It has been known that,the novel coronavirus,2019-nCoV,which is considered similar to SARS-CoV,invades human cells via the receptor angiotensin converting enzyme II(ACE2).Moreover,lung cells that have ACE2 expression ...It has been known that,the novel coronavirus,2019-nCoV,which is considered similar to SARS-CoV,invades human cells via the receptor angiotensin converting enzyme II(ACE2).Moreover,lung cells that have ACE2 expression may be the main target cells during 2019-nCoV infection.However,some patients also exhibit non-respiratory symptoms,such as kidney failure,implying that 2019-nCoV could also invade other organs.To construct a risk map of different human organs,we analyzed the single-cell RNA sequencing(scRNA-seq)datasets derived from major human physiological systems,including the respiratory,cardiovascular,digestive,and urinary systems.Through scRNA-seq data analyses,we identified the organs at risk,such as lung,heart,esophagus,kidney,bladder,and ileum,and located specific cell types(i.e.,type II alveolar cells(AT2),myocardial cells,proximal tubule cells of the kidney,ileum and esophagus epithelial cells,and bladder urothelial cells),which are vulnerable to 2019-nCoV infection.Based on the findings,we constructed a risk map indicating the vulnerability of different organs to 2019-nCoV infection.This study may provide potential clues for further investigation of the pathogenesis and route of 2019-nCoV infection.展开更多
It has long been thought that growth‐regulating factors（GRFs） gene family members act as transcriptional activators to play important roles in multiple plant developmental processes. However, the recent characteriz...It has long been thought that growth‐regulating factors（GRFs） gene family members act as transcriptional activators to play important roles in multiple plant developmental processes. However, the recent characterization of Arabidopsis GRF7 showed that it functions as a transcriptional repressor of osmotic stress‐responsive genes. This highlights the complex and diverse mechanisms by which different GRF members use to take action. In this study, the maize（Zea mays L.） GRF10 was functionally characterized to improve this concept. The deduced ZmGRF10 protein retains the N‐terminal QLQ and WRC domains, the characteristic regions as protein‐interacting and DNA‐binding domains, respectively. However,it lacks nearly the entire C‐terminal domain, the regions executing transactivation activity. Consistently, ZmGRF10 protein maintains the ability to interact with GRF‐interacting factors（GIFs） proteins, but lacks transactivation activity.Overexpression of ZmGRF10 in maize led to a reduction in leaf size and plant height through decreasing cell proliferation,whereas the yield‐related traits were not affected. Transcriptome analysis revealed that multiple biological pathways were affected by ZmGRF10 overexpression, including a few transcriptional regulatory genes, which have been demonstrated to have important roles in controlling plant growth and development. We propose that ZmGRF10 aids in fine‐tuning the homeostasis of the GRF‐GIF complex in the regulation of cell proliferation.展开更多
Bioinformatics methods for various RNA-seq data analyses are in fast evolution with the improvement of sequencing technologies. However, many challenges still exist in how to efficiently process the RNA-seq data to ob...Bioinformatics methods for various RNA-seq data analyses are in fast evolution with the improvement of sequencing technologies. However, many challenges still exist in how to efficiently process the RNA-seq data to obtain accurate and comprehensive results. Here we reviewed the strategies for improving diverse transcriptomic studies and the annotation of genetic variants based on RNA-seq data. Mapping RNA-seq reads to the genome and transcriptome represent two distinct methods for quantifying the expression of genes/transcripts. Besides the known genes annotated in current databases, many novel genes/transcripts(especially those long noncoding RNAs) still can be identified on the reference genome using RNA-seq. Moreover, owing to the incompleteness of current reference genomes, some novel genes are missing from them. Genome-guided and de novo transcriptome reconstruction are two effective and complementary strategies for identifying those novel genes/transcripts on or beyond the reference genome. In addition, integrating the genes of distinct databases to conduct transcriptomics and genetics studies can improve the results of corresponding analyses.展开更多
RNA-Seq, a high-throughput （HT） sequencing technique, has been used effectively in large-scale transcriptomic studies, and is particularly useful for improving gene structure information and mining of new genes. In ...RNA-Seq, a high-throughput （HT） sequencing technique, has been used effectively in large-scale transcriptomic studies, and is particularly useful for improving gene structure information and mining of new genes. In this study, RNA-Seq HT technology was employed to analyze the transcriptome of yak ovary. After lllurrlina-Solexa deep sequencing, 26826516 clean reads with a total of 4828772880 bp were obtained from the ovary library. Alignment analysis showed that 16992 yak genes mapped to the yak genome and 3734 of these genes were involved in alternative splicing. Gene structure refinement analysis showed that 7340 genes that were annotated in the yak genome could be extended at the 5＇ or 3＇ ends based on the alignments been the transcripts and the genome sequence. Novel transcript prediction analysis identified 6321 new transcripts with lengths ranging from 180 to 14884 bp, and 2267 of them were predicted to code proteins. BLAST analysis of the new transcripts showed that 1200-4933 mapped to the non-redundant （nr）, nucleotide （nt） and/or SwissProt sequence databases. Comparative statistical analysis of the new mapped transcripts showed that the majority of them were similar to genes in Bos taurus （41.4%）, Bos grunniens mutus （33.0%）, Ovis aries （6.3%）, Homo sapiens （2.8%）, Mus musculus （1.6%） and other species. Functional analy- sis showed that these expressed genes were involved in various Gene Ontology （GO） categories and Kyoto Encyclopedia of Genes and Genomes pathways. GO analysis of the new transcripts found that the largest proportion of them was associated with reproduction. The results of this study will provide a basis for describing the normal transcriptome map of yak ovary and for future studies on yak breeding performance. Moreover, the results confirmed that RNA-Seq HT technology is highly ad- vantageous in improving gene structure information and mining of new genes, as well as in providing valuable data to expand the yak genome information.展开更多
Rice false smut has become an increasingly serious disease in rice （Oryza sativa L.） production worldwide. The typical feature of this disease is that the fungal pathogen Ustilaginoidea virens （Uv） specifical y in...Rice false smut has become an increasingly serious disease in rice （Oryza sativa L.） production worldwide. The typical feature of this disease is that the fungal pathogen Ustilaginoidea virens （Uv） specifical y infects rice flower and forms false smut bal , the ustiloxin-containing bal-like fungal colony, of which the size is usual y several times larger than that of a mature rice seed. However, the underlying mechanisms of Uv-rice interac-tion are poorly understood. Here, we applied time-course microscopic and transcriptional approaches to investigate rice responses to Uv infection. The results demonstrated that the flower-opening process and expression of associated transcription factors, including ARF6 and ARF8, were inhibited in Uv-infected spikelets. The ovaries in infected spikelets were interrupted in fertilization and thus were unable to set seeds. However, a number of grain-fil ing-related genes, including seed storage protein genes, starch anabolism genes and endosperm-specific transcription factors （RISBZ1 and RPBF）, were highly transcribed as if the ovaries were fertilized. In addition, critical defense-related genes like NPR1 and PR1 were downregulated by;Uv infection. Our data imply that Uv may hijack host nutrient reservoir by activation of the grain-fil ing network because of growth and formation of false smut bal s.展开更多
基金This work was supported in part by the China National Science and Technology Major Project for Prevention and Treatment of Infectious Diseases(No.2017ZX10203207 to Z.-G.H.)National Natural Science Foundation of China(No.81672772 to Z.-G.H.,No.31601070 to J.H.,No.31800253 to K.C.)+1 种基金Interdisciplinary Program of Shanghai Jiao Tong University(Nos.2019TPA09 and ZH2018ZDA33 to Z.-G.H.,J.H.,and X.Z.)Shanghai Sailing Program(No.17YF1410400 to K.C.)and Innovative Research Team of High-Level Local Universities in Shanghai.
文摘It has been known that,the novel coronavirus,2019-nCoV,which is considered similar to SARS-CoV,invades human cells via the receptor angiotensin converting enzyme II(ACE2).Moreover,lung cells that have ACE2 expression may be the main target cells during 2019-nCoV infection.However,some patients also exhibit non-respiratory symptoms,such as kidney failure,implying that 2019-nCoV could also invade other organs.To construct a risk map of different human organs,we analyzed the single-cell RNA sequencing(scRNA-seq)datasets derived from major human physiological systems,including the respiratory,cardiovascular,digestive,and urinary systems.Through scRNA-seq data analyses,we identified the organs at risk,such as lung,heart,esophagus,kidney,bladder,and ileum,and located specific cell types(i.e.,type II alveolar cells(AT2),myocardial cells,proximal tubule cells of the kidney,ileum and esophagus epithelial cells,and bladder urothelial cells),which are vulnerable to 2019-nCoV infection.Based on the findings,we constructed a risk map indicating the vulnerability of different organs to 2019-nCoV infection.This study may provide potential clues for further investigation of the pathogenesis and route of 2019-nCoV infection.
基金supported by the National Transgene Research and Industrialization Project of China (2011ZX08003-003-00A)the National High Technology Research and Development Program of China (2012AA10A305)National Program on Key Basic Research Project of China (2014CB147300)
文摘It has long been thought that growth‐regulating factors（GRFs） gene family members act as transcriptional activators to play important roles in multiple plant developmental processes. However, the recent characterization of Arabidopsis GRF7 showed that it functions as a transcriptional repressor of osmotic stress‐responsive genes. This highlights the complex and diverse mechanisms by which different GRF members use to take action. In this study, the maize（Zea mays L.） GRF10 was functionally characterized to improve this concept. The deduced ZmGRF10 protein retains the N‐terminal QLQ and WRC domains, the characteristic regions as protein‐interacting and DNA‐binding domains, respectively. However,it lacks nearly the entire C‐terminal domain, the regions executing transactivation activity. Consistently, ZmGRF10 protein maintains the ability to interact with GRF‐interacting factors（GIFs） proteins, but lacks transactivation activity.Overexpression of ZmGRF10 in maize led to a reduction in leaf size and plant height through decreasing cell proliferation,whereas the yield‐related traits were not affected. Transcriptome analysis revealed that multiple biological pathways were affected by ZmGRF10 overexpression, including a few transcriptional regulatory genes, which have been demonstrated to have important roles in controlling plant growth and development. We propose that ZmGRF10 aids in fine‐tuning the homeostasis of the GRF‐GIF complex in the regulation of cell proliferation.
基金supported by the National High Technology Research and Development Program of China(2015AA020104)the China Human Proteome Project(2014DFB30010)+1 种基金the National Science Foundation of China(31471239,to Leming Shi)the 111 Project(B13016)
文摘Bioinformatics methods for various RNA-seq data analyses are in fast evolution with the improvement of sequencing technologies. However, many challenges still exist in how to efficiently process the RNA-seq data to obtain accurate and comprehensive results. Here we reviewed the strategies for improving diverse transcriptomic studies and the annotation of genetic variants based on RNA-seq data. Mapping RNA-seq reads to the genome and transcriptome represent two distinct methods for quantifying the expression of genes/transcripts. Besides the known genes annotated in current databases, many novel genes/transcripts(especially those long noncoding RNAs) still can be identified on the reference genome using RNA-seq. Moreover, owing to the incompleteness of current reference genomes, some novel genes are missing from them. Genome-guided and de novo transcriptome reconstruction are two effective and complementary strategies for identifying those novel genes/transcripts on or beyond the reference genome. In addition, integrating the genes of distinct databases to conduct transcriptomics and genetics studies can improve the results of corresponding analyses.
基金supported by the National Science&Technology Pillar Program of China(2012BAD13B06)the Special Fund for Agroscientific Research in the Public Interest(201203009)
文摘RNA-Seq, a high-throughput （HT） sequencing technique, has been used effectively in large-scale transcriptomic studies, and is particularly useful for improving gene structure information and mining of new genes. In this study, RNA-Seq HT technology was employed to analyze the transcriptome of yak ovary. After lllurrlina-Solexa deep sequencing, 26826516 clean reads with a total of 4828772880 bp were obtained from the ovary library. Alignment analysis showed that 16992 yak genes mapped to the yak genome and 3734 of these genes were involved in alternative splicing. Gene structure refinement analysis showed that 7340 genes that were annotated in the yak genome could be extended at the 5＇ or 3＇ ends based on the alignments been the transcripts and the genome sequence. Novel transcript prediction analysis identified 6321 new transcripts with lengths ranging from 180 to 14884 bp, and 2267 of them were predicted to code proteins. BLAST analysis of the new transcripts showed that 1200-4933 mapped to the non-redundant （nr）, nucleotide （nt） and/or SwissProt sequence databases. Comparative statistical analysis of the new mapped transcripts showed that the majority of them were similar to genes in Bos taurus （41.4%）, Bos grunniens mutus （33.0%）, Ovis aries （6.3%）, Homo sapiens （2.8%）, Mus musculus （1.6%） and other species. Functional analy- sis showed that these expressed genes were involved in various Gene Ontology （GO） categories and Kyoto Encyclopedia of Genes and Genomes pathways. GO analysis of the new transcripts found that the largest proportion of them was associated with reproduction. The results of this study will provide a basis for describing the normal transcriptome map of yak ovary and for future studies on yak breeding performance. Moreover, the results confirmed that RNA-Seq HT technology is highly ad- vantageous in improving gene structure information and mining of new genes, as well as in providing valuable data to expand the yak genome information.
基金supported by Sichuan Agricultural University start-up packages awarded to W.-M.W.and J.F.grants from the China Postdoctoral Science Foundation (2012M521679 to J.F.)grants from the Special Fund for Agro-Scientific Research in the Public Interest (200903039 to F.H.and W.-X.S.)
文摘Rice false smut has become an increasingly serious disease in rice （Oryza sativa L.） production worldwide. The typical feature of this disease is that the fungal pathogen Ustilaginoidea virens （Uv） specifical y infects rice flower and forms false smut bal , the ustiloxin-containing bal-like fungal colony, of which the size is usual y several times larger than that of a mature rice seed. However, the underlying mechanisms of Uv-rice interac-tion are poorly understood. Here, we applied time-course microscopic and transcriptional approaches to investigate rice responses to Uv infection. The results demonstrated that the flower-opening process and expression of associated transcription factors, including ARF6 and ARF8, were inhibited in Uv-infected spikelets. The ovaries in infected spikelets were interrupted in fertilization and thus were unable to set seeds. However, a number of grain-fil ing-related genes, including seed storage protein genes, starch anabolism genes and endosperm-specific transcription factors （RISBZ1 and RPBF）, were highly transcribed as if the ovaries were fertilized. In addition, critical defense-related genes like NPR1 and PR1 were downregulated by;Uv infection. Our data imply that Uv may hijack host nutrient reservoir by activation of the grain-fil ing network because of growth and formation of false smut bal s.
