Article
Multidisciplinary Sciences
Deshka S. Foster, Michael Januszyk, Kathryn E. Yost, Malini S. Chinta, Gunsagar S. Gulati, Alan T. Nguyen, Austin R. Burcham, Ankit Salhotra, R. Chase Ransom, Dominic Henn, Kellen Chen, Shamik Mascharak, Karen Tolentino, Ashley L. Titan, R. Ellen Jones, Oscar da Silva, W. Tripp Leavitt, Clement D. Marshall, Heather E. Des Jardins-Park, Michael S. Hu, Derrick C. Wan, Gerlinde Wernig, Dhananjay Wagh, John Coller, Jeffrey A. Norton, Geoffrey C. Gurtner, Aaron M. Newman, Howard Y. Chang, Michael T. Longaker
Summary: This study introduces a multimodal -omics platform to comprehensively study cell populations involved in wound healing across both time and space. By analyzing single cell chromatin landscapes and gene expression states, potential mechanisms controlling fibroblast fate during migration, proliferation, and differentiation following skin injury have been revealed.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Cell Biology
Maria A. Dimitriu, Irina Lazar-Contes, Martin Roszkowski, Isabelle M. Mansuy
Summary: Recent advances in single-cell analyses have led to comprehensive characterization of cellular and molecular states, with the development of multiplexed assays offering simultaneous analysis of multiple factors and processes. These technologies have rapidly evolved, providing better specificity, precision, and resolution. This review summarizes recent progress in single-cell multiomics approaches, focusing on innovative techniques that integrate genome, epigenome, and transcriptome profiling.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ricardo Mack, Or Gozani
Summary: The use of CRISPR technology and a high-content functional genomics screening platform sheds light on chromatin regulation and reveals a potential strategy for treating an aggressive type of leukemia.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Genetics & Heredity
Jaclyn M. Noshay, Zhikai Liang, Peng Zhou, Peter A. Crisp, Alexandre P. Marand, Candice N. Hirsch, Robert J. Schmitz, Nathan M. Springer
Summary: This study evaluates chromatin accessibility and DNA methylation patterns in a pan-genome context using de novo genome assemblies for four maize inbreds, revealing a more complete set of accessible chromatin regions and unmethylated regions when aligned to matched genomes. Shared UMRs and ACRs between genotypes exhibit dynamic boundaries, with most UMRs maintaining the unmethylated state across different genotypes.
G3-GENES GENOMES GENETICS
(2021)
Article
Agriculture, Dairy & Animal Science
Jingwei Yue, Xinhua Hou, Xin Liu, Ligang Wang, Hongmei Gao, Fuping Zhao, Lijun Shi, Liangyu Shi, Hua Yan, Tianyu Deng, Jianfei Gong, Lixian Wang, Longchao Zhang
Summary: Chromatin accessibility plays a crucial role in the regulation of embryonic muscle development in pigs by influencing the binding of transcription factors and controlling the temporal and spatial expression patterns of key genes involved in muscle development. The study highlights the importance of understanding the regulatory dynamics of genes in pig embryonic skeletal muscle development.
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY
(2021)
Article
Genetics & Heredity
Rita Jui-Hsien Lu, Yen-Ting Liu, Chih Wei Huang, Ming-Ren Yen, Chung-Yen Lin, Pao-Yang Chen
Summary: ATACgraph is a bioinformatics software designed for analyzing and visualizing ATAC-seq data, incorporating specific quality control and biological properties of chromatin accessibility. It profiles accessible chromatin regions, allows identification of differentially accessible regions, and provides an intuitive user experience for biologists.
FRONTIERS IN GENETICS
(2021)
Review
Biochemical Research Methods
Elias Orouji, Ayush T. Raman
Summary: The human genome is shaped by a variety of histone modifications, which play a crucial role in determining chromatin states and organization. Using statistical models and computational tools, noncoding regions of DNA can be annotated and combinatorial histone marks inferred. These marks enable the discovery of genomic function and activity, and their patterns change in different cell conditions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Cardiac & Cardiovascular Systems
Yuliang Feng, Liuyang Cai, Wanzi Hong, Chunxiang Zhang, Ning Tan, Mingyang Wang, Cheng Wang, Feng Liu, Xiaohong Wang, Jianyong Ma, Chen Gao, Mohit Kumar, Yuanxi Mo, Qingshan Geng, Changjun Luo, Yan Lin, Haiyang Chen, Shuang-Yin Wang, Michael J. Watson, Anil G. Jegga, Roger A. Pedersen, Ji-Dong Fu, Zhao Wang, Guo-Chang Fan, Sakthivel Sadayappan, Yigang Wang, Siim Pauklin, Feng Huang, Wei Huang, Lei Jiang
Summary: This study investigates the role of 3-dimensional chromatin topology in dilated cardiomyopathy (DCM) by analyzing the epigenome and transcriptome maps of DCM and nonfailing heart tissues. The research reveals that the reprogramming of chromatin topology is associated with transcriptional dysregulation in DCM, with the key transcription factor HAND1 implicated in the process. The findings provide insights into the pathogenesis of DCM and highlight the importance of chromatin organization in heart failure.
Article
Multidisciplinary Sciences
Lihua Zhang, Jing Zhang, Qing Nie
Summary: The emergence of single-cell multiomics data provides unprecedented opportunities to study the transcriptional regulatory mechanisms controlling cell identity. DIRECT-NET, a machine-learning method based on gradient boosting, allows us to identify genome-wide cis-regulatory elements (CREs) and their relationship to target genes from single-cell data. DIRECT-NET substantially improves the accuracy of inferring CRE-to-gene relationships and reveals cell subpopulation-specific and dynamic regulatory linkages.
Article
Biology
Siyu Yang, Dong Chen, Lei Xie, Xiaoxiao Zou, Yanyuan Xiao, Lin Rao, Tianxiong Yao, Qing Zhang, Liping Cai, Fei Huang, Bin Yang, Lusheng Huang
Summary: This study investigated the gene expression and chromatin accessibility in the pig hippocampus, revealing significant changes in different cell types during development and identifying key genes associated with neurogenesis and Alzheimer's disease. The findings of this study are helpful for utilizing pigs as a biomedical model for human neurodegenerative diseases.
SCIENCE CHINA-LIFE SCIENCES
(2023)
Article
Agriculture, Dairy & Animal Science
Tao Jiang, Ziqi Ling, Zhimin Zhou, Xiaoyun Chen, Liqing Chen, Sha Liu, Yingchun Sun, Jiawen Yang, Bin Yang, Jianzhen Huang, Lusheng Huang
Summary: This study presents a genome-wide landscape of chromatin accessibility in 20 tissues of pigs using ATAC-seq. It identifies tissue-specific regulatory elements and reveals their associations with tissue-relevant biological functions. The study also investigates the presence of transposable elements in open chromatin regions and prioritizes a potential causal variant for polyunsaturated fatty acid in muscle tissue.
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Yahui Gao, Shuli Liu, Ransom L. E. Baldwin, Erin E. B. Connor, John B. Cole, Li Ma, Lingzhao Fang, Cong-jun E. Li, George E. Liu
Summary: In this study, we characterized the landscapes of bovine regulatory elements and investigated the dynamic changes of chromatin states during rumen development. We identified specific chromatin states associated with gene expression, DNA methylation, and important economic traits in cattle.
Review
Cardiac & Cardiovascular Systems
Tatiana Gromova, Natalie D. Gehred, Thomas M. Vondriska
Summary: This review explores the biological significance of cellular heterogeneity in the heart through an analysis of single-cell transcriptomics. It evaluates new models for cardiac function and discusses the role of cell-to-cell variability in development and disease. Additionally, emerging epigenomic approaches combined with single-cell RNA-sequencing are presented as tools to understand gene regulation and cell phenotype variability.
CARDIOVASCULAR RESEARCH
(2023)
Article
Biology
Divya Khattar, Sharlene Fernandes, John Snowball, Minzhe Guo, Matthew C. Gillen, Suchi Singh Jain, Debora Sinner, William Zacharias, Daniel T. Swarr, Edward E. Morrisey
Summary: The tips of developing respiratory buds are home to important progenitor cells marked by the expression of SOX9 and ID2. The transcription factors and PI3K signaling play a crucial role in controlling the proliferation and differentiation of these progenitor cells during lung organogenesis. This study demonstrates the importance of paired RNA and ATAC seq in defining regulatory networks in development.
Article
Biochemical Research Methods
Yingxin Cao, Laiyi Fu, Jie Wu, Qinke Peng, Qing Nie, Jing Zhang, Xiaohui Xie
Summary: The proposed deep generative model framework SAILER aims to learn a low-dimensional nonlinear latent representation of each cell from scATAC-seq data, ensuring independence from extrinsic confounding factors. Experimental results demonstrate that SAILER outperforms other methods in learning biologically more meaningful cell representations, leading to significant improvements in downstream analyses. SAILER can easily scale to process millions of cells and has been implemented into a software package for large-scale scATAC-seq data analysis.
Article
Genetics & Heredity
Maci L. Mueller, John B. Cole, Natalie K. Connors, David J. Johnston, Imtiaz A. S. Randhawa, Alison L. Van Eenennaam
Summary: The study demonstrates that strong selection pressure on polled will be necessary due to the limited number of polled Australian Brahman bulls in order to significantly increase the number of polled animals in this population. Additionally, these scenarios illustrate how gene editing could be used as a tool to accelerate the development of high-genetic-merit homozygous polled sires in the Australian Brahman population to mitigate the trade-off of slower genetic gain associated with decreasing HORNED allele frequency.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Daniel E. Goszczynski, Michelle M. Halstead, Alma D. Islas-Trejo, Huaijun Zhou, Pablo J. Ross
Summary: This study characterized transcription start sites in the bovine genome at high resolution using the RAMPAGE approach, identifying known and novel sites and producing a promoter activity atlas. Coexpression networks revealed tissue-specific promoter usage, with enrichment of binding factor motifs around coexpressed modules. The comprehensive annotation of promoters in a large collection of tissues will enhance understanding of gene expression in cattle and other mammalian species.
Article
Agriculture, Dairy & Animal Science
Ricardo Zamorano-Algandar, Miguel A. Sanchez-Castro, Ana Hernandez-Cordero, R. Mark Enns, Scott E. Speidel, Milton G. Thomas, Juan F. Medrano, Gonzalo Rincon, Jose C. Leyva-Corona, Guillermo Luna-Nevarez, Javier R. Reyna-Granados, Pablo Luna-Nevarez
Summary: This study successfully constructed molecular breeding values for fertility traits in heat-stressed Holstein cattle using candidate gene SNPs from the prolactin and GH-IGF1 pathways. Some gene SNPs were found to be associated with days open and pregnancy rate, but these SNPs only explained a small portion of the variation in pregnancy rate. Further research using denser SNP panels and a larger population is suggested to improve the power of molecular breeding values as genetic predictors for fertility traits in lactating dairy cows managed under warm environmental conditions.
Article
Multidisciplinary Sciences
Colin Kern, Ying Wang, Xiaoqin Xu, Zhangyuan Pan, Michelle Halstead, Ganrea Chanthavixay, Perot Saelao, Susan Waters, Ruidong Xiang, Amanda Chamberlain, Ian Korf, Mary E. Delany, Hans H. Cheng, Juan F. Medrano, Alison L. Van Eenennaam, Chris K. Tuggle, Catherine Ernst, Paul Flicek, Gerald Quon, Pablo Ross, Huaijun Zhou
Summary: Gene regulatory elements play a crucial role in animal genomes, with a core set of regulatory elements found to be functionally conserved across different species. These datasets offer a unique opportunity for comparative epigenomics and the agricultural research community.
NATURE COMMUNICATIONS
(2021)
Review
Genetics & Heredity
Jason C. Lin, Alison L. Van Eenennaam
Summary: Introducing genome editing reagents into mammalian zygotes via electroporation provides a simpler and more streamlined approach compared to traditional methods. Studies have examined parameters for mouse and rat zygotes, with limited reports on livestock zygotes. Delivery of genome editing reagents via electroporation can help reduce mosaicism, especially in large livestock species.
FRONTIERS IN GENETICS
(2021)
Review
Agriculture, Dairy & Animal Science
A. L. Van Eenennaam, S. J. Werth
Summary: Discussions on sustainability often involve competing goals, leading to conflicting outcomes. The role of livestock in sustainable diets is contentious, and the emerging market for alternative meats aims to reduce GHG emissions and animal agriculture, but may overlook the nutritional importance of ASF. Technological innovations are crucial for improving the efficiency of animal source, plant source, and cultured meat production in order to meet future demand sustainably and counteract misinformation that may hinder global food security.
Article
Veterinary Sciences
Deepak, Sharif S. Aly, William J. Love, Patricia C. Blanchard, Beate Crossley, Alison L. Van Eenennaam, Terry W. Lehenbauer
Summary: The study estimated the association of BRD risk factors in pre-weaned dairy calves in California. Female calves were more negatively impacted by failure of passive immunity transfer compared to male calves. Different pathogens had varying odds ratios, with Mannheimia haemolytica and Pasteurella multocida showing high associations with BRD. Age, sex, immune status, and pathogens all played a role in BRD occurrence in pre-weaned dairy calves.
PREVENTIVE VETERINARY MEDICINE
(2021)
Article
Multidisciplinary Sciences
Sadie L. Hennig, Joseph R. Owen, Jason C. Lin, Bret R. McNabb, Alison L. Van Eenennaam, James D. Murray
Summary: Dehorning in cattle using CRISPR-Cas9 gene editing to remove a 133 bp region including a 10 bp sequence resulted in embryos with mutations, but not necessarily the desired polled phenotype. The timing of injection post-insemination and the use of synthetic gRNAs both affected the deletion rate in the embryos, highlighting the complexity of genetic factors influencing horn development in cattle.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Mazdak Salavati, Shernae A. Woolley, Yennifer Cortes Araya, Michelle M. Halstead, Claire Stenhouse, Martin Johnsson, Cheryl J. Ashworth, Alan L. Archibald, Francesc X. Donadeu, Musa A. Hassan, Emily L. Clark
Summary: This research identified regulatory sequences in the pig genome through Omni-ATAC-Seq analysis of semitendinosus muscle from 24 male piglets. Over 50% of the open chromatin regions were found near known transcription start sites. Differential analysis revealed genomic regions with significantly different chromatin accessibility across developmental time points.
G3-GENES GENOMES GENETICS
(2022)
Article
Agriculture, Dairy & Animal Science
Carly I. O'Malley, Juan P. Steibel, Ronald O. Bates, Catherine W. Ernst, Janice M. Siegford
Summary: Background: Aggression in pigs is a welfare concern in the pig industry; Objective: To understand the changes in affiliative behaviors in pigs after mixing and their relationship to aggression; Results: Affiliative behaviors remained stable after mixing, with nosing decreasing and play and non-agonistic contact increasing; Affiliative behaviors were negatively related to aggression at mixing, but nosing and play behaviors were positively related to aggression in the following weeks; Conclusion: Promoting non-agonistic contact and other positive social behaviors may help reduce aggression among pigs.
Article
Multidisciplinary Sciences
Sadie L. Hennig, Bret R. McNabb, Josephine F. Trott, Alison L. Van Eenennaam, James D. Murray
Summary: A long intergenic non-coding RNA (lincRNA#1) is highly expressed in the horn bud region of polled bovine fetuses, but its absence alone does not result in a hornless phenotype.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Carolyn J. Lawrence-Dill, Robyn L. Allscheid, Albert Boaitey, Todd Bauman, Edward S. Buckler, Jennifer L. Clarke, Christopher Cullis, Jack Dekkers, Cassandra J. Dorius, Shawn F. Dorius, David Ertl, Matthew Homann, Guiping Hu, Mary Losch, Eric Lyons, Brenda Murdoch, Zahra-Katy Navabi, Somashekhar Punnuri, Fahad Rafiq, James M. Reecy, Patrick S. Schnable, Nicole M. Scott, Moira Sheehan, Xavier Sirault, Margaret Staton, Christopher K. Tuggle, Alison Van Eenennaam, Rachael Voas
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Jinghui Li, Dailu Guan, Michelle M. Halstead, Alma D. Islas-Trejo, Daniel E. Goszczynski, Catherine W. Ernst, Hao Cheng, Pablo Ross, Huaijun Zhou
Summary: The annotation of the pig transcriptome using long-read sequencing technology identified numerous novel transcripts and unannotated loci, with the highest expression in the cerebellum. Comparison with existing databases revealed matches to known transcripts and proteins.
Article
Biotechnology & Applied Microbiology
R. J. Corbett, L. M. Ford, J. M. Grabowski, C. W. Ernst
Summary: Fetal myogenesis is a critical period of porcine skeletal muscle development, and we investigated the DNA methylation patterns and gene expression changes during this process. We identified differentially methylated regions (DMRs) and found that most of them were hypomethylated during later stages of gestation. Integration of methylation and transcriptomic data revealed strong associations between differential gene methylation and expression, as well as negative correlation between miRNA methylation and abundance. Motif analysis suggested that DNA hypomethylation may increase accessibility of muscle-specific transcription factors. Furthermore, developmental DMRs were found to be enriched for GWAS SNPs related to muscle and meat traits, indicating the potential influence of epigenetic processes on phenotypic diversity.
Article
Multidisciplinary Sciences
Julie A. Finzel, Austin R. Brown, Roselle C. Busch, Morgan P. Doran, John M. Harper, Daniel K. Macon, Rebecca K. Ozeran, Morgan R. Stegemiller, Karissa Isaacs, Alison Van Eenennaam
Summary: Despite being available for over a decade, adoption of electronic identification ear tags (EID) and DNA testing among commercial range sheep producers in the Western United States has been low. This project involved collaboration with five California sheep producers to demonstrate the potential of these technologies in improving flock health and reproductive management.