scholarly journals MicroRNA Expression Profiles Analysis in Sperm Reveals hsa-mir-191 is an Auspicious Omen of in Vitro Fertilization

2019 ◽  
Author(s):  
Hua Xu ◽  
Xin Wang ◽  
Zhikai Wang ◽  
Jianhui Li ◽  
Zhiming Xu ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Small Rna ◽  
Expression Profiles ◽  
Fertilization Rate ◽  
Small Rna Sequencing ◽  
High Quality ◽  
Potential Marker ◽  
Blastocyst Rate ◽  
The Relationship ◽  
Early Human

Abstract Background: MicroRNAs(miRNAs) are a class of non-coding small RNAs, which play important roles in many physiological processes by regulating gene expression. Previously studies show that the expression level of total miRNAs increased during the progression of mouse embryonic development, and some miRNAs control the regulatory network in the development progression. However, there are few studies focused on effects of miRNA on the early human embryonic development. The relationship of between miRNAs and early human embryogenesis is still unknown. Results In this study, 102 male sperm samples that were treated with assisted reproductive technology but with normal sperm index were collected for small RNA sequencing, and the relationships between differentially expressed small RNA and fertilization rate, blastocyst rate and high-quality embryo rate were analyzed. The results showed that the sperm samples with high expression of hsa-mir-191 had higher fertilization rate, blastocyst rate and high-quality embryo rate. Using hsa-mir-191 as a single indicator to predict high-quality embryo rate, the ROC curve has an AUC of 0.686. At the same time, we also found that the expression of hsa-mir-191 has a certain correlation with sperm abnormality rate (cor = 0.29, p< 0.01). In addition, we also evaluated the relationship between hsa-mir-34c and human early embryo development in these 102 sperm samples, and obtained negative results. Conclusions These findings suggest that higher hsa-mir-191-5p expression with better human early embryonic development, and indicate that the hsa-mir-191-5p could be a potential marker to access the quality of IVF.

scholarly journals MicroRNA Expression Profiles Analysis in Sperm Reveals hsa-mir-191 is an Auspicious Omen of in Vitro Fertilization

2019 ◽  
Author(s):  
Hua Xu ◽  
Xin Wang ◽  
Zhikai Wang ◽  
Jianhui Li ◽  
Zhiming Xu ◽  
...  
Keyword(s):  
In Vitro Fertilization ◽  
Embryonic Development ◽  
Roc Curve ◽  
Small Rnas ◽  
Expression Profiles ◽  
High Quality ◽  
Vitro Fertilization ◽  
The Relationship ◽  
Early Human

Abstract Background: MicroRNAs (miRNAs) are a class of noncoding small RNAs that play important roles in many physiological processes by regulating gene expression. Previous studies have shown that the expression levels of total miRNAs increase during mouse embryonic development, and some miRNAs control the regulatory network in development progression. However, few studies have focused on the effects of miRNAs on early human embryonic development. The relationship between miRNAs and early human embryogenesis is still unknown. Results:In this study, RNA-seq data collected from sperm samples from 102 patients with a normal sperm index but treated with assisted reproductive technology (ART) were analyzed for the relationships between differentially expressed small RNAs and the fertilization rate (FR), blastocyst rate and high-quality embryo rate (HQER). The sperm samples with high hsa-mir-191 expression had a higher FR, effective embryo rate (EER) and HQER. hsa-mir-191 was used as a single indicator to predict the HQER. The receiver operating characteristic (ROC) curve had an area under the ROC curve (AUC) of 0.686. We also found that hsa-mir-191 expression is correlated with an abnormal sperm rate (cor = 0.29, p< 0.01). We also evaluated the relationship between hsa-mir-34c and early human embryo development in these 102 sperm samples and obtained negative results. Conclusions: These findings suggest that high hsa-mir-191-5p expression in sperm is associated with early human embryonic quality and that hsa-mir-191-5p could be used as a potential marker to screen high-quality sperm to improve the success rates of in vitro fertilization (IVF).

scholarly journals MicroRNA Expression Profiles Analysis in Sperm Reveals hsa-mir-191 is an Auspicious Omen of in Vitro Fertilization

2019 ◽  
Author(s):  
Hua Xu ◽  
Xin Wang ◽  
Zhikai Wang ◽  
Jianhui Li ◽  
Zhiming Xu ◽  
...  
Keyword(s):  
In Vitro Fertilization ◽  
Embryonic Development ◽  
Roc Curve ◽  
Small Rnas ◽  
Small Rna Sequencing ◽  
High Quality ◽  
Vitro Fertilization ◽  
The Relationship ◽  
Early Human

Abstract Background : MicroRNAs (miRNAs) are a class of noncoding small RNAs that play important roles in many physiological processes by regulating gene expression. Previous studies have shown that the expression levels of total miRNAs increase during mouse embryonic development, and some miRNAs control the regulatory network in development progression. However, few studies have focused on the effects of miRNAs on early human embryonic development. The relationship between miRNAs and early human embryogenesis is still unknown. Results: In this study, sperm samples from 102 patients with a normal sperm index but treated with assisted reproductive technology (ART) were collected for small RNA sequencing, and the relationships between differentially expressed small RNAs and the fertilization rate (FR), blastocyst rate and high-quality embryo rate (HQER) were analyzed. The sperm samples with high hsa-mir-191 expression had a higher FR, effective embryo rate (EER) and HQER. hsa-mir-191 was used as a single indicator to predict the HQER. The receiver operating characteristic (ROC) curve had an area under the ROC curve (AUC) of 0.686. We also found that hsa-mir-191 expression is correlated with an abnormal sperm rate (cor = 0.29, p < 0.01). We also evaluated the relationship between hsa-mir-34c and early human embryo development in these 102 sperm samples and obtained negative results. Conclusions: These findings suggest that high hsa-mir-191-5p expression is associated with improved early human embryonic development and that hsa-mir-191-5p could be used as a potential marker to screen high-quality sperm to improve the success rates of in vitro fertilization (IVF).

scholarly journals MicroRNA Expression Profiles Analysis in Sperm Reveals hsa-mir-191 is an Auspicious Omen of in Vitro Fertilization

2019 ◽  
Author(s):  
Hua Xu ◽  
Xin Wang ◽  
Zhikai Wang ◽  
Jianhui Li ◽  
Zhiming Xu ◽  
...  
Keyword(s):  
In Vitro Fertilization ◽  
Embryonic Development ◽  
Roc Curve ◽  
Small Rnas ◽  
Expression Profiles ◽  
High Quality ◽  
Vitro Fertilization ◽  
The Relationship ◽  
Early Human

Abstract Background: MicroRNAs (miRNAs) are a class of noncoding small RNAs that play important roles in many physiological processes by regulating gene expression. Previous studies have shown that the expression levels of total miRNAs increase during mouse embryonic development, and some miRNAs control the regulatory network in development progression. However, few studies have focused on the effects of miRNAs on early human embryonic development. The relationship between miRNAs and early human embryogenesis is still unknown. Results:In this study, RNA-seq data collected from sperm samples from 102 patients with a normal sperm index but treated with assisted reproductive technology (ART) were analyzed for the relationships between differentially expressed small RNAs and the
fertilization rate (FR), blastocyst rate and high-quality embryo rate (HQER). The sperm samples with high hsa-mir-191 expression had a higher FR, effective embryo rate (EER) and HQER. hsa-mir-191 was used as a single indicator to predict the HQER. The receiver operating characteristic (ROC) curve had an area under the ROC curve (AUC) of 0.686. We also found that hsa-mir-191 expression is correlated with an abnormal sperm rate (cor = 0.29, p< 0.01). We also evaluated the relationship between hsa-mir-34c and early human embryo development in these 102 sperm samples and obtained negative results. Conclusions: These findings suggest that high hsa-mir-191-5p expression in sperm is associated with early human embryonic quality and that hsa-mir-191-5p could be used as a potential marker to screen high-quality sperm to improve the success rates of in vitro fertilization (IVF).

scholarly journals MicroRNA Expression Profiles Analysis in Sperm Reveals hsa-mir-191 is an Auspicious Omen of in Vitro Fertilization

2019 ◽  
Author(s):  
Hua Xu ◽  
Xin Wang ◽  
Zhikai Wang ◽  
Jianhui Li ◽  
Zhiming Xu ◽  
...  
Keyword(s):  
In Vitro Fertilization ◽  
Embryonic Development ◽  
Roc Curve ◽  
Small Rnas ◽  
Small Rna Sequencing ◽  
High Quality ◽  
Vitro Fertilization ◽  
The Relationship ◽  
Early Human

Abstract Background: MicroRNAs (miRNAs) are a class of noncoding small RNAs that play important roles in many physiological processes by regulating gene expression. Previous studies have shown that the expression levels of total miRNAs increase during mouse embryonic development, and some miRNAs control the regulatory network in development progression. However, few studies have focused on the effects of miRNAs on early human embryonic development. The relationship between miRNAs and early human embryogenesis is still unknown. Results: In this study, sperm samples from 102 patients with a normal sperm index but treated with assisted reproductive technology (ART) were collected for small RNA sequencing, and the relationships between differentially expressed small RNAs and the fertilization rate (FR), blastocyst rate and high-quality embryo rate (HQER) were analyzed. The sperm samples with high hsa-mir-191 expression had a higher FR, effective embryo rate (EER) and HQER. hsa-mir-191 was used as a single indicator to predict the HQER. The receiver operating characteristic (ROC) curve had an area under the ROC curve (AUC) of 0.686. We also found that hsa-mir-191 expression is correlated with an abnormal sperm rate (cor = 0.29, p< 0.01). We also evaluated the relationship between hsa-mir-34c and early human embryo development in these 102 sperm samples and obtained negative results. Conclusions: These findings suggest that high hsa-mir-191-5p expression in sperm is associated with early human embryonic quality and that hsa-mir-191-5p could be used as a potential marker to screen high-quality sperm to improve the success rates of in vitro fertilization (IVF). Keywords: miRNA, hsa-mir-191, hsa-mir-34c, RNA-Seq, Embryonic development

scholarly journals Identification and validation of miRNA reference genes in poplar under pathogen stress

2021 ◽  
Author(s):  
Lichun Zhang ◽  
Xiaoqian Yang ◽  
Yiyi Yin ◽  
Jinxing Wang ◽  
Yanwei Wang
Keyword(s):  
Gene Expression ◽  
Reference Gene ◽  
Small Rna ◽  
Reference Genes ◽  
Expression Profiles ◽  
Small Rna Sequencing ◽  
Rna Seq ◽  
Internal Standards ◽  
Qrt Pcr ◽  
Canker Pathogen

Abstract Quantitative real time polymerase chain reaction (qRT-PCR) is a common method to analyze gene expression. Due to differences in RNA quantity, quality, and reverse transcription efficiency between qRT-PCR samples, reference genes are used as internal standards to normalize gene expression. However, few universal genes especially miRNAs have been identified as reference so far. Therefore, it is essential to identify reference genes that can be used across various experimental conditions, stress treatments, or tissues. In this study, 14 microRNAs (miRNAs) and 5.8S rRNA were assessed for expression stability in poplar trees infected with canker pathogen. Using three reference gene analysis programs, we found that miR156g and miR156a exhibited stable expression throughout the infection process. miR156g and miR156a were then tested as internal standards to measure the expression of miR1447 and miR171c, and the results were compared to small RNA sequencing (RNA-seq) data. We found that when miR156a was used as the reference gene, the expression of miR1447 and miR171c were consistent with the small RNA-seq expression profiles. Therefore, miR156a was the most stable miRNAs examined in this study, and could be used as a reference gene in poplar under canker pathogen stress, which should enable comprehensive comparisons of miRNAs expression and avoid the bias caused by different lenth between detected miRNAs and traditional referece genes. The present study has expanded the miRNA reference genes available for gene expression studies in trees under biotic stress.

scholarly journals DBtRend: A Web-Server of tRNA Expression Profiles from Small RNA Sequencing Data in Humans

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1576
Author(s):  
Jin-Ok Lee ◽  
Minho Lee ◽  
Yeun-Jun Chung
Keyword(s):  
Small Rna ◽  
Molecular Subtype ◽  
Expression Profiles ◽  
Web Server ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Microrna Sequencing ◽  
User Friendly

Transfer RNA (tRNA), a key component of the translation machinery, plays critical roles in stress conditions and various diseases. While knowledge regarding the importance of tRNA function is increasing, its biological roles are still not well understood. There is currently no comprehensive database or web server providing the expression landscape of tRNAs across a variety of human tissues and diseases. Here, we constructed a user-friendly and interactive database, DBtRend, which provides a profile of mature tRNA expression across various biological conditions by reanalyzing the small RNA or microRNA sequencing data from the Cancer Genome Atlas (TCGA) and NCBI’s Gene Expression Omnibus (GEO) in humans. Users can explore not only the expression values of mature individual tRNAs in the human genome, but also those of isodecoders and isoacceptors based on our specific pipelines. DBtRend provides the expressed patterns of tRNAs, the differentially expressed tRNAs in different biological conditions, and the information of samples or patients, tissue types, and molecular subtype of cancers. The database is expected to help researchers interested in functional discoveries of tRNAs.

scholarly journals Effects of Different Types of Incubators on Embryo Development and Clinical Outcomes

2021 ◽  
Author(s):  
Ji Liu ◽  
Yan-Hua Zhou ◽  
Xiao-Xiao Wang ◽  
Ling-Xi Tong ◽  
Yan-Hong Li ◽  
...  
Keyword(s):  
Clinical Outcomes ◽  
Embryo Development ◽  
Recovery Time ◽  
Culture Media ◽  
Fertilization Rate ◽  
High Quality ◽  
Water Jacket ◽  
Different Types ◽  
Temperature Recovery ◽  
Blastocyst Rate

Main differences of incubators are humidity, temperature and gas control ways, which play important roles in regulating the steady state of culture media. In this study, we compared the effects of different types of incubators (air jacket incubators and water jacket incubators) on embryo development and clinical outcomes in human assisted reproduction. We found that temperature recovery time in air jacket incubators was significantly shorter than that in water jacket incubators. Although the O2 recovering time was also significantly shorter in air jacket incubators as compared with the water jacket incubator, no significant differences were observed in CO2 recovering time between two groups, which was also verified by pH recovering time of culture media. Besides, the temperature of culture medium in the dish covered with oil recovered more quickly in the air jacket incubators. However, there were no significant differences observed in the fertilization rate, Day 3 high-quality embryo rate, blastocyst rate, good blastocyst rate and clinical outcomes between two groups. These results indicate that the microenvironment, especially the temperature, in air jacket incubator recover faster than that in water jacket incubators, however, there were no significant differences in embryo development and clinical outcomes between two types of incubators.

scholarly journals Integrated mRNA and small RNA sequencing reveals microRNA regulatory network associated with internode elongation in sugarcane (Saccharum officinarum L.)

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Lihang Qiu ◽  
Rongfa Chen ◽  
Yegeng Fan ◽  
Xing Huang ◽  
Hanmin Luo ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Nitrogen Metabolism ◽  
Differentially Expressed Genes ◽  
Small Rna ◽  
Plant Hormone ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Internode Elongation ◽  
Mirna Regulation

Abstract Background Internode elongation is one of the most important traits in sugarcane because of its relation to crop productivity. Understanding the microRNA (miRNA) and mRNA expression profiles related to sugarcane internode elongation would help develop molecular improvement strategies but they are not yet well-investigated. To identify genes and miRNAs involved in internode elongation, the cDNA and small RNA libraries from the pre-elongation stage (EI), early elongation stage (EII) and rapid elongation stage (EIII) were sequenced and their expression were studied. Results Based on the sequencing results, 499,495,518 reads and 80,745 unigenes were identified from stem internodes of sugarcane. The comparisons of EI vs. EII, EI vs. EIII, and EII vs. EIII identified 493, 5035 and 3041 differentially expressed genes, respectively. Further analysis revealed that the differentially expressed genes were enriched in the GO terms oxidoreductase activity and tetrapyrrole binding. KEGG pathway annotation showed significant enrichment in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction”, which might be participating in internode elongation. miRNA identification showed 241 known miRNAs and 245 novel candidate miRNAs. By pairwise comparison, 11, 42 and 26 differentially expressed miRNAs were identified from EI and EII, EI and EIII, and EII and EIII comparisons, respectively. The target prediction revealed that the genes involved in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction” pathways are targets of the miRNAs. We found that the known miRNAs miR2592-y, miR1520-x, miR390-x, miR5658-x, miR6169-x and miR8154-x were likely regulators of genes with internode elongation in sugarcane. Conclusions The results of this study provided a global view of mRNA and miRNA regulation during sugarcane internode elongation. A genetic network of miRNA-mRNA was identified with miRNA-mediated gene expression as a mechanism in sugarcane internode elongation. Such evidence will be valuable for further investigations of the molecular regulatory mechanisms underpinning sugarcane growth and development.

scholarly journals Evaluating gastroenteropancreatic neuroendocrine tumors through microRNA sequencing

2019 ◽  
Vol 26 (1) ◽  
pp. 47-57 ◽  
Author(s):  
Nicole Panarelli ◽  
Kathrin Tyryshkin ◽  
Justin Jong Mun Wong ◽  
Adrianna Majewski ◽  
Xiaojing Yang ◽  
...  
Keyword(s):  
Neuroendocrine Tumors ◽  
Small Rna ◽  
Mirna Expression ◽  
Expression Profiles ◽  
Machine Learning Techniques ◽  
Disease Stage ◽  
Small Rna Sequencing ◽  
Gastroenteropancreatic Neuroendocrine Tumors ◽  
Mirna Expression Profiles ◽  
Microrna Sequencing

Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) can be challenging to evaluate histologically. MicroRNAs (miRNAs) are small RNA molecules that often are excellent biomarkers due to their abundance, cell-type and disease stage specificity and stability. To evaluate miRNAs as adjunct tissue markers for classifying and grading well-differentiated GEP-NETs, we generated and compared miRNA expression profiles from four pathological types of GEP-NETs. Using quantitative barcoded small RNA sequencing and state-of-the-art sequence annotation, we generated comprehensive miRNA expression profiles from archived pancreatic, ileal, appendiceal and rectal NETs. Following data preprocessing, we randomly assigned sample profiles to discovery (80%) and validation (20%) sets prior to data mining using machine-learning techniques. High expression analyses indicated that miR-375 was the most abundant individual miRNA and miRNA cistron in all samples. Leveraging prior knowledge that GEP-NET behavior is influenced by embryonic derivation, we developed a dual-layer hierarchical classifier for differentiating GEP-NET types. In the first layer, our classifier discriminated midgut (ileum, appendix) from non-midgut (rectum, pancreas) NETs based on miR-615 and -92b expression. In the second layer, our classifier discriminated ileal from appendiceal NETs based on miR-125b, -192 and -149 expression, and rectal from pancreatic NETs based on miR-429 and -487b expression. Our classifier achieved overall accuracies of 98.5% and 94.4% in discovery and validation sets, respectively. We also found provisional evidence that low- and intermediate-grade pancreatic NETs can be discriminated based on miR-328 expression. GEP-NETs can be reliably classified and potentially graded using a limited panel of miRNA markers, complementing morphological and immunohistochemistry-based approaches to histologic evaluation.

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