scholarly journals Different classes of small RNAs are essential for head regeneration in the planarian Dugesia japonica

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhonghong Cao ◽  
David Rosenkranz ◽  
Suge Wu ◽  
Hongjin Liu ◽  
Qiuxiang Pang ◽  
...  
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Evolutionary Conservation ◽  
Body Parts ◽  
Promising Candidate ◽  
Dugesia Japonica ◽  
Head Regeneration

Abstract Background Planarians reliably regenerate all body parts after injury, including a fully functional head and central nervous system. But until now, the expression dynamics and functional role of miRNAs and other small RNAs during the process of head regeneration are not well understood. Furthermore, little is known about the evolutionary conservation of the relevant small RNAs pathways, rendering it difficult to assess whether insights from planarians will apply to other taxa. Results In this study, we applied high throughput sequencing to identify miRNAs, tRNA fragments and piRNAs that are dynamically expressed during head regeneration in Dugesia japonica. We further show that knockdown of selected small RNAs, including three novel Dugesia-specific miRNAs, during head regeneration induces severe defects including abnormally small-sized eyes, cyclopia and complete absence of eyes. Conclusions Our findings suggest that a complex pool of small RNAs takes part in the process of head regeneration in Dugesia japonica and provide novel insights into global small RNA expression profiles and expression changes in response to head amputation. Our study reveals the evolutionary conserved role of miR-124 and brings further promising candidate small RNAs into play that might unveil new avenues for inducing restorative programs in non-regenerative organisms via small RNA mimics based therapies.

scholarly journals Genome-wide miRNA analysis and integrated network for flavonoid biosynthesis in Osmanthus fragrans

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yong Shi ◽  
Heng Xia ◽  
Xiaoting Cheng ◽  
Libin Zhang
Keyword(s):  
Secondary Metabolites ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Flavonoid Biosynthesis ◽  
Integrated Network ◽  
Osmanthus Fragrans ◽  
Flavonoid Synthesis ◽  
Genome Wide

AbstractBackgroundOsmanthus fragransis an important economical plant containing multiple secondary metabolites including flavonoids and anthocyanins. During the past years, the roles of miRNAs in regulating the biosynthesis of secondary metabolites in plants have been widely investigated. However, few studies on miRNA expression profiles and the potential roles in regulating flavonoid biosynthesis have been reported inO. fragrans.ResultsIn this study, we used high-throughput sequencing technology to analyze the expression profiles of miRNAs in leaf and flower tissues ofO. fragrans. As a result, 106 conserved miRNAs distributed in 47 families and 88 novel miRNAs were identified. Further analysis showed there were 133 miRNAs differentially expressed in leaves and flowers. Additionally, the potential target genes of miRNAs as well as the related metabolic pathways were predicted. In the end, flavonoid content was measured in flower and leaf tissues and potential role of miR858 in regulating flavonoid synthesis was illustrated inO. fragrans.ConclusionsThis study not only provided the genome-wide miRNA profiles in the flower and leaf tissue ofO. fragrans, but also investigated the potential regulatory role of miR858a in flavonoid synthesis inO. fragrans. The results specifically indicated the connection of miRNAs to the regulation of secondary metabolite biosynthesis in non-model economical plant.

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

Lupus ◽  
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.

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

Genes ◽  
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.

scholarly journals Protease-mediated processing of Argonaute proteins controls small RNA association

2020 ◽  
Author(s):  
Rajani Kanth Gudipati ◽  
Kathrin Braun ◽  
Foivos Gypas ◽  
Daniel Hess ◽  
Jan Schreier ◽  
...  
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Proteolytic Processing ◽  
Genome Integrity ◽  
Wild Type ◽  
Selfish Genetic Elements ◽  
Argonaute Proteins ◽  
Processing Activity ◽  
Rna Pathways

SummarySmall RNA pathways defend the germlines of animals against selfish genetic elements and help to maintain genomic integrity. At the same time, their activity needs to be well-controlled to prevent silencing of ‘self’ genes. Here, we reveal a proteolytic mechanism that controls endogenous small interfering (22G) RNA activity in the Caenorhabditis elegans germline to protect genome integrity and maintain fertility. We find that WAGO-1 and WAGO-3 Argonaute (Ago) proteins are matured through proteolytic processing of their unusually proline-rich N-termini. In the absence of DPF-3, a P-granule-localized N-terminal dipeptidase orthologous to mammalian DPP8/9, processing fails, causing a change of identity of 22G RNAs bound to these WAGO proteins. Desilencing of repeat- and transposon-derived transcripts, DNA damage and acute sterility ensue. These phenotypes are recapitulated when WAGO-1 and WAGO-3 are rendered resistant to DFP-3-mediated processing, identifying them as critical substrates of DPF-3. We conclude that N-terminal processing of Ago proteins regulates their activity and promotes discrimination of self from non-self by ensuring association with the proper complement of small RNAs.Graphical Abstract: The role of DPF-3 in the fertility of the animalsIn wild type animals, the WAGO-1 and WAGO-3 Argonaute proteins are produced as immature pro-proteins with N-termini (N) that are unusually rich in prolines (P). N-terminal processing by DPF-3 is required for loading of the proper small RNA cargo and stabilization of WAGO-3. Accordingly, loss of this processing activity causes desilencing of transposable elements (TE), cell death and sterility.

HyBra1, a Brachyury homologue, acts during head formation in Hydra

Development ◽  
1999 ◽  
Vol 126 (5) ◽  
pp. 999-1010 ◽  
Author(s):  
U. Technau ◽  
H.R. Bode
Keyword(s):  
Small Area ◽  
Evolutionary Conservation ◽  
Apical Part ◽  
T Box ◽  
Head Formation ◽  
Morphological Sign ◽  
Asexual Form ◽  
Head Regeneration ◽  
Transplantation Experiments

A homologue of the T-box gene, Brachyury, has been isolated from hydra. The gene, termed HyBra1, is expressed in the endoderm and is associated with the formation of the hypostome, the apical part of the head in four different developmental situations. In adults, which are continuously undergoing patterning, HyBra1 is continuously expressed in the hypostome. During budding, hydra's asexual form of reproduction, the gene is expressed in a small area that will eventually form the hypostome of the developing bud before any morphological sign of budding is apparent. The gene is also expressed very early during head regeneration and is confined to the region that will form the hypostome. During embryogenesis, HyBra1 is expressed shortly before hatching in the region that will form the apical end of the animal, the hypostome. The absence of expression at the apical end of decapitated animals of reg-16, a head formation-deficient mutant, provides additional evidence for a role of HyBra1 during head formation. Further, treatments that alter the head activation gradient have no effect on HyBra1 expression indicating the role of the gene is confined to head formation. Transplantation experiments indicate that the expression occurs before head determination has occurred, but expression does not irreversibly commit tissue to forming a head. A comparison of the function of the Brachyury homologues suggests an evolutionary conservation of a molecular mechanism that has been co-opted for a number of developmental processes throughout evolution.

scholarly journals Computational tools for plant small RNA detection and categorization

2017 ◽  
Vol 20 (4) ◽  
pp. 1181-1192 ◽  
Author(s):  
Lionel Morgado ◽  
Frank Johannes
Keyword(s):  
Small Rnas ◽  
High Throughput Sequencing ◽  
Short Length ◽  
Cellular Regulation ◽  
Rna Detection ◽  
Computational Tools ◽  
Bioinformatic Approaches ◽  
Regulatory Functions ◽  
Plant Small Rna

Abstract Small RNAs (sRNAs) are important short-length molecules with regulatory functions essential for plant development and plasticity. High-throughput sequencing of total sRNA populations has revealed that the largest share of sRNA remains uncategorized. To better understand the role of sRNA-mediated cellular regulation, it is necessary to create accurate and comprehensive catalogues of sRNA and their sequence features, a task that currently relies on nontrivial bioinformatic approaches. Although a large number of computational tools have been developed to predict features of sRNA sequences, these tools are mostly dedicated to microRNAs and none integrates the functionalities necessary to describe units from all sRNA pathways thus far discovered in plants. Here, we review the different classes of sRNA found in plants and describe available bioinformatics tools that can help in their detection and categorization.

scholarly journals miR-8b is involved in brain and eye regeneration of Dugesia japonica in head regeneration

Biology Open ◽  
2021 ◽  
Vol 10 (6) ◽  
Author(s):  
Hongjin Liu ◽  
Qian Song ◽  
Hui Zhen ◽  
Hongkuan Deng ◽  
Bosheng Zhao ◽  
...  
Keyword(s):  
Regulate Gene Expression ◽  
Planarian Regeneration ◽  
Evolutionarily Conserved ◽  
Proliferation And Differentiation ◽  
Important Regulator ◽  
Dugesia Japonica ◽  
Non Coding Rnas ◽  
Available Information ◽  
Head Regeneration

ABSTRACT MicroRNAs (miRNAs) are a class of evolutionarily conserved small non-coding RNAs that regulate gene expression at the translation level in cell growth, proliferation and differentiation. In addition, some types of miRNAs have been proven to be key modulators of both CNS development and plasticity, such as let-7, miR-9 and miR-124. In this research, we found miR-8b acts as an important regulator involved in brain and eyespot regeneration in Dugesia japonica. miR-8b was highly conserved among species and was abundantly expressed in central nervous system. Here, we detected the expression dynamics of miR-8b by qPCR during the head regeneration of D. japonica. Knockdown miR-8b by anti-MIRs method caused severe defects of eyes and CNS. Our study revealed the evolutionary conserved role of miR-8b in the planarian regeneration process, and further provided more research ideas and available information for planarian miRNAs.

scholarly journals A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6080
Author(s):  
Clicia Grativol ◽  
Flavia Thiebaut ◽  
Sara Sangi ◽  
Patricia Montessoro ◽  
Walaci da Silva Santos ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Small Rna ◽  
Genome Assembly ◽  
Inverted Repeat ◽  
Small Rnas ◽  
Distribution Patterns ◽  
Plant Genomes ◽  
Sugarcane Genome

Miniature inverted-repeat transposable elements (MITEs) have been associated with genic regions in plant genomes and may play important roles in the regulation of nearby genes via recruitment of small RNAs (sRNA) to the MITEs loci. We identified eight families of MITEs in the sugarcane genome assembly with MITE-Hunter pipeline. These sequences were found to be upstream, downstream or inserted into 67 genic regions in the genome. The position of the most abundant MITE (Stowaway-like) in genic regions, which we call AddIn-MITE, was confirmed in a WD40 gene. The analysis of four monocot species showed conservation of the AddIn-MITE sequence, with a large number of copies in their genomes. We also investigated the conservation of the AddIn-MITE’ position in the WD40 genes from sorghum, maize and, in sugarcane cultivars and wild Saccharum species. In all analyzed plants, AddIn-MITE has located in WD40 intronic region. Furthermore, the role of AddIn-MITE-related sRNA in WD40 genic region was investigated. We found sRNAs preferentially mapped to the AddIn-MITE than to other regions in the WD40 gene in sugarcane. In addition, the analysis of the small RNA distribution patterns in the WD40 gene and the structure of AddIn-MITE, suggests that the MITE region is a proto-miRNA locus in sugarcane. Together, these data provide insights into the AddIn-MITE role in Andropogoneae grasses.

scholarly journals Integrated analysis of high-throughput sequencing data reveals the key role of LINC00467 in the invasion and metastasis of testicular germ cell tumors

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Hao Bo ◽  
Fang Zhu ◽  
Zhizhong Liu ◽  
Qi Deng ◽  
Guangmin Liu ◽  
...  
Keyword(s):  
Germ Cell ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Germ Cell Tumors ◽  
Differentially Expressed ◽  
Migration And Invasion ◽  
Integrated Analysis ◽  
Sequencing Data ◽  
Testicular Germ Cell

AbstractLong noncoding RNAs (lncRNAs) are involved in various physiological and pathological processes. However, the role of lncRNAs in testicular germ cell tumor (TGCT) has been rarely reported. Our purpose is to comprehensively survey the expression and function of lncRNAs in TGCT. In this study, we used RNA sequencing to construct the lncRNA expression profiles of 13 TGCT tissues and 4 paraneoplastic tissues to explore the function of lncRNAs in TGCT. The bioinformatics analysis showed that many lncRNAs are differentially expressed in TGCT. GO and KEGG enrichment analyses revealed that the differentially expressed lncRNAs participated in various biological processes associated with tumorigenesis in cis and trans manners. Further, we found that the expression of LINC00467 was positively correlated with the poor prognosis and pathological grade of TGCT using WGCNA analysis and GEPIA database data mining. In vitro experiments revealed that LNC00467 could promote the migration and invasion of TGCT cells by regulating the expression of AKT3 and influencing total AKT phosphorylation. Further analysis of TCGA data revealed that the expression was negatively correlated with the infiltration of immune cells and the response to PD1 immunotherapy. In summary, this study is the first to construct the expression profile of lncRNAs in TGCT. It is also the first study to identify the metastasis-promoting role of LNC00467, which can be used as a potential predictor of TGCT prognosis and immunotherapeutic response to provide a clinical reference for the treatment and diagnosis of TGCT metastasis.

scholarly journals Expression profiles and functional analysis of plasma tRNA-derived small RNAs in children with fulminant myocarditis

Epigenomics ◽  
2021 ◽  
Author(s):  
Jing Wang ◽  
Bo Han ◽  
Yingchun Yi ◽  
Yan Wang ◽  
Li Zhang ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Small Rna ◽  
Small Rnas ◽  
Expression Profiles ◽  
Fulminant Myocarditis ◽  
Small Rna Sequencing ◽  
Quantitative Real Time Pcr ◽  
Extracellular Release ◽  
Larger Sample

Aim: Fulminant myocarditis (FM) has neither validated biomarkers nor well-established therapy. Roles of tRNA-derived small RNAs (tsRNAs) in FM remain unknown. Materials & methods: Small RNA sequencing was conducted in plasma from children with FM during acute and convalescent phase and matched healthy volunteers. Data were validated by quantitative real-time PCR in larger sample-sized groups and in vitro. Functional analysis was performed to explore the roles. Results: tiRNA-Gln-TTG-001 was overexpressed in children with FM during acute phase, and the generation and extracellular release of tiRNA-Gln-TTG-001 were higher after myocarditis-mimicked activity in vitro. Several pathways might participate in the pathogenesis of FM. Conclusion: tsRNAs may play an important role in FM, and tiRNA-Gln-TTG-001 might represent a novel and promising biomarker and therapeutic target.

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