scholarly journals Global survey of miRNAs and tRNA-derived small RNAs from the human parasitic protist Trichomonas vaginalis

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Zhen-Sheng Wang ◽  
Hong-Chang Zhou ◽  
Chun-Yan Wei ◽  
Zhi-Hua Wang ◽  
Xiao Hao ◽  
...  
Keyword(s):  
Small Rnas ◽  
Trichomonas Vaginalis ◽  
Stem Loop ◽  
Sexually Transmitted ◽  
Site Analysis ◽  
Reverse Transcription Pcr ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Parasitic Protist ◽  
Trna Halves

Abstract Background Small non-coding RNAs play critical regulatory roles in post-transcription. However, their characteristics in Trichomonas vaginalis, the causative agent of human sexually transmitted trichomoniasis, still remain to be determined. Methods Small RNA transcriptomes from Trichomonas trophozoites were deep sequenced using the Illumina NextSeq 500 system and comprehensively analyzed to identify Trichomonas microRNAs (miRNAs) and transfer RNA (tRNA)-derived small RNAs (tsRNAs). The tsRNA candidates were confirmed by stem-loop quantitative reverse transcription-PCR, and motifs to guide the cleavage of tsRNAs were predicted using the GLAM2 algorithm. Results The miRNAs were found to be present in T. vaginalis but at an extremely low abundance (0.0046%). Three categories of endogenous Trichomonas tsRNAs were identified, namely 5′tritsRNAs, mid-tritsRNAs and 3′tritsRNAs, with the 5′tritsRNAs constituting the dominant category (67.63%) of tsRNAs. Interestingly, the cleavage site analysis verified both conventional classes of tRNA-derived fragments (tRFs) and tRNA-halves in tritsRNAs, indicating the expression of tRNA-halves in the non-stress condition. A total of 25 tritsRNAs were experimentally confirmed, accounting for 78.1% of all tested candidates. Three motifs were predicted to guide the production of tritsRNAs. The results prove the expression of tRFs and tRNA-halves in the T. vaginalis transcriptome. Conclusions This is the first report of genome-wide investigation of small RNAs, particularly tsRNAs and miRNAs, from Trichomonas parasites. Our findings demonstrate the expression profile of tsRNAs in T. vaginalis, while miRNA was barely detected. These results may promote further research aimed at gaining a better understanding of the evolution of small non-coding RNA in T. vaginalis and their functions in the pathogenesis of trichomoniasis.

scholarly journals Global Survey of miRNAs and tRNA-derived Small RNAs From Human Parasitic Protist Trichomonas Vaginalis

2020 ◽  
Author(s):  
Zhensheng Wang ◽  
Hongchang Zhou ◽  
Chunyan Wei ◽  
Zhihua Wang ◽  
Xiao Hao ◽  
...  
Keyword(s):  
Small Rnas ◽  
Trichomonas Vaginalis ◽  
Stem Loop ◽  
Sexually Transmitted ◽  
Site Analysis ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Parasitic Protist ◽  
Non Coding Rnas ◽  
Trna Halves

Abstract BackgroundSmall non-coding RNAs play critical regulatory roles in post-transcription. However, their characteristics in Trichomonas vaginalis (T. vaginalis), the causative agent of human sexually transmitted trichomoniasis, still remain to be unveiled. MethodsSmall RNA transcriptomes from Trichomonas trophozoites were deeply sequenced through Illumina NextSeq 500 system and comprehensively analyzed to identify Trichomonas miRNAs and tRNA-derived small RNAs (tsRNAs). The tsRNAs candidates were confirmed by stem-loop RT-PCR and motifs to guide the cleavage of tsRNAs were predicted by performing GLAM2 algorithm. ResultsThe miRNAs were found at extremely low abundance (0.0046%) in T. vaginalis. Three categories of endogenous Trichomonas tsRNAs were identified as 5'tritsRNAs, mid-tritsRNAs and 3'tritsRNAs, with 5'tritsRNAs dominating (67.63%) in tsRNAs. Interestingly, the cleavage site analysis verified both conventional classes of tRFs and tRNA-halves in tritsRNAs, indicating the expression of tRNA-halves in non-stress condition. A total of 25 tritsRNAs were experimentally confirmed, accounting for 78.1% of all tested candidates. Three motifs were predicted to guide the production of tritsRNAs. This proved the expression of tRFs and tRNA-halves in T. vaginalis transcriptome. ConclusionsThis is the first report of genome-wide investigation of small RNAs, particularly tsRNAs and miRNAs, from Trichomonas parasites. Our findings demonstrate the expression profile of tsRNAs in T. vaginalis, while miRNA was hardly discovered. These results might promote the further research to better understand the evolution of small non-coding RNA in T. vaginalis and their functions in pathogenesis of trichomoniasis.

How to find small non-coding RNAs in bacteria

2005 ◽  
Vol 386 (12) ◽  
pp. 1219-1238 ◽  
Author(s):  
Jörg Vogel ◽  
Cynthia Mira Sharma
Keyword(s):  
Small Rnas ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Critical Role ◽  
Rna Molecules ◽  
Regulatory Circuit ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Response To Stress ◽  
Non Coding Rnas

AbstractSmall non-coding RNAs (sRNAs) have attracted considerable attention as an emerging class of gene expression regulators. In bacteria, a few regulatory RNA molecules have long been known, but the extent of their role in the cell was not fully appreciated until the recent discovery of hundreds of potential sRNA genes in the bacteriumEscherichia coli. Orthologs of theseE. colisRNA genes, as well as unrelated sRNAs, were also found in other bacteria. Here we review the disparate experimental approaches used over the years to identify sRNA molecules and their genes in prokaryotes. These include genome-wide searches based on the biocomputational prediction of non-coding RNA genes, global detection of non-coding transcripts using microarrays, and shotgun cloning of small RNAs (RNomics). Other sRNAs were found by either co-purification with RNA-binding proteins, such as Hfq or CsrA/RsmA, or classical cloning of abundant small RNAs after size fractionation in polyacrylamide gels. In addition, bacterial genetics offers powerful tools that aid in the search for sRNAs that may play a critical role in the regulatory circuit of interest, for example, the response to stress or the adaptation to a change in nutrient availability. Many of the techniques discussed here have also been successfully applied to the discovery of eukaryotic and archaeal sRNAs.

scholarly journals Adenine DNA methylation, 3D genome organization and gene expression in the parasiteTrichomonas vaginalis

2019 ◽  
Author(s):  
Ayelen Lizarraga ◽  
Zach Klapholz O’Brown ◽  
Konstantinos Boulias ◽  
Lara Roach ◽  
Eric Lieberman Greer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Trichomonas Vaginalis ◽  
Wide Distribution ◽  
Spatial Proximity ◽  
Regulation Of Transcription ◽  
Sexually Transmitted ◽  
Genome Wide ◽  
Methylation Mark ◽  
Intergenic Regions

ABSTRACTTrichomonas vaginalisis a common sexually transmitted parasite that colonizes the human urogenital tract causing infections that range from asymptomatic to highly inflammatory. Recent works have highlighted the importance of histone modifications in the regulation of transcription and parasite pathogenesis. However, the nature of DNA methylation in the parasite remains unexplored. Using a combination of immunological techniques and UHPLC, we analyzed the abundance of DNA methylation in strains with differential pathogenicity demonstrating that N6-methyladenine (6mA), and not 5-methylcytosine (5mC), is the main DNA methylation mark inT. vaginalis. Genome-wide distribution of 6mA reveals that this mark is enriched at intergenic regions, with a preference for certain super-families of DNA transposable elements. We show that 6mA inT. vaginalisis associated with silencing when present on genes. Interestingly, bioinformatics analysis revealed the presence of transcriptionally active or repressive intervals flanked by 6mA-enriched regions and results from chromatin conformation capture (3C) experiments suggest these 6mA flanked regions are in close spatial proximity. These associations were disrupted when parasites were treated with the demethylation activator ascorbic acid. This finding revealed a new role for 6mA in modulating 3D chromatin structure and gene expression in this divergent member of the Excavata.SIGNIFICANCE STATEMENTTrichomonas vaginaliscauses the most common non-viral sexually transmitted infection yet little is known about the regulation of gene expression in this eukaryotic parasite. We demonstrate that N6-methyladenine (6mA) is the main methylation mark in theT. vaginalisgenome. 6mA is widespread in DNA of eubacterial genera, but uncommon in genomes of most eukaryotes. Examination of the genome-wide distribution of 6mA reveals a preference for intergenic regions. Transcriptionally active or repressive intervals are found to be flanked by 6mA-enriched regions and data suggest 6mA flanked regions are in close 3D spatial proximity. Our findings describe for the first time the presence of DNA methylation inT. vaginalisand reveal a new role for 6mA in modulating 3D chromatin architecture.

Prevalence of Trichomonas Vaginalis and its Correlation with Socio-demographic Variables in Pregnant Women in Al-Diwaniya,Iraq

2018 ◽  
Vol 9 (SPL1) ◽  
Author(s):  
Shiren Ali Al Hamzawi
Keyword(s):  
Pregnant Women ◽  
Rural Areas ◽  
Trichomonas Vaginalis ◽  
Cross Sectional Study ◽  
Demographic Variables ◽  
Transmitted Infection ◽  
Cross Sectional ◽  
Sexually Transmitted ◽  
Vaginal Swabs ◽  
Low Education

Estimates of Trichomonas vaginalis prevalence in pregnant women are variable with few studies in Iraq.T. vaginalis is a worldwide prevalent sexually transmitted infection,but fortunately,it is very treatable. Researchers believed that pregnancy is one of the effective factors for T. vaginalis infection in women.A cross-sectional study performed in Obstetrics and Gynecology Department at Maternity and Children Teaching Hospital in Al-Diwaniya city on two hundred female pregnant patients between the ages of 16-45 years. These females had no intercourse for 2–3 days,not using drugs (antibiotics,antiprotozoal or steroids) for the last 15 days. Vaginal discharges of any type with or without itching,burning sensation or both were their main complaints. Vaginal swabs were taken from all participating patients for direct wet mount microscopy and culture for the detection of Trichomonas vaginalis infection. The study showed that twelve out of two hundred examined pregnant women (6%) presented with T. vaginalis infection. The infection was more in those with mothers’ age (26-35) years,housewives,low education,higher parity,and of rural residents. Other maternal variables were not significantly associated with T. vaginalis infection. The study showed a prevalence of (6%) of T. vaginalis infection in pregnant female attendees. Infection was more in those with mothers ’age (26-35) years,housewives,low educational level,higher parity,and living in rural areas.

scholarly journals Pharmacogenomics of Lithium Response in Bipolar Disorder

2021 ◽  
Vol 14 (4) ◽  
pp. 287
Author(s):  
Courtney M. Vecera ◽  
Gabriel R. Fries ◽  
Lokesh R. Shahani ◽  
Jair C. Soares ◽  
Rodrigo Machado-Vieira
Keyword(s):  
Bipolar Disorder ◽  
Association Studies ◽  
Mood Stabilizer ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Lithium Response ◽  
Genetic Loading ◽  
Long Non Coding Rna

Despite being the most widely studied mood stabilizer, researchers have not confirmed a mechanism for lithium’s therapeutic efficacy in Bipolar Disorder (BD). Pharmacogenomic applications may be clinically useful in the future for identifying lithium-responsive patients and facilitating personalized treatment. Six genome-wide association studies (GWAS) reviewed here present evidence of genetic variations related to lithium responsivity and side effect expression. Variants were found on genes regulating the glutamate system, including GAD-like gene 1 (GADL1) and GRIA2 gene, a mutually-regulated target of lithium. In addition, single nucleotide polymorphisms (SNPs) discovered on SESTD1 may account for lithium’s exceptional ability to permeate cell membranes and mediate autoimmune and renal effects. Studies also corroborated the importance of epigenetics and stress regulation on lithium response, finding variants on long, non-coding RNA genes and associations between response and genetic loading for psychiatric comorbidities. Overall, the precision medicine model of stratifying patients based on phenotype seems to derive genotypic support of a separate clinical subtype of lithium-responsive BD. Results have yet to be expounded upon and should therefore be interpreted with caution.

scholarly journals Functional genomics of autoimmune diseases

2021 ◽  
pp. annrheumdis-2019-216794
Author(s):  
Akari Suzuki ◽  
Matteo Maurizio Guerrini ◽  
Kazuhiko Yamamoto
Keyword(s):  
Autoimmune Diseases ◽  
Association Studies ◽  
Linkage Disequilibrium Block ◽  
Causal Variant ◽  
Genome Wide Association Studies ◽  
Coding Region ◽  
Risk Variants ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Long Non Coding Rna

For more than a decade, genome-wide association studies have been applied to autoimmune diseases and have expanded our understanding on the pathogeneses. Genetic risk factors associated with diseases and traits are essentially causative. However, elucidation of the biological mechanism of disease from genetic factors is challenging. In fact, it is difficult to identify the causal variant among multiple variants located on the same haplotype or linkage disequilibrium block and thus the responsible biological genes remain elusive. Recently, multiple studies have revealed that the majority of risk variants locate in the non-coding region of the genome and they are the most likely to regulate gene expression such as quantitative trait loci. Enhancer, promoter and long non-coding RNA appear to be the main target mechanisms of the risk variants. In this review, we discuss functional genetics to challenge these puzzles.

scholarly journals Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts

2019 ◽  
Vol 20 (13) ◽  
pp. 3315 ◽  
Author(s):  
Simona Cantarella ◽  
Davide Carnevali ◽  
Marco Morselli ◽  
Anastasia Conti ◽  
Matteo Pellegrini ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Cell Cycle Progression ◽  
Human Fibroblasts ◽  
Rna Polymerase Iii ◽  
Protein Coding ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Hela Cell Lines ◽  
Significant Enrichment ◽  
Alu Rna

Alu retroelements, whose retrotransposition requires prior transcription by RNA polymerase III to generate Alu RNAs, represent the most numerous non-coding RNA (ncRNA) gene family in the human genome. Alu transcription is generally kept to extremely low levels by tight epigenetic silencing, but it has been reported to increase under different types of cell perturbation, such as viral infection and cancer. Alu RNAs, being able to act as gene expression modulators, may be directly involved in the mechanisms determining cellular behavior in such perturbed states. To directly address the regulatory potential of Alu RNAs, we generated IMR90 fibroblasts and HeLa cell lines stably overexpressing two slightly different Alu RNAs, and analyzed genome-wide the expression changes of protein-coding genes through RNA-sequencing. Among the genes that were upregulated or downregulated in response to Alu overexpression in IMR90, but not in HeLa cells, we found a highly significant enrichment of pathways involved in cell cycle progression and mitotic entry. Accordingly, Alu overexpression was found to promote transition from G1 to S phase, as revealed by flow cytometry. Therefore, increased Alu RNA may contribute to sustained cell proliferation, which is an important factor of cancer development and progression.

scholarly journals Improved molecular laboratory productivity by consolidation of testing on the new random-access analyzer Alinity m

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Martin Obermeier ◽  
Monia Pacenti ◽  
Robert Ehret ◽  
Francesco Onelia ◽  
Rory Gunson ◽  
...  
Keyword(s):  
Trichomonas Vaginalis ◽  
Random Access ◽  
Mycoplasma Genitalium ◽  
Transmitted Infection ◽  
Sexually Transmitted ◽  
B Virus ◽  
Immunodeficiency Virus ◽  
International Multicenter Study ◽  
Laboratory Productivity ◽  
Laboratory Workflow

AbstractObjectivesAutomated molecular analyzers have accelerated diagnosis, allowing earlier intervention and better patient follow-up. A recently developed completely automated molecular analyzer, Alinity™ m (Abbott), offers consolidated, continuous, and random-access testing that may improve molecular laboratory workflow.MethodsAn international, multicenter study compared laboratory workflow metrics across various routine analyzers and Alinity m utilizing assays for human immunodeficiency virus type 1 (HIV-1), hepatitis C virus (HCV), hepatitis B virus (HBV), high-risk human papillomavirus (HR HPV), and sexually transmitted infection (STI) (Chlamydia trachomatis [CT]/Neisseria gonorrhoeae [NG]/Trichomonas vaginalis [TV]/Mycoplasma genitalium [MG]). Three turnaround times (TATs) were assessed: total TAT (sample arrival to result), sample onboard TAT (sample loading and test starting to result), and processing TAT (sample aspiration to result).ResultsTotal TAT was reduced from days with routine analyzers to hours with Alinity m, independent of requested assays. Sample onboard TATs for standard workflow using routine analyzers ranged from 7 to 32.5 h compared to 2.75–6 h for Alinity m. The mean sample onboard TAT for STAT samples on Alinity m was 2.36 h (±0.19 h). Processing TATs for Alinity m were independent of the combination of assays, with 100% of results reported within 117 min.ConclusionsThe consolidated, continuous, random-access workflow of Alinity m reduces TATs across various assays and is expected to improve both laboratory operational efficiency and patient care.

scholarly journals A Population-Specific Optimized GeneXpert Pooling Algorithm for Chlamydia trachomatis and Neisseria gonorrhoeae To Reduce Cost of Molecular Sexually Transmitted Infection Screening in Resource-Limited Settings

2020 ◽  
Vol 58 (9) ◽  
Author(s):  
Sarah Connolly ◽  
William Kilembe ◽  
Mubiana Inambao ◽  
Ana-Maria Visoiu ◽  
Tyronza Sharkey ◽  
...  
Keyword(s):  
Trichomonas Vaginalis ◽  
Molecular Testing ◽  
Resource Limited Settings ◽  
Syphilis Infection ◽  
Syndromic Management ◽  
Sexually Transmitted ◽  
Factors Associated ◽  
Resource Limited ◽  
The Cost ◽  
Low Prevalence

ABSTRACT The sexually transmitted infections (STIs) chlamydia (CT) and gonorrhea (NG) are often asymptomatic in women and undetected by syndromic management, leading to complications such as pelvic inflammatory disease, infertility, and ectopic pregnancy. Molecular testing, such as the GeneXpert CT/NG assay, is highly sensitive, but cost restraints preclude implementation of these technologies in resource-limited settings. Pooled testing is one strategy to reduce the cost per sample, but the extent of savings depends on disease prevalence. The current study describes a pooling strategy based on identification of sociodemographic and laboratory factors associated with CT/NG prevalence in a high-risk cohort of Zambian female sex workers and single mothers conducted from 2016 to 2019. Factors associated with testing positive for CT/NG via logistic regression modeling included city, younger age, lower education, long-acting reversible contraception usage, Trichomonas vaginalis infection, bacterial vaginosis, and incident syphilis infection. Based on these factors, the study population was stratified into high-, intermediate-, and low-prevalence subgroups and tested accordingly—individually, pools of 3, or pools of 4, respectively. The cost per sample was reduced from $18 to as low as $9.43 in the low-prevalence subgroup. The checklist tool and pooling approach described can be used in a variety of treatment algorithms to lower the cost per sample and increase access to molecular STI screening. This is particularly valuable in resource-limited settings to detect and treat asymptomatic CT/NG infections missed by traditional syndromic management.

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