Integrated Analysis of mRNA- and miRNA-Seq in the Ovary of Rare Minnow Gobiocypris rarus in Response to 17α-Methyltestosterone

17α-Methyltestosterone (MT) is a synthetic androgen. The objective of this study was to explore the effects of exogenous MT on the growth and gonadal development of female rare minnow Gobiocypris rarus. Female G. rarus groups were exposed to 25–100 ng/L of MT for 7 days. After exposure for 7 days, the total weight and body length were significantly decreased in the 50-ng/L MT groups. The major oocytes in the ovaries of the control group were vitellogenic oocytes (Voc) and cortical alveolus stage oocytes (Coc). In the MT exposure groups, some fish had mature ovaries with a relatively lower proportion of mature oocytes, and the diameter of the perinucleolar oocytes (Poc) was decreased compared with those of the control group. Ovarian VTG, FSH, LH, 11-KT, E2, and T were significantly increased after exposure to 50 ng/L of MT for 7 days. Unigenes (73,449), 24 known mature microRNAs (miRNAs), and 897 novel miRNAs in the gonads of G. rarus were found using high-throughput sequencing. Six mature miRNAs (miR-19, miR-183, miR-203, miR-204, miR-205, and miR-96) as well as six differentially expressed genes (fabp3, mfap4, abca1, foxo3, tgfb1, and zfp36l1) that may be associated with ovarian development and innate immune response were assayed using qPCR. Furthermore, the miR-183 cluster and miR-203 were differentially expressed in MT-exposed ovaries of the different G. rarus groups. This study provides some information about the role of miRNA–mRNA pairs in the regulation of ovarian development and innate immune system, which will facilitate future studies of the miRNA–RNA-associated regulation of teleost reproduction.

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Comprehensive analysis of miRNA-mRNA/lncRNA during gonadal development of triploid female rainbow trout (Oncorhynchus mykiss)

10.21203/rs.3.rs-31357/v2 ◽

2020 ◽

Author(s):

Tianqing Huang ◽

Wei Gu ◽

Enhui Liu ◽

Xiulan Shi ◽

Bingqian Wang ◽

...

Keyword(s):

Rainbow Trout ◽

High Throughput Sequencing ◽

Developmental Stages ◽

Expression Profiles ◽

Noncoding Rnas ◽

Gonadal Development ◽

Differentially Expressed ◽

Rainbow Trout Oncorhynchus Mykiss ◽

Oocyte Meiosis ◽

Non Coding Rna

Abstract Background: Chromosomal ploidy manipulation is one of the means to create excellent germplasm. Triploid fish could provide an ideal sterile model for the mechanism research of abnormality in meiosis. The complete understanding of the coding and noncoding RNAs regulating sterility caused by meiosis abnormality is still not well understood.Results: By high-throughput sequencing, we compared the expression profiles of gonadal mRNA, long non-coding RNA (lncRNA), and microRNA (miRNA) at different developmental stages [65 days post fertilisation (dpf), 180 dpf, and 600 dpf] between the diploid (XX) and triploid (XXX) female rainbow trout. A majority of differentially expressed (DE) RNAs were identified, and 22 DE mRNAs related to oocyte meiosis and homologous recombination were characterized. The predicted miRNA-mRNA/lncRNA networks of 3 developmental stages were constructed based on the target pairs of DE lncRNA-miRNA and DE mRNA-miRNA. According to the networks, meiosis-related gene of ccne1 was targeted by dre-miR-15a-5p_R+1, and 6 targeted DE lncRNAs were identified. Also, RT-qPCR was performed to validate the credibility of the network.Conclusions: This study explored the potential interplay between coding and noncoding RNAs during the gonadal development of polyploid fish. It provides full insights into polyploidy-associated effects on fertility of fish. These differentially expressed coding and noncoding RNAs provide a novel resource for studying genome diversity of polyploid induction.

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Non-monotonic dose–response effect of bisphenol A on rare minnow Gobiocypris rarus ovarian development

Chemosphere ◽

10.1016/j.chemosphere.2015.08.079 ◽

2016 ◽

Vol 144 ◽

pp. 304-311 ◽

Cited By ~ 27

Author(s):

Yingying Zhang ◽

Shiyu Tao ◽

Cong Yuan ◽

Yan Liu ◽

Zaizhao Wang

Keyword(s):

Bisphenol A ◽

Dose Response ◽

Ovarian Development ◽

Gobiocypris Rarus ◽

Response Effect ◽

Rare Minnow ◽

Dose Response Effect

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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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Immune-related miRNA-mRNA regulation network in the livers of DHAV-3-infected ducklings

10.21203/rs.2.13422/v3 ◽

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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Identification and characterization of heat-responsive microRNAs at the booting stage in two rice varieties 9311 and Nagina 22

Genome ◽

10.1139/gen-2020-0175 ◽

2021 ◽

Author(s):

Ying Luo ◽

Tao Wang ◽

Dan Yang ◽

Biao Luo ◽

Weiping Wang ◽

...

Keyword(s):

Stress Responses ◽

High Throughput Sequencing ◽

Target Genes ◽

Elevated Temperatures ◽

Differentially Expressed ◽

Control Group ◽

Microrna Target ◽

Rice Varieties ◽

Booting Stage ◽

Differentially Expressed Mirnas

Abstract: MicroRNAs (miRNAs) are small, non-coding, regulatory RNAs that play important roles in abiotic stress responses in plants. but their regulatory roles in the adaptive response to heat stress at the booting stage in two rice varieties 9311 and Nagina 22, remain largely unknown. In this study, 464 known miRNAs and 123 potential novel miRNAs were identified. Of these miRNAs, a total of 90 differential expressed miRNAs were obtained with 9311 libraries as control group, of which 54 upregulated and 36 downregulated miRNAs. To gain insight into functional significance, 2773 potential target genes of these 90 differentially expressed miRNAs were predicted. GO enrichment showed that the predicted target genes of differentially expressed miRNAs including NACs, LACs, CSD, and Hsp40. KEGG pathway analysis showed that target genes of these differentially expressed miRNAs were significantly enriched in plant hormone signal transduction pathway. The expression levels of ten differentially expressed miRNAs and their target genes obtained by qRT-PCR were largely consistent with the sequencing results. This study lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in rice at elevated temperatures. Key words: rice, heat-responsive, microRNA, target gene, booting stage, high-throughput sequencing

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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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Genome-wide analysis of microRNAs expression profiling in patients with primary IgA nephropathy

Genome ◽

10.1139/gen-2012-0159 ◽

2013 ◽

Vol 56 (3) ◽

pp. 161-169 ◽

Cited By ~ 27

Author(s):

Kuibi Tan ◽

Jing Chen ◽

Wuxian Li ◽

Yuyu Chen ◽

Weiguo Sui ◽

...

Keyword(s):

High Throughput Sequencing ◽

Target Genes ◽

Immunoglobulin A ◽

Differentially Expressed ◽

Control Group ◽

Pathological Changes ◽

Genome Wide ◽

Differentially Expressed Mirnas ◽

Specific Tissue ◽

Mirnas Expression

The aim of this study was to investigate the differential expression characteristics and the roles of the genome-wide microRNAs (miRNAs) in immunoglobulin A nephropathy (IgAN) kidney tissues. We used Illumina high-throughput sequencing technology to evaluate the miRNAs expression of six biopsy tissues from IgAN and six normal renal cortex specimens from patients with renal cell carcinoma. We observed a total of 85 miRNAs that were differentially expressed in the six IgAN patients, of which 11 miRNAs were up-regulated and 74 miRNAs were down-regulated in patients' tissues compared with control tissues. Additionally, we identified 55 candidate novel miRNAs in our study, which comprised seven candidates who were detected in the IgAN group and 49 candidates who were detected in the control group. Only one candidate (miR-n-9) was expressed in both groups. The bioinformatics showed that the regulated target genes of differentially expressed miRNAs were associated with immune and renal pathological changes. The identification of specific tissue miRNAs in our study not only helped clarify the genetics or immunology mechanisms involved in the pathogenesis of IgAN but also helped explain the pathological changes in the kidney tissues. We hypothesize that some significant miRNAs might potentially serve as novel diagnostic biomarkers in IgAN patients.

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An Integrated Analysis of Cashmere Fineness lncRNAs in Cashmere Goats

Genes ◽

10.3390/genes10040266 ◽

2019 ◽

Vol 10 (4) ◽

pp. 266 ◽

Cited By ~ 5

Author(s):

Yuan Y. Zheng ◽

Sheng D. Sheng ◽

Tai Y. Hui ◽

Chang Yue ◽

Jia M. Sun ◽

...

Keyword(s):

Intermediate Filament ◽

High Throughput Sequencing ◽

Target Genes ◽

Differentially Expressed ◽

Sphingolipid Metabolism ◽

Integrated Analysis ◽

Messenger Rnas ◽

Bioinformatics Analyses ◽

Anagen Phase ◽

Cashmere Goats

Animal growth and development are regulated by long non-coding RNAs (lncRNAs). However, the functions of lncRNAs in regulating cashmere fineness are poorly understood. To identify the key lncRNAs that are related to cashmere fineness in skin, we have collected skin samples of Liaoning cashmere goats (LCG) and Inner Mongolia cashmere goats (MCG) in the anagen phase, and have performed RNA sequencing (RNA-seq) approach on these samples. The high-throughput sequencing and bioinformatics analyses identified 437 novel lncRNAs, including 93 differentially expressed lncRNAs. We also identified 3,084 differentially expressed messenger RNAs (mRNAs) out of 27,947 mRNAs. Gene ontology (GO) analyses of lncRNAs and target genes in cis show a predominant enrichment of targets that are related to intermediate filament and intermediate filament cytoskeleton. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, sphingolipid metabolism is a significant pathway for lncRNA targets. In addition, this is the first report to reveal the possible lncRNA–mRNA regulatory network for cashmere fineness in cashmere goats. We also found that lncRNA XLOC_008679 and its target gene, KRT35, may be related to cashmere fineness in the anagen phase. The characterization and expression analyses of lncRNAs will facilitate future studies on the potential value of fiber development in LCG.

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