scholarly journals Role of SNPs in the Biogenesis of Mature miRNAs

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Ying Wang ◽  
Jidong Ru ◽  
Xianglian Meng ◽  
Jianhua Song ◽  
Qingfeng Jiang ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Mature Mirnas ◽  
Mirna Biogenesis ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Sequence Alignments ◽  
Whole Genome Analysis ◽  
Functional Snps ◽  
Mirna Sequencing

Single nucleotide polymorphisms (SNPs) play a significant role in microRNA (miRNA) generation, processing, and function and contribute to multiple phenotypes and diseases. Therefore, whole-genome analysis of how SNPs affect miRNA maturation mechanisms is important for precision medicine. The present study established an SNP-associated pre-miRNA (SNP-pre-miRNA) database, named miRSNPBase, and constructed SNP-pre-miRNA sequences. We also identified phenotypes and disease biomarker-associated isoform miRNA (isomiR) based on miRFind, which was developed in our previous study. We identified functional SNPs and isomiRs. We analyzed the biological characteristics of functional SNPs and isomiRs and studied their distribution in different ethnic groups using whole-genome analysis. Notably, we used individuals from Great Britain (GBR) as examples and identified isomiRs and isomiR-associated SNPs (iso-SNPs). We performed sequence alignments of isomiRs and miRNA sequencing data to verify the identified isomiRs and further revealed GBR ethnographic epigenetic dominant biomarkers. The SNP-pre-miRNA database consisted of 886 pre-miRNAs and 2640 SNPs. We analyzed the effects of SNP type, SNP location, and SNP-mediated free energy change during mature miRNA biogenesis and found that these factors were closely associated to mature miRNA biogenesis. Remarkably, 158 isomiRs were verified in the miRNA sequencing data for the 18 GBR samples. Our results indicated that SNPs affected the mature miRNA processing mechanism and contributed to the production of isomiRs. This mechanism may have important significance for epigenetic changes and diseases.

scholarly journals Role of SNPs in the biogenesis of mature miRNAs

2020 ◽  
Author(s):  
Ying Wang ◽  
Jidong Ru ◽  
Meng Xianglian
Keyword(s):  
Molecular Mechanisms ◽  
Mature Mirnas ◽  
Mirna Biogenesis ◽  
Sequencing Data ◽  
Whole Genome Analysis ◽  
Association Analyses ◽  
Genome Wide ◽  
Mirna Sequencing ◽  
And Function

Abstract BackgroundSNPs within pre-miRNA regions play a significant role in miRNA generation, processing and function by different molecular mechanisms and are thought to be major contributors to the variations in phenotypes and diseases. Therefore, whole-genome analysis of how SNPs affect mature miRNA biogenesis is important for precision medicine. ResultsIn this study, aiming to analyze the role of SNPs in mature miRNA biogenesis genome-wide, we constructed a SNP-pre-miRNA database, named miRSNPBase, consisting of 886 pre-miRNAs and 2640 SNPs based on the latest data. Then, we identified 10574 SNP-pre-miRNAs based on 886 pre-miRNAs and their associated 2640 SNPs, and we performed genome-wide association analyses to identify isoform miRNAs (isomiRs) based on miRFind that are associated with the mechanism of SNPs affecting miRNA maturation. A total of 4235 nor-SNP-pre-miRNAs based on 480 nor-pre-miRNAs and 1250 nor-SNPs were identified. We analyzed the effects of SNP type, SNP location and SNP-mediated free energy change during mature miRNA biogenesis and found that they are closely related to mature miRNA biogenesis. In addition, the MAF distribution of the iso-pre-miRNAs and nor-SNPs was analyzed based on the 1000 Genomes Project. The results demonstrated that individuals who contained the iso-SNPs were in the minority, and those who contained the nor-SNPs were in the majority. Notably, to verify our method and identify important biomarkers, we identified isomiRs and iso-SNPs in 18 GBR individuals of European origin. In the results, 209 iso-pre-miRNA candidates and 71 verified iso-pre-miRNAs of the 18 GBR samples were identified, and 2667 isomiRs of 209 pre-miRNAs were verified by miRNA sequencing data.ConclusionsOur results clearly indicated that SNPs that altered the mature miRNA splicing mechanism and led to the production of isomiRs, were closely related to and affected normal life processes, and led to epigenetic changes and diseases.

scholarly journals An Approach to Identify Individual Functional Single Nucleotide Polymorphisms and Isoform MicroRNAs

2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Ying Wang ◽  
Jidong Ru ◽  
Tao Jin ◽  
Ming Sun ◽  
Lizhu Jia ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Single Nucleotide Polymorphisms ◽  
Disease Risk ◽  
Software Tool ◽  
Mature Mirnas ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
1000 Genomes ◽  
Mirna Sequencing

MicroRNAs (miRNAs) and single nucleotide polymorphisms (SNPs) play important roles in disease risk and development, especially cancer. Importantly, when SNPs are located in pre-miRNAs, they affect their splicing mechanism and change the function of miRNAs. To improve disease risk assessment, we propose an approach and developed a software tool, IsomiR_Find, to identify disease/phenotype-related SNPs and isomiRs in individuals. Our approach is based on the individual’s samples, with SNP information extracted from the 1000 Genomes Project. SNPs were mapped to pre-miRNAs based on whole-genome coordinates and then SNP-pre-miRNA sequences were constructed. Moreover, we developed matpred2, a software tool to identify the four splicing sites of mature miRNAs. Using matpred2, we identified isomiRs and then verified them by searching within individual miRNA sequencing data. Our approach yielded biomarkers for biological experiments, mined functions of miRNAs and SNPs, improved disease risk assessment, and provided a way to achieve individualized precision medicine.

scholarly journals Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562

2017 ◽  
Author(s):  
Bo Zhou ◽  
Steve S. Ho ◽  
Stephanie U. Greer ◽  
Xiaowei Zhu ◽  
John M. Bell ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Genome Analysis ◽  
Large Scale ◽  
Wide Spectrum ◽  
Whole Genome ◽  
Sequencing Data ◽  
Whole Genome Analysis ◽  
Multiple Allele ◽  
Specific Expression ◽  
Allele Specific

ABSTRACTK562 is widely used in biomedical research. It is one of three tier-one cell lines of ENCODE and also most commonly used for large-scale CRISPR/Cas9 screens. Although its functional genomic and epigenomic characteristics have been extensively studied, its genome sequence and genomic structural features have never been comprehensively analyzed. Such information is essential for the correct interpretation and understanding of the vast troves of existing functional genomics and epigenomics data for K562. We performed and integrated deep-coverage whole-genome (short-insert), mate-pair, and linked-read sequencing as well as karyotyping and array CGH analysis to identify a wide spectrum of genome characteristics in K562: copy numbers (CN) of aneuploid chromosome segments at high-resolution, SNVs and Indels (both corrected for CN in aneuploid regions), loss of heterozygosity, mega-base-scale phased haplotypes often spanning entire chromosome arms, structural variants (SVs) including small and large-scale complex SVs and non-reference retrotransposon insertions. Many SVs were phased, assembled, and experimentally validated. We identified multiple allele-specific deletions and duplications within the tumor suppressor geneFHIT. Taking aneuploidy into account, we re-analyzed K562 RNA-seq and whole-genome bisulfite sequencing data for allele-specific expression and allele-specific DNA methylation. We also show examples of how deeper insights into regulatory complexity are gained by integrating genomic variant information and structural context with functional genomics and epigenomics data. Furthermore, using K562 haplotype information, we produced an allele-specific CRISPR targeting map. This comprehensive whole-genome analysis serves as a resource for future studies that utilize K562 as well as a framework for the analysis of other cancer genomes.

scholarly journals Population Genomics of American Mink Using Whole Genome Sequencing Data

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 258
Author(s):  
Karim Karimi ◽  
Duy Ngoc Do ◽  
Mehdi Sargolzaei ◽  
Younes Miar
Keyword(s):  
Population Genomics ◽  
Association Studies ◽  
American Mink ◽  
Population History ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Effective Population ◽  
Cross Validation Error

Characterizing the genetic structure and population history can facilitate the development of genomic breeding strategies for the American mink. In this study, we used the whole genome sequences of 100 mink from the Canadian Centre for Fur Animal Research (CCFAR) at the Dalhousie Faculty of Agriculture (Truro, NS, Canada) and Millbank Fur Farm (Rockwood, ON, Canada) to investigate their population structure, genetic diversity and linkage disequilibrium (LD) patterns. Analysis of molecular variance (AMOVA) indicated that the variation among color-types was significant (p < 0.001) and accounted for 18% of the total variation. The admixture analysis revealed that assuming three ancestral populations (K = 3) provided the lowest cross-validation error (0.49). The effective population size (Ne) at five generations ago was estimated to be 99 and 50 for CCFAR and Millbank Fur Farm, respectively. The LD patterns revealed that the average r2 reduced to <0.2 at genomic distances of >20 kb and >100 kb in CCFAR and Millbank Fur Farm suggesting that the density of 120,000 and 24,000 single nucleotide polymorphisms (SNP) would provide the adequate accuracy of genomic evaluation in these populations, respectively. These results indicated that accounting for admixture is critical for designing the SNP panels for genotype-phenotype association studies of American mink.

scholarly journals Whole-genome analysis uncovers loss of blaZ associated to carriage isolates belonging to MRSA clone ST5-VI in Cape Verde

2021 ◽  
Author(s):  
Magdalena Wysocka ◽  
Tamar Monteiro ◽  
Carine de Pina ◽  
Deisy Gonçalves ◽  
Sandrine de Pina ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Cape Verde ◽  
Whole Genome ◽  
Whole Genome Analysis

Whole‐genome analysis identifying candidate genes of altitude adaptive ecological thresholds in yak populations

2019 ◽  
Vol 136 (5) ◽  
pp. 371-377 ◽  
Author(s):  
Guang‐Xin E ◽  
Wang‐Dui Basang ◽  
Yan‐Bin Zhu
Keyword(s):  
Candidate Genes ◽  
Genome Analysis ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Ecological Thresholds
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