Bovine Genome Database: new tools for gleaning function from the<i>Bos taurus</i>genome

Elsik, Christine G.; Unni, Deepak; Diesh, Colin; Tayal, Aditi; Emery, Marianne L.; Nguyen, Hung N.; Hagen, Darren E.

doi:10.1093/nar/gkv1077

Cited by 96 publications

(83 citation statements)

References 49 publications

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“…For exosomal RNAs, 91.8% to 99.4% of the mates had no hits to the database and only a few had a hit with two or less mismatches (Table S1). Next, all back-splicing mates were mapped to the bovine genome34 both linearly and using the back-splicing detection algorithm. The linear mapping percentages were close to 0 for all samples, and no more than 2.2% of the back-splicing mates could be back-splicing-mapped to the bovine genome (Table S2).…”

Section: Resultsmentioning

confidence: 99%

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Circular RNAs are down-regulated in KRAS mutant colon cancer cells and can be transferred to exosomes

Dou

Diana

Franklin

et al. 2016

Sci Rep

284

240

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Recent studies have shown that circular RNAs (circRNAs) are abundant, widely expressed in mammals, and can display cell-type specific expression. However, how production of circRNAs is regulated and their precise biological function remains largely unknown. To study how circRNAs might be regulated during colorectal cancer progression, we used three isogenic colon cancer cell lines that differ only in KRAS mutation status. Cellular RNAs from the parental DLD-1 cells that contain both wild-type and G13D mutant KRAS alleles and isogenically-matched derivative cell lines, DKO-1 (mutant KRAS allele only) and DKs-8 (wild-type KRAS allele only) were analyzed using RNA-Seq. We developed a bioinformatics pipeline to identify and evaluate circRNA candidates from RNA-Seq data. Hundreds of high-quality circRNA candidates were identified in each cell line. Remarkably, circRNAs were significantly down-regulated at a global level in DLD-1 and DKO-1 cells compared to DKs-8 cells, indicating a widespread effect of mutant KRAS on circRNA abundance. This finding was confirmed in two independent colon cancer cell lines HCT116 (KRAS mutant) and HKe3 (KRAS WT). In all three cell lines, circRNAs were also found in secreted extracellular-vesicles, and circRNAs were more abundant in exosomes than cells. Our results suggest that circRNAs may serve as promising cancer biomarkers.

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Section: Resultsmentioning

confidence: 99%

“…All back-splicing mates were blasted48 (ncbi-blast-2.3.0+) against the database with default parameters. Next, back-splicing mates were linearly mapped to the bovine genome34 by Tophat2 (version 2.0.12) with up to 2 mismatches49. Moreover, these mates were mapped to the bovine genome using the back-splicing detection algorithm described above.…”

Section: Methodsmentioning

confidence: 99%

Circular RNAs are down-regulated in KRAS mutant colon cancer cells and can be transferred to exosomes

Dou

Diana

Franklin

et al. 2016

Sci Rep

284

240

View full text Add to dashboard Cite

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“…Raw sequencing data (publicly available on the GEO database accession GSE83509, [27]) were analysed using the sRNAbench 1.0 tool [28, 29]. Briefly, the software was run in genome mode using default settings, with the bovine genome (bosTau4) and miRBase 21 (accessed on 30 April 2015) [30, 31] as reference in order to identify bovine miRNAs (bta-miR) and human miRNA homologues (hsa-miR). A single nucleotide mismatch was allowed when mapping raw reads to known miRNA sequences and reads without sequencing adaptor, with undetermined bases and reads below 15 nucleotides (nt) in length being automatically removed from the analysis.…”

Section: Methodsmentioning

confidence: 99%

Changes in circulating microRNA levels can be identified as early as day 8 of pregnancy in cattle

Ioannidis

Donadeu

2017

PLoS ONE

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Poor reproductive performance remains a major issue in the dairy industry, with low conception rates having a significant impact on milk production through extended calving intervals. A major limiting factor is the lack of reliable methods for early pregnancy diagnosis. Identification of animals within a herd that fail to conceive within 3 weeks after insemination would allow early re-insemination and shorten calving intervals. In a previous study, we found an increase in plasma miR-26a levels in Day 16-pregnant relative to non-pregnant heifers, however changes in miRNA levels that early during pregnancy were very small which likely prevented the identification of robust biomarkers. In this study, we extended our analyses to a wider interval during pregnancy (Days 8 to 60, n = 11 heifers) with the rationale that this may facilitate the identification of additional early pregnancy miRNA biomarkers. Using small RNA sequencing we identified a total of 77 miRNAs that were differentially expressed on Day 60 relative to Day 0 of pregnancy. We selected 14 miRNAs for validation by RT-qPCR and confirmed significant differences in the expression of let-7f, let-7c, miR-30c, miR-101, miR-26a, miR-205 and miR-143 between Days 0 and 60. RT-qPCR profiling throughout Days 0, 8, 16 and 60 of pregnancy showed a distinct increase in circulating levels of miR-26a (3.1-fold, P = 0.046) as early as Day 8 of pregnancy. In summary, in contrast to earlier stages of pregnancy (≤ Day 24), marked differences in the levels of multiple miRNAs can be detected in circulation by Day 60 in cattle. Retrospective analyses showed miR-26a levels to be increased in circulation as early as Day 8, sooner than previously reported in any species, suggesting a biological role for this miRNA in the very early events of pregnancy.

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“…Candidate genes identified from SNP concordance analyses, GWAS, and homozygosity mapping were uploaded to the BovineMine warehouse47 to compare the list of candidate genes with the list of bovine genes associated with the GO term “hindlimb morphogenesis” (GO: 0035137). Network analyses were performed on the set of candidate genes associated with the GO term “hindlimb morphogenesis” and all candidate genes identified from GWAS using GeneMANIA48.…”

Section: Methodsmentioning

confidence: 99%

Elucidating the genetic basis of an oligogenic birth defect using whole genome sequence data in a non-model organism, Bubalus bubalis

Whitacre

Hoff

Schnabel

et al. 2017

Sci Rep

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Recent strong selection for dairy traits in water buffalo has been associated with higher levels of inbreeding, leading to an increase in the prevalence of genetic diseases such as transverse hemimelia (TH), a congenital developmental abnormality characterized by absence of a variable distal portion of the hindlimbs. Limited genomic resources available for water buffalo required an original approach to identify genetic variants associated with the disease. The genomes of 4 bilateral and 7 unilateral affected cases and 14 controls were sequenced. A concordance analysis of SNPs and INDELs requiring homozygosity unique to all unilateral and bilateral cases revealed two genes, WNT7A and SMARCA4, known to play a role in embryonic hindlimb development. Additionally, SNP alleles in NOTCH1 and RARB were homozygous exclusively in the bilateral cases, suggesting an oligogenic mode of inheritance. Homozygosity mapping by whole genome de novo assembly also supported oligogenic inheritance; implicating 13 genes involved in hindlimb development in bilateral cases and 11 in unilateral cases. A genome-wide association study (GWAS) predicted additional modifier genes. Although our data show a complex inheritance of TH, we predict that homozygous variants in WNT7A and SMARCA4 are necessary for expression of TH and selection against these variants should eradicate TH.

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Bovine Genome Database: new tools for gleaning function from theBos taurusgenome

Cited by 96 publications

References 49 publications

Circular RNAs are down-regulated in KRAS mutant colon cancer cells and can be transferred to exosomes

Circular RNAs are down-regulated in KRAS mutant colon cancer cells and can be transferred to exosomes

Changes in circulating microRNA levels can be identified as early as day 8 of pregnancy in cattle

Elucidating the genetic basis of an oligogenic birth defect using whole genome sequence data in a non-model organism, Bubalus bubalis

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