Expression profiles and potential roles of transfer RNA‐derived small RNAs in atherosclerosis

Abstract Background: MicroRNAs (miRNAs) are a class of noncoding small RNAs that play important roles in many physiological processes by regulating gene expression. Previous studies have shown that the expression levels of total miRNAs increase during mouse embryonic development, and some miRNAs control the regulatory network in development progression. However, few studies have focused on the effects of miRNAs on early human embryonic development. The relationship between miRNAs and early human embryogenesis is still unknown. Results:In this study, RNA-seq data collected from sperm samples from 102 patients with a normal sperm index but treated with assisted reproductive technology (ART) were analyzed for the relationships between differentially expressed small RNAs and the fertilization rate (FR), blastocyst rate and high-quality embryo rate (HQER). The sperm samples with high hsa-mir-191 expression had a higher FR, effective embryo rate (EER) and HQER. hsa-mir-191 was used as a single indicator to predict the HQER. The receiver operating characteristic (ROC) curve had an area under the ROC curve (AUC) of 0.686. We also found that hsa-mir-191 expression is correlated with an abnormal sperm rate (cor = 0.29, p< 0.01). We also evaluated the relationship between hsa-mir-34c and early human embryo development in these 102 sperm samples and obtained negative results. Conclusions: These findings suggest that high hsa-mir-191-5p expression in sperm is associated with early human embryonic quality and that hsa-mir-191-5p could be used as a potential marker to screen high-quality sperm to improve the success rates of in vitro fertilization (IVF).

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Dysregulation of tRNA-derived small RNAs and their potential roles in lupus nephritis

Lupus ◽

10.1177/09612033211061482 ◽

2021 ◽

pp. 096120332110614

Author(s):

Yan Liang ◽

Ji Zhang ◽

Wenxian Qiu ◽

Bo Chen ◽

Ying Zhou ◽

...

Keyword(s):

Lupus Nephritis ◽

Signaling Pathway ◽

Small Rnas ◽

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Mapk Signaling ◽

Pcr Analysis ◽

Clinical Indicators ◽

Qrt Pcr

Objective Lupus nephritis (LN) is a major end-organ complication of systemic lupus erythematosus (SLE), and the molecular mechanism of LN is not completely clear. Accumulating pieces of evidence indicate the potential vital role of tRNA-derived small RNAs (tsRNAs) in human diseases. Current study aimed to investigate the potential roles of tsRNAs in LN. Methods We herein employed high‐throughput sequencing to screen the expression profiles of tsRNAs in renal tissues of the LN and control groups. To validate the sequencing data, we performed quantitative real-time PCR (qRT-PCR) analysis. Correlational analysis of verified tsRNAs expression and clinical indicators was conducted using linear regression. The potential target genes were also predicted. The biological functions of tsRNAs were annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Results Our findings revealed that the expression profiles of tsRNAs were significantly altered in the kidney tissues from LN patients compared with control. Overall, 160 tsRNAs were significantly dysregulated in the LN group, of which 79 were upregulated, whereas 81 were downregulated. Subsequent qRT-PCR results confirmed the different expression of candidate tsRNAs. Correlation analysis results found that expression of verified tsRNAs were correlated to clinical indicators. The target prediction results revealed that verified tsRNAs might act on 712 target genes. Further bioinformatics analysis uncovered tsRNAs might participate in the pathogenesis of LN through several associated pathways, including cell adhesion molecules, MAPK signaling pathway, PI3K-Akt signaling pathway and B cell receptor signaling pathway. Conclusion This study provides a novel insight for studying the mechanism of LN.

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Integration of Transcriptomes, Small RNAs, and Degradome Sequencing to Identify Putative miRNAs and their Targets Related to Eu-Rubber Biosynthesis in Eucommia ulmoides

Genes ◽

10.3390/genes10080623 ◽

2019 ◽

Vol 10 (8) ◽

pp. 623

Author(s):

Jing Ye ◽

Wenjing Han ◽

Ruisheng Fan ◽

Minhao Liu ◽

Long Li ◽

...

Keyword(s):

Regulatory Network ◽

Small Rnas ◽

High Throughput Sequencing ◽

Expression Profiles ◽

Vital Role ◽

Eucommia Ulmoides ◽

Messenger Rnas ◽

Rubber Biosynthesis ◽

Degradome Sequencing ◽

The Eu

Eucommia ulmoides has attracted much attention as a valuable natural rubber (Eu-rubber) production tree. As a strategic material, Eu-rubber plays a vital role in general and defence industries. However, the study of Eu-rubber biosynthesis at a molecular level is scarce, and the regulatory network between microRNAs (miRNAs) and messenger RNAs (mRNAs) in Eu-rubber biosynthesis has not been assessed. In this study, we comprehensively analyzed the transcriptomes, small RNAs (sRNAs) and degradome to reveal the regulatory network of Eu-rubber biosynthesis in E. ulmoides. A total of 82,065 unigenes and 221 miRNAs were identified using high-throughput sequencing; 20,815 targets were predicted using psRNATarget software. Of these targets, 779 miRNA-target pairs were identified via degradome sequencing. Thirty-one miRNAs were differentially expressed; 22 targets of 34 miRNAs were annotated in the terpenoid backbone biosynthesis pathway (ko00900) based on the Kyoto Encyclopedia of Genes and Genomes (KEGG). These miRNAs were putatively related to Eu-rubber biosynthesis. A regulatory network was constructed according to the expression profiles of miRNAs and their targets. These results provide a comprehensive analysis of transcriptomics, sRNAs and degradome to reveal the Eu-rubber accumulation, and provide new insights into genetic engineering techniques which may improve the content of Eu-rubber in E. ulmoides.

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Transfer RNA-derived small RNAs in plants

Science China Life Sciences ◽

10.1007/s11427-017-9167-5 ◽

2017 ◽

Vol 61 (2) ◽

pp. 155-161 ◽

Cited By ~ 7

Author(s):

Lei Zhu ◽

David W. Ow ◽

Zhicheng Dong

Keyword(s):

Small Rnas ◽

Transfer Rna

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Mechanisms by Which Small RNAs Affect Bacterial Activity

Journal of Dental Research ◽

10.1177/0022034519876898 ◽

2019 ◽

Vol 98 (12) ◽

pp. 1315-1323

Author(s):

L. Lei ◽

Y. Yang ◽

S. Wu ◽

X. Ma ◽

...

Keyword(s):

Stress Responses ◽

Small Rnas ◽

Environmental Changes ◽

Expression Profiles ◽

Bacterial Flora ◽

Oral Disease ◽

Bacterial Gene ◽

Bacterial Physiology ◽

Cellular Processes ◽

Regulatory Rnas

The oral cavity contains a distinct habitat that supports diverse bacterial flora. Recent observations have provided additional evidence that sRNAs are key regulators of bacterial physiology and pathogenesis. These sRNAs have been divided into 5 functional groups: cis-encoded RNAs, trans-encoded RNAs, RNA regulators of protein activity, bacterial CRISPR (clustered regularly interspaced short palindromic repeat) RNAs, and a novel category of miRNA-size small RNAs (msRNAs). In this review, we discuss a critical group of key commensal and opportunistic oral pathogens. In general, supragingival bacterial sRNAs function synergistically to fine-tune the regulation of cellular processes and stress responses in adaptation to environmental changes. Particularly in the cariogenic bacteria Streptococcus mutans, both the antisense vicR RNA and msRNA1657 can impede the metabolism of bacterial exopolysaccharides, prevent biofilm formation, and suppress its cariogenicity. In Enterococcus faecalis, selected sRNAs control the expression of proteins involved in diverse cellular processes and stress responses. In subgingival plaques, sRNAs from periodontal pathogens can function as novel bacterial signaling molecules that mediate bacterial-human interactions in periodontal homeostasis. In Porphyromonas gingivalis, the expression profiles of putative sRNA101 and sRNA42 were found to respond to hemin availability after hemin starvation. Regarding Aggregatibacter actinomycetemcomitans (previously Actinobacillus actinomycetemcomitans), a major periodontal pathogen associated with aggressive periodontitis, the predicted sRNAs interact with several virulence genes, including those encoding leukotoxin and cytolethal distending toxin. Furthermore, in clinical isolates, these associated RNAs could be explored not only as potential biomarkers for oral disease monitoring but also as alternative types of regulators for drug design. Thus, this emerging subspecialty of bacterial regulatory RNAs could reshape our understanding of bacterial gene regulation from their key roles of endogenous regulatory RNAs to their activities in pathologic processes.

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Genome-wide analysis of hippocampal transfer RNA-derived small RNAs identifies new potential therapeutic targets of Bushen Tiansui formula against Alzheimer’s disease

Journal of Integrative Medicine ◽

10.1016/j.joim.2020.12.005 ◽

2020 ◽

Author(s):

Zhe-yu Zhang ◽

Chun-hu Zhang ◽

Jing-jing Yang ◽

Pan-pan Xu ◽

Peng-ji Yi ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Small Rnas ◽

Therapeutic Targets ◽

Transfer Rna ◽

Genome Wide Analysis ◽

Genome Wide

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Two novel members of the LhrC family of small RNAs in Listeria monocytogenes with overlapping regulatory functions but distinctive expression profiles

RNA Biology ◽

10.1080/15476286.2016.1208332 ◽

2016 ◽

Vol 13 (9) ◽

pp. 895-915 ◽

Cited By ~ 19

Author(s):

Maria Storm Mollerup ◽

Joseph Andrew Ross ◽

Anne-Catherine Helfer ◽

Kristine Meistrup ◽

Pascale Romby ◽

...

Keyword(s):

Listeria Monocytogenes ◽

Small Rnas ◽

Expression Profiles ◽

Regulatory Functions

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Divergent degeneration of creA antitoxin genes from minimal CRISPRs and the convergent strategy of tRNA-sequestering CreT toxins

Nucleic Acids Research ◽

10.1093/nar/gkab821 ◽

2021 ◽

Vol 49 (18) ◽

pp. 10677-10688

Author(s):

Feiyue Cheng ◽

Rui Wang ◽

Haiying Yu ◽

Chao Liu ◽

Jun Yang ◽

...

Keyword(s):

Adaptive Immunity ◽

Deep Sequencing ◽

Small Rnas ◽

Transfer Rna ◽

Open Reading Frame ◽

Type I ◽

Essential Information ◽

Reading Frame ◽

Crea Gene

Abstract Aside from providing adaptive immunity, type I CRISPR-Cas was recently unearthed to employ a noncanonical RNA guide (CreA) to transcriptionally repress an RNA toxin (CreT). Here, we report that, for most archaeal and bacterial CreTA modules, the creA gene actually carries two flanking ‘CRISPR repeats’, which are, however, highly divergent and degenerated. By deep sequencing, we show that the two repeats give rise to an 8-nt 5′ handle and a 22-nt 3′ handle, respectively, i.e., the conserved elements of a canonical CRISPR RNA, indicating they both retained critical nucleotides for Cas6 processing during divergent degeneration. We also uncovered a minimal CreT toxin that sequesters the rare transfer RNA for isoleucine, tRNAIleCAU, with a six-codon open reading frame containing two consecutive AUA codons. To fully relieve its toxicity, both tRNAIleCAU overexpression and supply of extra agmatine (modifies the wobble base of tRNAIleCAU to decipher AUA codons) are required. By replacing AUA to AGA/AGG codons, we reprogrammed this toxin to sequester rare arginine tRNAs. These data provide essential information on CreTA origin and for future CreTA prediction, and enrich the knowledge of tRNA-sequestering small RNAs that are employed by CRISPR-Cas to get addictive to the host.

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