unclear. In this study, we attempted to characterize the structure of NF90 binding pri-miRNAs by informatics analysis and RNA-electrophoretic mobility shift assay (RNA-EMSA). We used genome-wide approaches including ENCODE and small RNA-seq to identify pri-miRNAs that are associated with NF90. As a result, we found that NF90-targerted pri-miRNAs are highly stable, having a lower free energy and fewer mismatches compared to all pri-miRNAs. To confirm this, we performed RNA-EMSA probed with mutated pri-miRNAs. Pri-miR-3173 and pri-miR-186, the NF90-targeted pri-miRNA, were mutated to unstable structure by making bulges in the stem structure, whereas pri-miR-200a, which exhibits low affinity to NF90, was changed to more stable structure by forming long duplex in the stem. Consequently, we found that the mutated pri-miR-3173 and pri-miR-186 lead to a reduction in binding activity of NF90 to the pri-miRNAs. On the other hand, the binding affinity of NF90 to pri-miR-200a was dramatically elevated by forming the long duplex in the structure. These results suggest that NF90 preferentially binds pri-miRNAs having less mismatches and highly stable stem structure.
{"title":"Characteristic analysis of a secondary structure of primary microRNA bound to a double-strand RNA-binding protein, NF90","authors":"Takuma Higuchi, R. Kiernan, S. Sakamoto","doi":"10.2198/ELECTROPH.65.13","DOIUrl":"https://doi.org/10.2198/ELECTROPH.65.13","url":null,"abstract":"unclear. In this study, we attempted to characterize the structure of NF90 binding pri-miRNAs by informatics analysis and RNA-electrophoretic mobility shift assay (RNA-EMSA). We used genome-wide approaches including ENCODE and small RNA-seq to identify pri-miRNAs that are associated with NF90. As a result, we found that NF90-targerted pri-miRNAs are highly stable, having a lower free energy and fewer mismatches compared to all pri-miRNAs. To confirm this, we performed RNA-EMSA probed with mutated pri-miRNAs. Pri-miR-3173 and pri-miR-186, the NF90-targeted pri-miRNA, were mutated to unstable structure by making bulges in the stem structure, whereas pri-miR-200a, which exhibits low affinity to NF90, was changed to more stable structure by forming long duplex in the stem. Consequently, we found that the mutated pri-miR-3173 and pri-miR-186 lead to a reduction in binding activity of NF90 to the pri-miRNAs. On the other hand, the binding affinity of NF90 to pri-miR-200a was dramatically elevated by forming the long duplex in the structure. These results suggest that NF90 preferentially binds pri-miRNAs having less mismatches and highly stable stem structure.","PeriodicalId":369290,"journal":{"name":"Electrophoresis Letters","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128548568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Firstly, small number of cells (1–100) were manually collected, and they were chemically and/or enzymatically processed in a PCR tube with a micropi-pette. The obtained sample solution was then introduced into a capillary, preconcentrated by LDIS, electrophoretical-ly separated, and detected by highly sensitive detector like laser-induced fluorescence (LIF) or mass spectrometry (MS). The obtained data were processed via a database search and finally metabolome and glycome analyses were achieved for 1–100 cells.
{"title":"Trace omics analysis by ultra-sensitive capillary electrophoresis","authors":"T. Kawai","doi":"10.2198/electroph.64.23","DOIUrl":"https://doi.org/10.2198/electroph.64.23","url":null,"abstract":"Firstly, small number of cells (1–100) were manually collected, and they were chemically and/or enzymatically processed in a PCR tube with a micropi-pette. The obtained sample solution was then introduced into a capillary, preconcentrated by LDIS, electrophoretical-ly separated, and detected by highly sensitive detector like laser-induced fluorescence (LIF) or mass spectrometry (MS). The obtained data were processed via a database search and finally metabolome and glycome analyses were achieved for 1–100 cells.","PeriodicalId":369290,"journal":{"name":"Electrophoresis Letters","volume":"77 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134058736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Development of a fully automated enzymatic lipoprotein fractionation method for staining total cholesterol and triglycerides","authors":"M. Matsushita, Natsumi Yamaguchi, Marina Tanaka","doi":"10.2198/electroph.65.69","DOIUrl":"https://doi.org/10.2198/electroph.65.69","url":null,"abstract":"","PeriodicalId":369290,"journal":{"name":"Electrophoresis Letters","volume":"20 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131757394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Trajectory of autoantibody-based cancer biomarker research","authors":"Makoto Kobayashi, K. Sugimoto, H. Chiba","doi":"10.2198/electroph.66.43","DOIUrl":"https://doi.org/10.2198/electroph.66.43","url":null,"abstract":"","PeriodicalId":369290,"journal":{"name":"Electrophoresis Letters","volume":"100 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127067680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yasunori Sugiyama, Tatsuto Nakane, Shuji Sakmoto, K. Murao
{"title":"Novel signaling pathways that regulate suppression of insulin gene expression in type 2 diabetes","authors":"Yasunori Sugiyama, Tatsuto Nakane, Shuji Sakmoto, K. Murao","doi":"10.2198/electroph.65.47","DOIUrl":"https://doi.org/10.2198/electroph.65.47","url":null,"abstract":"","PeriodicalId":369290,"journal":{"name":"Electrophoresis Letters","volume":"54 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129466367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Multi-omics analysis based on proteomics is fun! : development of proteogenomic software generating sample-specific proteome database and comprehensive kinase activity analysis","authors":"Rei Noguchi","doi":"10.2198/electroph.67.5","DOIUrl":"https://doi.org/10.2198/electroph.67.5","url":null,"abstract":"","PeriodicalId":369290,"journal":{"name":"Electrophoresis Letters","volume":"35 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123827612","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Heat-denatured protein analysis by SDS-PAGE with low concentration of SDS. in the extraction medium","authors":"M. Oh‐ishi, Sahara Watanabe, Kaimu Matsumoto","doi":"10.2198/electroph.66.59","DOIUrl":"https://doi.org/10.2198/electroph.66.59","url":null,"abstract":"","PeriodicalId":369290,"journal":{"name":"Electrophoresis Letters","volume":"80 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126259073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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