levels among the cell types. Results demonstrate that miR&moRe2 is a valid tool for a comprehensive study of small RNAs generated from microRNA precursors and could help to investigate their biogenesis and function.

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Dysregulation of a family of short noncoding RNAs, tsRNAs, in human cancer

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1604266113 ◽

2016 ◽

Vol 113 (18) ◽

pp. 5071-5076 ◽

Cited By ~ 77

Author(s):

Yuri Pekarsky ◽

Veronica Balatti ◽

Alexey Palamarchuk ◽

Lara Rizzotto ◽

Dario Veneziano ◽

...

Keyword(s):

Lung Cancer ◽

Small Rnas ◽

Northern Blot Analysis ◽

Human Cancer ◽

Noncoding Rnas ◽

Lymphocytic Leukemia ◽

P Element ◽

Human Leukemia ◽

Hematopoietic Malignancies ◽

Small Noncoding Rnas

Chronic lymphocytic leukemia (CLL) is the most common human leukemia, and transgenic mouse studies indicate that activation of the T-cell leukemia/lymphoma 1 (TCL1) oncogene is a contributing event in the pathogenesis of the aggressive form of this disease. While studying the regulation of TCL1 expression, we identified the microRNA cluster miR-4521/3676 and discovered that these two microRNAs are associated with tRNA sequences and that this region can produce two small RNAs, members of a recently identified class of small noncoding RNAs, tRNA-derived small RNAs (tsRNAs). We further proved that miR-3676 and miR-4521 are tsRNAs using Northern blot analysis. We found that, like ts-3676, ts-4521 is down-regulated and mutated in CLL. Analysis of lung cancer samples revealed that both ts-3676 and ts-4521 are down-regulated and mutated in patient tumor samples. Because tsRNAs are similar in nature to piRNAs [P-element–induced wimpy testis (Piwi)-interacting small RNAs], we investigated whether ts-3676 and ts-4521 can interact with Piwi proteins and found these two tsRNAs in complexes containing Piwi-like protein 2 (PIWIL2). To determine whether other tsRNAs are involved in cancer, we generated a custom microarray chip containing 120 tsRNAs 16 bp or more in size. Microarray hybridization experiments revealed tsRNA signatures in CLL and lung cancer, indicating that, like microRNAs, tsRNAs may have an oncogenic and/or tumor-suppressor function in hematopoietic malignancies and solid tumors. Thus, our results show that tsRNAs are dysregulated in human cancer.

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mi-IsoNet: systems-scale microRNA landscape reveals rampant isoform-mediated gain of target interaction diversity and signaling specificity

Briefings in Bioinformatics ◽

10.1093/bib/bbab091 ◽

2021 ◽

Author(s):

Li Guo ◽

Yongsheng Li ◽

Kara M Cirillo ◽

Robert A Marick ◽

Zhe Su ◽

...

Keyword(s):

Gene Regulation ◽

Small Rna ◽

Small Rnas ◽

Regulatory Networks ◽

Circuit Complexity ◽

Selective Advantage ◽

Functional Variation ◽

Signaling Specificity ◽

Gene Regulation Network ◽

Novel Target

Abstract MicroRNA (miRNA) is not a single sequence, but a series of multiple variants (also termed isomiRs) with sequence and expression heterogeneity. Whether and how these isoforms contribute to functional variation and complexity at the systems and network levels remain largely unknown. To explore this question systematically, we comprehensively analyzed the expression of small RNAs and their target sites to interrogate functional variations between novel isomiRs and their canonical miRNA sequences. Our analyses of the pan-cancer landscape of miRNA expression indicate that multiple isomiRs generated from the same miRNA locus often exhibit remarkable variation in their sequence, expression and function. We interrogated abundant and differentially expressed 5′ isomiRs with novel seed sequences via seed shifting and identified many potential novel targets of these 5′ isomiRs that would expand interaction capabilities between small RNAs and mRNAs, rewiring regulatory networks and increasing signaling circuit complexity. Further analyses revealed that some miRNA loci might generate diverse dominant isomiRs that often involved isomiRs with varied seeds and arm-switching, suggesting a selective advantage of multiple isomiRs in regulating gene expression. Finally, experimental validation indicated that isomiRs with shifted seed sequences could regulate novel target mRNAs and therefore contribute to regulatory network rewiring. Our analysis uncovers a widespread expansion of isomiR and mRNA interaction networks compared with those seen in canonical small RNA analysis; this expansion suggests global gene regulation network perturbations by alternative small RNA variants or isoforms. Taken together, the variations in isomiRs that occur during miRNA processing and maturation are likely to play a far more complex and plastic role in gene regulation than previously anticipated.

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