miRNAs are a class of small, single-stranded, non-coding RNAs that perform post-transcriptional repression of target genes by binding to 3＇ untranslated regions. Research has found that miRNAs involved in the regulat...miRNAs are a class of small, single-stranded, non-coding RNAs that perform post-transcriptional repression of target genes by binding to 3＇ untranslated regions. Research has found that miRNAs involved in the regulation of many metabolic processes. Here we uncovered that the beef quality of Angus cattle sharply diversified after acute stress. By performing miRNA microarray analysis, 13 miRNAs were significantly differentially expressed in stressed group compared to control group. Using a bioinformatics method, 135 protein-coding genes were predicted as the targets of significant differentially expressed miRNAs. Gene Ontology （GO） term and Ingenuity Pathway Analysis （IPA） mined that these target genes involved in some important pathways, which may have impact on meat quality and beef tenderness.展开更多
A resource that provides candidate transcription factor binding sites （TFBSs） does not currently exist for cattle. Such data is necessary, as predicted sites may serve as excellent starting locations for future omic...A resource that provides candidate transcription factor binding sites （TFBSs） does not currently exist for cattle. Such data is necessary, as predicted sites may serve as excellent starting locations for future omics studies to develop transcriptional regulation hypotheses. In order to generate this resource, we employed a phylogenetic footprinting approach--using sequence conservation across cattle, human and dog and position-specific scoring matrices to identify 379,333 putative TFBSs upstream of nearly 8000 Mammalian Gene Collection （MGC） annotated genes within the cattle genome. Comparisons of our predictions to known binding site loci within the PCKI, ACTA1 and G6PC promoter regions revealed 75% sensitivity for our method of discovery. Additionally, we intersected our predictions with known cattle SNP variants in dbSNP and on the lllumina BovineHD 770k and Bos 1 SNP chips, finding 7534, 444 and 346 overlaps, respectively. Due to our stringent filtering criteria, these results represent high quality predictions of putative TFBSs within the cattle genome. All binding site predictions are freely available at http：//bfgl. anri.barc.usda.gov/BovineTFBS/or http：//199.133.54.77/BovineTFBS.展开更多
A systematic phylogenetic footprinting approach was performed to identify conserved transcription factor binding sites （TFBSs） in mammalian promoter regions using human, mouse and rat sequence alignments. We found t...A systematic phylogenetic footprinting approach was performed to identify conserved transcription factor binding sites （TFBSs） in mammalian promoter regions using human, mouse and rat sequence alignments. We found that the score distributions of most binding site models did not follow the Gaussian distribution required by many statistical methods. Therefore, we performed an empirical test to establish the optimal threshold for each model. We gauged our computational predictions by comparing with previously known TFBSs in the PCK1 gene promoter of the cytosolic isoform of phosphoenolpyruvate carboxykinase, and achieved a sensitivity of 75% and a specificity of approximately 32% Almost all known sites overlapped with predicted sites, and several new putative TFBSs were also identified. We validated a predicted SP1 binding site in the control of PCK1 transcription using gel shift and reporter assays. Finally, we applied our computational approach to the prediction of putative TFBSs within the promoter regions of all available RefSeq genes. Our full set of TFBS predictions is freely available at http：//bfgl.anri.barc.usda.gov/tfbsConsSites.展开更多
基金supported by Maryland Agricultural Experiment Station and Jorgensen Endowment Funds
文摘miRNAs are a class of small, single-stranded, non-coding RNAs that perform post-transcriptional repression of target genes by binding to 3＇ untranslated regions. Research has found that miRNAs involved in the regulation of many metabolic processes. Here we uncovered that the beef quality of Angus cattle sharply diversified after acute stress. By performing miRNA microarray analysis, 13 miRNAs were significantly differentially expressed in stressed group compared to control group. Using a bioinformatics method, 135 protein-coding genes were predicted as the targets of significant differentially expressed miRNAs. Gene Ontology （GO） term and Ingenuity Pathway Analysis （IPA） mined that these target genes involved in some important pathways, which may have impact on meat quality and beef tenderness.
基金supported by the National Research Institute and the Agricultural and Food Research Initiative(Grant No. 2007-35205-17869 and 2011-67015-30183) from the United States Department of Agriculture Cooperative State Research, Education and Extension Service(now the National Institute of Food and Agriculture)Project form the US Department of Agriculture--Agricultural Research Service(ARS)(Grant No. 1265-31000-098-00)
文摘A resource that provides candidate transcription factor binding sites （TFBSs） does not currently exist for cattle. Such data is necessary, as predicted sites may serve as excellent starting locations for future omics studies to develop transcriptional regulation hypotheses. In order to generate this resource, we employed a phylogenetic footprinting approach--using sequence conservation across cattle, human and dog and position-specific scoring matrices to identify 379,333 putative TFBSs upstream of nearly 8000 Mammalian Gene Collection （MGC） annotated genes within the cattle genome. Comparisons of our predictions to known binding site loci within the PCKI, ACTA1 and G6PC promoter regions revealed 75% sensitivity for our method of discovery. Additionally, we intersected our predictions with known cattle SNP variants in dbSNP and on the lllumina BovineHD 770k and Bos 1 SNP chips, finding 7534, 444 and 346 overlaps, respectively. Due to our stringent filtering criteria, these results represent high quality predictions of putative TFBSs within the cattle genome. All binding site predictions are freely available at http：//bfgl. anri.barc.usda.gov/BovineTFBS/or http：//199.133.54.77/BovineTFBS.
基金This work was supported in part by CRIS Project (No.1265-31000-090-00D and 1265-31000-081-00D) from US Department of Agricul-ture and by NIH Grant DK-25541 (to RWH)JY was supported by the NIH Metabolism Training Program (DK-07139)
文摘A systematic phylogenetic footprinting approach was performed to identify conserved transcription factor binding sites （TFBSs） in mammalian promoter regions using human, mouse and rat sequence alignments. We found that the score distributions of most binding site models did not follow the Gaussian distribution required by many statistical methods. Therefore, we performed an empirical test to establish the optimal threshold for each model. We gauged our computational predictions by comparing with previously known TFBSs in the PCK1 gene promoter of the cytosolic isoform of phosphoenolpyruvate carboxykinase, and achieved a sensitivity of 75% and a specificity of approximately 32% Almost all known sites overlapped with predicted sites, and several new putative TFBSs were also identified. We validated a predicted SP1 binding site in the control of PCK1 transcription using gel shift and reporter assays. Finally, we applied our computational approach to the prediction of putative TFBSs within the promoter regions of all available RefSeq genes. Our full set of TFBS predictions is freely available at http：//bfgl.anri.barc.usda.gov/tfbsConsSites.
