scholarly journals Differential expression of miRNAs and their target genes in senescing leaves and siliques: insights from deep sequencing of small RNAs and cleaved target RNAs

2014 ◽  
Vol 38 (1) ◽  
pp. 188-200 ◽  
Author(s):  
SHAWN R. THATCHER ◽  
SHAUL BURD ◽  
CHRISTOPHER WRIGHT ◽  
AMNON LERS ◽  
PAMELA J. GREEN
Keyword(s):  
Differential Expression ◽  
Deep Sequencing ◽  
Small Rnas ◽  
Target Genes

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 Deep Sequencing of Guinea Pig (Cavia Porcellus) Lung Small RNAs Reveals Differential Expression of microRNAs between Non-infected and BCG-Infected Lungs

2021 ◽  
Author(s):  
Xiaoqi jing ◽  
Biqiong Jiang ◽  
Long Cheng ◽  
Yong Li
Keyword(s):  
Immune Responses ◽  
Guinea Pig ◽  
Differential Expression ◽  
Deep Sequencing ◽  
Target Genes ◽  
Transforming Growth Factor ◽  
Expression Profiles ◽  
Mitogen Activated Protein Kinase ◽  
Public Health Burden ◽  
Small Noncoding Rnas

Abstract Background: Pulmonary tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) infection remains a major public health burden worldwide. It has been well documented that a group of small noncoding RNAs, microRNAs (miRNAs) are involved in the development and pathogenesis many diseases, including the TB. Guinea pigs are considered as one of the best animal models for biomedical research in TB, the potential roles of miRNAs in the innate immune regulation of guinea pig lung against Mtb infection are not well understood. Methods: In this study, we investigated the differential expression of miRNA profiles between the un-infected lungs and Mycobacterium bovis bacillus Calmette-Guérin (BCG)-infected lungs of guinea pigs via deep sequencing and bioinformatics analysis. Results: A total of 2508 miRNAs were identified, among them 1187 were conserved miRNAs and 56 were novel miRNAs in the uninfected lungs, and 1202 were identified as conserved miRNAs and 63 were novel miRNAs in the BCG-infected lungs. Interestingly, comparison analysis further identified 902 co-expressed miRNAs and 585 distinct miRNAs between these two groups. Of the 15 most abundantly conserved miRNAs in guinea pig lungs, which belong to 7 miRNA families, including miR23, miR29, miR145, miR320, miR378, miR451, and miR423. 13 of these 15 most abundant miRNAs were significantly downregulated and 2 of them were significantly upregulated in the BCG-infected lungs. Individually, miRNA Let-7f-5p, let-7f, let-7-5p and let-7b-5p were the most abundant in both profiles of the non-infected and BCG-infected guinea pig lungs. The predicted target genes of specific miRNAs found in guinea pig lungs were involved in regulation signaling pathways related to immune responses, including Toll-like receptors (TLRs), nuclear factor (NF)-kappa B, Wnt, mitogen-activated protein kinase (MAPK), and transforming growth factor (TGF)-beta signaling, as well as related to autophagy signaling mTOR and apoptotic molecule p53. Conclusions: These data of comprehensive analysis of miRNA transcriptome demonstrated the differential expression profiles of miRNAs during M. tuberculosis infection of guinea pig lungs. These results could facilitate the future exploitation of the roles of miRNAs in regulation of immune responses to M. tuberculosis infection using the guinea pig model.

scholarly journals Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection

mBio ◽  
2011 ◽  
Vol 2 (6) ◽  
Author(s):  
Xinxia Peng ◽  
Lisa Gralinski ◽  
Martin T. Ferris ◽  
Matthew B. Frieman ◽  
Matthew J. Thomas ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Virus Infection ◽  
Differential Expression ◽  
Deep Sequencing ◽  
Small Rnas ◽  
Host Response ◽  
Mouse Strains ◽  
Sequencing Analysis ◽  
Virus Infections ◽  
Protein Coding

ABSTRACT We previously reported widespread differential expression of long non-protein-coding RNAs (ncRNAs) in response to virus infection. Here, we expanded the study through small RNA transcriptome sequencing analysis of the host response to both severe acute respiratory syndrome coronavirus (SARS-CoV) and influenza virus infections across four founder mouse strains of the Collaborative Cross, a recombinant inbred mouse resource for mapping complex traits. We observed differential expression of over 200 small RNAs of diverse classes during infection. A majority of identified microRNAs (miRNAs) showed divergent changes in expression across mouse strains with respect to SARS-CoV and influenza virus infections and responded differently to a highly pathogenic reconstructed 1918 virus compared to a minimally pathogenic seasonal influenza virus isolate. Novel insights into miRNA expression changes, including the association with pathogenic outcomes and large differences between in vivo and in vitro experimental systems, were further elucidated by a survey of selected miRNAs across diverse virus infections. The small RNAs identified also included many non-miRNA small RNAs, such as small nucleolar RNAs (snoRNAs), in addition to nonannotated small RNAs. An integrative sequencing analysis of both small RNAs and long transcripts from the same samples showed that the results revealing differential expression of miRNAs during infection were largely due to transcriptional regulation and that the predicted miRNA-mRNA network could modulate global host responses to virus infection in a combinatorial fashion. These findings represent the first integrated sequencing analysis of the response of host small RNAs to virus infection and show that small RNAs are an integrated component of complex networks involved in regulating the host response to infection. IMPORTANCE Most studies examining the host transcriptional response to infection focus only on protein-coding genes. However, mammalian genomes transcribe many short and long non-protein-coding RNAs (ncRNAs). With the advent of deep-sequencing technologies, systematic transcriptome analysis of the host response, including analysis of ncRNAs of different sizes, is now possible. Using this approach, we recently discovered widespread differential expression of host long (>200 nucleotide [nt]) ncRNAs in response to virus infection. Here, the samples described in the previous report were again used, but we sequenced another fraction of the transcriptome to study very short (about 20 to 30 nt) ncRNAs. We demonstrated that virus infection also altered expression of many short ncRNAs of diverse classes. Putting the results of the two studies together, we show that small RNAs may also play an important role in regulating the host response to virus infection.

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

2020 ◽  
Author(s):  
Sevan Majed ◽  
Suhad 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 26843 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 breast cancer. DVL3, PPP2R2D, THSD4, CREB1, SYT7, and PRKACA are newly identified to be targeted by miR-1275.

scholarly journals Deep Sequencing of Small RNAs in the Whitefly Bemisia tabaci Reveals Novel MicroRNAs Potentially Associated with Begomovirus Acquisition and Transmission

Insects ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 562
Author(s):  
Daniel K. Hasegawa ◽  
Md Shamimuzzaman ◽  
Wenbo Chen ◽  
Alvin M. Simmons ◽  
Zhangjun Fei ◽  
...  
Keyword(s):  
Bemisia Tabaci ◽  
Deep Sequencing ◽  
Small Rnas ◽  
Target Genes ◽  
Expression Profiles ◽  
Virus Transmission ◽  
Plant Viruses ◽  
Insect Vector ◽  
Regulatory Effects ◽  
Leaf Curl Virus

The whitefly Bemisia tabaci (Gennadius) is a notorious insect vector that transmits hundreds of plant viruses, affecting food and fiber crops worldwide, and results in the equivalent of billions of U.S. dollars in crop loss annually. To gain a better understanding of the mechanism in virus transmission, we conducted deep sequencing of small RNAs on the whitefly B. tabaci MEAM1 (Middle East-Asia Minor 1) that fed on tomato plants infected with tomato yellow leaf curl virus (TYLCV). Overall, 160 miRNAs were identified, 66 of which were conserved and 94 were B. tabaci-specific. Among the B. tabaci-specific miRNAs, 67 were newly described in the present study. Two miRNAs, with predicted targets encoding a nuclear receptor (Bta05482) and a very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 2 (Bta10702), respectively, were differentially expressed in whiteflies that fed on TYLCV-infected versus uninfected plants. To better understand the regulatory effects of identified miRNAs and their target genes, we correlated expression profiles of miRNAs and their target transcripts and found that, interestingly, miRNA expression was inversely correlated with the expression of ~50% of the predicted target genes. These analyses could serve as a model to study gene regulation in other systems involving arthropod transmission of viruses to plants and animals.

scholarly journals Identification of Tumor-Suppressive miRNA-1275 as a Novel Marker for Breast Cancer (BC) by MACE-Sequencing and RT-qPCR Techniques

2020 ◽  
Author(s):  
Sevan Omer Majed ◽  
Suhad Asad Mustafa
Keyword(s):  
Breast Cancer ◽  
Differential Expression ◽  
Small Rnas ◽  
Target Genes ◽  
The Cancer Genome Atlas ◽  
Expression Level ◽  
Formalin Fixed Paraffin ◽  
Number Of Patients ◽  
Sequencing Technique ◽  
Formalin Fixed Paraffin Embedded

Abstract IntroductionDisruption of cellular processes in the breast by abnormally expressed miRNA is characterized to develop cancer. We aimed to determine the differential expression of coding and non-coding RNAs in formalin fixed paraffin embedded (FFPE) blocks of breast cancer (BC) tissue and normal adjacent tissue (NAT). Another aim is to determine differential expression of has-miR-1275 as novel biomarker for BC and identify its target genes using prediction sites and experimentally expression level of them via the MACE-sequencing technique. MethodsMACE-sequencing technique was utilized to analyze differential expression of coding RNAs and small RNAs (sRNAs). Among small RNAs, miRNA-1275 expression was focused and confirmed using RT-qPCR technique in 20 Kurdish cases with BC . Moreover, clinical significance of miR- 1275 and its target genes was studied in a large number of patients with BC using the data obtained from The Cancer Genome Atlas database.ResultsThe MACE-seq findings showed that 1400 sRNAs and 26843 coding RNAs were differentially expressed in FFPE of BC tissue compared to NAT. Among these sRNAs, miRNA-1275 expression was found to be decreased in BC tissue compared to NAT. The decreased expression level of which was then confirmed via RT-qPCR technique to farther prove in 20 Kurdish cases with BC . Furthermore, the correlation between the expression level of miRNA-1275 and clinical data were evaluated to be highly corrected in cases with BC (overall survival rate: P = 0.0401). However, putative target genes ( DVL3, PPP 2R2D, THSD4, CREB1, SYT7, and PRKACA) were computationally identified as direct targets of miRNA-1275 in several target predicted sites. Among coding RNAs, the expression level of these targets was increased in BC tissue compared to NAT. The levels of these targets were negatively associated with miRNA-1275 expression. Finally, the role of down-expressed miRNA-1275 and its targets in BC cells were identified to attenuated biological mechanisms; including cell growth, proliferation, movement, invasion, metastasis, and apoptosis.Conclusiondown-expressed miR-1275 , a tumor suppressor, is as a novel biomarker for early detection of breast cancer. DVL3, PPP 2R2D, THSD4, CREB1, SYT7, and PRKACA are novely identified to be targeted by miR-1275 in BC cells.

scholarly journals Genome-Wide Changes of Regulatory Non-Coding RNAs Reveal Pollen Development Initiated at Ecodormancy in Peach

2021 ◽  
Vol 8 ◽  
Author(s):  
Jiali Yu ◽  
Dennis Bennett ◽  
Christopher Dardick ◽  
Tetyana Zhebentyayeva ◽  
Albert G. Abbott ◽  
...  
Keyword(s):  
Differential Expression ◽  
Small Rnas ◽  
Noncoding Rna ◽  
Target Genes ◽  
Prunus Persica ◽  
Developmental Time ◽  
Microrna Target ◽  
Time Points ◽  
Genome Wide ◽  
Non Coding Rnas

Bud dormancy is under the regulation of complex mechanisms including genetic and epigenetic factors. To study the function of regulatory non-coding RNAs in winter dormancy release, we analyzed the small RNA and long non-coding RNA (lncRNA) expression from peach (Prunus persica) floral buds in endodormancy, ecodormancy and bud break stages. Small RNAs underwent a major shift in expression primarily between dormancy and flowering with specific pairs of microRNAs and their mRNA target genes undergoing coordinated differential expression. From endodormancy to ecodormancy, ppe-miR6285 was significantly upregulated while its target gene, an ASPARAGINE-RICH PROTEIN involved in the regulation of abscisic acid signaling, was downregulated. At ecodormancy, ppe-miR2275, a homolog of meiosis-specific miR2275 across angiosperms, was significantly upregulated, supporting microsporogenesis in anthers at a late stage of dormancy. The expression of 785 lncRNAs, unlike the overall expression pattern in the small RNAs, demonstrated distinctive expression signatures across all dormancy and flowering stages. We predicted that a subset of lncRNAs were targets of microRNAs and found 18 lncRNA/microRNA target pairs with both differentially expressed across time points. The genome-wide differential expression and network analysis of non-coding RNAs and mRNAs from the same tissues provide new candidate loci for dormancy regulation and suggest complex noncoding RNA interactions control transcriptional regulation across these key developmental time points.

scholarly journals The Non-Canonical Aspects of MicroRNAs: Many Roads to Gene Regulation

Cells ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 1465 ◽  
Author(s):  
Christiaan J. Stavast ◽  
Stefan J. Erkeland
Keyword(s):  
Rna Polymerase Ii ◽  
Transcriptional Activation ◽  
Small Rnas ◽  
Target Genes ◽  
Biological Functions ◽  
Rnase Iii ◽  
Mrna Targets ◽  
Argonaute Proteins ◽  
Epigenetic Modifiers ◽  
Encoding Genes

MicroRNAs (miRNAs) are critical regulators of gene expression. As miRNAs are frequently deregulated in many human diseases, including cancer and immunological disorders, it is important to understand their biological functions. Typically, miRNA-encoding genes are transcribed by RNA Polymerase II and generate primary transcripts that are processed by RNase III-endonucleases DROSHA and DICER into small RNAs of approximately 21 nucleotides. All miRNAs are loaded into Argonaute proteins in the RNA-induced silencing complex (RISC) and act as post-transcriptional regulators by binding to the 3′- untranslated region (UTR) of mRNAs. This seed-dependent miRNA binding inhibits the translation and/or promotes the degradation of mRNA targets. Surprisingly, recent data presents evidence for a target-mediated decay mechanism that controls the level of specific miRNAs. In addition, several non-canonical miRNA-containing genes have been recently described and unexpected functions of miRNAs have been identified. For instance, several miRNAs are located in the nucleus, where they are involved in the transcriptional activation or silencing of target genes. These epigenetic modifiers are recruited by RISC and guided by miRNAs to specific loci in the genome. Here, we will review non-canonical aspects of miRNA biology, including novel regulators of miRNA expression and functions of miRNAs in the nucleus.

Screening candidate microR-15a- IRAK2 regulatory pairs for predicting the response to Staphylococcus aureus-induced mastitis in dairy cows

2019 ◽  
Vol 86 (4) ◽  
pp. 425-431 ◽  
Author(s):  
Zhi Chen ◽  
Jingpeng Zhou ◽  
Xiaolong Wang ◽  
Yang Zhang ◽  
Xubin Lu ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Differential Expression ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Interleukin 1 ◽  
Differentially Expressed ◽  
Luciferase Reporter ◽  
Expression Of Genes ◽  
Chinese Holstein Cows ◽  
Reporter Assays

AbstractWe established a mastitis model using exogenous infection of the mammary gland of Chinese Holstein cows with Staphylococcus aureus and extracted total RNA from S. aureus-infected and healthy mammary quarters. Differential expression of genes due to mastitis was evaluated using Affymetrix technology and results revealed a total of 1230 differentially expressed mRNAs. A subset of affected genes was verified via Q-PCR and pathway analysis. In addition, Solexa high-throughput sequencing technology was used to analyze profiles of miRNA in infected and healthy quarters. These analyses revealed a total of 52 differentially expressed miRNAs. A subset of those results was verified via Q-PCR. Bioinformatics techniques were used to predict and analyze the correlations among differentially expressed miRNA and mRNA. Results revealed a total of 329 pairs of negatively associated miRNA/mRNA, with 31 upregulated pairs of mRNA and 298 downregulated pairs of mRNA. Differential expression of miR-15a and interleukin-1 receptor-associated kinase-like 2 (IRAK2), were evaluated by western blot and luciferase reporter assays. We conclude that miR-15a and miR-15a target genes (IRAK2) constitute potential miRNA–mRNA regulatory pairs for use as biomarkers to predict a mastitis response.

Sign in / Sign up

Export Citation Format

Share Document