Object： To identify transcript variants and expression patterns of porcine Mitf. Materials and methods： A pairwise BLAST search at NCBI database was performed to deduce the structure of porcine Mitf gene. Subsequent...Object： To identify transcript variants and expression patterns of porcine Mitf. Materials and methods： A pairwise BLAST search at NCBI database was performed to deduce the structure of porcine Mitf gene. Subsequently, 5＇ RACE and fluorescent quantitative RT-PCR were used to analyze the expression pattern of porcine Mitf in different tissues. Results： Four transcript variants of porcine Mitf, MITF-A, MITF-H, MITF-M and MITF-SUS were identified, all sharing high homology with those in humans, except Mitf-SUS.Conclusion： The sequence of porcine Mitf appear highly homologous to human MITF. However, only 4 transcript variants of porcine Mitf were identified in these minipigs, less than the 9 transcript variants in human MITF.展开更多
Objective： To study the expression level and role of apoptosis-associated speck-like protein containing a caspase recruitment domain （PYCARD） gene transcript variant mRNA in peripheral blood mononuclear cells （PB...Objective： To study the expression level and role of apoptosis-associated speck-like protein containing a caspase recruitment domain （PYCARD） gene transcript variant mRNA in peripheral blood mononuclear cells （PBMCs） of primary gout （PG） patients with different Chinese medicine （CM） syndromes. Methods： The expressions of PYCARD gene transcript variant mRNA and interleukin-1β （IL-1β） mRNA in PBMCs were investigated in 96 PG patients with acute phase （APPG, 44 cases） and non-acute phase （NAPPG, 52 cases） and 30 healthy controls （HCs） by reverse transcription-polymerase chain reaction （PCR） and/or real-time quantitative PCR. PYCARD and nuclear factor-κB （p50） [NF-κB （p50）] protein was detected by Western blot in PBMCs respectively. IL-1β, IL-4 and IL-10 protein levels in plasma of HCs and PG patients were measured by enzyme-linked immuno sorbent assay. Results： The main CM syndromes in APPG patients were obstruction of dampness and heat syndrome （ODHS, 36.36%） and intermingled phlegm-blood stasis syndrome （IPBSS, 27.27%）, while in NAPPG patients were Pi （Spleen）-deficiency induced dampness syndrome （PDIDS, 40.38%） and qi-blood deficiency syndrome （QBDS, 26.92%）. It showed statistical significances of the expressions of PYCARD gene and its transcript variant mRNA, the protein of PYCARD and NF-κB （p50） and the plasma IL-1β, IL-4 and IL-10 in APPG, NAPPG, ODHS, IPBSS, PDIDS and QBDS groups, compared with the HC group respectively （P〈0.05 or P〈0.01）. There were also significant differences of mRNA expressions of PYCARD-1 and PYCARD-2 as well as protein expressions of IL-1β, IL-4 and IL-10 among the 4 CM syndromes groups （P〈0.05 or P〈0.01）. Correlation analysis showed positive correlation between the mRNA expressions of PYCARD-1 gene transcript variant and IL-1β in APPG patients （r=0.3088, P=0.0183）. Conclusion： PYCARD gene and its transcript variant may play a critical and regulative role in the inflammatory response of PG patients with different phases and CM syndromes.展开更多
Understanding the functional effects of genetic variants is crucial in modern genomics and genetics. Transcription factor binding sites （TFBSs） are one of the most important cis-regulatory elements. While multiple t...Understanding the functional effects of genetic variants is crucial in modern genomics and genetics. Transcription factor binding sites （TFBSs） are one of the most important cis-regulatory elements. While multiple tools have been developed to assess functional effects of genetic variants at TFBSs, they usually assume that each variant works in isolation and neglect the potential ＂interference＂ among multiple variants within the same TFBS. In this study, we presented COPE-TFBS （Context-Oriented Predictor for variant Effect on Transcription Factor Binding Site）, a novel method that considers sequence context to accurately predict variant effects on TFBSs. We systematically re-analyzed the sequencing data from both the 1000 Genomes Project and the Genotype-Tissue Expression （GTEx） Project via COPE-TFBS, and identified numbers of novel TFBSs, transformed TFBSs and discordantly annotated TFBSs resulting from multiple variants, further highlighting the necessity of sequence context in accurately annotating genetic variants.展开更多
基金supported by grants from the Major State Basic Research Development Program of China(973 Program)(#2011CBA01000)the National Basic Research Program of China(973 Program)(#2012CB967900)the National Natural Science Foundation of China(81400472)
文摘Object： To identify transcript variants and expression patterns of porcine Mitf. Materials and methods： A pairwise BLAST search at NCBI database was performed to deduce the structure of porcine Mitf gene. Subsequently, 5＇ RACE and fluorescent quantitative RT-PCR were used to analyze the expression pattern of porcine Mitf in different tissues. Results： Four transcript variants of porcine Mitf, MITF-A, MITF-H, MITF-M and MITF-SUS were identified, all sharing high homology with those in humans, except Mitf-SUS.Conclusion： The sequence of porcine Mitf appear highly homologous to human MITF. However, only 4 transcript variants of porcine Mitf were identified in these minipigs, less than the 9 transcript variants in human MITF.
基金Supported by the National Natural Science Foundation of China(No.81603441)Educational Commission of Sichuan Province(No.16ZA0282)the China Postdoctoral Science Foundation(No.2016M590872),China
文摘Objective： To study the expression level and role of apoptosis-associated speck-like protein containing a caspase recruitment domain （PYCARD） gene transcript variant mRNA in peripheral blood mononuclear cells （PBMCs） of primary gout （PG） patients with different Chinese medicine （CM） syndromes. Methods： The expressions of PYCARD gene transcript variant mRNA and interleukin-1β （IL-1β） mRNA in PBMCs were investigated in 96 PG patients with acute phase （APPG, 44 cases） and non-acute phase （NAPPG, 52 cases） and 30 healthy controls （HCs） by reverse transcription-polymerase chain reaction （PCR） and/or real-time quantitative PCR. PYCARD and nuclear factor-κB （p50） [NF-κB （p50）] protein was detected by Western blot in PBMCs respectively. IL-1β, IL-4 and IL-10 protein levels in plasma of HCs and PG patients were measured by enzyme-linked immuno sorbent assay. Results： The main CM syndromes in APPG patients were obstruction of dampness and heat syndrome （ODHS, 36.36%） and intermingled phlegm-blood stasis syndrome （IPBSS, 27.27%）, while in NAPPG patients were Pi （Spleen）-deficiency induced dampness syndrome （PDIDS, 40.38%） and qi-blood deficiency syndrome （QBDS, 26.92%）. It showed statistical significances of the expressions of PYCARD gene and its transcript variant mRNA, the protein of PYCARD and NF-κB （p50） and the plasma IL-1β, IL-4 and IL-10 in APPG, NAPPG, ODHS, IPBSS, PDIDS and QBDS groups, compared with the HC group respectively （P〈0.05 or P〈0.01）. There were also significant differences of mRNA expressions of PYCARD-1 and PYCARD-2 as well as protein expressions of IL-1β, IL-4 and IL-10 among the 4 CM syndromes groups （P〈0.05 or P〈0.01）. Correlation analysis showed positive correlation between the mRNA expressions of PYCARD-1 gene transcript variant and IL-1β in APPG patients （r=0.3088, P=0.0183）. Conclusion： PYCARD gene and its transcript variant may play a critical and regulative role in the inflammatory response of PG patients with different phases and CM syndromes.
基金supported by funds from the National Key R&D Program of China (2016YFC0901603)the China 863 Program (2015AA020108)+1 种基金the State Key Laboratory of Protein and Plant Gene Researchsupported in part by the National Program for Support of Top-notch Young Professionals
文摘Understanding the functional effects of genetic variants is crucial in modern genomics and genetics. Transcription factor binding sites （TFBSs） are one of the most important cis-regulatory elements. While multiple tools have been developed to assess functional effects of genetic variants at TFBSs, they usually assume that each variant works in isolation and neglect the potential ＂interference＂ among multiple variants within the same TFBS. In this study, we presented COPE-TFBS （Context-Oriented Predictor for variant Effect on Transcription Factor Binding Site）, a novel method that considers sequence context to accurately predict variant effects on TFBSs. We systematically re-analyzed the sequencing data from both the 1000 Genomes Project and the Genotype-Tissue Expression （GTEx） Project via COPE-TFBS, and identified numbers of novel TFBSs, transformed TFBSs and discordantly annotated TFBSs resulting from multiple variants, further highlighting the necessity of sequence context in accurately annotating genetic variants.
