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Single-cell transcriptome analysis reveals widespread monoallelic gene expression in individual rice mesophyll cells

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Science Bulletin 2017年第19期62卷 1304-1314页

作者： Yingying Han Xiao Chu Haopeng Yu Ying-Ke Ma Xiu-Jie Wang Wenfeng Qian Yuling Jiao State Key Laboratory of Plant genomics Institute of Genetics and Developmental BiologyChinese Academy of Sciences University of Chinese Academy of Sciences department of Biological Chemistry School of MedicineUniversity of California Key Laboratory of Genetic Network Biology Institute of Genetics and Developmental BiologyChinese Academy of Sciences Beijing Institute of genomics Chinese Academy of Sciences

Monoallelic gene expression refers to the phenomenon that all transcripts of a gene in a cell are expressed from only one of the two alleles in a diploid organism. Although monoallelic gene expression has been occasionally reported with bulk transcriptome analysis in plants, how prevalent it is in individual plant cells remains unknown. Here, we developed a single-cell RNA-seq protocol in rice and investigated allelic expression patterns in mesophyll cells of indica （93-11 ） and japonica （Nipponbare） inbred lines, as well as their F1 reciprocal hybrids. We observed pervasive monoallelic gene expression in individual mesophyll cells, which could be largely explained by stochastic and independent transcription of two alleles. By con- trast, two mechanisms that were proposed previously based on bulk transcriptome analyses, parent-of- origin effects and allelic repression, were not well supported by our data. Furthermore, monoallelically expressed genes exhibited a number of characteristics, such as lower expression levels, narrower H3K4me3/H3K9acJH3K27me3 peaks, and larger expression divergences between 93-11 and Nipponbare. Taken together, the development of a single-cell RNA-seq protocol in this study offers us an excellent opportunity to investigate the origins and prevalence of monoallelic gene expression in plant cells.

关键词： Monoallelic gene expressionSingle-cell RNA-seqRice mesophyll cellsIndependent allelic expression

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New gene therapy strategies for hepatic fibrosis

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World Journal of Gastroenterology 2015年第13期21卷 3813-3825页

作者： Adriana M Salazar-Montes Luis D Hernández-Ortega Martha S Lucano-Landeros Juan Armendariz-Borunda department of Molecular Biology and genomics Institute for Molecular Biology and Gene TherapyUniversity of GuadalajaraGuadalajaraJalisco 44281México

The liver is the largest internal organ of the body, which may suffer acute or chronic injury induced by many factors, leading to cirrhosis and hepatocarcinoma. Cirrhosis is the irreversible end result of fibrous scarring and hepatocellular regeneration, characterized by diffuse disorganization of the normal hepatic structure, regenerative nodules and fibrotic tissue. Cirrhosis is associated with a high co-morbidity and mortality without effective treatment, and much research has been aimed at developing new therapeutic strategies to guarantee recovery. Liver-based gene therapy has been used to downregulate specific genes, to block the expression of deleterious genes, to delivery therapeutic genes, to prevent allograft rejection and to augment liver regeneration. Viral and non-viral vectors have been used, with viral vectors proving to be more efficient. This review provides an overview of the main strategies used in liver-gene therapy represented by non-viral vectors, viral vectors, novel administration methods like hydrodynamic injection, hybrids of two viral vectors and blocking molecules, with the hope of translating findings from the laboratory to the patient′s bed-side.

关键词： Gene therapy Hepatic fibrosis Viral vectors Non-vi

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The transfer RNA genes in Oryza sativa ***

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Science China(Life Sciences) 2002年第5期45卷 504-511页

作者：王希胤史晓黎郝柏林 College of Life Science Peking University Beijing China Beijing genomics Institute/Center of genomics and Bioinformatics Chinese Academy of Sciences Beijing China department of Mathematics and Physics Hebei Institute of Science and Technology Tangshan China The T-life Research Center Fudan University Shanghai China

The availability of the draft genome sequence of Oryza sativa L. ssp. indica has made it possible to study the rice tRNA genes. A total of 596 tRNA genes, including 3 selenocysteine tRNA genes and one suppressor tRNA gene are identified in 127551 rice contigs. There are 45 species of tRNA genes and the revised wobble hypothesis proposed by Guthrie and Abelson is perfectly obeyed. The relationship between codon usage and the number of corresponding tRNA genes is discussed. Redundancy may exist in the present list of tRNA genes and novel ones may be found in the future. A set of 33 tRNA genes is discovered in the complete chloroplast genome of Oryza sativa L. ssp. indica. These tRNA genes are identical to those in ssp. japonica identified by us independently from the origional annotation.

关键词： tRNA gene, wobble hypothesis, codon usage, pseudo-tRNA gene, Oryza sativa, chloroplast.

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Recent Advances in Cloning and Characterization of Disease Resistance Genes in Rice

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Journal of Integrative Plant Biology 2007年第1期49卷 112-119页

作者： Liang-Ying Dai Xiong-Lun Liu Ying-Hui Xiao Guo-Liang Wang Rice genomics Laboratory Hunan Agricultural University Changsha 410128 China department of Plant Pathology The Ohio State University Columbus OH 43210 USA

Rice diseases caused by fungi, bacteria and viruses are one of the major constraints for sustainable rice （Oryza sativa L.） production worldwide. The use of resistant cultivars is considered the most economical and effective method to control rice diseases. In the last decade, a dozen resistance genes against the fungal pathogen Magnaporthe grisea and the bacterial pathogen Xanthomonas oryzae pv. oryzae have been cloned. Approximately half of them encode nuclear binding site （NBS） and leucine rich repeat （LRR）-containing proteins, the most common type of cloned plant resistance genes. Interestingly, four of them encode novel proteins which have not been identified in other plant species, suggesting that unique mechanisms might be involved in rice defense responses. This review summarizes the recent advances in cloning and characterization of disease resistance genes in rice and presents future perspectives for in-depth molecular analysis of the function and evolution of rice resistance genes and their interaction with avirulence genes in pathogens.

关键词： rice blast bacterial blight Oryza sativa Magnaporthe grisea Xanthomonas oryzae pv. oryzae

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Single nucleotide polymorphisms of the SCN5A gene in Han Chinese and their relation with Brugada syndrome

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Chinese Medical Journal 2004年第5期117卷 652-656页

作者：陈君柱谢旭东王兴祥陶明尚云鹏郭晓钢 department of Cardiovascular Diseases genomics & Bioinformatics Center

Background Mutations in the cardiac sodium channel gene (SCN5A) may lead to a broad spectrum of familial arrhythmias, including long QT syndrome (LQTS), idiopathic ventricular fibrillation (IVF), and isolated cardiac conduction diseases Recent studies have shown that polymorphisms in the SCN5A gene also play an important role in the manifestation of disorders involving cardiac excitability In this study, we investigated the polymorphisms of the SCN5A gene in Han Chinese and its relation to Brugada syndrome (BS) Methods Genomic DNA was isolated from 120 unrelated healthy volunteers and 48 unrelated Brugada syndrome patients by means of standard procedures All exons including the putative splicing sites of the SCN5A gene were amplified by PCR and sequenced directly or after subcloning using an ABI Prism 377 DNA sequencer Results A total of 5 single nucleotide polymorphisms (SNPs) were identified in the Han Chinese population, including 3 novel ones: G87A(A29A), 4245+82A>G, and G6174A The allele frequencies of each SNP in the Han Chinese population were as follows: G87A (A29A) 27 5%, A1673G (H558R) 10 4%, 4245+82A>G 32 8%, C5457T (D1819D) 41 3%, and G6174A 44 9% S1102Y and 10 other SNPs identified in other ethnic populations were not detected in this study There was no significant difference in the allele frequency of A1673G (H558R) between different ethnic populations (all P >0 5) On the other hand, the allele frequency of C5457T (D1819D) among Han Chinese was similar to its frequency among Japanese ( P >0 5), but higher than that among Americans ( P <0 005) The allele G1673 (R558) was over-represented in BS patients compared to controls ( P <0 005), but there was no significant difference in genotype frequencies at this locus There were also no differences in either the allele or genotype frequencies of the 4 other identified SNPs when comparing BS patients with healthy controls Conclusions The distribution of SCN5A SN

关键词： polymorphism genetics · SCN5A gene · Brugada syndrome · arrhythmia

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Cloning ＆ sequence identification of Hsp27 gene and expression analysis of the protein on thermal stress in Lucilia cuprina

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Insect Science 2016年第4期23卷 555-568页

作者： Manish K. Singh Pramod K. Tiwari Center for genomics Molecular & Human Genetics Jiwaji University Gwafior 474011 Cytogenetics Laboratory Department of Zoology Banaras Hindu University Varanasi 221005 India

Hsp27, a highly conserved small molecular weight heat shock protein, is widely known to be developmentally regulated and heat inducible. Its role in thermotolerance is also implicated. This study is a sequel of our earlier studies to understand the molecular organization of heat shock genes/proteins and their role in development and thermal adaptation in a sheep pest, Lucilia cuprina （blowfly）, which exhibits unusually high adaptability to a variety of environmental stresses, including heat and chemicals. In this report our aim was to understand the evolutionary relationship of Lucilia hsp27 gene/protein with those of other species and its role in thermal adaptation. We sequence characterized the Lchsp27 gene （coding region） and analyzed its expression in various larval and adult tissues under normal as well as heat shock conditions. The nucleotide sequence analysis of 678 bps long-coding region of Lchsp27 exhibited closest evolutionary proximity with Drosophila （90.09%）, which belongs to the same order, Diptera. Heat shock caused significant en- hancement in the expression ofLchsp27 gene in all the larval and adult tissues examined, however, in a tissue specific manner. Significantly, in Malpighian tubules, while the heatinduced level ofhsp27 transcript （mRNA） appeared increased as compared to control, the protein level remained unaltered and nuclear localized. We infer that Lchsp27 may have significant role in the maintenance of cellular homeostasis, particularly, during summer months, when the fly remains exposed to high heat in its natural habitat.

关键词： heat shock protein Hsp27 Lucilia cuprina thermal stress

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Go green with plant organelle genome editing

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Molecular Plant 2021年第9期14卷 1415-1417页

作者： Hongwoo Lee Cheljong Hong Jaewoong Hwang Pil Joon Seo department of Chemistry Seoul National UniversitySeoul 08826Korea Plant genomics and Breeding Institute Seoul National UniversitySeoul 08826Korea

Programmable genome-editing technologies that enable efficient and precise genetic manipulation at targeted genomic regions,in eluding zinc fin ger nucleases,tran scripti on activator-like effector nu cleases(TALENs),and clustered regularly in terspaced short palindromic repeat(CRISPR)systems,have become invaluable tools for plant biotech no logy and precision breedi ng(Sedeek et al.,2019).Genome-editing systems have been utilized in a variety of plant species to characterize nuclear gene functions and improve agricultural traits,such as crop yields,nutritional values,and biotic and abiotic stress toleranee(Sedeek et al„2019).

关键词： plant organelle traits

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Glutamine analogs promote cytoophidium assembly in human and Drosophila cells

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Journal of Genetics and genomics 2011年第9期38卷 391-402页

作者： mr Yilmaz Tastan Zillah Anne Deussen Mayte Yu-Yin Siswick Medical Research Council Functional genomics Unit Department of Physiology Anatomy and GeneticsUniversity of OxfordOxford OXI 3QXUnited Kingdom

CTP synthase is compartmentalized within a subcellular structure,termed the cytoophidium,in a range of organisms including bacteria, yeast,fruit fly and *** we show that CTP synthase is also compartmentalized into cytoophidia in human ***,the occurrence of cytoophidia in human cells increases upon treatment with a glutamine analog 6-diazo-5-oxo-L-norleucine（DON）,an inhibitor of glutamine-dependent enzymes including CTP *** in flies confirmed that DON globally promotes cytoophidium *** analysis via CTP synthase RNA interference in somatic cells indicates that CTP synthase expression level is critical for the formation of ***,DON facilitates cytoophidium assembly even when CTP synthase level is low.A second glutamine analog azaserine also promotes cytoophidum *** data demonstrate that glutamine analogs serve as useful tools in the study of cytoophidia.

关键词： Azaserine CTP synthase Cytoophidium 6-diazo-5-oxo-L-norleucine Drosophila HeLa cell lntracellular compartmentation

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New Insights into Plant Isoprenoid Metabolism

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Molecular Plant 2012年第5期5卷 964-967页

作者： Pablo Pulido Catalina Perello Manuel Rodriguez-Concepcion department of Molecular Genetics Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB Campus UAB Bellaterra 08193 BarcelonaSpain

Isoprenoids are a hugely diverse family of compounds derived from the C5 precursors isopentenyl diphosphate （IPP） and dimethylallyl diphosphate （DMAPP）. Although all free-living organisms synthesize isoprenoids, they are particularly abun- dant and diverse in plants, with tens of thousands structures known to date. The highest variety of plant isoprenoids are specialized （secondary） metabolites that participate in the interaction of plants with their environment. These include pigments, volatiles, and defense compounds, some of which have applications in industry and agriculture.

关键词： Metabolism Insight Plant

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Insufficient TRPM5 Mediates Lipotoxicity-induced Pancreaticβ-cell Dysfunction

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Current Medical Science 2024年第2期44卷 346-354页

作者： Kai-yuan WANG Shi-mei WU Zheng-jian YAO Yun-xia ZHU Xiao HAN Key Laboratory of Human Functional genomics of Jiangsu Province Department of Biochemistry and Molecular BiologyNanjing Medical UniversityNanjing 211166China

Objective:While the reduction of transient receptor potential channel subfamily M member 5(TRPM5)has been reported in islet cells from type 2 diabetic(T2D)mouse models,its role in lipotoxicity-induced pancreaticβ-cell dysfunction remains *** study aims to study its ***:Pancreas slices were prepared from mice subjected to a high-fat-diet(HFD)at different time points,and TRPM5 expression in the pancreaticβcells was examined using immunofluorescence ***-stimulated insulin secretion(GSIS)defects caused by lipotoxicity were mimicked by saturated fatty acid palmitate(Palm).Primary mouse islets and mouse insulinoma MIN6 cells were treated with Palm,and the TRPM5 expression was detected using qRT-PCR and Western ***-induced GSIS defects were measured following siRNA-based Trpm5 *** detrimental effects of Palm on primary mouse islets were also assessed after overexpressing Trpm5 via an adenovirus-derived Trpm5(Ad-Trpm5).Results:HFD feeding decreased the mRNA levels and protein expression of TRPM5 in mouse pancreatic *** reduced TRPM5 protein expression in a time-and dose-dependent manner in MIN6 *** also inhibited TRPM5 expression in primary mouse *** of Trpm5 inhibited insulin secretion upon high glucose stimulation but had little effect on insulin *** of Trpm5 reversed Palm-induced GSIS defects and the production of functional maturation molecules unique toβ***:Our findings suggest that lipotoxicity inhibits TRPM5 expression in pancreaticβcells both in vivo and in vitro and,in turn,drivesβ-cell dysfunction.

关键词： type 2 diabetes β-cell dysfunction lipotoxicity TRPM5

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