scholarly journals Nucleotide modifications in messenger RNA and their role in development and disease

2016 ◽  
Vol 44 (5) ◽  
pp. 1385-1393 ◽  
Author(s):  
Veronica Dezi ◽  
Chavdar Ivanov ◽  
Irmgard U. Haussmann ◽  
Matthias Soller
Keyword(s):  
High Throughput ◽  
Messenger Rna ◽  
Reverse Genetics ◽  
High Throughput Sequencing ◽  
Modified Nucleotides ◽  
Genes Encoding ◽  
Dynamic Landscape ◽  
Over 40 Years

Modified nucleotides in messenger RNA (mRNA) have been discovered over 40 years ago, but until recently little was known about which transcripts contain them and what their function is. High-throughput sequencing approaches revealed a dynamic landscape of the ‘Epitranscriptome’ for many mRNA modifications in various organisms from yeast to humans. Meanwhile, also many genes encoding mRNA-modifying enzymes and auxiliary proteins have been identified yielding functional insights by reverse genetics into their role in development and disease.

scholarly journals Reverse Genetics and High Throughput Sequencing Methodologies for Plant Functional Genomics

2016 ◽  
Vol 17 (6) ◽  
pp. 460-475 ◽  
Author(s):  
Anis Ben-Amar ◽  
Samia Daldoul ◽  
Götz M. Reustle ◽  
Gabriele Krczal ◽  
Ahmed Mliki
Keyword(s):  
Functional Genomics ◽  
High Throughput ◽  
Reverse Genetics ◽  
High Throughput Sequencing

scholarly journals Detection of novel allelic variations in soybean mutant population using Tilling by Sequencing

2019 ◽  
Author(s):  
Reneth Millas ◽  
Mary Espina ◽  
CM Sabbir Ahmed ◽  
Angelina Bernardini ◽  
Ekundayo Adeleke ◽  
...  
Keyword(s):  
Fatty Acid ◽  
High Throughput ◽  
Reverse Genetics ◽  
High Throughput Sequencing ◽  
Fatty Acid Biosynthesis ◽  
Induced Mutations ◽  
Mutant Population ◽  
Sequencing Technologies ◽  
Allelic Variations ◽  
Tilling By Sequencing

ABSTRACTOne of the most important tools in genetic improvement is mutagenesis, which is a useful tool to induce genetic and phenotypic variation for trait improvement and discovery of novel genes. JTN-5203 (MG V) mutant population was generated using an induced ethyl methane sulfonate (EMS) mutagenesis and was used for detection of induced mutations in FAD2-1A and FAD2-1B genes using reverse genetics approach. Optimum concentration of EMS was used to treat 15,000 bulk JTN-5203 seeds producing 1,820 M2 population. DNA was extracted, normalized, and pooled from these individuals. Specific primers were designed from FAD2-1A and FAD2-1B genes that are involved in the fatty acid biosynthesis pathway for further analysis using next-generation sequencing. High throughput mutation discovery through TILLING-by-Sequencing approach was used to detect novel allelic variations in this population. Several mutations and allelic variations with high impacts were detected for FAD2-1A and FAD2-1B. This includes GC to AT transition mutations in FAD2-1A (20%) and FAD2-1B (69%). Mutation density for this population is estimated to be about 1/136kb. Through mutagenesis and high-throughput sequencing technologies, novel alleles underlying the mutations observed in mutants with reduced polyunsaturated fatty acids will be identified, and these mutants can be further used in breeding soybean lines with improved fatty acid profile, thereby developing heart-healthy-soybeans.

scholarly journals Small RNA Expression Profiling by High-Throughput Sequencing: Implications of Enzymatic Manipulation

2012 ◽  
Vol 2012 ◽  
pp. 1-15 ◽  
Author(s):  
Fanglei Zhuang ◽  
Ryan T. Fuchs ◽  
G. Brett Robb
Keyword(s):  
High Throughput ◽  
Expression Profiling ◽  
Messenger Rna ◽  
High Throughput Sequencing ◽  
Biological Processes ◽  
Cellular Processes ◽  
Disease States ◽  
Powerful Approach ◽  
Sequencing Library ◽  
Rna Expression Profiling

Eukaryotic regulatory small RNAs (sRNAs) play significant roles in many fundamental cellular processes. As such, they have emerged as useful biomarkers for diseases and cell differentiation states. sRNA-based biomarkers outperform traditional messenger RNA-based biomarkers by testing fewer targets with greater accuracy and providing earlier detection for disease states. Therefore, expression profiling of sRNAs is fundamentally important to further advance the understanding of biological processes, as well as diagnosis and treatment of diseases. High-throughput sequencing (HTS) is a powerful approach for both sRNA discovery and expression profiling. Here, we discuss the general considerations for sRNA-based HTS profiling methods from RNA preparation to sequencing library construction, with a focus on the causes of systematic error. By examining the enzymatic manipulation steps of sRNA expression profiling, this paper aims to demystify current HTS-based sRNA profiling approaches and to aid researchers in the informed design and interpretation of profiling experiments.

scholarly journals PCR Primers to Study the Diversity of Expressed Fungal Genes Encoding Lignocellulolytic Enzymes in Soils Using High-Throughput Sequencing

PLoS ONE ◽  
2014 ◽  
Vol 9 (12) ◽  
pp. e116264 ◽  
Author(s):  
Florian Barbi ◽  
Claudia Bragalini ◽  
Laurent Vallon ◽  
Elsa Prudent ◽  
Audrey Dubost ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Pcr Primers ◽  
Lignocellulolytic Enzymes ◽  
Genes Encoding ◽  
Fungal Genes

Exosomal hsa-miR-129-2 and hsa-miR-889 from a 6-microRNA signature might be a potential biomarker for predicting prognosis of papillary thyroid carcinoma

2021 ◽  
Vol 24 ◽  
Author(s):  
Ying Xin ◽  
Kexin Meng ◽  
Haiwei Guo ◽  
Bin Chen ◽  
Chuanming Zheng ◽  
...  
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
High Throughput ◽  
Messenger Rna ◽  
High Throughput Sequencing ◽  
The Cancer Genome Atlas ◽  
Papillary Thyroid ◽  
Control Groups ◽  
Potential Biomarker ◽  
And Control

Background: Papillary thyroid carcinoma (PTC) is a subtype of thyroid cancer with increasing incidence over time. Objective: This study aimed to build a risk score (RS) system for PTC patients. Methods: PTC microRNA (miRNA) and messenger RNA (mRNA) expression data were extracted from The Cancer Genome Atlas (TCGA) database. The 491 PTC samples were randomly divided into training and validation sets. Using the limma software package, differentially expressed mRNAs (DEGs) and miRNAs (DEMs) between the tumor and control groups were screened. In order to construct an RS system, a survival package was used to select independent miRNAs related to prognosis. Enrichment analysis was performed, and a miRNA-mRNA co-expression network was constructed. High-throughput sequencing was also used to verify the prognostic miRNAs in exosomes. Results: We found 1363 DEGs and 171 DEMs between the tumor and control groups. After identifying 26 DEMs that were significantly related to prognosis, 6 independent prognosis-associated miRNAs were selected to build an RS system. The areas under the curves of the overall survival rates of the training, validation, and entire sets were 0.847, 0.772, and 0.819, respectively. By conducting pathway analysis using the miRNA-mRNA co-expression network, one overlapping factor and five overlapping pathways were obtained. In addition, high-throughput sequencing revealed that the hsa-miR-129-2, hsa-miR-548j, hsa-miR-6734, and hsa-miR-889 expression levels in TCGA tumor tissues and exosomes were consistent, and those of hsa-miR-129-2 and hsa-miR-889 between patients and controls were significantly different in exosomes. Conclusion: The six-miRNA RS system in exosomes may comprise independent signatures for predicting PTC patient prognosis.

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