scholarly journals Functional profiling of the endometrium transcriptome during preimplantation development in Finnsheep, Texel and their F1 crosses

2020 ◽  
Vol 29 (4) ◽  
Author(s):  
Kisun Pokharel ◽  
Jaana Peippo ◽  
Meng-Hua Li ◽  
Juha Kantanen
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Transcriptome Profiling ◽  
Preimplantation Development ◽  
Endogenous Retroviruses ◽  
P Value ◽  
Comparative Transcriptome ◽  
Functional Profiling ◽  
Genetic Mechanisms ◽  
Gene Expression Dynamics

Carefully coordinated interaction between the endometrium and embryo is critical for the establishment and maintenance of pregnancy in mammals. By exploring the gene expression dynamics of this tissue during preimplantation development, we may be able to get insight into the genetic mechanisms of reproduction during early pregnancy. Here, we have performed comparative transcriptome profiling of the endometrium in response to spherical (Day 7 to Day 12) and elongated (Day 13 to Day 17) embryos in Finnsheep, Texel and their F1 crosses using RNA sequencing (RNA-seq) approach. A total of 21125 genes were expressed in our dataset of which 554 were significantly (absolute log2 fold change > 2.5; adjusted p-value < 0.01) upregulated in the endometrium with elongated embryos. Highly abundant autosomal genes in the endometrium were associated with biological processes such as facilitation of maternal recognition of pregnancy, trophoblast elongation and implantation (LGALS15, CST3, CST6, and EEF1A1). Several endogenous retroviruses (ERVs) including a novel ERV gene located in a reduced FecL locus potentially associated with sheep prolificacy were expressed in our dataset. Comparative transcriptome profiling of the endometrium having spherical and elongated embryos revealed distinct gene expression patterns. Genes that were upregulated in response to elongated embryos indicated the importance of immune system at the maternal-embryo interface prior to implantation.

scholarly journals Combined Metabolome and Transcriptome Profiling Reveal Optimal Harvest Strategy Model Based on Different Production Purposes in Olive

Foods ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 360
Author(s):  
Guodong Rao ◽  
Jianguo Zhang ◽  
Xiaoxia Liu ◽  
Xue Li ◽  
Chenhe Wang
Keyword(s):  
Gene Expression ◽  
Olive Oil ◽  
Expression Patterns ◽  
Transcriptome Profiling ◽  
Minor Components ◽  
Harvest Time ◽  
Rna Seq ◽  
Optimal Harvest ◽  
Harvest Strategy ◽  
Different Color

Olive oil has been favored as high-quality edible oil because it contains balanced fatty acids (FAs) and high levels of minor components. The contents of FAs and minor components are variable in olive fruits of different color at harvest time, which render it difficult to determine the optimal harvest strategy for olive oil producing. Here, we combined metabolome, Pacbio Iso-seq, and Illumina RNA-seq transcriptome to investigate the association between metabolites and gene expression of olive fruits at harvest time. A total of 34 FAs, 12 minor components, and 181 other metabolites (including organic acids, polyols, amino acids, and sugars) were identified in this study. Moreover, we proposed optimal olive harvesting strategy models based on different production purposes. In addition, we used the combined Pacbio Iso-seq and Illumina RNA-seq gene expression data to identify genes related to the biosynthetic pathways of hydroxytyrosol and oleuropein. These data lay the foundation for future investigations of olive fruit metabolism and gene expression patterns, and provide a method to obtain olive harvesting strategies for different production purposes.

scholarly journals Host Gene Regulation by Transposable Elements: The New, the Old and the Ugly

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1089 ◽  
Author(s):  
Rocio Enriquez-Gasca ◽  
Poppy A. Gould ◽  
Helen M. Rowe
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Transposable Elements ◽  
Essential Gene ◽  
Expression Patterns ◽  
Genetic Material ◽  
Endogenous Retroviruses ◽  
Host Gene ◽  
New Genes ◽  
Host Genes

The human genome has been under selective pressure to evolve in response to emerging pathogens and other environmental challenges. Genome evolution includes the acquisition of new genes or new isoforms of genes and changes to gene expression patterns. One source of genome innovation is from transposable elements (TEs), which carry their own promoters, enhancers and open reading frames and can act as ‘controlling elements’ for our own genes. TEs include LINE-1 elements, which can retrotranspose intracellularly and endogenous retroviruses (ERVs) that represent remnants of past retroviral germline infections. Although once pathogens, ERVs also represent an enticing source of incoming genetic material that the host can then repurpose. ERVs and other TEs have coevolved with host genes for millions of years, which has allowed them to become embedded within essential gene expression programmes. Intriguingly, these host genes are often subject to the same epigenetic control mechanisms that evolved to combat the TEs that now regulate them. Here, we illustrate the breadth of host gene regulation through TEs by focusing on examples of young (The New), ancient (The Old), and disease-causing (The Ugly) TE integrants.

scholarly journals Transcriptome Profiling across Five Tissues of Giant Panda

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Feng Li ◽  
Chengdong Wang ◽  
Zhongxian Xu ◽  
Mingzhou Li ◽  
Linhua Deng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Giant Panda ◽  
Expression Patterns ◽  
Genetic Research ◽  
Gene Expression Pattern ◽  
Transcriptome Profiling ◽  
Ailuropoda Melanoleuca ◽  
Ppi Network ◽  
Illumina Hiseq ◽  
Lung And Kidney

Gene differential expression studies can serve to explore and understand the laws and characteristics of animal life activities, and the difference in gene expression between different animal tissues has been well demonstrated and studied. However, for the world-famous rare and protected species giant panda (Ailuropoda melanoleuca), only the transcriptome of the blood and spleen has been reported separately. Here, in order to explore the transcriptome differences between the different tissues of the giant panda, transcriptome profiles of the heart, liver, spleen, lung, and kidney from five captive giant pandas were constructed with Illumina HiSeq 2500 platform. The comparative analysis of the intertissue gene expression patterns was carried out based on the generated RNA sequencing datasets. Analyses of Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network were performed according to the identified differentially expressed genes (DEGs). We generated 194.52 GB clean base data from twenty-five sequencing libraries and identified 18,701 genes, including 3492 novel genes. With corrected p value <0.05 and |log2FoldChange| >2, we finally obtained 921, 553, 574, 457, and 638 tissue-specific DEGs in the heart, liver, spleen, lung, and kidney, respectively. In addition, we identified TTN, CAV3, LDB3, TRDN, and ACTN2 in the heart; FGA, AHSG, and SERPINC1 in the liver; CD19, CD79B, and IL21R in the spleen; NKX2-4 and SFTPB in the lung; GC and HRG in the kidney as hub genes in the PPI network. The results of the analyses showed a similar gene expression pattern between the spleen and lung. This study provided for the first time the heart, liver, lung, and kidney’s transcriptome resources of the giant panda, and it provided a valuable resource for further genetic research or other potential research.

scholarly journals What can we learn from gene expression profiling of mouse oocytes?

Reproduction ◽  
2008 ◽  
Vol 135 (5) ◽  
pp. 581-592 ◽  
Author(s):  
Toshio Hamatani ◽  
Mitsutoshi Yamada ◽  
Hidenori Akutsu ◽  
Naoaki Kuji ◽  
Yoshiyuki Mochimaru ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Oocyte Quality ◽  
Preimplantation Development ◽  
Preimplantation Embryos ◽  
Gene Expressions ◽  
Oocyte Competence

Mammalian ooplasm supports the preimplantation development and reprograms the introduced nucleus transferred from a somatic cell to confer pluripotency in a cloning experiment. However, the underlying molecular mechanisms of oocyte competence remain unknown. Recent advances in microarray technologies have allowed gene expression profiling of such tiny specimens as oocytes and preimplantation embryos, generating a flood of information about gene expressions. So, what can we learn from it? Here, we review the initiative global gene expression studies of mouse and/or human oocytes, focusing on the lists of maternal transcripts and their expression patterns during oogenesis and preimplantation development. Especially, the genes expressed exclusively in oocytes should contribute to the uniqueness of oocyte competence, driving mammalian development systems of oocytes and preimplantation embryos. Furthermore, we discuss future directions for oocyte gene expression profiling, including discovering biomarkers of oocyte quality and exploiting the microarray data for ‘making oocytes’.

scholarly journals Aberrant Whole Blood Gene Expression in the Lumen of Human Intracranial Aneurysms

Diagnostics ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1442
Author(s):  
Vincent M. Tutino ◽  
Yongjun Lu ◽  
Daizo Ishii ◽  
Kerry E. Poppenberg ◽  
Hamidreza Rajabzadeh-Oghaz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Whole Blood ◽  
Quantitative Polymerase Chain Reaction ◽  
Expression Patterns ◽  
Transcriptome Profiling ◽  
Circulating Biomarkers ◽  
Post Contrast ◽  
Blood Gene Expression ◽  
Transcriptional Changes ◽  
Polymerase Chain

The rupture of an intracranial aneurysm (IA) causes devastating hemorrhagic strokes. Yet, most IAs remain asymptomatic and undetected until they rupture. In the search for circulating biomarkers of unruptured IAs, we previously performed transcriptome profiling on whole blood and identified an IA-associated panel of 18 genes. In this study, we seek to determine if these genes are also differentially expressed within the IA lumen, which could provide a mechanistic link between the disease and the observed circulating gene expression patterns. To this end, we collected blood from the lumen of 37 IAs and their proximal parent vessels in 31 patients. The expression levels of 18 genes in the lumen and proximal vessel were then measured by quantitative polymerase chain reaction. This analysis revealed that the expression of 6/18 genes (CBWD6, MT2A, MZT2B, PIM3, SLC37A3, and TNFRSF4) was significantly higher in intraluminal blood, while the expression of 3/18 genes (ST6GALNAC1, TCN2, and UFSP1) was significantly lower. There was a significant, positive correlation between intraluminal and proximal expression of CXCL10, MT2A, and MZT2B, suggesting local increases of these genes is reflected in the periphery. Expression of ST6GALNAC1 and TIFAB was significantly positively correlated with IA size, while expression of CCDC85B was significantly positively correlated with IA enhancement on post-contrast MRI, a metric of IA instability and risk. In conclusion, intraluminal expression differences in half of the IA-associated genes observed in this study provide evidence for IA tissue-mediated transcriptional changes in whole blood. Additionally, some genes may be informative in assessing IA risk, as their intraluminal expression was correlated to IA size and aneurysmal wall enhancement.

scholarly journals The Potential Role of Genetic Assimilation during Maize Domestication

2017 ◽  
Author(s):  
Anne Lorant ◽  
Sarah Pedersen ◽  
Irene Holst ◽  
Matthew B. Hufford ◽  
Klaus Winter ◽  
...  
Keyword(s):  
Gene Expression ◽  
Zea Mays ◽  
Potential Role ◽  
Expression Patterns ◽  
Genetic Assimilation ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Mechanisms ◽  
Maize Domestication

ABSTRACTDomestication research has largely focused on identification of morphological and genetic differences between extant populations of crops and their wild relatives. Little attention has been paid to the potential effects of environment despite substantial known changes in climate from the time of domestication to modern day. Recent research, in which maize and teosinte (i.e., wild maize) were exposed to environments similar to the time of domestication, resulted in a plastic induction of domesticated phenotypes in teosinte and little response to environment in maize. These results suggest that early agriculturalists may have selected for genetic mechanisms that cemented domestication phenotypes initially induced by a plastic response of teosinte to environment, a process known as genetic assimilation. To better understand this phenomenon and the potential role of environment in maize domestication, we examined differential gene expression in maize (Zea mays ssp. mays) and teosinte (Zea mays ssp. parviglumis) between past and present conditions. We identified a gene set of over 2000 loci showing a change in expression across environmental conditions in teosinte and invariance in maize. In fact, overall we observed both greater plasticity in gene expression and more substantial re-wiring of expression networks in teosinte across environments when compared to maize. While these results suggest genetic assimilation played at least some role in domestication, genes showing expression patterns consistent with assimilation are not significantly enriched for previously identified domestication candidates, indicating assimilation did not have a genome-wide effect.

scholarly journals Evaluating Alteration of Blood Transcriptome Affected by Storage Conditions Using RNA Sequencing

2020 ◽  
Author(s):  
Eun Jung Koh ◽  
So Yeon Yu ◽  
Seung Jun Kim ◽  
Eun-Il Lee ◽  
Seung Yong Hwang
Keyword(s):  
Gene Expression ◽  
Rna Sequencing ◽  
Whole Blood ◽  
Expression Patterns ◽  
Rna Degradation ◽  
Biological Research ◽  
P Value ◽  
Sample Handling ◽  
Rna Quality

Abstract BackgroundWhole blood is one of the most widely utilized human samples in biological research and is useful for analysing the mechanisms of diverse bio-molecular phenomena. However, owing to its fluidic properties, whole blood is relatively unstable in the frozen state compared to other biopsy samples. Because RNA is structurally unstable, sample damage can severely affect RNA quality, thereby reducing its usability. This study aimed to assess the quality of RNA prepared from blood stored at different temperatures and times prior to freezing, as well as the effect of freezer storage time. ResultsThe quality of the RNA derived from different blood samples was assessed by determining the RNA integrity number and RNA sequencing to identify genes (|fold-change (FC)| > 1.5, p-value < 0.05, false discovery rate (FDR) < 0.05) that were differentially expressed between the differently prepared RNA samples. We found that improper sample handling critically influenced both RNA quality and gene expression patterns. In particular, storing blood at room temperature over 12 h before freezing led to RNA degradation. Differential gene expression analysis revealed that expression of the CXCR1 gene was substantially reduced when using impaired RNA. ConclusionsThis study emphasizes the importance of proper sample management for obtaining reliable downstream application outcomes and suggests the CXCR1 gene as a candidate screening marker for RNA damage caused by improper sample handling.

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