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

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.

scholarly journals Of rodents and ruminants: a comparison of small noncoding RNA requirements in mouse and bovine reproduction

2021 ◽  
Vol 99 (3) ◽  
Author(s):  
Lauren G Chukrallah ◽  
Aditi Badrinath ◽  
Kelly Seltzer ◽  
Elizabeth M Snyder
Keyword(s):  
Germ Cell ◽  
Germ Cells ◽  
Noncoding Rna ◽  
Reproductive Potential ◽  
Noncoding Rnas ◽  
Model Organism ◽  
Cell Physiology ◽  
Male Germ Cells ◽  
Small Noncoding Rna ◽  
Small Noncoding Rnas

Abstract Ruminants are major producers of meat and milk, thus managing their reproductive potential is a key element in cost-effective, safe, and efficient food production. Of particular concern, defects in male germ cells and female germ cells may lead to significantly reduced live births relative to fertilization. However, the underlying molecular drivers of these defects are unclear. Small noncoding RNAs, such as piRNAs and miRNAs, are known to be important regulators of germ-cell physiology in mouse (the best-studied mammalian model organism) and emerging evidence suggests that this is also the case in a range of ruminant species, in particular bovine. Similarities exist between mouse and bovids, especially in the case of meiotic and postmeiotic male germ cells. However, fundamental differences in small RNA abundance and metabolism between these species have been observed in the female germ cell, differences that likely have profound impacts on their physiology. Further, parentally derived small noncoding RNAs are known to influence early embryos and significant species-specific differences in germ-cell born small noncoding RNAs have been observed. These findings demonstrate the mouse to be an imperfect model for understanding germ-cell small noncoding RNA biology in ruminants and highlight the need to increase research efforts in this underappreciated aspect of animal reproduction.

scholarly journals Visualization of the small RNA transcriptome using seqclusterViz

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 232 ◽  
Author(s):  
Lorena Pantano ◽  
Francisco Pantano ◽  
Eulalia Marti ◽  
Shannan Ho Sui
Keyword(s):  
Gene Regulation ◽  
Small Rna ◽  
Small Rnas ◽  
Noncoding Rnas ◽  
Model Organisms ◽  
Visualization Tool ◽  
Rna Seq ◽  
Small Noncoding Rnas ◽  
Different Types ◽  
Genomic Locations

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.

scholarly journals Visualization of the small RNA transcriptome using seqclusterViz

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 232
Author(s):  
Lorena Pantano ◽  
Francisco Pantano ◽  
Eulalia Marti ◽  
Shannan Ho Sui
Keyword(s):  
Gene Regulation ◽  
Small Rna ◽  
Small Rnas ◽  
Noncoding Rnas ◽  
Model Organisms ◽  
Visualization Tool ◽  
Rna Seq ◽  
Small Noncoding Rnas ◽  
Different Types ◽  
Genomic Locations

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 .

scholarly journals Identification of a Functional Small Noncoding RNA of African Swine Fever Virus

2020 ◽  
Vol 94 (21) ◽  
Author(s):  
Laura E. M. Dunn ◽  
Alasdair Ivens ◽  
Christopher L. Netherton ◽  
David A. G. Chapman ◽  
Philippa M. Beard
Keyword(s):  
Small Rnas ◽  
Noncoding Rna ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Hemorrhagic Disease ◽  
Small Noncoding Rna ◽  
Small Noncoding Rnas ◽  
Log Reduction ◽  
Complex Interactions

ABSTRACT African swine fever virus (ASFV) causes a lethal hemorrhagic disease of domestic pigs, against which no vaccine is available. ASFV has a large, double-stranded DNA genome that encodes over 150 proteins. Replication takes place predominantly in the cytoplasm of the cell and involves complex interactions with host cellular components, including small noncoding RNAs (sncRNAs). A number of DNA viruses are known to manipulate sncRNA either by encoding their own or disrupting host sncRNA. To investigate the interplay between ASFV and sncRNAs, a study of host and viral small RNAs extracted from ASFV-infected primary porcine macrophages (PAMs) was undertaken. We discovered that ASFV infection had only a modest effect on host miRNAs, with only 6 miRNAs differentially expressed during infection. The data also revealed 3 potential novel small RNAs encoded by ASFV, ASFVsRNA1-3. Further investigation of ASFVsRNA2 detected it in lymphoid tissue from pigs with ASF. Overexpression of ASFVsRNA2 led to an up to 1-log reduction in ASFV growth, indicating that ASFV utilizes a virus-encoded small RNA to disrupt its own replication. IMPORTANCE African swine fever (ASF) poses a major threat to pig populations and food security worldwide. The disease is endemic to Africa and Eastern Europe and is rapidly emerging into Asia, where it has led to the deaths of millions of pigs in the last 12 months. The development of safe and effective vaccines to protect pigs against ASF has been hindered by lack of understanding of the complex interactions between ASFV and the host cell. We focused our work on characterizing the interactions between ASFV and sncRNAs. Although comparatively modest changes to host sncRNA abundances were observed upon ASFV infection, we discovered and characterized a novel functional ASFV-encoded sncRNA. The results from this study add important insights into ASFV host-pathogen interactions. This knowledge may be exploited to develop more effective ASFV vaccines that take advantage of the sncRNA system.

scholarly journals Identification of a σB-Dependent Small Noncoding RNA in Listeria monocytogenes

2008 ◽  
Vol 190 (18) ◽  
pp. 6264-6270 ◽  
Author(s):  
Jesper Sejrup Nielsen ◽  
Anders Steno Olsen ◽  
Mette Bonde ◽  
Poul Valentin-Hansen ◽  
Birgitte H. Kallipolitis
Keyword(s):  
Listeria Monocytogenes ◽  
Stress Tolerance ◽  
Sigma Factor ◽  
Noncoding Rna ◽  
Noncoding Rnas ◽  
Alternative Sigma Factor ◽  
Dependent Manner ◽  
Small Noncoding Rna ◽  
Small Noncoding Rnas ◽  
Regulatory Circuits

ABSTRACT In Listeria monocytogenes, the alternative sigma factor σB plays important roles in stress tolerance and virulence. Here, we present the identification of SbrA, a novel small noncoding RNA that is produced in a σB-dependent manner. This finding adds the σB regulon to the growing list of stress-induced regulatory circuits that include small noncoding RNAs.

scholarly journals Interaction between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer

mSystems ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Ce Yuan ◽  
Michael B. Burns ◽  
Subbaya Subramanian ◽  
Ran Blekhman
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Gut Microbiota ◽  
Mirna Expression ◽  
Gut Microbiome ◽  
Noncoding Rna ◽  
Microbial Community Composition ◽  
Host Cells ◽  
Microbiome Composition ◽  
Small Noncoding Rna

ABSTRACT Although variation in gut microbiome composition has been linked with colorectal cancer (CRC), the factors that mediate the interactions between CRC tumors and the microbiome are poorly understood. MicroRNAs (miRNAs) are known to regulate CRC progression and are associated with patient survival outcomes. In addition, recent studies suggested that host miRNAs can also regulate bacterial growth and influence the composition of the gut microbiome. Here, we investigated the association between miRNA expression and microbiome composition in human CRC tumor and normal tissues. We identified 76 miRNAs as differentially expressed (DE) in tissue from CRC tumors and normal tissue, including the known oncogenic miRNAs miR-182, miR-503, and mir-17~92 cluster. These DE miRNAs were correlated with the relative abundances of several bacterial taxa, including Firmicutes , Bacteroidetes , and Proteobacteria . Bacteria correlated with DE miRNAs were enriched with distinct predicted metabolic categories. Additionally, we found that miRNAs that correlated with CRC-associated bacteria are predicted to regulate targets that are relevant for host-microbiome interactions and highlight a possible role for miRNA-driven glycan production in the recruitment of pathogenic microbial taxa. Our work characterized a global relationship between microbial community composition and miRNA expression in human CRC tissues. IMPORTANCE Recent studies have found an association between colorectal cancer (CRC) and the gut microbiota. One potential mechanism by which the microbiota can influence host physiology is through affecting gene expression in host cells. MicroRNAs (miRNAs) are small noncoding RNA molecules that can regulate gene expression and have important roles in cancer development. Here, we investigated the link between the gut microbiota and the expression of miRNA in CRC. We found that dozens of miRNAs are differentially regulated in CRC tumors and adjacent normal colon and that these miRNAs are correlated with the abundance of microbes in the tumor microenvironment. Moreover, we found that microbes that have been previously associated with CRC are correlated with miRNAs that regulate genes related to interactions with microbes. Notably, these miRNAs likely regulate glycan production, which is important for the recruitment of pathogenic microbial taxa to the tumor. This work provides a first systems-level map of the association between microbes and host miRNAs in the context of CRC and provides targets for further experimental validation and potential interventions.

scholarly journals Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Sonia Tarallo ◽  
Giulio Ferrero ◽  
Gaetano Gallo ◽  
Antonio Francavilla ◽  
Giuseppe Clerico ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Gut Microbiota ◽  
Small Rna ◽  
Gut Microbiome ◽  
Small Rnas ◽  
Area Under The Curve ◽  
Small Rna Sequencing ◽  
Predictive Tool ◽  
Cross Sectional ◽  
Stool Samples

ABSTRACT Dysbiotic configurations of the human gut microbiota have been linked to colorectal cancer (CRC). Human small noncoding RNAs are also implicated in CRC, and recent findings suggest that their release in the gut lumen contributes to shape the gut microbiota. Bacterial small RNAs (bsRNAs) may also play a role in carcinogenesis, but their role has been less extensively explored. Here, we performed small RNA and shotgun sequencing on 80 stool specimens from patients with CRC or with adenomas and from healthy subjects collected in a cross-sectional study to evaluate their combined use as a predictive tool for disease detection. We observed considerable overlap and a correlation between metagenomic and bsRNA quantitative taxonomic profiles obtained from the two approaches. We identified a combined predictive signature composed of 32 features from human and microbial small RNAs and DNA-based microbiome able to accurately classify CRC samples separately from healthy and adenoma samples (area under the curve [AUC] = 0.87). In the present study, we report evidence that host-microbiome dysbiosis in CRC can also be observed by examination of altered small RNA stool profiles. Integrated analyses of the microbiome and small RNAs in the human stool may provide insights for designing more-accurate tools for diagnostic purposes. IMPORTANCE The characteristics of microbial small RNA transcription are largely unknown, while it is of primary importance for a better identification of molecules with functional activities in the gut niche under both healthy and disease conditions. By performing combined analyses of metagenomic and small RNA sequencing (sRNA-Seq) data, we characterized both the human and microbial small RNA contents of stool samples from healthy individuals and from patients with colorectal carcinoma or adenoma. With the integrative analyses of metagenomic and sRNA-Seq data, we identified a human and microbial small RNA signature which can be used to improve diagnosis of the disease. Our analysis of human and gut microbiome small RNA expression is relevant to generation of the first hypotheses about the potential molecular interactions occurring in the gut of CRC patients, and it can be the basis for further mechanistic studies and clinical tests.

scholarly journals Exosomal miRNA: Small Molecules, Big Impact in Colorectal Cancer

2019 ◽  
Vol 2019 ◽  
pp. 1-18 ◽  
Author(s):  
Valentin Vautrot ◽  
Gaëtan Chanteloup ◽  
Mohammed Elmallah ◽  
Marine Cordonnier ◽  
François Aubin ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Biology ◽  
Noncoding Rna ◽  
Cell Types ◽  
Response To Therapy ◽  
Bioactive Molecules ◽  
Premetastatic Niche ◽  
Rna Molecules ◽  
Small Noncoding Rna ◽  
Exosomal Mirna

Colorectal cancer (CRC) is one of the major causes of cancer-related deaths worldwide. Tumor microenvironment (TME) contains many cell types including stromal cells, immune cells, and endothelial cells. The TME modulation explains the heterogeneity of response to therapy observed in patients. In this context, exosomes are emerging as major contributors in cancer biology. Indeed, exosomes are implicated in tumor proliferation, angiogenesis, invasion, and premetastatic niche formation. They contain bioactive molecules such as proteins, lipids, and RNAs. More recently, many studies on exosomes have focused on miRNAs, small noncoding RNA molecules able to influence protein expression. In this review, we describe miRNAs transported by exosomes in the context of CRC and discuss their influence on TME and their potential as circulating biomarkers. This overview underlines emerging roles for exosomal miRNAs in cancer research for the near future.

172 IDENTIFICATION OF MICRORNAS IN BOVINE OVARY

2009 ◽  
Vol 21 (1) ◽  
pp. 185
Author(s):  
M. M. Hossain ◽  
M. Hoelker ◽  
C. Phatsara ◽  
E. Tholen ◽  
K. Schellander ◽  
...  
Keyword(s):  
Small Rna ◽  
Hormonal Regulation ◽  
Small Rnas ◽  
Noncoding Rna ◽  
Bovine Genome ◽  
Functional Characterization ◽  
Sequence Length ◽  
P Value ◽  
Template Switching ◽  
Bovine Ovary

Tightly regulated expression and interaction of a multitude of genes for ovarian folliculogenesis leading to successful oocyte development could be regulated by recently identified new class of small RNAs of ~22 nt (i.e. microRNAs), which are already proved as one of the vital transcriptional regulators in different biological processes including development. But their presence and expression in bovine ovary has not yet been determined. Here, we have attempted to identify miRNAs in bovine ovary by small RNA-cDNA library construction through 5 ligation independent cloning. For this purpose, total RNA enriched with small RNA was isolated from ovary and size fractionated (18 to 24 nt) by denaturing PAGE. Extracted RNA was first 3′ linkered and after template switching by RT, the second 3′ linkering of the first strand cDNA was performed. These linkered small RNA-cDNAs were then amplified with linker-specific primers consisting of BAN I restriction sites, concatemerized by serial ligation, cloned into TOPO TA vector, and transformed into TOP 10 chemically competent cells. After screening, colonies were picked and sequenced. Bioinformatic analysis was done according to the published criteria for the small RNAs. From 233 clones a total of 479 reads were identified. Frequency of sequence length found in the library was 26.8% for ≤18 nt, 55.1% for 19 to 22 nt, and 18.1% for ≥23 nt. The total 479 sequences identified in the library represent 35% miRNAs, 12% mRNA, 12.1% rRNA, 5.6% tRNA, 4.2% repeat associated siRNA, 3.8% non-repeat-associated siRNA, 4% tiny noncoding RNA, 1% small nuclear RNA, and 16% sequences not matched to bovine genome. All 171 miR sequences comprised 79 distinct miRNAs, of which 45 miRNAs already annotated in miRBase for bovine and the other 34 miRNAs are new discoveries. Of the 34 newly identified miRNAs, 12 are described in other species but not yet in bovine. Most of the miRNAs cloned into multiple times, where let-7a cloned for 10, let-7b for 28, let-7c for 13, miR-21 for 4, miR-23b for 11, miR-24 for 7, miR-27a for 6, miR-126 for 4, and miR-143 for 11 times. Based on best hit score, P-value and free energy by online target prediction, some of the bta-miR identified in the library (let-7b, 15b, 18a, 23b, 101, 125b, 126, 140, 145, 199a) are found to target hundreds of genes related to follicular development, ovulation and hormonal regulation. Further functional characterization of some selected miRNAs including expression profiling and in situ localization in follicles of different size and cycles may supplement the results of this study and will enable us to gain insight into their relation to female fertility.

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