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Meiotic transcriptional reprogramming mediated by cell-cell communications in humans and mice revealed by scatacseq and scRNA-seq

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Zoological Research 2024年第3期45卷 601-616页

作者： Hai-Quan Wang Xiao-Long Wu Jing Zhang Si-Ting Wang Yong-Juan Sang Kang Li Chao-Fan Yang Fei Sun Chao-Jun Li State Key Laboratory of Reproductive Medicine and Offspring Health Center for Global HealthSchool of Public HealthNanjing Medical UniversityNanjingJiangsu 211166China Medical School Nanjing UniversityNanjingJiangsu 210093China Zhejiang University School of Medicine HangzhouZhejiang 310016China Department of Urology and Andrology Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouZhejiang 310000China Model Animal Research Center of Medical School Nanjing UniversityNanjingNanjingJiangsu 210093China Liangzhu Laboratory Zhejiang UniversityHangzhouZhejiang 311121China

Meiosis is a highly complex process significantly influenced by transcriptional ***,studies on the mechanisms that govern transcriptomic changes during meiosis,especially in prophase I,are ***,we performed single-cell atac-seq of human testis tissues and observed reprogramming during the transition from zygotene to pachytene *** event,conserved in mice,involved the deactivation of genes associated with meiosis after reprogramming and the activation of those related to spermatogenesis before their functional ***,we identified 282 transcriptional regulators(TRs)that underwent activation or deactivation subsequent to this *** suggested that physical contact signals from Sertoli cells may regulate these TRs in spermatocytes,while secreted ENHO signals may alter metabolic patterns in these *** results further indicated that defective transcriptional reprogramming may be associated with non-obstructive azoospermia(NOA).This study revealed the importance of both physical contact and secreted signals between Sertoli cells and germ cells in meiotic progression.

关键词： single-cell RNA-seq single-cell atac-seq Spermatogenesis Meiosis Transcriptional reprogramming cell-cell communication

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Spatially resolved expression landscape and generegulatory network of human gastric corpus epithelium

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Protein & cell 2023年第6期14卷 433-447页

作者： Ji Dong Xinglong Wu Xin Zhou Yuan Gao Changliang Wang Wendong Wang Weiya He Jingyun Li Wenjun Deng Jiayu Liao Xiaotian Wu Yongqu Lu Antony KChen Lu Wen Wei Fu Fuchou Tang Biomedical Pioneering Innovation Center Department of General SurgeryCollege of Life SciencesThird HospitalPeking UniversityBeijing 100871China GMU-GIBH Joint School of Life Sciences Guangzhou LaboratoryGuangzhou Medical UniversityGuangzhou 510799China College of Animal Science and Technology Hebei Agricultural UniversityBaoding 071001China Department of Biomedical Engineering College of EngineeringPeking UniversityBeijing 100871China Beijing Advanced Innovation Center for Genomics(ICG) Ministry of Education Key Laboratory of Cell Proliferation and DifferentiationBeijing 100871China Peking University Third Hospital Cancer Center Beijing 100191China Peking-Tsinghua Center for Life Sciences Peking UniversityBeijing 100871China Bioland Laboratory(Guangzhou Regenerative Medicine and Health Guangdong Laboratory) Guangzhou 510320China

Molecular knowledge of human gastric corpus epithelium remains ***,by integrated analyses using single-cell RNA sequencing(scRNA-seq),spatial transcriptomics,and single-cell assay for transposase accessible chromatin sequencing(scatac-seq)techniques,we uncovered the spatially resolved expression landscape and gene-regulatory network of human gastric corpus ***,we identified a stem/progenitor cell population in the isthmus of human gastric corpus,where EGF and WNT signaling pathways were ***,LGR4,but not LGR5,was responsible for the activation of WNT signaling ***,FABP5 and NME1 were identified and validated as crucial for both normal gastric stem/progenitor cells and gastric cancer ***,we explored the epigenetic regulation of critical genes for gastric corpus epithelium at chromatin state level,and identified several important cell-type-specific transcription *** summary,our work provides novel insights to systematically understand the cellular diversity and homeostasis of human gastric corpus epithelium in vivo.

关键词： human gastric corpus gastric corpus stem/progenitor cell single-cell omics sequencing single-cell atac-seq spatial transcriptomics regulatory network

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A combinatorial indexing strategy for low-cost epigenomic profiling of plant single cells

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Plant Communications 2022年第4期3卷 72-82页

作者： Xiaoyu Tu Alexandre P.Marand Robert J.Schmitz Silin Zhong Joint Center for single cell Biology School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China Shanghai Collaborative Innovation Center of Agri-Seeds School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China Department of Genetics University of GeorgiaAthensGA 30602USA State Key Laboratory of Agrobiotechnology School of Life SciencesThe Chinese University of Hong KongHong KongChina

Understanding how cis-regulatory elements facilitate gene expression is a key question in *** advances in single-cell genomics have led to the discovery of cell-specific chromatin landscapes that underlie transcription programs in animal ***,the high equipment and reagent costs of commercial systems limit their applications for many *** this study,we developed a combinatorial index and dual PCR barcode strategy to profile the Arabidopsis thaliana root single-cell epigenome without any specialized *** generated chromatin accessibility profiles for 13576 root nuclei with an average of 12784 unique Tn5 integrations per *** of the single-cell assay for transposaseaccessible chromatin sequencing and RNA sequencing data sets enabled the identification of 24 cell clusters with unique transcription,chromatin,and cis-regulatory *** with single-cell data generated using the commercial microfluidic platform from 10X Genomics revealed that this low-cost combinatorial index method is capable of unbiased identification of cell-type-specific chromatin *** anticipate that,by removing cost,instrumentation,and other technical obstacles,this method will be a valuable tool for routine investigation of single-cell epigenomes and provide new insights into plant growth and development and plant interactions with the environment.

关键词： combinatorial indexing single-cell atac-seq epigenome

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Profiling Chromatin Accessibility at single-cell Resolution

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Genomics, Proteomics & Bioinformatics 2021年第2期19卷 172-190页

作者： Sarthak Sinha Ansuman T.Satpathy Weiqiang Zhou Hongkai Ji Jo A.Stratton Arzina Jaffer Nizar Bahlis Sorana Morrissy Jeff A.Biernaskie Department of Comparative Biology&Experimental Medicine Faculty of Veterinary MedicineUniversity of CalgaryCalgaryAB T2N 4N1Canada Department of Pathology Stanford University School of MedicineStanfordCA 94305USA Department of Biostatistics Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMD 21205USA Alberta Children’s Hospital Research Institute University of CalgaryCalgaryAB T2N 4N1Canada Hotchkiss Brain Institute University of CalgaryCalgaryAB T2N 4N1Canada Arnie Charbonneau Cancer Institute University of CalgaryCalgaryAB T2N 4Z6Canada Department of Biochemistry and Molecular Biology Cumming School of MedicineUniversity of CalgaryCalgaryAB T2N 4N1Canada

How distinct transcriptional programs are enacted to generate cellular heterogeneity and plasticity,and enable complex fate decisions are important open *** key regulator is the cell’s epigenome state that drives distinct transcriptional programs by regulating chromatin ***-wide chromatin accessibility measurements can impart insights into regulatory sequences(in)accessible to DNA-binding proteins at a single-cell *** review outlines molecular methods and bioinformatic tools for capturing cell-to-cell chromatin variation using single-cell assay for transposase-accessible chromatin using sequencing(scatac-seq)in a scalable *** also covers joint profiling of chromatin with transcriptome/proteome measurements,computational strategies to integrate multi-omic measurements,and predictive bioinformatic tools to infer chromatin accessibility from single-cell transcriptomic *** refinements that increase power for cell discovery through robust chromatin coverage and integrate measurements from multiple modalities will further expand our understanding of gene regulation during homeostasis and disease.

关键词： single-cell atac-seq Gene regulation Epigenetics single-cell multi-omics Cis-regulatory elements

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