A systematic phylogenetic footprinting approach was performed to identify con-served transcription factor binding sites (TFBSs) in mammalian promoter regions using human,mouse and rat sequence alignments. We found tha...A systematic phylogenetic footprinting approach was performed to identify con-served transcription factor binding sites (TFBSs) in mammalian promoter regions using human,mouse and rat sequence alignments. We found that the score dis-tributions 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 pro-moter 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 tran-scription 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
LncRNAs and metabolism represents two factors involved in cancer initiation and progression.However,the interaction between lncRNAs and metabolism remains to be fully explored.In this study,lncRNA FEZF1-AS1(FEZF1-AS1)...LncRNAs and metabolism represents two factors involved in cancer initiation and progression.However,the interaction between lncRNAs and metabolism remains to be fully explored.In this study,lncRNA FEZF1-AS1(FEZF1-AS1)was found upregulated in colon cancer after screening all the lncRNAs of colon cancer tissues deposited in TCGA,the result of which was further confirmed by RNAscope staining on a colon tissue chip.The results obtained using FEZF1-AS1 knockout colon cancer cells(SW480 KO and HCT-116 KO)constructed using CRISPR/Cas9 system confirmed the proliferation,invasion,and migration-promoting function of FEZF1-AS1 in vitro.Mechanistically,FEZF1-AS1 associated with the mitochondrial protein phosphoenolpyruvate carboxykinase(PCK2),which plays an essential role in regulating energy metabolism in the mitochondria.Knockdown of FEZF1-AS1 greatly decreased PCK2 protein levels,broke the homeostasis of energy metabolism in the mitochondria,and inhibited proliferation,invasion,and migration of SW480 and HCT-116 cells.PCK2 overexpression in FEZF1-AS1 knockout cells partially rescued the tumor inhibitory effect on colon cancer cells both in vitro and in vivo.Moreover,PCK2 overexpression specifically rescued the abnormal accumulation of Flavin mononucleotide(FMN)and succinate,both of which play an important role in oxidative phosphorylation(OXPHOS).Overall,these results indicate that FEZF1-AS1 is an oncogene through regulating energy metabolism of the cell.This research reveals a new mechanism for lncRNAs to regulate colon cancer and provides a potential target for colon cancer diagnosis and treatment.展开更多
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 con-served transcription factor binding sites (TFBSs) in mammalian promoter regions using human,mouse and rat sequence alignments. We found that the score dis-tributions 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 pro-moter 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 tran-scription 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.
基金supported by the GDAS Special Project of Science and Technology Development (2019GDASYL-0103058)Guangdong Basic and Applied Basic Research Foundation,Natural Science Foundation of Guangdong Province (2019A1515011456).
文摘LncRNAs and metabolism represents two factors involved in cancer initiation and progression.However,the interaction between lncRNAs and metabolism remains to be fully explored.In this study,lncRNA FEZF1-AS1(FEZF1-AS1)was found upregulated in colon cancer after screening all the lncRNAs of colon cancer tissues deposited in TCGA,the result of which was further confirmed by RNAscope staining on a colon tissue chip.The results obtained using FEZF1-AS1 knockout colon cancer cells(SW480 KO and HCT-116 KO)constructed using CRISPR/Cas9 system confirmed the proliferation,invasion,and migration-promoting function of FEZF1-AS1 in vitro.Mechanistically,FEZF1-AS1 associated with the mitochondrial protein phosphoenolpyruvate carboxykinase(PCK2),which plays an essential role in regulating energy metabolism in the mitochondria.Knockdown of FEZF1-AS1 greatly decreased PCK2 protein levels,broke the homeostasis of energy metabolism in the mitochondria,and inhibited proliferation,invasion,and migration of SW480 and HCT-116 cells.PCK2 overexpression in FEZF1-AS1 knockout cells partially rescued the tumor inhibitory effect on colon cancer cells both in vitro and in vivo.Moreover,PCK2 overexpression specifically rescued the abnormal accumulation of Flavin mononucleotide(FMN)and succinate,both of which play an important role in oxidative phosphorylation(OXPHOS).Overall,these results indicate that FEZF1-AS1 is an oncogene through regulating energy metabolism of the cell.This research reveals a new mechanism for lncRNAs to regulate colon cancer and provides a potential target for colon cancer diagnosis and treatment.
