scholarly journals The most common technologies and tools for functional genome analysis

2017 ◽  
Vol 24 (1) ◽  
pp. 1-11 ◽  
Author(s):  
Evelina Gasperskaja ◽  
Vaidutis Kučinskas
Keyword(s):  
Functional Analysis ◽  
Human Genome ◽  
Genome Analysis ◽  
Bioinformatic Analysis ◽  
Genome Wide ◽  
Polymerase Chain ◽  
Scientific Results ◽  
The Right ◽  
Generation Sequencing ◽  
Functional Genome

Since the  sequence of the  human genome is complete, the  main issue is how to understand the information written in the DNA sequence. Despite numerous genome-wide studies that have already been performed, the challenge to determine the function of genes, gene products, and also their interaction is still open. As changes in the human genome are highly likely to cause pathological conditions, functional analysis is vitally important for human health. For many years there have been a  variety of technologies and tools used in functional genome analysis. However, only in the  past decade there has been rapid revolutionizing progress and improvement in high-throughput methods, which are ranging from traditional real-time polymerase chain reaction to more complex systems, such as next-generation sequencing or mass spectrometry. Furthermore, not only laboratory investigation, but also accurate bioinformatic analysis is required for reliable scientific results. These methods give an opportunity for accurate and comprehensive functional analysis that involves various fields of studies: genomics, epigenomics, proteomics, and interactomics. This is essential for filling the  gaps in the  knowledge about dynamic biological processes at both cellular and organismal level. However, each method has both advantages and limitations that should be taken into account before choosing the right method for particular research in order to ensure successful study. For this reason, the present review paper aims to describe the most frequent and widely-used methods for the comprehensive functional analysis.

Endometrial Liquid Biopsy Provides a miRNA Roadmap of the Secretory Phase of the Human Endometrium

2019 ◽  
Vol 105 (3) ◽  
pp. 877-889 ◽  
Author(s):  
Alessia Grasso ◽  
Roser Navarro ◽  
Nuria Balaguer ◽  
Inmaculada Moreno ◽  
Pilar Alama ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Ribonucleic Acid ◽  
Liquid Biopsy ◽  
Bioinformatic Analysis ◽  
Endometrial Receptivity ◽  
Mirna Signature ◽  
Secretory Phase ◽  
Messenger Ribonucleic Acid ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Context Endometrial liquid biopsy (ELB) is a minimally invasive alternative for research and diagnosis in endometrial biology. Objective We sought to establish an endometrial micro ribonucleic acid (miRNA) roadmap based on ELB during the secretory phase of the menstrual cycle in both natural and hormonal replacement therapy (HRT) cycles. Design Human ELB samples (n = 58) were obtained from healthy ovum donors undergoing a natural and an HRT cycle consecutively. miRNA profiles were identified using next-generation sequencing (NGS). For functional analysis, messenger ribonucleic acid targets were chosen among those reported in the endometrial receptivity analysis. Results The human endometrial secretory phase is characterized by a dynamic miRNA secretion pattern that varies from the prereceptive to the receptive stages. No differences in miRNA profiles were found among natural versus HRT cycles in the same women, reinforcing the similarities in functional and clinical outcomes in natural versus medicated cycles. Bioinformatic analysis revealed 62 validated interactions and 81 predicted interactions of miRNAs differentially expressed in the HRT cycle. Annotation of these genes linked them to 51 different pathways involved in endometrial receptivity. Conclusion This NGS-based study describes the miRNA signature in human ELB during the secretory phase of natural and HRT cycles. A consistent endometrial miRNA signature was observed in the acquisition of endometrial receptivity. Interestingly, no significant differences in miRNA expression were found in natural versus HRT cycles reinforcing the functional clinical similarities between both approaches.

scholarly journals Genome-wide Identification and Expression Pattern Analysis of BRI1-EMS–suppressor Transcription Factors in Tomato under Abiotic Stresses

2018 ◽  
Vol 143 (1) ◽  
pp. 84-90 ◽  
Author(s):  
Yingmei Gao ◽  
Jingkang Hu ◽  
Tingting Zhao ◽  
Xiangyang Xu ◽  
Jingbin Jiang ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Expression Patterns ◽  
Bioinformatic Analysis ◽  
Functional Identification ◽  
Tomato Plants ◽  
Protein Motifs ◽  
Genome Wide ◽  
Polymerase Chain ◽  
Regulated Gene Expression ◽  
Insight Into

BRI1-EMS-suppressor 1 (BES1) is a transcription factor (TF) that functions as a master regulator of brassinosteroid (BR)-regulated gene expression. Here, we provide a complete overview of Solanum lycopersicum BES1 (SLB) genes, including phylogeny, gene structure, protein motifs, chromosome locations and expression characteristics. Through bioinformatic analysis, we compared the sequences of SLB genes, arabidopsis (Arabidopsis thaliana) genes, and chinese cabbage (Brassica pekinensis) genes. All of the gene sequences were divided into three groups by cluster analysis. SLB genes were mapped to the eight tomato (S. lycopersicum) chromosomes. Bioinformatic analysis showed that SLB genes shares similarities with the proteins from other plants, though different species exhibit specific features. The expression patterns of SLB genes in various tissues and under different abiotic conditions were analyzed by quantitative reverse transcription polymerase chain reaction. SLB genes were found to be induced by multiple stresses, particularly salt stress, indicating that SLB genes may have important roles in the response to unfavorable environmental changes. This study provides insight into the evolution of SLB genes and may aid in the further functional identification of BES1 proteins and the response of tomato plants to different stresses.

Functional Genome-wide Analysis: a Technical Review, Its Developments and Its Relevance to Cancer Research

2013 ◽  
Vol 7 (2) ◽  
pp. 157-166 ◽  
Author(s):  
James Powell ◽  
Mark Bennett ◽  
Raymond Waters ◽  
Nigel Skinner ◽  
Simon Reed
Keyword(s):  
Cancer Research ◽  
Genome Wide Analysis ◽  
Technical Review ◽  
Genome Wide ◽  
Functional Genome

scholarly journals Genome wide effects of oleic acid on cultured bovine granulosa cells: evidence for the activation of pathways favoring folliculo-luteal transition

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Vengala Rao Yenuganti ◽  
Dirk Koczan ◽  
Jens Vanselow
Keyword(s):  
Oleic Acid ◽  
Granulosa Cells ◽  
System Development ◽  
Circulatory System ◽  
Bioinformatic Analysis ◽  
Negative Energy ◽  
Tissue Remodelling ◽  
Gonadotropin Secretion ◽  
Genome Wide

Abstract Background Metabolic stress, as negative energy balance on one hand or obesity on the other hand can lead to increased levels of free fatty acids in the plasma and follicular fluid of animals and humans. In an earlier study, we showed that increased oleic acid (OA) concentrations affected the function of cultured bovine granulosa cells (GCs). Here, we focus on genome wide effects of increased OA concentrations. Results Our data showed that 413 genes were affected, of which 197 were down- and 216 up-regulated. Specifically, the expression of FSH-regulated functional key genes, CCND2, LHCGR, INHA and CYP19A1 and 17-β-estradiol (E2) production were reduced by OA treatment, whereas the expression of the fatty acid transporter CD36 was increased and the morphology of the cells was changed due to lipid droplet accumulation. Bioinformatic analysis revealed that associated pathways of the putative upstream regulators “FSH” and “Cg (choriogonadotropin)” were inhibited and activated, respectively. Down-regulated genes are over-represented in GO terms “reproductive structure/system development”, “ovulation cycle process”, and “(positive) regulation of gonadotropin secretion”, whereas up-regulated genes are involved in “circulatory system development”, “vasculature development”, “angiogenesis” or “extracellular matrix/structure organization”. Conclusions From these data we conclude that besides inhibiting GC functionality, increased OA levels seemingly promote angiogenesis and tissue remodelling, thus suggestively initiating a premature fulliculo-luteal transition. In vivo this may lead to impeded folliculogenesis and ovulation, and cause sub-fertility.

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