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Single-cell omics: experimental workflow, data analyses and applications

Science China Life Sciences 2025年第1期68卷 5-102页

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin Wang Xin Dong Bin Duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han Qi Liu Xiaohui Fan Chen Li Chenfei Wang Tieliu Shi Department of Clinical Laboratory the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City) Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research Institute of Intelligent Computing Zhejiang Lab Shanghai Research Institute for Intelligent Autonomous Systems center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of Medicine National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University center for Bioinformatics and Computational biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University Beijing Institutes of Life Science Chinese Academy of Sciences Peking-Tsinghua center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology (CQB)Peking University Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women's HospitalZhejiang University School of Medicine Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal University

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell rna technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome,proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial sc rna-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

关键词： single-cell sequencing genome epigenome proteomics metabolomics multimodal spatial transcriptomics CRISPR screening

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Viroids:Small Probes for Exploring the Vast Universe of rna Trafficking in Plants

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Journal of Integrative Plant biology 2010年第1期52卷 28-39页

作者： Ying Wang Biao Ding Department of Plant Cellular and Molecular biology and Plant Biotechnology center The Ohio State University the center for rna biology The Ohio State University Molecular Cellular and DeVelopmental Biology Program The Ohio State University Columbus OH 43210 USA

Cell-to-cell and long-distance trafficking of rna is a rapidly evolving frontier of integrative plant biology that broadly impacts studies on plant growth and development, spread of infectious agents and plant defense responses. The fundamental questions being pursued at the forefronts revolve around function, mechanism and evolution. In the present review, we will first use specific examples to illustrate the biological importance of cell-to-cell and long-distance trafficking of rna. We then focus our discussion on research findings obtained using viroids that have advanced our understanding of the underlying mechanisms involved in rna trafficking. We further use viroid examples to illustrate the great diversity of trafficking machinery evolved by plants, as well as the promise for new insights in the years ahead. Finally, we discuss the prospect of integrating findings from different experimental systems to achieve a systems-based understanding of rna trafficking function, mechanism and evolution.

关键词： no English key word

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Transfer rna:A dancer between charging and mis-charging for protein biosynthesis

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Science China(Life Sciences) 2013年第10期56卷 921-932页

作者： ZHOU XiaoLong WANG EnDuo center for rna Research State Key Laboratory of Molecular BiologyInstitute of Biochemistry and Cell BiologyShanghai Institutes for Biological SciencesChinese Academy of Sciences

Transfer rna plays a fundamental role in the protein biosynthesis as an adaptor molecule by functioning as a biological link between the genetic nucleotide sequence in the mrna and the amino acid sequence in the *** perform its role in protein biosynthesis,it has to be accurately recognized by aminoacyl-trna synthetases(aaRSs)to generate aminoacyl-trnas(aa-trnas).The correct pairing between an amino acid with its cognate trna is crucial for translational quality *** and utilization of mis-charged trnas are usually detrimental for all the species,resulting in cellular *** aa-trnas formation is collectively controlled by aaRSs with distinct mechanisms and/or other ***,in very limited instances,mis-charged trnas are intermediate for specific pathways or essential components for the translational ***,from the point of accuracy in trna charging,we review our understanding about the mechanism ensuring correct aa-trna *** addition,some unique mis-charged trna species necessary for the organism are also briefly described.

关键词： trna aminoacyl-trna synthetase aminoacylation editing

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Viral Regulation of rna Granules in Infected Cells

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Virologica Sinica 2019年第2期34卷 175-191页

作者： Qiang Zhang Nishi R. Sharma Zhi-Ming Zheng Mingzhou Chen State Key Laboratory of Virology and Modern Virology Research center College of Life Sciences Wuhan UniversityWuhan 430072 China Tumor Virus rna biology Section RNA Biology Laboratory National Cancer Institute National Institutes of Health Frederick MD 21702 USA

rna granules are cytoplasmic, microscopically visible, non-membrane ribo-nucleoprotein structures and are important posttranscriptional regulators in gene expression by controlling rna translation and stability. TIA/G3BP/PABP-specific stress granules(SG) and GW182/DCP-specific rna processing bodies(PB) are two major distinguishable rna granules in somatic cells and contain various ribosomal subunits, translation factors, scaffold proteins, rna-binding proteins, rna decay enzymes and helicases to exclude m rnas from the cellular active translational pool. Although SG formation is inducible due to cellular stress, PB exist physiologically in every cell. Both rna granules are important components of the host antiviral defense. Virus infection imposes stress on host cells and thus induces SG formation. However, both rna and DNA viruses must confront the hostile environment of host innate immunity and apply various strategies to block the formation of SG and PB for their effective infection and multiplication. This review summarizes the current research development in the field and the mechanisms of how individual viruses suppress the formation of host SG and PB for virus production.

关键词： Stress granules (SG) P-bodies (PB) rna virus - DNA virus

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On Bioinformatic Resources

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Genomics, Proteomics & Bioinformatics 2015年第1期13卷 1-3页

作者： Runsheng Chen CAS Key Laboratory of rna biology Institute of Biophysics Chinese Academy of Sciences

A starting point of curating bioinformatic resources for the public is marked by the establishment of the US National center for Biotechnology Information（NCBI）in 1988[1].One of its many purposes is certainly to echo the initiative of the Human Genome Project（HGP）––when two landmark reports were published at the same time：‘‘Mapping and Sequencing the Human Genome’’by the National Research Council[2]and‘‘Mapping Our Genes––The Genome Project：How Big,How Fast？’’by the US Congress[3].

关键词： Genome Mapping Biotechnology Sequencing initiative landmark disciplines genomic sequenced starting

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rna-dependent pseudouridylation catalyzed by box H/ACA RNPs

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Frontiers in biology 2018年第1期13卷 1-10页

作者： Meemanage D. De Zoysa Yi-Tao Yu University of Rochester Medical center Department of Biochemistry and Biophysics Center for RNA Biology 601 Elmwood AvenueRochester NY14642 USA

BACKGROUND： Pseudouridine （Ψ） is the most abundant post-transcriptionally modified nucleotide found in rna. ~ is clustered in functionally important and evolutionary conserved regions of rnas in all three domains of life. Pseudouridylation is catalyzed by two distinct mechanisms： an rna-independent and an rna-dependent mechanism. The former involves a group of stand-alone protein enzymes, and the latter involves a family of complex enzymes called box H/ACA RNPs, each of which consists of one rna （box H/ACA rna） and a set of four core proteins. Over the years, the mechanism of rna- dependent pseudouridylation has been extensively studied. The crystal structures of partial and complete box H/ACA RNP have been solved. However, the detailed picture of rna-dependent pseudouridylation is still not entirely clear. OBJECTIVE： In this work, we review what is known about box H/ACA RNP and the mechanism by which box H/ACA RNP catalyzes rna-dependent pseudouridylation. We also discuss some examples of the dual nature and redundancy of box H/ ACA RNPs that deviate from the usual mechanism. METHODS： A methodical literature search was performed using the Pubmed central search engine and International Digital Publishing Forum （EPUB） using the following keywords：＂pseudouridylation,＂＂pseudouridine,＂ and ＂box H/ACA RNP.＂ The necessary information was extracted and cited. RESULTS： A detailed introduction is made including the discovery, mechanism and crystal structure of box H/ACA RNP. Three sequence/structural requirements for box H/ACA rna-guided pseudouridylation are discussed and the exceptions to those rules are explored. CONCLUSION： Over the years, box H/ACA RNP-catalyzed pseudouridylation has been extensively studied, generating fruitful results. However, a detailed picture regarding the mechanism of this reaction is still to be deciphered. More work is needed to fully understand box H/ACA RNP-catalyzed pseudouridylation.

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Endoplasmic reticulum stress and autophagy in cerebral ischemia/reperfusion injury:PERK as a potential target for intervention

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Neural Regeneration Research 2025年第5期20卷 1455-1466页

作者： Ju Zheng Yixin Li Ting Zhang Yanlin Fu Peiyan Long Xiao Gao Zhengwei Wang Zhizhong Guan Xiaolan Qi Wei Hong Yan Xiao Key Laboratory of Endemic and Ethnic Diseases Ministry of Education&Key Laboratory of Medical Molecular Biology of Guizhou ProvinceGuizhou Medical UniversityGuiyangGuizhou ProvinceChina Guizhou center for Disease Control and Prevention GuiyangGuizhou ProvinceChina Department of Histology and Embryology Guizhou Medical UniversityGuiyangGuizhou ProvinceChina Collaborative Innovation center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry GuiyangGuizhou ProvinceChina

Several studies have shown that activation of unfolded protein response and endoplasmic reticulum(ER)stress plays a crucial role in severe cerebral ischemia/reperfusion *** occurs within hours after cerebral ischemia,but the relationship between ER stress and autophagy remains *** this study,we established experimental models using oxygen-glucose deprivation/reoxygenation in PC12 cells and primary neurons to simulate cerebral ischemia/reperfusion *** found that prolongation of oxygen-glucose deprivation activated the ER stress pathway protein kinase-like endoplasmic reticulum kinase(PERK)/eukaryotic translation initiation factor 2 subunit alpha(e IF2α)-activating transcription factor 4(ATF4)-C/EBP homologous protein(CHOP),increased neuronal apoptosis,and induced ***,inhibition of ER stress using inhibitors or by si rna knockdown of the PERK gene significantly attenuated excessive autophagy and neuronal apoptosis,indicating an interaction between autophagy and ER stress and suggesting PERK as an essential target for regulating *** autophagy with chloroquine exacerbated ER stress-induced apoptosis,indicating that normal levels of autophagy play a protective role in neuronal injury following cerebral ischemia/reperfusion *** from this study indicate that cerebral ischemia/reperfusion injury can trigger neuronal ER stress and promote autophagy,and suggest that PERK is a possible target for inhibiting excessive autophagy in cerebral ischemia/reperfusion injury.

关键词： apoptosis ATF4 autophagy C/EBP homologous protein cerebral ischemia/reperfusion injury eIF2α endoplasmic reticulum stress PERK

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Pseudouridines in spliceosomal snrnas

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Protein & Cell 2011年第9期2卷 712-725页

作者： Andrew T.Yu Junhui Ge Yi-Tao Yu Department of Biochemistry and Biophysics Center for RNA BiologyUniversity of Rochester Medical Center601 Elmwood AvenueRochesterNY 14642USA Department of Pathology Changzheng HospitalSecond Military Medical UniversityShanghai 200003China

Spliceosomal rnas are a family of small nuclear rnas(snrnas)that are essential for pre-mrna *** vertebrate spliceosomal snrnas are extensively pseudouridylated after *** in spliceosomal snrnas are generally clustered in regions that are functionally important during *** of these modified nucleotides are conserved across species *** studies have demonstrated that spliceosomal snrna pseudouridylation is catalyzed by two different mechanisms:an rna-dependent mechanism and an rna-independent *** functions of the pseudouridines in spliceosomal snrnas(U2 snrna in particular)have also been extensively *** data indicate that virtually all pseudouridines in U2 snrna are functionally *** the currently known pseudouridines(constitutive modifications),recent work has also indicated that pseudouridylation can be induced at novel positions under stress conditions,thus strongly suggesting that pseudouridylation is also a regulatory modification.

关键词： small nuclear rnas(snrnas) pseudouridine spliceosome small nuclear ribonucleoproteins(snRNPs)

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HPV18 Utilizes Two Alternative Branch Sites for E6*I Splicing to Produce E7 Protein

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Virologica Sinica 2019年第2期34卷 211-221页

作者： Ayslan Castro Brant Vladimir Majerciak Miguel Angelo Martins Moreira Zhi-Ming Zheng Tumor Virus rna biology Section RNA Biology Laboratory Center for Cancer Research National Cancer Institute NIH Frederick MD 21702 USA Genetics Post-Graduation Program Rio de Janeiro Federal University Rio de Janeiro Brazil Genetics Program Nacional Cancer Institute INCA Rio de Janeiro 20231-050 Brazil

Human papillomavirus 18(HPV18) E6 and E7 oncogenes are transcribed as a single bicistronic E6 E7 pre-mrna. The E6 ORF region in the bicistronic E6 E7 pre-mrna contains an intron. Splicing of this intron disrupts the E6 ORF integrity and produces a spliced E6*I rna for efficient E7 translation. Here we report that the E6 intron has two overlapped branch point sequences(BPS) upstream of its 30 splice site, with an identical heptamer AACUAAC, for E6*I splicing. One heptamer has a branch site adenosine(underlined) at nt 384 and the other at nt 388. E6*I splicing efficiency correlates to the expression level of E6 and E7 proteins and depends on the selection of which branch site. In general, E6*I splicing prefers the 30 ss-proximal branch site at nt 388 over the distal branch site at nt 384. Inactivation of the nt 388 branch site was found to activate a cryptic acceptor site at nt 636 for aberrant rna splicing. Together, these data suggest that HPV18 modulates its production ratio of E6 and E7 proteins by alternative selection of the two mapped branch sites for the E6*I splicing, which could be beneficial in its productive or oncogenic infection according to the host cell environment.

关键词： Human papillomavirus 18 (HPV18) HPV splicing Branch point E6,E7,E6 intron HPV oncogenes

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Microrna in rectal cancer

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World Journal of Gastrointestinal Oncology 2016年第5期8卷 416-426页

作者： azadeh azizian jens gruber b michael ghadimi jochen gaedcke depart-ment of general visceral and pediatric surgeryuniversity medical center gottingen37075 GottingenGermany junior research group medical rna biology german primate center37075 GottingenGermany

In rectal cancer,one of the most common cancers worldwide,the proper staging of the disease determines the subsequent *** those with locally advancedrectal cancer,a neoadjuvant chemoradiotherapy(CRT) is recommended before any ***,response to CRT ranges from complete response(responders) to complete resistance(non-responders).To date we are not able to separate in advance the first group from the second,due to the absence of a valid *** all patients receive the same therapy regardless of whether they reap *** the other hand almost all patients receive a surgical resection after the CRT,although a watch-and-wait procedure or an endoscopic resection might be sufficient for those who responded well to the *** highly conserved regulators of gene expression,micro rnas(mi rnas) seem to be promising candidates for *** studies have been analyzing the mi rnas expressed in rectal cancer tissue to determine a specific mi rna profile for the ***,there is only a small overlap of identified mi rnas between different studies,posing the question as to whether different methods or differences in tissue storage may contribute to that fact or if the results simply are not reproducible,due to unknown factors with undetected influences on mi rna *** studies sought to find mi rnas which correlate to clinical parameters(tumor grade,nodal stage,metastasis,survival) and therapy *** several mi rnas seem to have an impact on the response to CRT or might predict nodal stage,there is still only little overlap between different *** here aimed to summarize the current literature on rectal cancer and mi rna expression with respect to the different relevant clinical parameters.

关键词： Polymorphism Micro rna Rectal cancer Response Chemoradiotherapy Expression

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