scholarly journals Heterologous Expression of Salvia miltiorrhiza MicroRNA408 Enhances Tolerance to Salt Stress in Nicotiana benthamiana

2018 ◽  
Vol 19 (12) ◽  
pp. 3985 ◽  
Author(s):  
Xiaorong Guo ◽  
Junfeng Niu ◽  
Xiaoyan Cao
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Transgenic Tobacco ◽  
Small Rna ◽  
Small Rnas ◽  
Target Genes ◽  
Salvia Miltiorrhiza ◽  
Promoter Sequence ◽  
Oxygen Species ◽  
Gus Staining

MicroRNAs (miRNAs) are a class of endogenous small RNAs that regulate the expression of target genes post-transcriptionally; they are known to play major roles in development and responses to abiotic stress. MicroRNA408 (miR408) is a conserved small RNA in plants; it was reported that miR408 genes were involved in abiotic stress in Arabidopsis. However, miR408 in Salvia miltiorrhiza has been rarely investigated. In this study, we cloned Sm-MIR408, the miR408 precursor sequence, and its promoter sequence from S. miltiorrhiza and the role in tolerance to salt stress is described. The effects of salt stress on miR408 expression were studied by using β-glucuronidase (GUS) staining. Our data indicated that transgenic tobacco overexpressing Sm-MIR408 promoted seed germination and reduced the accumulation of reactive oxygen species under salt stress. Transcript levels of antioxidative genes, i.e., NbSOD, NbPOD, and NbCAT, and their enzyme activities increased in salinity-stressed transgenic tobacco plants, suggesting a better antioxidant system to cope the oxidative damage caused by salinity stress. Taken together, these findings indicated that miR408 functions in positive responses to salt tolerance in tobacco.

scholarly journals Analysis of miRNAs in the Heads of Different Castes of the Bumblebee Bombus lantschouensis (Hymenoptera: Apidae)

Insects ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 349 ◽  
Author(s):  
Liu ◽  
Huang ◽  
Zhang ◽  
Liu ◽  
An
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Target Genes ◽  
Solexa Sequencing ◽  
Biological Functions ◽  
Putative Target ◽  
Differentially Expressed Mirnas ◽  
Rna Deep Sequencing ◽  
Small Rna Deep Sequencing ◽  
Go Terms

Bumblebees are important insect pollinators for many wildflowers and crops. MicroRNAs (miRNAs) are endogenous non-coding small RNAs that regulate different biological functions in insects. In this study, the miRNAs in the heads of the three castes of the bumblebee Bombus lantschouensis were identified and characterized by small RNA deep sequencing. The significant differences in the expression of miRNAs and their target genes were analyzed. The results showed that the length of the small RNA reads from males, queens, and workers was distributed between 18 and 30 nt, with a peak at 22 nt. A total of 364 known and 89 novel miRNAs were identified from the heads of the three castes. The eight miRNAs with the highest expressed levels in males, queens, and workers were identical, although the order of these miRNAs based on expression differed. The male vs. queen, male vs. worker, and worker vs. queen comparisons identified nine, fourteen, and four miRNAs with significant differences in expression, respectively. The different castes were clustered based on the differentially expressed miRNAs (DE miRNAs), and the expression levels of the DE miRNAs obtained by RT-qPCR were consistent with the read counts obtained through Solexa sequencing. The putative target genes of these DE miRNAs were enriched in 29 Gene Ontology (GO) terms, and catalytic activity was the most enriched GO term, as demonstrated by its association with 2837 target genes in the male vs. queen comparison, 3535 target genes in the male vs. worker comparison, and 2185 target genes in the worker vs. queen comparison. This study highlights the characteristics of the miRNAs in the three B. lantschouensis castes and will aid further studies on the functions of miRNAs in bumblebees.

scholarly journals Small RNAs in parasitic nematodes – forms and functions

Parasitology ◽  
2019 ◽  
Vol 147 (8) ◽  
pp. 855-864
Author(s):  
Collette Britton ◽  
Roz Laing ◽  
Eileen Devaney
Keyword(s):  
Gene Expression ◽  
Small Rna ◽  
Small Rnas ◽  
Target Genes ◽  
Parasitic Nematodes ◽  
Small Rna Sequencing ◽  
Small Interfering Rnas ◽  
Rna Sequences ◽  
C Elegans

AbstractSmall RNAs are important regulators of gene expression. They were first identified in Caenorhabditis elegans, but it is now apparent that the main small RNA silencing pathways are functionally conserved across diverse organisms. Availability of genome data for an increasing number of parasitic nematodes has enabled bioinformatic identification of small RNA sequences. Expression of these in different lifecycle stages is revealed by small RNA sequencing and microarray analysis. In this review we describe what is known of the three main small RNA classes in parasitic nematodes – microRNAs (miRNAs), Piwi-interacting RNAs (piRNAs) and small interfering RNAs (siRNAs) – and their proposed functions. miRNAs regulate development in C. elegans and the temporal expression of parasitic nematode miRNAs suggest modulation of target gene levels as parasites develop within the host. miRNAs are also present in extracellular vesicles released by nematodes in vitro, and in plasma from infected hosts, suggesting potential regulation of host gene expression. Roles of piRNAs and siRNAs in suppressing target genes, including transposable elements, are also reviewed. Recent successes in RNAi-mediated gene silencing, and application of small RNA inhibitors and mimics will continue to advance understanding of small RNA functions within the parasite and at the host–parasite interface.

scholarly journals Comparative profiling of small RNAs of pig seminal plasma and ejaculated and epididymal sperm

Reproduction ◽  
2017 ◽  
Vol 153 (6) ◽  
pp. 785-796 ◽  
Author(s):  
Cai Chen ◽  
Han Wu ◽  
Dan Shen ◽  
Saisai Wang ◽  
Li Zhang ◽  
...  
Keyword(s):  
Seminal Plasma ◽  
Small Rna ◽  
Small Rnas ◽  
Target Genes ◽  
Large Population ◽  
Small Nuclear Rna ◽  
Epididymal Sperm ◽  
Zygote Development ◽  
Similarities And Differences ◽  
Small Rna Species

The similarities and differences of small RNAs in seminal plasma, epididymal sperm and ejaculated sperm remain largely undefined. We conducted a systematic comparative analysis of small RNA profiles in pig ejaculated sperm, epididymal sperm and seminal plasma and found that the diversity distribution of small RNA species was generally similar, whereas the abundance of small RNAs is dramatically different across the three libraries; miRNAs and small RNAs derived from rRNA, tRNA, small nuclear RNA, 7SK RNA, NRON RNA and cis-regulatory RNA were enriched in the three libraries, but piRNA was absent. A large population of small RNAs from ejaculated sperm are ejaculated sperm specific, and only 8–30% of small RNAs overlapped with those of epididymal sperm or seminal plasma and a small proportion (5–18%) of small RNAs were shared in the three libraries, suggesting that, in addition to the testes, sperm RNAs may also originate from seminal plasma, epididymis as well as other resources. Most miRNAs were co-distributed but differentially expressed across the three libraries, with epididymal sperm exhibiting the highest abundance, followed by ejaculated sperm and seminal plasma. The prediction of target genes of the top 10 highly expressed miRNAs across the three libraries revealed that these miRNAs may be involved in spermatogenesis, zygote development and the interaction between the environment and animals. Our study provides the first description of the similarities and differences of small RNA profiles in ejaculated sperm, epididymal sperm and seminal plasma and indicates that sperm RNA may have origins other than the testes.

scholarly journals Integrative analysis of microRNA and mRNA expression in response to salt stress by UMI

2019 ◽  
Author(s):  
Jing jing Zhan ◽  
Yang yang Diao ◽  
Yan yan Zhao ◽  
Chao Li ◽  
Xiao Han ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Salinity Stress ◽  
Target Genes ◽  
Plant Responses ◽  
Tolerance Mechanism ◽  
Significant Differential Expression ◽  
Function Annotation ◽  
Functional Studies ◽  
Processing Stability

Abstract Background Small RNAs play an important role in regulating plant responses to abiotic stress through modulation of the processing, stability, and translation of larger RNAs. Plants employ complex mechanisms of gene regulation to respond to salinity stress. Results In this study, we constructed 12 small RNA libraries, 12 mRNA libraries, and a degradome library to systematically investigate the miRNAs response to salt stress. A total of 312 cotton miRNAs were identified and of these, 80 were known ghr-miRNAs. 144 genes showed significant differential expression under salt stress combined with the targeting relationship between the sRNA data and mRNA data. We found 56 miRNA-mRNA pairs which were positively correlated, and 91 pairs which were negatively correlated. Using degradome sequencing, 72 target genes were identified associated with 25 miRNA families. Gene ontology and KEGG analysis indicated some targets were involved in vital biological pathways of salinity stress tolerance: 14 were involved in responses to abiotic stress, two were associated with an environmental adaptation pathway, and a total of 16 NAC and MYB family transcription factors were related to salinity stress. Conclusions The present study identified a large number of cotton miRNAs and identified relationships between miRNA and mRNA, with function annotation revealing their possible biological roles in response to salt stress. Our findings will further functional studies of cotton miRNAs and the salt tolerance mechanism.

scholarly journals Comparative Analysis of Cotton Small RNAs and Their Target Genes in Response to Salt Stress

Genes ◽  
2017 ◽  
Vol 8 (12) ◽  
pp. 369 ◽  
Author(s):  
Zujun Yin ◽  
Xiulan Han ◽  
Yan Li ◽  
Junjuan Wang ◽  
Delong Wang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Comparative Analysis ◽  
Small Rnas ◽  
Target Genes

scholarly journals TEsmall identifies small RNAs associated with targeted inhibitor resistance in melanoma

2018 ◽  
Author(s):  
Kathryn O’Neill ◽  
Wen-Wei Liao ◽  
Ami Patel ◽  
Molly Gale Hammell
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Target Genes ◽  
Mapk Pathway ◽  
Single Agent ◽  
Resistance Mechanisms ◽  
Melanoma Cells ◽  
Cancer Therapies ◽  
Mrna Targets ◽  
Inhibitor Resistance

MicroRNAs (miRNAs) are small 21-22nt RNAs that act to regulate the expression of mRNA target genes through direct binding to mRNA targets. While miRNAs typically dominate small RNA transcriptomes, many other classes are present including tRNAs, snoRNAs, snRNAs, Y-RNAs, piRNAs, and siRNAs. Interactions between processing machinery and targeting networks of these various small RNA classes remains unclear, largely because these small RNAs are typically analyzed separately. Here we present TEsmall, a tool that allows for the simultaneous processing and analysis of small RNAs from each annotated class in a single integrated workflow. The pipeline begins with raw fastq reads and proceeds all the way to producing count tables formatted for differential expression. Several interactive charts are also produced to look at overall distributions in length and annotation classes. We next applied the TEsmall pipeline to small RNA libraries generated from melanoma cells responding to targeted inhibitors of the MAPK pathway. Targeted oncogene inhibitors have emerged as way to tailor cancer therapies to the particular mutations present in a given tumor. While these targeted strategies are typically effective for short intervals, the emergence of resistance is extremely common, limiting the effectiveness of single-agent therapeutics and driving the need for a better understanding of resistance mechanisms. Using TEsmall, we identified several microRNAs and other small RNA classes that are enriched in inhibitor resistant melanoma cells in multiple melanoma cell lines and may be able to serve as markers of resistant populations more generally.

scholarly journals Non-Templated Oligo-Adenylation of Small RNAs in the Parasite Entamoeba: Potential Roles for Small RNA Control in Single Celled Eukaryotic Pathogen

2020 ◽  
Author(s):  
Hanbang Zhang ◽  
Gretchen M Ehrenkaufer ◽  
Neil Hall ◽  
Upinder Singh
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Cellular Localization ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Protozoan Parasite ◽  
Rnai Pathway ◽  
Regulation Mechanism ◽  
Protozoan Parasites ◽  
Modification Process

Abstract Background: The RNA interference (RNAi) pathway is a gene regulation mechanism that uitilizes small RNA (sRNA) and Argonaute (Ago) proteins to silence target genes. Our previous work identified a functional RNAi pathway in the protozoan parasite Entamoeba histolytica, including abundant 27nt antisense sRNA populations derived from the secondary RNAi pathway which associate with EhAgo2-2 protein. However, there is lack of understanding about sRNAs that are bound to two other EhAgos (EhAgo2-1 and 2-3), and the mechanism of sRNA regulation itself is unclear in this parasite. Results: In the present study, we sequenced sRNA libraries from both total RNAs and EhAgo bound RNAs. We identified a new population of 31nt sRNAs that results from the addition of a non-templated 3-4 adenosine nucleotides at the 3´-end of the 27nt sRNA populations, indicating a non-templated RNA-tailing event in the parasite. We found that both sRNA populations (27nt and 31nt) are unchanged during the development of E. invadens. However, we detected an alteration in their relative abundance for the targeted gene in parasites transfected with a trigger-gene silencing construct, indicating that non-templated RNA-tailing is likely a pathway for sRNA turnover when the targeted gene is unable to be silenced in this parasite. In sequencing the sRNAs associating with the three EhAgo proteins, we observed that despite distinct cellular localization, all three EhAgo sRNA libraries contain 27nt sRNAs with 5´-polyphosphate (5´-polyP) structure and a largely overlapping sRNA repertoire, mainly targeting retrotransposons and a subset of ~226 genes that are endogenously silenced. Furthermore, our data show that 31nt sRNA populations paritally associate with wildtype EhAgo2-2 but not with its mutant protein (EhAgo2-2 C-terminal deletion), indicating an intact RISC is essential for the sRNA modification process.Conclusion: High-throughput sequencing of sRNA in Entamoeba has identified a new population of sRNA with non-templated adenylation modification, which is the first such observation amongst single cell protozoan parasites. Our sRNA sequencing libraries provide the first comprehensive sRNA dataset for all three Entamoeba Ago proteins, which can serve as a useful database for the amoeba community.

scholarly journals Integrative analysis of microRNA and mRNA expression in response to salt stress by UMI

2019 ◽  
Author(s):  
Jing jing Zhan ◽  
Yang yang Diao ◽  
Yan yan Zhao ◽  
Chao Li ◽  
Xiao Han ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Salinity Stress ◽  
Target Genes ◽  
Plant Responses ◽  
Tolerance Mechanism ◽  
Significant Differential Expression ◽  
Function Annotation ◽  
Functional Studies ◽  
Processing Stability

Abstract Background Small RNAs play an important role in regulating plant responses to abiotic stress through modulation of the processing, stability, and translation of larger RNAs. Plants employ complex mechanisms of gene regulation to respond to salinity stress. Results In this study, we constructed 12 small RNA libraries, 12 mRNA libraries, and a degradome library to systematically investigate the miRNAs response to salt stress. A total of 312 cotton miRNAs were identified and of these, 80 were known ghr-miRNAs. 144 genes showed significant differential expression under salt stress combined with the targeting relationship between the sRNA data and mRNA data. We found 56 miRNA-mRNA pairs which were positively correlated, and 91 pairs which were negatively correlated. Using degradome sequencing, 72 target genes were identified associated with 25 miRNA families. Gene ontology and KEGG analysis indicated some targets were involved in vital biological pathways of salinity stress tolerance: 14 were involved in responses to abiotic stress, two were associated with an environmental adaptation pathway, and a total of 16 NAC and MYB family transcription factors were related to salinity stress. Conclusions The present study identified a large number of cotton miRNAs and identified relationships between miRNA and mRNA, with function annotation revealing their possible biological roles in response to salt stress. Our findings will further functional studies of cotton miRNAs and the salt tolerance mechanism.

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