Chromosomes are well-organized carriers of genetic information in eukaryotes and are usually quite long,carrying hundreds and thousands of genes.Intriguingly,a clade of single-celled ciliates,Spirotrichea,feature nano...Chromosomes are well-organized carriers of genetic information in eukaryotes and are usually quite long,carrying hundreds and thousands of genes.Intriguingly,a clade of single-celled ciliates,Spirotrichea,feature nanochromosomes—also called“gene-sized chromosomes”.These chromosomes predominantly carry only one gene,flanked by short telomere sequences.However,the organization and copy number variation of the chromosomes in these highly fragmented genomes remain unexplored in many groups of Spirotrichea,including the marine Strombidium.Using deep genome sequencing,we assembled the macronuclear genome of Strombidium stylifer into more than 18,000 nanochromosomes(~2.4 Kb long on average).Our results show that S.stylifer occupies an intermediate position during the evolutionary history of Strombidium lineage and experienced significant expansions in several gene families related to guanyl ribonucleotide binding.Based on the nucleotide distribution bias analysis and conserved motifs search in non-genic regions,we found that the subtelomeric regions have a conserved adenine-thymine(AT)-rich sequence motif.We also found that the copy number of nanochromosomes lacks precise regulation.This work sheds light on the unique features of chromosome structure in eukaryotes with highly fragmented genomes and reveals that a rather specialized evolutionary strategy at the genomic level has resulted in great diversity within the ciliated lineages.展开更多
Late-stage ovarian cancer(OC)has a poor prognosis and a high metastasis rate,but the underlying molecular mechanism is unclear.RNA binding proteins(RBPs)play important roles in posttranscriptional regulation in the co...Late-stage ovarian cancer(OC)has a poor prognosis and a high metastasis rate,but the underlying molecular mechanism is unclear.RNA binding proteins(RBPs)play important roles in posttranscriptional regulation in the contexts of neoplasia and tumor metastasis.In this study,we explored the molecular functions of a canonical RBP,Transformer 2βhomolog(TRA2B),in cancer cells.TRA2B knockdown in HeLa cells and subsequent wholetranscriptome RNA sequencing(RNA-seq)analysis revealed the TRA2B-regulated alternative splicing(AS)profile.We disrupted TRA2B expression in epithelial OC cells and performed a series of experiments to confirm the resulting effects on OC cell proliferation,apoptosis and invasion.TRA2B-regulated AS was tightly associated with the mitotic cell cycle,apoptosis and several cancer pathways.Moreover,the expression of hundreds of genes was regulated by TRA2B,and these genes were enriched in the functions of cell proliferation,cell adhesion and angiogenesis,which are related to the malignant phenotype of OC.By integrating the alternatively spliced and differentially expressed genes,we found that AS events and gene expression were regulated independently.We then explored and validated the oncogenic functions of TRA2B by knocking down its expression in OC cells.The high TRA2B expression was associated with poor prognosis in patients with OC.In ovarian tissue,TRA2B expression showed a gradual increasing trend with increasing malignancy.We demonstrated the important roles of TRA2B in ovarian neoplasia and aggressive OC behaviors and identified the underlying molecular mechanisms,facilitating the targeted treatment of OC.展开更多
Transferrin receptor 1(TfR1),encoded by the TFRC gene,is the gatekeeper of cellular iron uptake for cells.A variety of molecular mechanisms are at work to tightly regulate TfR1 expression,and abnormal TfR1 expression ...Transferrin receptor 1(TfR1),encoded by the TFRC gene,is the gatekeeper of cellular iron uptake for cells.A variety of molecular mechanisms are at work to tightly regulate TfR1 expression,and abnormal TfR1 expression has been associated with various diseases.In the current study,to determine the regulation pattern of TfR1,we cloned and overexpressed the human TFRC gene in HeLa cells.RNA-sequencing(RNA-seq)was used to analyze the global transcript levels in overexpressed(OE)and normal control(NC)samples.A total of 1669 differentially expressed genes(DEGs)were identified between OE and NC.Gene ontology(GO)analysis was carried out to explore the functions of the DEGs.It was found that multiple DEGs were associated with ion transport and immunity.Moreover,the regulatory network was constructed on basis of DEGs associated with ion transport and immunity,highlighting that TFRC was the node gene of the network.These results together suggested that precisely controlled TfR1 expression might be not only essential for iron homeostasis,but also globally important for cell physiology,including ion transport and immunity.展开更多
We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database（YPED） that is used by investigators at more than 300 institutions worldwide. YPED ...We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database（YPED） that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a singlelaboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry（LC–MS/MS） database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring（MRM）/selective reaction monitoring（SRM） assay development. We have linked YPED＇s database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.展开更多
Posterior to the discovery of the doublestranded RNA mediated gene silencing two decades ago,RNA interference or RNA-mediated gene silencing has received unusual intensity of study in the biology-related research fiel...Posterior to the discovery of the doublestranded RNA mediated gene silencing two decades ago,RNA interference or RNA-mediated gene silencing has received unusual intensity of study in the biology-related research fields.RNA silencing represents a large spectrum of gene regulation mechanisms in all kingdoms of eukaryotes.The power and necessity of RNA silencing has been unambiguously appreciated in both animals and plants,although the mechanisms engaged are divergent in some aspects.Interestingly,as comprehensively reviewed by Schumann et al.in this issue,RNA silencing in the simple eukaryotic fungi strikingly differs from those of animals and plants,and among fungal species as well.展开更多
基金This work was supported by the project of the National Natural Science Foundation of China(32030015)the Fundamental Research Funds for the Central Universities(862101013143,202141007).
文摘Chromosomes are well-organized carriers of genetic information in eukaryotes and are usually quite long,carrying hundreds and thousands of genes.Intriguingly,a clade of single-celled ciliates,Spirotrichea,feature nanochromosomes—also called“gene-sized chromosomes”.These chromosomes predominantly carry only one gene,flanked by short telomere sequences.However,the organization and copy number variation of the chromosomes in these highly fragmented genomes remain unexplored in many groups of Spirotrichea,including the marine Strombidium.Using deep genome sequencing,we assembled the macronuclear genome of Strombidium stylifer into more than 18,000 nanochromosomes(~2.4 Kb long on average).Our results show that S.stylifer occupies an intermediate position during the evolutionary history of Strombidium lineage and experienced significant expansions in several gene families related to guanyl ribonucleotide binding.Based on the nucleotide distribution bias analysis and conserved motifs search in non-genic regions,we found that the subtelomeric regions have a conserved adenine-thymine(AT)-rich sequence motif.We also found that the copy number of nanochromosomes lacks precise regulation.This work sheds light on the unique features of chromosome structure in eukaryotes with highly fragmented genomes and reveals that a rather specialized evolutionary strategy at the genomic level has resulted in great diversity within the ciliated lineages.
基金supported by the National Natural Science Foundation of China(81572563)the National Science Foundations of HUBEI(2018CFB235).
文摘Late-stage ovarian cancer(OC)has a poor prognosis and a high metastasis rate,but the underlying molecular mechanism is unclear.RNA binding proteins(RBPs)play important roles in posttranscriptional regulation in the contexts of neoplasia and tumor metastasis.In this study,we explored the molecular functions of a canonical RBP,Transformer 2βhomolog(TRA2B),in cancer cells.TRA2B knockdown in HeLa cells and subsequent wholetranscriptome RNA sequencing(RNA-seq)analysis revealed the TRA2B-regulated alternative splicing(AS)profile.We disrupted TRA2B expression in epithelial OC cells and performed a series of experiments to confirm the resulting effects on OC cell proliferation,apoptosis and invasion.TRA2B-regulated AS was tightly associated with the mitotic cell cycle,apoptosis and several cancer pathways.Moreover,the expression of hundreds of genes was regulated by TRA2B,and these genes were enriched in the functions of cell proliferation,cell adhesion and angiogenesis,which are related to the malignant phenotype of OC.By integrating the alternatively spliced and differentially expressed genes,we found that AS events and gene expression were regulated independently.We then explored and validated the oncogenic functions of TRA2B by knocking down its expression in OC cells.The high TRA2B expression was associated with poor prognosis in patients with OC.In ovarian tissue,TRA2B expression showed a gradual increasing trend with increasing malignancy.We demonstrated the important roles of TRA2B in ovarian neoplasia and aggressive OC behaviors and identified the underlying molecular mechanisms,facilitating the targeted treatment of OC.
基金The work was supported by the General Fund of Health Commission of Hubei Province(No.WJ2019M147).
文摘Transferrin receptor 1(TfR1),encoded by the TFRC gene,is the gatekeeper of cellular iron uptake for cells.A variety of molecular mechanisms are at work to tightly regulate TfR1 expression,and abnormal TfR1 expression has been associated with various diseases.In the current study,to determine the regulation pattern of TfR1,we cloned and overexpressed the human TFRC gene in HeLa cells.RNA-sequencing(RNA-seq)was used to analyze the global transcript levels in overexpressed(OE)and normal control(NC)samples.A total of 1669 differentially expressed genes(DEGs)were identified between OE and NC.Gene ontology(GO)analysis was carried out to explore the functions of the DEGs.It was found that multiple DEGs were associated with ion transport and immunity.Moreover,the regulatory network was constructed on basis of DEGs associated with ion transport and immunity,highlighting that TFRC was the node gene of the network.These results together suggested that precisely controlled TfR1 expression might be not only essential for iron homeostasis,but also globally important for cell physiology,including ion transport and immunity.
基金supported in part by the National Institutes of Health of the United States(Grant Nos.UL1 RR024139 to Yale Clinical and Translational Science Award,1S10OD018034-01 to 6500 QTrap Mass Spectrometer for Yale University,1S10RR026707-01 to 5500QTrap Mass Spectrometer for Yale University,P30DA018343 to Yale/NIDA Neuroproteomics Center and NIDDK-K01DK089006 awarded to JR)
文摘We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database（YPED） that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a singlelaboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry（LC–MS/MS） database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring（MRM）/selective reaction monitoring（SRM） assay development. We have linked YPED＇s database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.
文摘Posterior to the discovery of the doublestranded RNA mediated gene silencing two decades ago,RNA interference or RNA-mediated gene silencing has received unusual intensity of study in the biology-related research fields.RNA silencing represents a large spectrum of gene regulation mechanisms in all kingdoms of eukaryotes.The power and necessity of RNA silencing has been unambiguously appreciated in both animals and plants,although the mechanisms engaged are divergent in some aspects.Interestingly,as comprehensively reviewed by Schumann et al.in this issue,RNA silencing in the simple eukaryotic fungi strikingly differs from those of animals and plants,and among fungal species as well.
