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Sparling BA, Ng TT, Carlo-Allende A, McCarthy FM, Taylor RL, Drechsler Y. Immunoglobulin-like receptors in chickens: identification, functional characterization, and renaming to cluster homolog of immunoglobulin-like receptors. Poult Sci 2024; 103:103292. [PMID: 38100950 PMCID: PMC10764270 DOI: 10.1016/j.psj.2023.103292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
The cluster homolog of immunoglobulin-like receptors (CHIRs), previously known as the "chicken homolog of immunogloublin-like receptors," represents is a large group of transmembrane glycoproteins that direct the immune response. However, the full repertoire of putatively activating, inhibitory, or dual function CHIRA, CHIRB, and CHIRAB on chickens' immune responses is poorly understood. Herein, the study objective was to determine the genes encoding CHIR proteins and predict their function by searching canonical protein structure. A bioinformatics pipeline based on previous work was employed to search for the CHIRs from the newly updated broiler and layer genomes. The categorization into CHIRA, CHIRB, and CHIRAB types was assigned through motif searches, multiple sequence alignment, and phylogeny. In total, 150 protein-encoding genes on Chromosome 31 were identified as CHIRs. Gene members of each functional group (CHIRA, CHIRB, CHIRAB) were classified in accordance with previously recognized proteins. The genes were renamed to "cluster homolog of immunoglobulin-like receptors" (CHIRs) to allow for the naming of orthologous genes in other avian species. Additionally, expression analysis of the classified CHIRs across various reinforces their importance as immune regulators and activation in inflammatory tissues. Furthermore, over 1,000 diverse and rare CHIRs variants associated with differential Marek's disease response (P < 0.05) emphasize the impact of CHIRs on shaping avian immune responses in diverse contexts. The practical applications of these findings encompass advancing immunology, improving poultry health management, optimizing breeding programs for disease resistance, and enhancing overall animal health through a deeper understanding of the roles and functions of CHIRA, CHIRB, and CHIRAB types in avian immune responses.
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Affiliation(s)
- Brandi A Sparling
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766, USA; Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Theros T Ng
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Anaid Carlo-Allende
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Fiona M McCarthy
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Robert L Taylor
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Yvonne Drechsler
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766, USA; Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA.
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2
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Roth C, Venu V, Job V, Lubbers N, Sanbonmatsu KY, Steadman CR, Starkenburg SR. Improved quality metrics for association and reproducibility in chromatin accessibility data using mutual information. BMC Bioinformatics 2023; 24:441. [PMID: 37990143 PMCID: PMC10664258 DOI: 10.1186/s12859-023-05553-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Correlation metrics are widely utilized in genomics analysis and often implemented with little regard to assumptions of normality, homoscedasticity, and independence of values. This is especially true when comparing values between replicated sequencing experiments that probe chromatin accessibility, such as assays for transposase-accessible chromatin via sequencing (ATAC-seq). Such data can possess several regions across the human genome with little to no sequencing depth and are thus non-normal with a large portion of zero values. Despite distributed use in the epigenomics field, few studies have evaluated and benchmarked how correlation and association statistics behave across ATAC-seq experiments with known differences or the effects of removing specific outliers from the data. Here, we developed a computational simulation of ATAC-seq data to elucidate the behavior of correlation statistics and to compare their accuracy under set conditions of reproducibility. RESULTS Using these simulations, we monitored the behavior of several correlation statistics, including the Pearson's R and Spearman's [Formula: see text] coefficients as well as Kendall's [Formula: see text] and Top-Down correlation. We also test the behavior of association measures, including the coefficient of determination R[Formula: see text], Kendall's W, and normalized mutual information. Our experiments reveal an insensitivity of most statistics, including Spearman's [Formula: see text], Kendall's [Formula: see text], and Kendall's W, to increasing differences between simulated ATAC-seq replicates. The removal of co-zeros (regions lacking mapped sequenced reads) between simulated experiments greatly improves the estimates of correlation and association. After removing co-zeros, the R[Formula: see text] coefficient and normalized mutual information display the best performance, having a closer one-to-one relationship with the known portion of shared, enhanced loci between simulated replicates. When comparing values between experimental ATAC-seq data using a random forest model, mutual information best predicts ATAC-seq replicate relationships. CONCLUSIONS Collectively, this study demonstrates how measures of correlation and association can behave in epigenomics experiments. We provide improved strategies for quantifying relationships in these increasingly prevalent and important chromatin accessibility assays.
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Affiliation(s)
- Cullen Roth
- Los Alamos National Laboratory, Genomics and Bioanalytics, Los Alamos, NM, USA.
| | - Vrinda Venu
- Los Alamos National Laboratory, Climate, Ecosystems, and Environmental Science, Los Alamos, NM, USA
| | - Vanessa Job
- Los Alamos National Laboratory, High Performance Computing and Design, Los Alamos, NM, USA
| | - Nicholas Lubbers
- Los Alamos National Laboratory, Information Sciences, Los Alamos, NM, USA
| | - Karissa Y Sanbonmatsu
- Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, NM, USA
| | - Christina R Steadman
- Los Alamos National Laboratory, Climate, Ecosystems, and Environmental Science, Los Alamos, NM, USA
| | - Shawn R Starkenburg
- Los Alamos National Laboratory, Genomics and Bioanalytics, Los Alamos, NM, USA
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3
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Pan Z, Wang Y, Wang M, Wang Y, Zhu X, Gu S, Zhong C, An L, Shan M, Damas J, Halstead MM, Guan D, Trakooljul N, Wimmers K, Bi Y, Wu S, Delany ME, Bai X, Cheng HH, Sun C, Yang N, Hu X, Lewin HA, Fang L, Zhou H. An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics. SCIENCE ADVANCES 2023; 9:eade1204. [PMID: 37134160 PMCID: PMC10156120 DOI: 10.1126/sciadv.ade1204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A comprehensive characterization of regulatory elements in the chicken genome across tissues will have substantial impacts on both fundamental and applied research. Here, we systematically identified and characterized regulatory elements in the chicken genome by integrating 377 genome-wide sequencing datasets from 23 adult tissues. In total, we annotated 1.57 million regulatory elements, representing 15 distinct chromatin states, and predicted about 1.2 million enhancer-gene pairs and 7662 super-enhancers. This functional annotation of the chicken genome should have wide utility on identifying regulatory elements accounting for gene regulation underlying domestication, selection, and complex trait regulation, which we explored. In short, this comprehensive atlas of regulatory elements provides the scientific community with a valuable resource for chicken genetics and genomics.
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Affiliation(s)
- Zhangyuan Pan
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ying Wang
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Mingshan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650000, China
| | - Yuzhe Wang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Xiaoning Zhu
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Shenwen Gu
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Conghao Zhong
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Liqi An
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Mingzhu Shan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Joana Damas
- The Genome Center, University of California, Davis, CA 95616, USA
| | - Michelle M Halstead
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Dailu Guan
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Nares Trakooljul
- Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Klaus Wimmers
- Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
- Faculty of Agricultural and Environmental Sciences, University Rostock, Rostock, Germany
| | - Ye Bi
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Shang Wu
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Mary E Delany
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Xuechen Bai
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Hans H Cheng
- USDA-ARS, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, USA
| | - Congjiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Xiaoxiang Hu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650000, China
| | - Harris A Lewin
- The Genome Center, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, DK
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
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4
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Wong YY, Harbison JE, Hope CM, Gundsambuu B, Brown KA, Wong SW, Brown CY, Couper JJ, Breen J, Liu N, Pederson SM, Köhne M, Klee K, Schultze J, Beyer M, Sadlon T, Barry SC. Parallel recovery of chromatin accessibility and gene expression dynamics from frozen human regulatory T cells. Sci Rep 2023; 13:5506. [PMID: 37016052 PMCID: PMC10073253 DOI: 10.1038/s41598-023-32256-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 03/24/2023] [Indexed: 04/06/2023] Open
Abstract
Epigenetic features such as DNA accessibility dictate transcriptional regulation in a cell type- and cell state- specific manner, and mapping this in health vs. disease in clinically relevant material is opening the door to new mechanistic insights and new targets for therapy. Assay for Transposase Accessible Chromatin Sequencing (ATAC-seq) allows chromatin accessibility profiling from low cell input, making it tractable on rare cell populations, such as regulatory T (Treg) cells. However, little is known about the compatibility of the assay with cryopreserved rare cell populations. Here we demonstrate the robustness of an ATAC-seq protocol comparing primary Treg cells recovered from fresh or cryopreserved PBMC samples, in the steady state and in response to stimulation. We extend this method to explore the feasibility of conducting simultaneous quantitation of chromatin accessibility and transcriptome from a single aliquot of 50,000 cryopreserved Treg cells. Profiling of chromatin accessibility and gene expression in parallel within the same pool of cells controls for cellular heterogeneity and is particularly beneficial when constrained by limited input material. Overall, we observed a high correlation of accessibility patterns and transcription factor dynamics between fresh and cryopreserved samples. Furthermore, highly similar transcriptomic profiles were obtained from whole cells and from the supernatants recovered from ATAC-seq reactions. We highlight the feasibility of applying these techniques to profile the epigenomic landscape of cells recovered from cryopreservation biorepositories.
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Affiliation(s)
- Ying Y Wong
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Jessica E Harbison
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
- Women's and Children's Hospital, North Adelaide, Australia
| | - Christopher M Hope
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
- Women's and Children's Hospital, North Adelaide, Australia
| | | | - Katherine A Brown
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Soon W Wong
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Cheryl Y Brown
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
- Women's and Children's Hospital, North Adelaide, Australia
| | - Jennifer J Couper
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
- Women's and Children's Hospital, North Adelaide, Australia
| | - Jimmy Breen
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Ning Liu
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Stephen M Pederson
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Maren Köhne
- German Center for Neurodegenerative Diseases, University of Bonn, Bonn, Germany
| | - Kathrin Klee
- German Center for Neurodegenerative Diseases, University of Bonn, Bonn, Germany
| | - Joachim Schultze
- German Center for Neurodegenerative Diseases, University of Bonn, Bonn, Germany
| | - Marc Beyer
- German Center for Neurodegenerative Diseases, University of Bonn, Bonn, Germany
| | - Timothy Sadlon
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
- Women's and Children's Hospital, North Adelaide, Australia
| | - Simon C Barry
- Robinson Research Institute, University of Adelaide, Adelaide, Australia.
- Women's and Children's Hospital, North Adelaide, Australia.
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5
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de Vos J, Crooijmans RP, Derks MF, Kloet SL, Dibbits B, Groenen MA, Madsen O. Detailed molecular and epigenetic characterization of the pig IPEC-J2 and chicken SL-29 cell lines. iScience 2023; 26:106252. [PMID: 36936794 PMCID: PMC10018572 DOI: 10.1016/j.isci.2023.106252] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 12/05/2022] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The pig IPEC-J2 and chicken SL-29 cell lines are of interest because of their untransformed nature and wide use in functional studies. Molecular characterization of these cell lines is important to gain insight into possible molecular aberrations. The aim of this paper is to provide a molecular and epigenetic characterization of the IPEC-J2 and SL-29 cell lines, a cell-line reference for the FAANG community, and future biomedical research. Whole genome sequencing, gene expression, DNA methylation, chromatin accessibility, and ChIP-seq of four histone marks (H3K4me1, H3K4me3, H3K27ac, H3K27me3) and an insulator (CTCF) are used to achieve these aims. Heteroploidy (aneuploidy) of various chromosomes was observed from whole genome sequencing analysis in both cell lines. Furthermore, higher gene expression for genes located on chromosomes with aneuploidy in comparison to diploid chromosomes was observed. Regulatory complexity of gene expression, DNA methylation, and chromatin accessibility was investigated through an integrative approach.
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Affiliation(s)
- Jani de Vos
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen 6708PB, the Netherlands
- Corresponding author
| | | | - Martijn F.L. Derks
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen 6708PB, the Netherlands
| | - Susan L. Kloet
- Human Genetics, Leids Universitair Medisch Centrum, Leiden 2333ZC, the Netherlands
| | - Bert Dibbits
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen 6708PB, the Netherlands
| | - Martien A.M. Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen 6708PB, the Netherlands
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen 6708PB, the Netherlands
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6
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Peng S, Dahlgren AR, Donnelly CG, Hales EN, Petersen JL, Bellone RR, Kalbfleisch T, Finno CJ. Functional annotation of the animal genomes: An integrated annotation resource for the horse. PLoS Genet 2023; 19:e1010468. [PMID: 36862752 PMCID: PMC10013926 DOI: 10.1371/journal.pgen.1010468] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/14/2023] [Accepted: 01/28/2023] [Indexed: 03/03/2023] Open
Abstract
The genomic sequence of the horse has been available since 2009, providing critical resources for discovering important genomic variants regarding both animal health and population structures. However, to fully understand the functional implications of these variants, detailed annotation of the horse genome is required. Due to the limited availability of functional data for the equine genome, as well as the technical limitations of short-read RNA-seq, existing annotation of the equine genome contains limited information about important aspects of gene regulation, such as alternate isoforms and regulatory elements, which are either not transcribed or transcribed at a very low level. To solve above problems, the Functional Annotation of the Animal Genomes (FAANG) project proposed a systemic approach to tissue collection, phenotyping, and data generation, adopting the blueprint laid out by the Encyclopedia of DNA Elements (ENCODE) project. Here we detail the first comprehensive overview of gene expression and regulation in the horse, presenting 39,625 novel transcripts, 84,613 candidate cis-regulatory elements (CRE) and their target genes, 332,115 open chromatin regions genome wide across a diverse set of tissues. We showed substantial concordance between chromatin accessibility, chromatin states in different genic features and gene expression. This comprehensive and expanded set of genomics resources will provide the equine research community ample opportunities for studies of complex traits in the horse.
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Affiliation(s)
- Sichong Peng
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Anna R. Dahlgren
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Callum G. Donnelly
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Erin N. Hales
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Jessica L. Petersen
- Department of Animal Science, University of Nebraska—Lincoln, Lincoln, Nebraska, United States of America
| | - Rebecca R. Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Ted Kalbfleisch
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, United States of America
| | - Carrie J. Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
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7
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Zhu XN, Wang YZ, Li C, Wu HY, Zhang R, Hu XX, Zhang R, Hu XX. Chicken chromatin accessibility atlas accelerates epigenetic annotation of birds and gene fine-mapping associated with growth traits. Zool Res 2023; 44:53-62. [PMID: 36317479 PMCID: PMC9841184 DOI: 10.24272/j.issn.2095-8137.2022.228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The development of epigenetic maps, such as the ENCODE project in humans, provides resources for gene regulation studies and a reference for research of disease-related regulatory elements. However, epigenetic information, such as a bird-specific chromatin accessibility atlas, is currently lacking for the thousands of bird species currently described. The major genomic difference between birds and mammals is their shorter introns and intergenic distances, which seriously hinders the use of humans and mice as a reference for studying the function of important regulatory regions in birds. In this study, using chicken as a model bird species, we systematically compiled a chicken chromatin accessibility atlas using 53 Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) samples across 11 tissues. An average of 50 796 open chromatin regions were identified per sample, cumulatively accounting for 20.36% of the chicken genome. Tissue specificity was largely reflected by differences in intergenic and intronic peaks, with specific functional regulation achieved by two mechanisms: recruitment of several sequence-specific transcription factors and direct regulation of adjacent functional genes. By integrating data from genome-wide association studies, our results suggest that chicken body weight is driven by different regulatory variants active in growth-relevant tissues. We propose CAB39L (active in the duodenum), RCBTB1 (muscle and liver), and novel long non-coding RNA ENSGALG00000053256 (bone) as candidate genes regulating chicken body weight. Overall, this study demonstrates the value of epigenetic data in fine-mapping functional variants and provides a compendium of resources for further research on the epigenetics and evolution of birds and mammals.
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Affiliation(s)
- Xiao-Ning Zhu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yu-Zhe Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China,National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing 100193, China,E-mail:
| | - Chong Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Han-Yu Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China,National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing 100193, China
| | - Ran Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiao-Xiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China,National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing 100193, China,
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8
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Jiang H, Sun M, Zhao Y, Liu G, Zhong L, Xue H, Chen X, Zheng Y, Wang M. The early function of cortisol in liver during Aeromonas hydrophila infection: Dynamics of the transcriptome and accessible chromatin landscapes. Front Immunol 2022; 13:989075. [PMID: 36532002 PMCID: PMC9751032 DOI: 10.3389/fimmu.2022.989075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/17/2022] [Indexed: 12/02/2022] Open
Abstract
In China, channel catfish (Ictalurus punctatus) is an important aquaculture species; however, haemorrhagic disease (Aeromonas hydrophila induced disease) in these fish has caused tremendous economic loss due to high morbidity and mass mortality in the breeding industry. The role of cortisol in bacterial diseases, particularly in the acute phase, remains unclear. In this study, liver transcriptome (RNA-seq) and chromatin accessibility (ATAC-seq) analyses were employed to investigate the early functional role of cortisol in Aeromonas hydrophila-stimulated responses. Our experiments confirmed that A. hydrophila infection can initially significantly increase serum cortisol levels at 1 h after infection. At this time point, the increased serum cortisol levels can significantly regulate A. hydrophila-regulated genes by affecting both transcriptome and chromatin accessibility. Cross-analysis of RNA-seq and ATAC-seq revealed that a certain gene group (92 target_DEGs) was regulated at an early time point by cortisol. KEGG enrichment analysis revealed that the top three pathways according to target_DEGs were cancer, glutathione metabolism, and the Notch signalling pathway. The protein-protein interaction analysis of target_DEGs revealed that they may be primarily involved in cell proliferation, CD8+ T cell function, glutathione synthesis, and activation of the NF-κB signalling pathway. This suggests that after the emergence of immune stress, the early regulation of cortisol is positive against the immune response. It is possible that in this situation, the animal is attempting to avoid dangerous situations and risks and then cope with the imbalance produced by the stressor to ultimately restore homeostasis. Our results will contribute to future research on fish and provide valuable insight regarding the mechanism of immune regulation by cortisol and the study of bacterial haemorrhagic disease in channel catfish.
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9
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Jafari E, Johnson T, Wang Y, Liu Y, Huang K, Wang Y. AIscEA: unsupervised integration of single-cell gene expression and chromatin accessibility via their biological consistency. Bioinformatics 2022; 38:5236-5244. [PMID: 36250795 PMCID: PMC9710555 DOI: 10.1093/bioinformatics/btac683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION The integrative analysis of single-cell gene expression and chromatin accessibility measurements is essential for revealing gene regulation, but it is one of the key challenges in computational biology. Gene expression and chromatin accessibility are measurements from different modalities, and no common features can be directly used to guide integration. Current state-of-the-art methods lack practical solutions for finding heterogeneous clusters. However, previous methods might not generate reliable results when cluster heterogeneity exists. More importantly, current methods lack an effective way to select hyper-parameters under an unsupervised setting. Therefore, applying computational methods to integrate single-cell gene expression and chromatin accessibility measurements remains difficult. RESULTS We introduce AIscEA-Alignment-based Integration of single-cell gene Expression and chromatin Accessibility-a computational method that integrates single-cell gene expression and chromatin accessibility measurements using their biological consistency. AIscEA first defines a ranked similarity score to quantify the biological consistency between cell clusters across measurements. AIscEA then uses the ranked similarity score and a novel permutation test to identify cluster alignment across measurements. AIscEA further utilizes graph alignment for the aligned cell clusters to align the cells across measurements. We compared AIscEA with the competing methods on several benchmark datasets and demonstrated that AIscEA is highly robust to the choice of hyper-parameters and can better handle the cluster heterogeneity problem. Furthermore, AIscEA significantly outperforms the state-of-the-art methods when integrating real-world SNARE-seq and scMultiome-seq datasets in terms of integration accuracy. AVAILABILITY AND IMPLEMENTATION AIscEA is available at https://figshare.com/articles/software/AIscEA_zip/21291135 on FigShare as well as {https://github.com/elhaam/AIscEA} onGitHub. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Elham Jafari
- Computer Science Department, Indiana University, Bloomington, IN 47408, USA
| | - Travis Johnson
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yue Wang
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yunlong Liu
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Kun Huang
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yijie Wang
- Computer Science Department, Indiana University, Bloomington, IN 47408, USA
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10
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Chen Y, Zhang T, Xian M, Zhang R, Yang W, Su B, Yang G, Sun L, Xu W, Xu S, Gao H, Xu L, Gao X, Li J. A draft genome of Drung cattle reveals clues to its chromosomal fusion and environmental adaptation. Commun Biol 2022; 5:353. [PMID: 35418663 PMCID: PMC9008013 DOI: 10.1038/s42003-022-03298-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 03/21/2022] [Indexed: 12/02/2022] Open
Abstract
Drung cattle (Bos frontalis) have 58 chromosomes, differing from the Bos taurus 2n = 60 karyotype. To date, its origin and evolution history have not been proven conclusively, and the mechanisms of chromosome fusion and environmental adaptation have not been clearly elucidated. Here, we assembled a high integrity and good contiguity genome of Drung cattle with 13.7-fold contig N50 and 4.1-fold scaffold N50 improvements over the recently published Indian mithun assembly, respectively. Speciation time estimation and phylogenetic analysis showed that Drung cattle diverged from Bos taurus into an independent evolutionary clade. Sequence evidence of centromere regions provides clues to the breakpoints in BTA2 and BTA28 centromere satellites. We furthermore integrated a circulation and contraction-related biological process involving 43 evolutionary genes that participated in pathways associated with the evolution of the cardiovascular system. These findings may have important implications for understanding the molecular mechanisms of chromosome fusion, alpine valleys adaptability and cardiovascular function.
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Affiliation(s)
- Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Tianliu Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Ming Xian
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Rui Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Weifei Yang
- 1 Gene Co., Ltd, 310051, Hangzhou, P.R. China
- Annoroad Gene Technology (Beijing) Co., Ltd, 100176, Beijing, P.R. China
| | - Baqi Su
- Drung Cattle Conservation Farm in Jiudang Wood, Drung and Nu Minority Autonomous County, Gongshan, 673500, Kunming, Yunnan, P.R. China
| | - Guoqiang Yang
- Livestock and Poultry Breed Improvement Center, Nujiang Lisu Minority Autonomous Prefecture, 673199, Kunming, Yunnan, P.R. China
| | - Limin Sun
- Yunnan Animal Husbandry Service, 650224, Kunming, Yunnan, P.R. China
| | - Wenkun Xu
- Yunnan Animal Husbandry Service, 650224, Kunming, Yunnan, P.R. China
| | - Shangzhong Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China.
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China.
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11
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Merrill CB, Pabon MA, Montgomery AB, Rodan AR, Rothenfluh A. Optimized assay for transposase-accessible chromatin by sequencing (ATAC-seq) library preparation from adult Drosophila melanogaster neurons. Sci Rep 2022; 12:6043. [PMID: 35411004 PMCID: PMC9001676 DOI: 10.1038/s41598-022-09869-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/14/2022] [Indexed: 01/07/2023] Open
Abstract
Assay for transposase-accessible chromatin by sequencing (ATAC-seq) is rapidly becoming the assay of choice to investigate chromatin-mediated gene regulation, largely because of low input requirements, a fast workflow, and the ability to interrogate the entire genome in an untargeted manner. Many studies using ATAC-seq use mammalian or human-derived tissues, and established protocols work well in these systems. However, ATAC-seq is not yet widely used in Drosophila. Vinegar flies present several advantages over mammalian systems that make them an excellent model for ATAC-seq studies, including abundant genetic tools that allow straightforward targeting, transgene expression, and genetic manipulation that are not available in mammalian models. Because current ATAC-seq protocols are not optimized to use flies, we developed an optimized workflow that accounts for several complicating factors present in Drosophila. We examined parameters affecting nuclei isolation, including input size, freezing time, washing, and possible confounds from retinal pigments. Then, we optimized the enzymatic steps of library construction to account for the smaller Drosophila genome size. Finally, we used our optimized protocol to generate ATAC-seq libraries that meet ENCODE quality metrics. Our optimized protocol enables extensive ATAC-seq experiments in Drosophila, thereby leveraging the advantages of this powerful model system to understand chromatin-mediated gene regulation.
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Affiliation(s)
- Collin B. Merrill
- grid.223827.e0000 0001 2193 0096Department of Psychiatry, Huntsman Mental Health Institute, University of Utah, Salt Lake City, UT 84108 USA
| | - Miguel A. Pabon
- grid.223827.e0000 0001 2193 0096Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112 USA
| | - Austin B. Montgomery
- grid.223827.e0000 0001 2193 0096Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112 USA
| | - Aylin R. Rodan
- grid.223827.e0000 0001 2193 0096Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112 USA ,grid.223827.e0000 0001 2193 0096Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah, Salt Lake City, UT 84112 USA ,grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 USA ,grid.280807.50000 0000 9555 3716Medical Service, Veterans Affairs Salt Lake City Health Care System, Salt Lake City, UT 84148 USA
| | - Adrian Rothenfluh
- grid.223827.e0000 0001 2193 0096Department of Psychiatry, Huntsman Mental Health Institute, University of Utah, Salt Lake City, UT 84108 USA ,grid.223827.e0000 0001 2193 0096Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112 USA ,grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 USA ,grid.223827.e0000 0001 2193 0096Department of Neurobiology, University of Utah, Salt Lake City, UT 84112 USA
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12
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Salavati M, Woolley SA, Cortés Araya Y, Halstead MM, Stenhouse C, Johnsson M, Ashworth CJ, Archibald AL, Donadeu FX, Hassan MA, Clark EL. Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions. G3 (BETHESDA, MD.) 2022; 12:6460335. [PMID: 34897420 PMCID: PMC9210303 DOI: 10.1093/g3journal/jkab424] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the "Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)" to identify putative regulatory regions in flash-frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest-, average-, and largest-sized male piglets from each litter through five developmental time points. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs.
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Affiliation(s)
- Mazdak Salavati
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Shernae A Woolley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Yennifer Cortés Araya
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Michelle M Halstead
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA
| | - Claire Stenhouse
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA
| | - Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Cheryl J Ashworth
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Alan L Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Francesc X Donadeu
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Musa A Hassan
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Emily L Clark
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
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13
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Cao X, Cheng J, Huang Y, Lan X, Lei C, Chen H. Comparative Enhancer Map of Cattle Muscle Genome Annotated by ATAC-Seq. Front Vet Sci 2022; 8:782409. [PMID: 34977215 PMCID: PMC8715921 DOI: 10.3389/fvets.2021.782409] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/12/2021] [Indexed: 11/13/2022] Open
Abstract
Annotating regulatory elements could benefit the interpretation of the molecular mechanism of genome-wide association study (GWAS) hits. In this work, we performed transposase-accessible chromatin with sequencing (ATAC-seq) to annotate the cattle muscle genome's functional elements. A total of 10,023 and 11,360 peaks were revealed in muscle genomes of adult and embryo cattle, respectively. The two peak sets produced 8,850 differentially accessible regions (DARs), including 2,515 promoters and 4,319 putative enhancers. These functional elements were associated with the cell cycle, muscle development, and lipid metabolism. A total of 15 putative enhancers were selected for a dual-luciferase reporter assay, and 12 of them showed enhancer activity in cattle myoblasts. Interestingly, the GeneHancer database has annotated the interactions of eight active enhancers with gene promoters, such as embryo-specific peak1053 (log2FC = 1.81, embryo/adult, E/A) with ligand-dependent nuclear receptor corepressor-like protein (LCORL) and embryo-specific peak4218 (log2FC = 1.81) with FERM domain-containing 8 (FRMD8). A total of 295 GWAS loci from the animal QTL database were mapped to 183 putative enhancers, including rs109554838 (associated with cattle body weight and average daily gain) to peak1053 and rs110294629 (associated with beef shear force and tenderness score) to peak4218. Notably, peak4218 has been found to be involved in mouse embryo development. Deleting peak4218 clearly reduced luciferase activity (P = 3.30E-04). Our comparative enhancer map is expected to benefit the area of beef cattle breeding.
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Affiliation(s)
- Xiukai Cao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Jie Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,College of Animal Science, Xinjiang Agricultural University, Urumqi, China
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14
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Peng S, Petersen JL, Bellone RR, Kalbfleisch T, Kingsley NB, Barber AM, Cappelletti E, Giulotto E, Finno CJ. Decoding the Equine Genome: Lessons from ENCODE. Genes (Basel) 2021; 12:genes12111707. [PMID: 34828313 PMCID: PMC8625040 DOI: 10.3390/genes12111707] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/24/2021] [Accepted: 10/26/2021] [Indexed: 12/23/2022] Open
Abstract
The horse reference genome assemblies, EquCab2.0 and EquCab3.0, have enabled great advancements in the equine genomics field, from tools to novel discoveries. However, significant gaps of knowledge regarding genome function remain, hindering the study of complex traits in horses. In an effort to address these gaps and with inspiration from the Encyclopedia of DNA Elements (ENCODE) project, the equine Functional Annotation of Animal Genome (FAANG) initiative was proposed to bridge the gap between genome and gene expression, providing further insights into functional regulation within the horse genome. Three years after launching the initiative, the equine FAANG group has generated data from more than 400 experiments using over 50 tissues, targeting a variety of regulatory features of the equine genome. In this review, we examine how valuable lessons learned from the ENCODE project informed our decisions in the equine FAANG project. We report the current state of the equine FAANG project and discuss how FAANG can serve as a template for future expansion of functional annotation in the equine genome and be used as a reference for studies of complex traits in horse. A well-annotated reference functional atlas will also help advance equine genetics in the pan-genome and precision medicine era.
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Affiliation(s)
- Sichong Peng
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA; (S.P.); (R.R.B.); (N.B.K.)
| | - Jessica L. Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE 68583-0908, USA; (J.L.P.); (A.M.B.)
| | - Rebecca R. Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA; (S.P.); (R.R.B.); (N.B.K.)
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Ted Kalbfleisch
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40503, USA;
| | - N. B. Kingsley
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA; (S.P.); (R.R.B.); (N.B.K.)
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Alexa M. Barber
- Department of Animal Science, University of Nebraska, Lincoln, NE 68583-0908, USA; (J.L.P.); (A.M.B.)
| | - Eleonora Cappelletti
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (E.C.); (E.G.)
| | - Elena Giulotto
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (E.C.); (E.G.)
| | - Carrie J. Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA; (S.P.); (R.R.B.); (N.B.K.)
- Correspondence:
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15
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Pan Z, Yao Y, Yin H, Cai Z, Wang Y, Bai L, Kern C, Halstead M, Chanthavixay G, Trakooljul N, Wimmers K, Sahana G, Su G, Lund MS, Fredholm M, Karlskov-Mortensen P, Ernst CW, Ross P, Tuggle CK, Fang L, Zhou H. Pig genome functional annotation enhances the biological interpretation of complex traits and human disease. Nat Commun 2021; 12:5848. [PMID: 34615879 PMCID: PMC8494738 DOI: 10.1038/s41467-021-26153-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 09/20/2021] [Indexed: 02/08/2023] Open
Abstract
The functional annotation of livestock genomes is crucial for understanding the molecular mechanisms that underpin complex traits of economic importance, adaptive evolution and comparative genomics. Here, we provide the most comprehensive catalogue to date of regulatory elements in the pig (Sus scrofa) by integrating 223 epigenomic and transcriptomic data sets, representing 14 biologically important tissues. We systematically describe the dynamic epigenetic landscape across tissues by functionally annotating 15 different chromatin states and defining their tissue-specific regulatory activities. We demonstrate that genomic variants associated with complex traits and adaptive evolution in pig are significantly enriched in active promoters and enhancers. Furthermore, we reveal distinct tissue-specific regulatory selection between Asian and European pig domestication processes. Compared with human and mouse epigenomes, we show that porcine regulatory elements are more conserved in DNA sequence, under both rapid and slow evolution, than those under neutral evolution across pig, mouse, and human. Finally, we provide biological insights on tissue-specific regulatory conservation, and by integrating 47 human genome-wide association studies, we demonstrate that, depending on the traits, mouse or pig might be more appropriate biomedical models for different complex traits and diseases.
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Affiliation(s)
- Zhangyuan Pan
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Yuelin Yao
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Hongwei Yin
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Zexi Cai
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, 8300, Denmark
| | - Ying Wang
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Lijing Bai
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Colin Kern
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Michelle Halstead
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Ganrea Chanthavixay
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | | | - Klaus Wimmers
- Leibniz-Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, 8300, Denmark
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, 8300, Denmark
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, 8300, Denmark
| | - Merete Fredholm
- Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederikgsberg C, 1870, Denmark
| | - Peter Karlskov-Mortensen
- Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederikgsberg C, 1870, Denmark
| | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Pablo Ross
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | | | - Lingzhao Fang
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, EH4 2XU, UK.
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, Davis, CA, USA.
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16
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Peng S, Bellone R, Petersen JL, Kalbfleisch TS, Finno CJ. Successful ATAC-Seq From Snap-Frozen Equine Tissues. Front Genet 2021; 12:641788. [PMID: 34220931 PMCID: PMC8242358 DOI: 10.3389/fgene.2021.641788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/21/2021] [Indexed: 11/20/2022] Open
Abstract
An assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) has become an increasingly popular method to assess genome-wide chromatin accessibility in isolated nuclei from fresh tissues. However, many biobanks contain only snap-frozen tissue samples. While ATAC-seq has been applied to frozen brain tissues in human, its applicability in a wide variety of tissues in horse remains unclear. The Functional Annotation of Animal Genome (FAANG) project is an international collaboration aimed to provide high quality functional annotation of animal genomes. The equine FAANG initiative has generated a biobank of over 80 tissues from two reference female animals and experiments to begin to characterize tissue specificity of genome function for prioritized tissues have been performed. Due to the logistics of tissue collection and storage, extracting nuclei from a large number of tissues for ATAC-seq at the time of collection is not always practical. To assess the feasibility of using stored frozen tissues for ATAC-seq and to provide a guideline for the equine FAANG project, we compared ATAC-seq results from nuclei isolated from frozen tissue to cryopreserved nuclei (CN) isolated at the time of tissue harvest in liver, a highly cellular homogenous tissue, and lamina, a relatively acellular tissue unique to the horse. We identified 20,000-33,000 accessible chromatin regions in lamina and 22-61,000 in liver, with consistently more peaks identified using CN isolated at time of tissue collection. Our results suggest that frozen tissues are an acceptable substitute when CN are not available. For more challenging tissues such as lamina, nuclei extraction at the time of tissue collection is still preferred for optimal results. Therefore, tissue type and accessibility to intact nuclei should be considered when designing ATAC-seq experiments.
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Affiliation(s)
- Sichong Peng
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Rebecca Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Jessica L. Petersen
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Theodore S. Kalbfleisch
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY, United States
| | - Carrie J. Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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17
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Kern C, Wang Y, Xu X, Pan Z, Halstead M, Chanthavixay G, Saelao P, Waters S, Xiang R, Chamberlain A, Korf I, Delany ME, Cheng HH, Medrano JF, Van Eenennaam AL, Tuggle CK, Ernst C, Flicek P, Quon G, Ross P, Zhou H. Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research. Nat Commun 2021; 12:1821. [PMID: 33758196 PMCID: PMC7988148 DOI: 10.1038/s41467-021-22100-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/01/2021] [Indexed: 01/31/2023] Open
Abstract
Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. The Functional Annotation of Animal Genomes consortium was formed to collaboratively annotate the functional elements in animal genomes, starting with domesticated animals. Here we present an expansive collection of datasets from eight diverse tissues in three important agricultural species: chicken (Gallus gallus), pig (Sus scrofa), and cattle (Bos taurus). Comparative analysis of these datasets and those from the human and mouse Encyclopedia of DNA Elements projects reveal that a core set of regulatory elements are functionally conserved independent of divergence between species, and that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes are also conserved. These datasets represent a unique opportunity for the emerging field of comparative epigenomics, as well as the agricultural research community, including species that are globally important food resources.
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Affiliation(s)
- Colin Kern
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Ying Wang
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Xiaoqin Xu
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Zhangyuan Pan
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Michelle Halstead
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Ganrea Chanthavixay
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Perot Saelao
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Susan Waters
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Ruidong Xiang
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Amanda Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Ian Korf
- Genome Center, University of California, Davis, Davis, CA, USA
| | - Mary E Delany
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Hans H Cheng
- USDA-ARS, Avian Disease and Oncology Laboratory, East Lansing, MI, USA
| | - Juan F Medrano
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | | | - Chris K Tuggle
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Catherine Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Gerald Quon
- Department of Molecular and Cellular Biology, University of California, David, Davis, CA, USA
| | - Pablo Ross
- Department of Animal Science, University of California, Davis, Davis, CA, USA.
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, Davis, CA, USA.
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Pietrobon V, Cesano A, Marincola F, Kather JN. Next Generation Imaging Techniques to Define Immune Topographies in Solid Tumors. Front Immunol 2021; 11:604967. [PMID: 33584676 PMCID: PMC7873485 DOI: 10.3389/fimmu.2020.604967] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
In recent years, cancer immunotherapy experienced remarkable developments and it is nowadays considered a promising therapeutic frontier against many types of cancer, especially hematological malignancies. However, in most types of solid tumors, immunotherapy efficacy is modest, partly because of the limited accessibility of lymphocytes to the tumor core. This immune exclusion is mediated by a variety of physical, functional and dynamic barriers, which play a role in shaping the immune infiltrate in the tumor microenvironment. At present there is no unified and integrated understanding about the role played by different postulated models of immune exclusion in human solid tumors. Systematically mapping immune landscapes or "topographies" in cancers of different histology is of pivotal importance to characterize spatial and temporal distribution of lymphocytes in the tumor microenvironment, providing insights into mechanisms of immune exclusion. Spatially mapping immune cells also provides quantitative information, which could be informative in clinical settings, for example for the discovery of new biomarkers that could guide the design of patient-specific immunotherapies. In this review, we aim to summarize current standard and next generation approaches to define Cancer Immune Topographies based on published studies and propose future perspectives.
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Affiliation(s)
| | | | | | - Jakob Nikolas Kather
- Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
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Halstead MM, Kern C, Saelao P, Wang Y, Chanthavixay G, Medrano JF, Van Eenennaam AL, Korf I, Tuggle CK, Ernst CW, Zhou H, Ross PJ. A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues. BMC Genomics 2020; 21:698. [PMID: 33028202 PMCID: PMC7541309 DOI: 10.1186/s12864-020-07078-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/17/2020] [Indexed: 12/25/2022] Open
Abstract
Background Although considerable progress has been made towards annotating the noncoding portion of the human and mouse genomes, regulatory elements in other species, such as livestock, remain poorly characterized. This lack of functional annotation poses a substantial roadblock to agricultural research and diminishes the value of these species as model organisms. As active regulatory elements are typically characterized by chromatin accessibility, we implemented the Assay for Transposase Accessible Chromatin (ATAC-seq) to annotate and characterize regulatory elements in pigs and cattle, given a set of eight adult tissues. Results Overall, 306,304 and 273,594 active regulatory elements were identified in pig and cattle, respectively. 71,478 porcine and 47,454 bovine regulatory elements were highly tissue-specific and were correspondingly enriched for binding motifs of known tissue-specific transcription factors. However, in every tissue the most prevalent accessible motif corresponded to the insulator CTCF, suggesting pervasive involvement in 3-D chromatin organization. Taking advantage of a similar dataset in mouse, open chromatin in pig, cattle, and mice were compared, revealing that the conservation of regulatory elements, in terms of sequence identity and accessibility, was consistent with evolutionary distance; whereas pig and cattle shared about 20% of accessible sites, mice and ungulates only had about 10% of accessible sites in common. Furthermore, conservation of accessibility was more prevalent at promoters than at intergenic regions. Conclusions The lack of conserved accessibility at distal elements is consistent with rapid evolution of enhancers, and further emphasizes the need to annotate regulatory elements in individual species, rather than inferring elements based on homology. This atlas of chromatin accessibility in cattle and pig constitutes a substantial step towards annotating livestock genomes and dissecting the regulatory link between genome and phenome.
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Affiliation(s)
- Michelle M Halstead
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - Colin Kern
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - Perot Saelao
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - Ying Wang
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - Ganrea Chanthavixay
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - Juan F Medrano
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | | | - Ian Korf
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | | | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, 48824, MI, USA
| | - Huaijun Zhou
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA.
| | - Pablo J Ross
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA.
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Mass Spectrometry to Study Chromatin Compaction. BIOLOGY 2020; 9:biology9060140. [PMID: 32604817 PMCID: PMC7345930 DOI: 10.3390/biology9060140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/19/2020] [Accepted: 06/23/2020] [Indexed: 12/26/2022]
Abstract
Chromatin accessibility is a major regulator of gene expression. Histone writers/erasers have a critical role in chromatin compaction, as they “flag” chromatin regions by catalyzing/removing covalent post-translational modifications on histone proteins. Anomalous chromatin decondensation is a common phenomenon in cells experiencing aging and viral infection. Moreover, about 50% of cancers have mutations in enzymes regulating chromatin state. Numerous genomics methods have evolved to characterize chromatin state, but the analysis of (in)accessible chromatin from the protein perspective is not yet in the spotlight. We present an overview of the most used approaches to generate data on chromatin accessibility and then focus on emerging methods that utilize mass spectrometry to quantify the accessibility of histones and the rest of the chromatin bound proteome. Mass spectrometry is currently the method of choice to quantify entire proteomes in an unbiased large-scale manner; accessibility on chromatin of proteins and protein modifications adds an extra quantitative layer to proteomics dataset that assist more informed data-driven hypotheses in chromatin biology. We speculate that this emerging new set of methods will enhance predictive strength on which proteins and histone modifications are critical in gene regulation, and which proteins occupy different chromatin states in health and disease.
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