Article
Immunology
Jiali Wu, Yuwei Li, Delong Feng, Yaqin Yu, Haojun Long, Zhi Hu, Qianjin Lu, Ming Zhao
Summary: This study used ATAC-seq and RNA-seq techniques to identify abnormal gene expression and chromatin accessibility changes in CD4+ T cells from SLE patients. Functional analysis revealed that these differentially accessible regions were associated with T cell differentiation, the cell cycle, and signaling pathways. Knockdown experiments confirmed the role of the transcription factor ZNF770 in regulating the expression of immune-related genes. The findings provide potential therapeutic targets for the treatment of SLE.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2023)
Article
Cell Biology
Jianbo Li, Congjiao Sun, Jiangxia Zheng, Junying Li, Guoqiang Yi, Ning Yang
Summary: This study provides a comprehensive profile of four representative stages of chicken gonadal development at the transcriptional and chromatin levels. The findings suggest that candidate genes involved in morphogenesis, meiosis, and subcellular structure formation may contribute to asymmetric gonadal development. Further analysis reveals that chromatin accessibility and transcriptional activity of these candidate genes may be regulated by nearby open chromatin regions, acting as potential cis-regulatory elements.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemical Research Methods
Liheng Luo, Michael Gribskov, Sufang Wang
Summary: With recent advances in high-throughput next-generation sequencing, this article reviews the literature on ATAC-seq, describes its characteristics and introduces the principles and features of RNA-seq, ChIP-seq, and ATAC-seq. The article also analyzes the accumulation of ATAC-seq data from different species and summarizes the findings from human diseases and other species, emphasizing the role of multi-omics data analysis in current research. In addition, the article collects and compares ATAC-seq analysis pipelines to assist biological researchers without programming skills. Overall, the article highlights the importance of multi-omics analysis and single-cell sequencing technology in future research.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Han Zhang, Zhexi Liu, Ji Wang, Tong Zeng, Xiaohua Ai, Keliang Wu
Summary: This study used ATAC-seq and RNA-seq to analyze the differences in endometrial tissues between Meishan pigs and Duroc pigs, and identified key transcription factors and differentially expressed genes that may play important roles in promoting fertility.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Honggui Wu, Xiang Li, Fanchong Jian, Ayijiang Yisimayi, Yinghui Zheng, Longzhi Tan, Dong Xing, X. Sunney Xie
Summary: Recent advances in single-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) and its coassays have transformed the field of single-cell epigenomics and transcriptomics. However, the low detection efficiency of current methods has limited our understanding of the true complexity of chromatin accessibility and its relationship with gene expression in single cells. In this study, a high-sensitivity scATAC-seq method called multiplexed end-tagging amplification of transposase accessible chromatin (METATAC) is reported, which detects a large number of accessible sites per cell and is compatible with automation. The study also investigated allele-specific accessibility in the mouse cerebral cortex and combined METATAC with high-sensitivity single-cell RNA sequencing to develop a joint ATAC-RNA assay (M2C-seq) that achieved significant improvements compared to previous methods.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Veterinary Sciences
Jianfang Wang, Bingzhi Li, Xinran Yang, Chengcheng Liang, Sayed Haidar Abbas Raza, Yueting Pan, Ke Zhang, Linsen Zan
Summary: In this study, RNA-seq and ATAC-seq techniques were used to identify differentially expressed genes specifically expressed in bovine skeletal muscle. The results revealed key regulatory genes that are involved in skeletal muscle development. Motif analysis further identified potential target genes of the transcription factor MEF2C.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Monika Chanu Chongtham, Tamer Butto, Kanak Mungikar, Susanne Gerber, Jennifer Winter
Summary: This study compared the application of INTACT and FANS in isolating sfGFP+ nuclei, revealing differences in the efficiency of isolation, nuclear size, as well as transcriptional and chromatin accessibility states. The findings offer guidance for researchers in selecting the most suitable methodology for their individual experimental design.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Nutrition & Dietetics
Zhong Xu, Junjing Wu, Jiawei Zhou, Yu Zhang, Mu Qiao, Hua Sun, Zipeng Li, Lianghua Li, Nanqi Chen, Favour Oluwapelumi Oyelami, Xianwen Peng, Shuqi Mei
Summary: This study used ATAC-seq and RNA-seq analysis to examine the accessible chromatin and gene expression in Xidu black pigs, identifying key genes and regulatory pathways associated with meat quality and fat deposition.
FRONTIERS IN NUTRITION
(2022)
Article
Biochemistry & Molecular Biology
Shicong Wang, Jieqiang He, Mengting Deng, Caixia Wang, Ruifeng Wang, Jinjiao Yan, Minrong Luo, Fengwang Ma, Qingmei Guan, Jidi Xu
Summary: Drought resistance in plants is influenced by multiple signaling pathways and epigenetic modifications, with changes in chromatin accessibility playing an important role in abiotic stress. Analysis in apples under drought conditions revealed 23,466 upregulated peaks and 2447 downregulated peaks in chromatin accessibility. Drought-induced chromatin accessibility changes genes enriched in metabolism, stimulus, and binding pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Junhong Wang, Chunwei Shi, Mingyang Cheng, Yiyuan Lu, Xiaoyu Zhang, Fengdi Li, Yu Sun, Xiaoxu Li, Xinyang Li, Yan Zeng, Chunfeng Wang, Xin Cao
Summary: Our experimental results for the first time elucidate the significance of the Zbtb1 gene in T cell development, lymphocyte production, and apoptosis from the perspectives of chromosome spatial structure and chromatin opening degree.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Min Ding, Weijian Huang, Guifen Liu, Bo Zhai, Hexin Yan, Yong Zhang
Summary: This study found that HepLPCs exhibited an aged phenotype characterized by the activation of inflammatory factors during long-term culture. FOSL2, highly enriched in lp-HepLPCs, was found to be involved in the regulation of age-related genes. Depletion of FOSL2 attenuated the aging phenotype in lp-HepLPCs. This study provides a novel approach for the long-term in vitro culture of HepLPCs.
Article
Genetics & Heredity
Lili Yu, Hao Zhang, Rongxia Guan, Yinghui Li, Yong Guo, Lijuan Qiu
Summary: Promoters are crucial for controlling gene expression in higher plant growth and development. Tissue-specific promoters are a solution to the limitations of constitutive promoters in plant genetic engineering. This study identified 10 tissue-specific genes and their corresponding promoters through transcriptome analysis and real-time quantitative PCR. The findings demonstrate the effectiveness of high-throughput transcriptional data in tissue-specific promoter discovery.
Article
Cell Biology
Anil Upreti, Stephanie. L. L. Padula, Jared. A. A. Tangeman, Brad. D. D. Wagner, Michael. J. J. O'Connell, Tycho. J. J. Jaquish, Raye. K. K. Palko, Courtney. J. J. Mantz, Deepti Anand, Frank. J. J. Lovicu, Salil. A. A. Lachke, Michael. L. L. Robinson
Summary: Lens epithelial explants cultured with vitreous humor showed increased chromatin accessibility and gene expression associated with fiber differentiation and immune response. However, the accessibility and gene expression of highly expressed genes in the lens epithelium were not significantly affected by vitreous. Analysis of differentially accessible regions revealed enrichment of cis-regulatory motifs for certain transcription factors.
Article
Multidisciplinary Sciences
Lukas M. Weber, Arkajyoti Saha, Abhirup Datta, Kasper D. Hansen, Stephanie C. Hicks
Summary: nnSVG is a scalable approach based on nearest-neighbor Gaussian processes for identifying spatially variable genes. It can identify genes that show continuous variation in expression across the entire tissue or within specific spatial domains, and it scales linearly with the number of spatial locations. We demonstrate its performance using experimental data and simulations.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Lingyu Qiu, Chen Liang, Yidong Zheng, Huayu Kang, Aiyue Chen, Chunlin Chen, Xinlong Wang, Jielin Yang, Qiongfang Fang, Xinjie Hui, Yueming Hu, Zewei Chen, Ou Sha, Wei-Guo Zhu, Yejun Wang
Summary: This research systematically investigates stable expressed genes (SEGs) in humans at the single-cell level and observes their specificity in development, tissue, and cell types. The study identifies a list of 408 spatial-temporal SEGs and finds development-specific SEGs as well as tissue-specific SEGs with immune and RNA splicing functions. The research also explores the application of SEGs in cell decomposition and accurately predicts the proportions of major immune cells in peripheral blood samples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Ashish Jain, Toshihiko Ezashi, R. Michael Roberts, Geetu Tuteja
SCIENTIFIC REPORTS
(2017)
Review
Developmental Biology
Majd Abdulghani, Ashish Jain, Geetu Tuteja
Article
Biochemical Research Methods
Ashish Jain, Geetu Tuteja
Article
Biochemical Research Methods
Huy N. Nguyen, Ashish Jain, Oliver Eulenstein, Iddo Friedberg
Article
Multidisciplinary Sciences
Megan A. Sheridan, Ying Yang, Ashish Jain, Alex S. Lyons, Penghua Yang, Sambasiva R. Brahmasani, Aihua Dai, Yuchen Tian, Mark R. Ellersieck, Geetu Tuteja, Danny J. Schust, Laura C. Schulz, Toshihiko Ezashi, R. Michael Roberts
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Multidisciplinary Sciences
Jiude Mao, Ashish Jain, Nancy D. Denslow, Mohammad-Zaman Nouri, Sixue Cheng, Tingting Wang, Ning Zhu, Jin Koh, Saurav J. Sarma, Barbara W. Sumner, Zhentian Lei, Lloyd W. Sumner, Nathan J. Bivens, R. Michael Roberts, Geetu Tuteja, Cheryl S. Rosenfeld
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Developmental Biology
Ashish Jain, Geetu Tuteja
Summary: The development of PlacentaCellEnrich provides a tool for assessing the enrichment of gene sets with placenta cell-specific expression patterns based on human placenta scRNA-Seq data. The tool is freely available for non-profit academic use under the MIT license.
Article
Multidisciplinary Sciences
Regan L. Scott, Ha T. H. Vu, Ashish Jain, Khursheed Iqbal, Geetu Tuteja, Michael J. Soares
Summary: This study characterized the transcriptome of the invasive trophoblast cell lineage, as well as other cell populations within the rat uterine-placental interface, using single-cell RNA sequencing. The results identified key transcripts that define invasive trophoblast cells and showed that the maturation stage of invasive trophoblast cell development can be determined by changes in transcript expression during gestation. Importantly, a subset of rat invasive trophoblast cell transcripts is conserved in the invasive extravillous trophoblast cell lineage of the human placenta.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)