scholarly journals Differentially Expressed tRNA-Derived Small RNAs Co-Sediment Primarily with Non-Polysomal Fractions in Drosophila

Genes ◽  
2017 ◽  
Vol 8 (11) ◽  
pp. 333 ◽  
Author(s):  
Çağdaş Göktaş ◽  
Hatice Yiğit ◽  
Mehmet Coşacak ◽  
Bünyamin Akgül
Keyword(s):  
Small Rnas ◽  
Differentially Expressed

scholarly journals Oxidative Medicine and Cellular Longevity Changes in the Small RNA Expression in Endothelial Cells in Response to Inflammatory Stimulation

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Peixi Liu ◽  
Liuxun Hu ◽  
Yuan Shi ◽  
Yingjun Liu ◽  
Guo Yu ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Small Rna ◽  
Small Rnas ◽  
Cerebrovascular Diseases ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Rna Expression ◽  
Tissue Specific ◽  
Qrt Pcr ◽  
Tnf Α

Objective. Endothelial cell inflammation is a common pathophysiological process in many cardiovascular and cerebrovascular diseases. Small RNA is a kind of short nonprotein coding RNA molecule. Changes in the small RNA expression in endothelial cells have been linked to the development of cardiovascular and cerebrovascular diseases. We investigated and verified differentially expressed small RNAs in endothelial cells in response to inflammatory stimulation. Methods. Primary rat endothelial cells were obtained from Sprague-Dawley rats and treated with 10 ng/ml TNF-α for 24 hours. Small RNA sequencing was used to generate extensive small RNA data. Significantly differentially expressed small RNAs identified in the analysis were further confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Then, we investigated the tissue-specific small RNA expression after RNA extraction from different tissues. Results. Small RNA sequencing demonstrated that 17 miRNAs, 1 piRNA, 10 snoRNAs, and 7 snRNAs were significantly differentially expressed. qRT-PCR identified 3 miRNAs, 2 snoRNAs, and 2 snRNAs with significantly different expression. Analysis of the tissue-specific expression showed that rno-miR-126a-5p was predominantly expressed in the lung, rno-miR-146a-5p in the intestines, and rno-novel-178 in the heart. Rno-piR-017330 was mainly expressed in the muscle. snoR-8966.1 was predominantly expressed in the bone. snoR-6253.1 was mostly expressed in the vessels and bone. snR-29469.1 was mainly expressed in the bone, and snR-85806.1 was predominantly expressed in the vessels and bone. Conclusions. We report for the first time the expression of small RNAs in endothelial cells under inflammatory conditions. TNF-α can regulate the expression of small RNAs in endothelial cells, and their expression is tissue-specific.

scholarly journals fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Roshan Regmi ◽  
Toby E. Newman ◽  
Lars G. Kamphuis ◽  
Mark C. Derbyshire
Keyword(s):  
Disease Resistance ◽  
Small Rnas ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Differentially Expressed ◽  
Disease Resistance Gene ◽  
Ethylene Response Factor ◽  
Post Inoculation ◽  
Necrotrophic Pathogen ◽  
Degradome Sequencing

Abstract Background Small RNAs are short non-coding RNAs that are key gene regulators controlling various biological processes in eukaryotes. Plants may regulate discrete sets of sRNAs in response to pathogen attack. Sclerotinia sclerotiorum is an economically important pathogen affecting hundreds of plant species, including the economically important oilseed B. napus. However, there are limited studies on how regulation of sRNAs occurs in the S. sclerotiorum and B. napus pathosystem. Results We identified different classes of sRNAs from B. napus using high throughput sequencing of replicated mock and infected samples at 24 h post-inoculation (HPI). Overall, 3999 sRNA loci were highly expressed, of which 730 were significantly upregulated during infection. These 730 up-regulated sRNAs targeted 64 genes, including disease resistance proteins and transcriptional regulators. A total of 73 conserved miRNA families were identified in our dataset. Degradome sequencing identified 2124 cleaved mRNA products from these miRNAs from combined mock and infected samples. Among these, 50 genes were specific to infection. Altogether, 20 conserved miRNAs were differentially expressed and 8 transcripts were cleaved by the differentially expressed miRNAs miR159, miR5139, and miR390, suggesting they may have a role in the S. sclerotiorum response. A miR1885-triggered disease resistance gene-derived secondary sRNA locus was also identified and verified with degradome sequencing. We also found further evidence for silencing of a plant immunity related ethylene response factor gene by a novel sRNA using 5′-RACE and RT-qPCR. Conclusions The findings in this study expand the framework for understanding the molecular mechanisms of the S. sclerotiorum and B. napus pathosystem at the sRNA level.

scholarly journals Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

2020 ◽  
Author(s):  
Pawel Sega ◽  
Katarzyna Kruszka ◽  
Dawid Bielewicz ◽  
Wojciech Karlowski ◽  
Przemyslaw Nuc ◽  
...  
Keyword(s):  
Small Rnas ◽  
Plant Stress ◽  
Perfect Match ◽  
Regulatory Elements ◽  
Differentially Expressed ◽  
Proximal Promoter ◽  
Nutrient Mobilization ◽  
Pi Starvation ◽  
Low Pi Stress ◽  
Pi Stress

Abstract Background: Small RNAs (sRNAs) are 18–24 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration triggers plant responses to balance the internal Pi level. Results: In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs. We find that differentially and significantly expressed miRNAs (DEMs, p-value < 0.05) are represented by 162 (44.88 % of total differentially expressed small RNAs) molecules in shoot and 138 (7.14 %) in root; mainly various miR399 and miR827 isomiRs. The remaining small RNAs (i.e., those without perfect match to reference sequences deposited in miRBase) are considered as differentially expressed other sRNAs (DESs, Bonferroni correction). In roots, a more abundant and diverse set of other sRNAs (1796 unique sequences, 0.13 % from total unique reads obtained under low-Pi) contributes more to the compensation of low-Pi stress than that in shoots (199 unique sequences, 0.01 %). More than 80 % of differentially expressed other sRNAs are upregulated in both organs. Additionally, in barley shoots, upregulation of small RNAs is accompanied by strong induction of two nucleases (S1/P1 endonuclease and 3’-5’ exonuclease). This suggests that most small RNAs may be generated upon endonucleolytic cleavage to increase the internal Pi pool. Transcriptomic profiling of Pi-starved barley shoots identify 98 differentially expressed genes (DEGs). A majority of the DEGs possess characteristic Pi-responsive cis-regulatory elements (P1BS and/or PHO element), located mostly in the proximal promoter regions. GO analysis shows that the discovered DEGs primarily alter plant defense, plant stress response, nutrient mobilization, or pathways involved in the gathering and recycling of phosphorus from organic pools.Conclusions: Our results provide comprehensive data to demonstrate complex responses at the RNA level in barley to maintain Pi homeostasis and indicate that barley adapts to Pi scarcity through elicitation of RNA degradation. Novel P-responsive genes were selected as putative candidates to overcome low-Pi stress in barley plants.

scholarly journals MACE-Seq-based coding RNA and TrueQuant-based small RNA profile in breast cancer: tumor-suppressive miRNA-1275 identified as a novel marker

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Sevan Omer Majed ◽  
Suhad Asad Mustafa
Keyword(s):  
Breast Cancer ◽  
Differential Expression ◽  
Small Rnas ◽  
Target Genes ◽  
Target Prediction ◽  
Ffpe Tissue ◽  
Differentially Expressed ◽  
Expression Level ◽  
Formalin Fixed Paraffin Embedded ◽  
Cancer Tumor

Abstract Introduction Disruption of cellular processes in the breast by abnormally expressed miRNA is characterized to develop cancer. We aimed to identify the differential expression of small RNAs (sRNAs) and mRNAs in formalin-fixed paraffin-embedded (FFPE) tissue of the breast cancer (BC) and normal adjacent tissue (NAT). Another aim is to determine the differential expression of miR-1275 as a novel biomarker for BC and also identify its target genes. Methods TrueQuant method for analysis of sRNA expression and MACE-sequencing method for analysis of gene expression were used analyzing. The RT-qPCR technique was used to confirm miR-1275 down expression. Target genes of miR-1275 were computationally identified using target prediction sites and also the expression level of them was experimentally determined among the expressed genes. Results TrueQuant findings showed that 1400 sRNAs were differentially expressed in the FFPE tissue of two Kurdish cases with BC, as compared to NAT. Among the sRNAs, 29 small RNAs were shown to be significantly downregulated in BC cells. The RT-qPCR results confirmed that miR-1275 was significantly down-expressed in 20 Kurdish cases with BC compared to NAT. However, Overall survival (OS) analysis revealed that the correlation between the expression level of miR-1275 and clinical significance was highly corrected in cases with BC (OS rate: P = 0.0401). The MACE-seq results revealed that 26,843 genes were differentially expressed in the BC tissue compared to NAT, but 7041 genes were displayed in a scatter plot. Furthermore, putative target genes (DVL3, PPP2R2D, THSD4, CREB1, SYT7, and PRKACA) were computationally identified as direct targets of miR-1275 in several target predicted sites. The MACE-seq results revealed that the expression level of these targets was increased in BC tissue compared to NAT. The level of these targets was negatively associated with miR-1275 expression. Finally, the role of down-regulated miR-1275 on its targets in biological mechanisms of BC cells was identified; including cell growth, proliferation, movement, invasion, metastasis, and apoptosis. Conclusion Down-expressed miR-1275, a tumor suppressor, is a novel biomarker for early detection of BC. DVL3, PPP2R2D, THSD4, CREB1, SYT7, and PRKACA are newly identified to be targeted by miR-1275.

scholarly journals Comparative transcriptomics identifies the transcription factors BRANCHED1 and TCP4, as well as the microRNA miR166 as candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae)

2021 ◽  
Author(s):  
Lydia Gramzow ◽  
Katharina Klupsch ◽  
Noe Fernandez Pozo ◽  
Martin Hoelzer ◽  
Manja Marz ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Differentially Expressed Genes ◽  
Small Rnas ◽  
Model System ◽  
Differentially Expressed ◽  
Evolutionary Transition ◽  
Floral Buds ◽  
Genetic Mechanisms ◽  
Transcription Factor 4 ◽  
Synthesis And Degradation

Background: Fruits are the seed-bearing structures of flowering plants and are highly diverse in terms of morphology, texture and maturation. Dehiscent fruits split open upon maturation to discharge their seeds while indehiscent fruits are dispersed as a whole. Indehiscent fruits evolved from dehiscent fruits several times independently in the crucifer family (Brassicaceae). The fruits of Lepidium appelianum, for example, are indehiscent while the fruits of the closely related L. campestre are dehiscent. Here, we investigate the molecular and genetic mechanisms underlying the evolutionary transition from dehiscent to indehiscent fruits using these two Lepidium species as model system. Results: We have sequenced the transcriptomes and small RNAs of floral buds, flowers and fruits of L. appelianum and L. campestre and analyzed differentially expressed genes (DEGs) and differently differentially expressed genes (DDEGs). DEGs are genes that show significantly different transcript levels in the same structures (buds, flowers and fruits) in different species, or in different structures in the same species. DDEGs are genes for which the change in expression level between two structures is significantly different in one species than in the other. Comparing the two species, the highest number of DEGs was found in flowers, followed by fruits and floral buds while the highest number of DDEGs was found in fruits versus flowers followed by flowers versus floral buds. Several gene ontology terms related to cell wall synthesis and degradation were overrepresented in different sets of DEGs highlighting the importance of these processes for fruit opening. Furthermore, the fruit valve identity genes FRUITFUL and YABBY3 were among the DEGs identified. Finally, the microRNA miR166 as well as the TCP transcription factors BRANCHED1 (BRC1) and TCP FAMILY TRANSCRIPTION FACTOR 4 (TCP4) were found to be DDEGs. Conclusions: Our study reveals differences in gene expression between dehiscent and indehiscent fruits and uncovers miR166, BRC1 and TCP4 as possible causes for the evolutionary transition from dehiscent to indehiscent fruits in Lepidium.

scholarly journals Finding differentially expressed sRNA-Seq regions with srnadiff

2019 ◽  
Author(s):  
Matthias Zytnicki ◽  
Ignacio González
Keyword(s):  
Small Rnas ◽  
New Method ◽  
Differentially Expressed ◽  
Reference Sequence ◽  
External Information ◽  
Small Rna Sequencing ◽  
Small Interfering Rnas ◽  
Genomic Annotation ◽  
Micro Rnas ◽  
Wide Range

AbstractSmall RNAs (sRNAs) encompass a great variety of different molecules of different kinds, such as micro RNAs, small interfering RNAs, Piwi-associated RNA, among other. These sRNA have a wide range of activities, which include gene regulation, protection against virus, transposable element silencing, and have been identified as a key actor to study and understand the development of the cell. Small RNA sequencing is thus routinely used to assess the expression of the diversity of sRNAs, usually in the context of differentially expression, where two conditions are compared. Many tools have been presented to detect differentially expressed micro RNAs, because they are well documented, and the associated genes are well defined. However, tools are lacking to detect other types of sRNAs, which are less studied, and have an imprecise “gene” structure. We present here a new method, called srnadiff, to find all kinds of differentially expressed sRNAs. To the extent of our knowledge, srnadiff is the first tool that detects differentially expressed sRNAs without the use of external information, such as genomic annotation or reference sequence of sRNAs.Author summaryWe present here a new method for the ab initio discovery of differentially expressed small RNAs. The standard method, sometimes named annotate-then-identify, first finds possible genes, and tests for differential expression. In contrast, our method skips the first step and scans the genome for potential differentially expressed regions (the identify-then-annotate strategy). Since our method is the first one to use the identify-then-annotate strategy on sRNAs, we compared our method against a similar method, developed for long RNAs (derfinder), and to the annotate-then-identify strategy, where the sRNAs have been identified beforehand using a segmentation tool, on three published datasets, and a simulated one. Results show that srnadiff gives much better results than derfinder, and is also better than the annotate-then-identify strategy on many aspects. srnadiff is available as a Bioconductor package, together with a detailed manual: https://bioconductor.org/packages/release/bioc/html/srnadiff.html

Integration of small RNAs, degradome, and transcriptome sequencing in Populus × euramericana “Neva” provides insights into the allelopathic interference of para-hydroxybenzoic acid

2020 ◽  
Vol 50 (4) ◽  
pp. 422-437 ◽  
Author(s):  
Guoting Liang ◽  
Jing Guo ◽  
Shuyong Zhang ◽  
Guangcan Zhang
Keyword(s):  
Small Rnas ◽  
Mirna Target ◽  
Target Genes ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Hydroxybenzoic Acid ◽  
Differentially Expressed Mirnas ◽  
Leaves And Roots

Allelopathy is a hot topic of research; however, little is known regarding microRNA (miRNA) expression profiles in plants in response to allelochemicals. In this study, we combined the analyses of the transcriptome, small RNAs (sRNAs), and the degradome to identify key regulatory miRNA-targeted circuits under para-hydroxybenzoic acid (pHBA) stress. A total of 739 and 673 miRNAs were identified in leaves and roots, respectively. Of those, 214 and 148 miRNAs were significantly differentially expressed and identified as pHBA-responsive miRNAs in leaves and roots, respectively. The target genes for the pHBA-responsive miRNAs are involved in signal transduction, response to stress, and secondary metabolite pathways. Furthermore, an integrated analysis of the miRNA–target expression profiles was used to screen the 60 differentially expressed target genes from the 46 differentially expressed miRNAs in the leaves and the 51 differentially expressed target genes from the 36 differentially expressed miRNAs in roots. This integrated analysis revealed 17 and 30 pairs of miRNA targets in the leaves and roots, respectively, which had negatively correlated expression profiles. According to a real-time quantitative polymerase chain reaction (PCR) analysis, 14 miRNA–target pairs also exhibited negative correlations. Moreover, four coexpression regulatory networks were constructed based on the profiles of the differentially expressed miRNA–target pairs. These results suggest that comprehensive analyses of transcriptomes, sRNAs, and the degradome provide a useful platform for investigating the molecular mechanism underlying the pHBA-induced stress response in plants.

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