Integrated analysis of miRNA-seq and mRNA-seq reveals immune related miRNA-mRNA regulation network in the DHAV-3-infected duckling liver

Abstract Background: Duck hepatitis A virus type 3 (DHAV-3) is one of the most harmful pathogens in the duck industry. However, the molecular mechanism underlying DHAV-3 infection in ducklings is remain poorly understood. To elucidate the genetic regulatory network for miRNA-mRNA and the signaling pathways involved in DHAV-3 infection in ducklings, we conducted global miRNA and mRNA expression profiling of duckling liver tissues infected with lethal DHAV-3 using high-throughput sequencing. Results: We found 156 differentially expressed miRNAs (DEMs) and 7717 differentially expressed miRNAs (DEGs) between mock-infected and DHAV-3-infected duckling livers. A total of 19,606 miRNA-mRNA pairs with negatively correlated expression patterns were identified in miRNA-mRNA networks constructed on the basis of these DEMs and DEGs. Moreover, immune-related pathways including the cytokine-cytokine receptor interaction, apoptosis, Toll-like receptor, Jak-STAT, and RIG-I-like receptor signaling pathway were significantly enriched through analyzing functions of mRNAs in the network in response to DHAV-3 infection. Besides, apl-miR-32-5p, apl-miR-125-5p, apl-miR-128-3p, apl-miR-460-5p, and novel-m0012-3p were identified as potential regulators in the immune-related signaling pathways during the DHAV-3 infection. Conclusions: To our knowledge, this is the first report on integrated analysis of miRNA-seq and mRNA-seq in DHAV-3-infected ducklings. The results indicated the important roles of miRNAs in regulating immune response genes and revealed the immune related miRNA-mRNA regulation network in the DHAV-3-infected duckling liver. Our findings may provide valuable information to further investigate the roles of miRNAs and their target genes in DHAV-3 replication and pathogenesis; additionally, they may offer clues for further understanding host-virus interactions.

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Integrated analysis of miRNA-seq and mRNA-seq reveals immune related miRNA-mRNA regulation network in the DHAV-3-infected duckling liver

10.21203/rs.2.13422/v2 ◽

2019 ◽

Author(s):

Fengyao Wu ◽

Fengying Lu ◽

Xin Fan ◽

Jin Chao ◽

Chuanmin Liu ◽

...

Keyword(s):

Signaling Pathways ◽

High Throughput Sequencing ◽

Expression Patterns ◽

Differentially Expressed ◽

Receptor Interaction ◽

Integrated Analysis ◽

Mrna Regulation ◽

Duck Hepatitis ◽

Differentially Expressed Mirnas ◽

Regulation Network

Abstract Background: Duck hepatitis A virus type 3 (DHAV-3) is one of the most harmful pathogens in the duck industry. However, the molecular mechanism underlying DHAV-3 infection in ducklings is remain poorly understood. To elucidate the genetic regulatory network for miRNA-mRNA and the signaling pathways involved in DHAV-3 infection in ducklings, we conducted global miRNA and mRNA expression profiling of duckling liver tissues infected with lethal DHAV-3 using high-throughput sequencing. Results: We found 156 differentially expressed miRNAs (DEMs) and 7717 differentially expressed miRNAs (DEGs) between mock-infected and DHAV-3-infected duckling livers. A total of 19,606 miRNA-mRNA pairs with negatively correlated expression patterns were identified in miRNA-mRNA networks constructed on the basis of these DEMs and DEGs. Moreover, immune-related pathways including the cytokine-cytokine receptor interaction, apoptosis, Toll-like receptor, Jak-STAT, and RIG-I-like receptor signaling pathway were significantly enriched through analyzing functions of mRNAs in the network in response to DHAV-3 infection. Besides, apl-miR-32-5p, apl-miR-125-5p, apl-miR-128-3p, apl-miR-460-5p, and novel-m0012-3p were identified as potential regulators in the immune-related signaling pathways during the DHAV-3 infection. Conclusions: To our knowledge, this is the first report on integrated analysis of miRNA-seq and mRNA-seq in DHAV-3-infected ducklings. The results indicated the important roles of miRNAs in regulating immune response genes and revealed the immune related miRNA-mRNA regulation network in the DHAV-3-infected duckling liver. Our findings may provide valuable information to further investigate the roles of miRNAs and their target genes in DHAV-3 replication and pathogenesis; additionally, they may offer clues for further understanding host-virus interactions.

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Integrated analysis of miRNA and mRNA expression profiles in testes of Duroc and Meishan boars

10.21203/rs.2.15327/v1 ◽

2019 ◽

Author(s):

Haisheng Ding ◽

Min Liu ◽

Changfan Zhou ◽

Xiangbin You ◽

Tao Su ◽

...

Keyword(s):

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Male Gamete ◽

Mirna Expression Profile ◽

Mapk Signaling ◽

Differentially Expressed ◽

Integrated Analysis ◽

Testis Development ◽

Differentially Expressed Mirnas

Abstract Background: MicroRNAs (miRNAs) are small non-coding RNAs playing vital roles in regulating posttranscriptional gene expression. Elucidating the expression regulation of miRNAs underlying pig testis development will contribute to a better understanding of boar fertility and spermatogenesis. Results: In this study, miRNA expression profile was investigated in testes of Duroc and Meishan boars at 20, 75, and 270 days of age by high-throughput sequencing. Forty-five differentially expressed miRNAs were identified from testes of Duroc and Meishan boars before and after puberty. Integrated analysis of miRNA and mRNA profiles predicted many miRNA-mRNA pairs. Gene ontology and biological pathway analyses revealed that predicted target genes of ssc-mir-423-5p, ssc-mir-34c, ssc-mir-107, ssc-165 mir-196b-5p, ssc-mir-92a, ssc-mir-320, ssc-mir-10a-5p, and ssc-mir-181b were involved in sexual reproduction, male gamete generation, and spermatogenesis, and GnRH, Wnt, and MAPK signaling pathway. Four significantly differentially expressed miRNAs and their predicted target genes were validated by quantitative real-time polymerase chain reaction, and phospholipase C beta 1 ( PLCβ1) gene was verified to be a target of ssc-mir-423-5p . Conclusions: This study provides an insight into the functional roles of miRNAs in testis development and spermatogenesis and offers useful resources for understanding differences in sexual function development caused by the change in miRNAs expression between Duroc and Meishan boars.

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Integrated analysis of miRNA and mRNA expression profiles in testes of Duroc and Meishan boars

BMC Genomics ◽

10.1186/s12864-020-07096-7 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Haisheng Ding ◽

Min Liu ◽

Changfan Zhou ◽

Xiangbin You ◽

Tao Su ◽

...

Keyword(s):

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Male Gamete ◽

Mirna Expression Profile ◽

Mapk Signaling ◽

Differentially Expressed ◽

Integrated Analysis ◽

Testis Development ◽

Differentially Expressed Mirnas

Abstract Background MicroRNAs (miRNAs) are small non-coding RNAs playing vital roles in regulating posttranscriptional gene expression. Elucidating the expression regulation of miRNAs underlying pig testis development will contribute to a better understanding of boar fertility and spermatogenesis. Results In this study, miRNA expression profile was investigated in testes of Duroc and Meishan boars at 20, 75, and 270 days of age by high-throughput sequencing. Forty-five differentially expressed miRNAs were identified from testes of Duroc and Meishan boars before and after puberty. Integrated analysis of miRNA and mRNA profiles predicted many miRNA-mRNA pairs. Gene ontology and biological pathway analyses revealed that predicted target genes of ssc-mir-423-5p, ssc-mir-34c, ssc-mir-107, ssc-mir-196b-5p, ssc-mir-92a, ssc-mir-320, ssc-mir-10a-5p, and ssc-mir-181b were involved in sexual reproduction, male gamete generation, and spermatogenesis, and GnRH, Wnt, and MAPK signaling pathway. Four significantly differentially expressed miRNAs and their predicted target genes were validated by quantitative real-time polymerase chain reaction, and phospholipase C beta 1 (PLCβ1) gene was verified to be a target of ssc-mir-423-5p. Conclusions This study provides an insight into the functional roles of miRNAs in testis development and spermatogenesis and offers useful resources for understanding differences in sexual function development caused by the change in miRNAs expression between Duroc and Meishan boars.

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Identification and Characterization of miRNAs in Self-Rooted and Grafted Malus Reveals Critical Networks Associated with Flowering

International Journal of Molecular Sciences ◽

10.3390/ijms19082384 ◽

2018 ◽

Vol 19 (8) ◽

pp. 2384 ◽

Cited By ~ 2

Author(s):

Na An ◽

Sheng Fan ◽

Yang Yang ◽

Xilong Chen ◽

Feng Dong ◽

...

Keyword(s):

Regulatory Networks ◽

High Throughput Sequencing ◽

Expression Patterns ◽

Fruit Trees ◽

Differentially Expressed ◽

Flowering Genes ◽

Differentially Expressed Mirnas ◽

Flowering Rate ◽

Carbohydrate Contents

Grafting can improve the agricultural traits of crop plants, especially fruit trees. However, the regulatory networks and differentially expressed microRNAs (miRNAs) related to grafting in apple remain unclear. Herein, we conducted high-throughput sequencing and identified differentially expressed miRNAs among self-rooted Fuji, self-rooted M9, and grafted Fuji/M9. We analyzed the flowering rate, leaf morphology, and nutrient and carbohydrate contents in the three materials. The flowering rate, element and carbohydrate contents, and expression levels of flowering genes were higher in Fuji/M9 than in Fuji. We detected 206 known miRNAs and 976 novel miRNAs in the three materials, and identified those that were up- or downregulated in response to grafting. miR156 was most abundant in Fuji, followed by Fuji/M9, and then self-rooted M9, while miR172 was most abundant in M9, followed by Fuji/M9, and then Fuji. These expression patterns suggest that that these miRNAs were related to grafting. A Gene Ontology (GO) analysis showed that the differentially expressed miRNAs controlled genes involved in various biological processes, including cellular biosynthesis and metabolism. The expression of differentially expressed miRNAs and flowering-related genes was verified by qRT-PCR. Altogether, this comprehensive analysis of miRNAs related to grafting provides valuable information for breeding and grafting of apple and other fruit trees.

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Differentially expressed circulating microRNAs in Brazilian patients with COVID-19: a preliminary study on potential biomarkers for diagnosis and severity

10.21203/rs.3.rs-630726/v1 ◽

2021 ◽

Author(s):

Aline de Souza Nicoletti ◽

Marília Berlofa Visacri ◽

Carla Regina da Silva Correa da Ronda ◽

Pedro Eduardo do Nascimento Silva Vasconcelos ◽

Julia Coelho França Quintanilha ◽

...

Keyword(s):

Signaling Pathways ◽

Mirna Expression ◽

High Throughput Sequencing ◽

Viral Infections ◽

Differentially Expressed ◽

Stat3 Signaling ◽

Differentially Expressed Mirnas ◽

Critical Patients ◽

Novel Coronavirus ◽

Potential Biomarkers

Abstract Background: Coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is known that host microRNAs (miRNAs) can be modulated to favor viral infection or to protect the host. Objective: The aim of this study was to identify differentially expressed circulating miRNAs in Brazilian patients with COVID-19 as potential biomarkers for diagnosis and severity. Methods: miRNAs were extracted from the blood plasma of eight patients with COVID-19 (four patients with mild/moderate COVID-19 and four patients with severe/critical COVID-19) and four healthy controls. The patients and controls were matched for sex and age. miRNA expression levels were detected using high-throughput sequencing. Differential miRNA expression and enrichment analyses were further evaluated. Results: A total of 18 human miRNAs were differentially expressed between patients with COVID-19 (n = 8) and controls (n = 4), with 13 significantly upregulated and five significantly downregulated miRNAs. miR-4433b-5p, miR-6780b-3p, miR-6883-3p, miR-320b, miR-7111-3p, miR-4755-3p, miR-320c, and miR-6511a-3p were the most important miRNAs found significantly involved in the PI3K/AKT, Wnt/β-catenin, and STAT3 signaling pathways, which have a crucial role in viral infections. Moreover, 42 miRNAs were differentially expressed between severe/critical patients with COVID-19 (n = 4) and mild/moderate patients with COVID-19 (n = 4). miR-451a, miR-101-3p, miR-185-5p, miR-30d-5p, miR-25-3p, miR-342-3p, miR-30e-5p, miR-150-5p, miR-15b-5p, and miR-29c-3p were the most important miRNAs found to be significantly involved in the Wnt/β-catenin, NF-κβ, and STAT3 signaling pathways, which play crucial roles in immune response and inflammation. Conclusions: Differentially expressed miRNAs found in this study may be used as potential biomarkers for the diagnosis and severity of COVID-19. Larger studies are needed to validate these miRNAs as biomarkers of COVID-19.

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Integrated analysis of miRNA and mRNA expression profiles in testes of Duroc and Meishan boars

10.21203/rs.2.15327/v4 ◽

2020 ◽

Author(s):

Haisheng Ding ◽

Min Liu ◽

Changfan zhou ◽

Xiangbin You ◽

Tao Su ◽

...

Keyword(s):

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Male Gamete ◽

Mirna Expression Profile ◽

Mapk Signaling ◽

Differentially Expressed ◽

Integrated Analysis ◽

Testis Development ◽

Differentially Expressed Mirnas

Abstract Background: MicroRNAs (miRNAs) are small non-coding RNAs playing vital roles in regulating posttranscriptional gene expression. Elucidating the expression regulation of miRNAs underlying pig testis development will contribute to a better understanding of boar fertility and spermatogenesis. Results: In this study, miRNA expression profile was investigated in testes of Duroc and Meishan boars at 20, 75, and 270 days of age by high-throughput sequencing. Forty-five differentially expressed miRNAs were identified from testes of Duroc and Meishan boars before and after puberty. Integrated analysis of miRNA and mRNA profiles predicted many miRNA-mRNA pairs. Gene ontology and biological pathway analyses revealed that predicted target genes of ssc-mir-423-5p, ssc-mir-34c, ssc-mir-107, ssc-165 mir-196b-5p, ssc-mir-92a, ssc-mir-320, ssc-mir-10a-5p, and ssc-mir-181b were involved in sexual reproduction, male gamete generation, and spermatogenesis, and GnRH, Wnt, and MAPK signaling pathway. Four significantly differentially expressed miRNAs and their predicted target genes were validated by quantitative real-time polymerase chain reaction, and phospholipase C beta 1 ( PLCβ1) gene was verified to be a target of ssc-mir-423-5p . Conclusions: This study provides an insight into the functional roles of miRNAs in testis development and spermatogenesis and offers useful resources for understanding differences in sexual function development caused by the change in miRNAs expression between Duroc and Meishan boars.

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Identification of miRNAs and Their Target Genes Involved in Cucumber Fruit Expansion Using Small RNA and Degradome Sequencing

Biomolecules ◽

10.3390/biom9090483 ◽

2019 ◽

Vol 9 (9) ◽

pp. 483 ◽

Cited By ~ 1

Author(s):

Sun ◽

Luo ◽

Chang ◽

Li ◽

Zhou ◽

...

Keyword(s):

Small Rna ◽

High Throughput Sequencing ◽

Target Genes ◽

Expression Patterns ◽

Differentially Expressed ◽

Sequencing Data ◽

Degradome Sequencing ◽

Complex Biological Process ◽

Cucumber Fruit ◽

Differentially Expressed Mirnas

Fruit expansion is an essential and very complex biological process. Regulatory roles of microRNAs (miRNAs) and miRNA–mRNA modules in the cucumber fruit expansion are not yet to be investigated. In this work, 1253 known and 1269 novel miRNAs were identified from nine cucumber fruit small RNA (sRNA) libraries through high-throughput sequencing. A total of 105 highly differentially expressed miRNAs were recognized in the fruit on five days post anthesis with pollination (EXP_5d) sRNA library. Further, expression patterns of 11 differentially expressed miRNAs were validated by quantitative real-time PCR (qRT-PCR). The expression patterns were similar to sRNAs sequencing data. Transcripts of 1155 sequences were predicted as target genes of differentially expressed miRNAs by degradome sequencing. Gene Ontology (GO) enrichment showed that these target genes were involved in 24 biological processes, 15 cell components and nine molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that these target genes were significantly enriched in 19 pathways and the enriched KEGG pathways were associated with environmental adaptation, signal transduction and translation. Based on the functional prediction of miRNAs and target genes, our findings suggest that miRNAs have a potential regulatory role in cucumber fruit expansion by targeting their target genes, which provide important data for understanding the miRNA-mediated regulatory networks controlling fruit expansion in cucumber. Specific miRNAs could be selected for further functional research and molecular breeding in cucumber.

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Integrated analysis of miRNA and mRNA expression profiles in testes of Duroc and Meishan boars

10.21203/rs.2.15327/v3 ◽

2020 ◽

Author(s):

Haisheng Ding ◽

Min Liu ◽

Changfan zhou ◽

Xiangbin You ◽

Tao Su ◽

...

Keyword(s):

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Male Gamete ◽

Mirna Expression Profile ◽

Mapk Signaling ◽

Differentially Expressed ◽

Integrated Analysis ◽

Testis Development ◽

Differentially Expressed Mirnas

Abstract Background: MicroRNAs (miRNAs) are small non-coding RNAs playing vital roles in regulating posttranscriptional gene expression. Elucidating the expression regulation of miRNAs underlying pig testis development will contribute to a better understanding of boar fertility and spermatogenesis. Results: In this study, miRNA expression profile was investigated in testes of Duroc and Meishan boars at 20, 75, and 270 days of age by high-throughput sequencing. Forty-five differentially expressed miRNAs were identified from testes of Duroc and Meishan boars before and after puberty. Integrated analysis of miRNA and mRNA profiles predicted many miRNA-mRNA pairs. Gene ontology and biological pathway analyses revealed that predicted target genes of ssc-mir-423-5p, ssc-mir-34c, ssc-mir-107, ssc-165 mir-196b-5p, ssc-mir-92a, ssc-mir-320, ssc-mir-10a-5p, and ssc-mir-181b were involved in sexual reproduction, male gamete generation, and spermatogenesis, and GnRH, Wnt, and MAPK signaling pathway. Four significantly differentially expressed miRNAs and their predicted target genes were validated by quantitative real-time polymerase chain reaction, and phospholipase C beta 1 (PLCβ1) gene was verified to be a target of ssc-mir-423-5p. Conclusions: This study provides an insight into the functional roles of miRNAs in testis development and spermatogenesis and offers useful resources for understanding differences in sexual function development caused by the change in miRNAs expression between Duroc and Meishan boars.

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Integrated analysis of miRNA and mRNA expression profiles in testes of Duroc and Meishan boars

10.21203/rs.2.15327/v6 ◽

2020 ◽

Author(s):

Haisheng Ding ◽

Min Liu ◽

Changfan zhou ◽

Xiangbin You ◽

Tao Su ◽

...

Keyword(s):

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Male Gamete ◽

Mirna Expression Profile ◽

Mapk Signaling ◽

Differentially Expressed ◽

Integrated Analysis ◽

Testis Development ◽

Differentially Expressed Mirnas

Abstract Background: MicroRNAs (miRNAs) are small non-coding RNAs playing vital roles in regulating posttranscriptional gene expression. Elucidating the expression regulation of miRNAs underlying pig testis development will contribute to a better understanding of boar fertility and spermatogenesis. Results: In this study, miRNA expression profile was investigated in testes of Duroc and Meishan boars at 20, 75, and 270 days of age by high-throughput sequencing. Forty-five differentially expressed miRNAs were identified from testes of Duroc and Meishan boars before and after puberty. Integrated analysis of miRNA and mRNA profiles predicted many miRNA-mRNA pairs. Gene ontology and biological pathway analyses revealed that predicted target genes of ssc-mir-423-5p, ssc-mir-34c, ssc-mir-107, ssc-165 mir-196b-5p, ssc-mir-92a, ssc-mir-320, ssc-mir-10a-5p, and ssc-mir-181b were involved in sexual reproduction, male gamete generation, and spermatogenesis, and GnRH, Wnt, and MAPK signaling pathway. Four significantly differentially expressed miRNAs and their predicted target genes were validated by quantitative real-time polymerase chain reaction, and phospholipase C beta 1 (PLCβ1) gene was verified to be a target of ssc-mir-423-5p. Conclusions: This study provides an insight into the functional roles of miRNAs in testis development and spermatogenesis and offers useful resources for understanding differences in sexual function development caused by the change in miRNAs expression between Duroc and Meishan boars.

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