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Functional annotation of regulatory elements in cattle genome reveals the roles of extracellular interaction and dynamic change of chromatin states in rumen development during weaning. Genomics 2022; 114:110296. [PMID: 35143887 DOI: 10.1016/j.ygeno.2022.110296] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 12/20/2021] [Accepted: 02/01/2022] [Indexed: 12/24/2022]
Abstract
We profiled landscapes of bovine regulatory elements and explored dynamic changes of chromatin states in rumen development during weaning. The regulatory elements (15 chromatin states) and their coordinated activities in cattle were defined through genome-wide profiling of four histone modifications, CTCF-binding, DNA accessibility, DNA methylation, and transcriptome in rumen epithelial tissues. Each chromatin state presented specific enrichment for sequence ontology, methylation, trait-associated variants, transcription, gene expression-associated variants, selection signatures, and evolutionarily conserved elements. During weaning, weak enhancers and flanking active transcriptional start sites (TSS) were the most dynamic chromatin states and occurred in tandem with significant variations in gene expression and DNA methylation, significantly associated with stature, production, and reproduction economic traits. By comparing with in vitro cultured epithelial cells and in vivo rumen tissues, we showed the commonness and uniqueness of these results, especially the roles of cell interactions and mitochondrial activities in tissue development.
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Cheng X, Yan J, Liu Y, Wang J, Taubert S. eVITTA: a web-based visualization and inference toolbox for transcriptome analysis. Nucleic Acids Res 2021; 49:W207-W215. [PMID: 34019643 PMCID: PMC8218201 DOI: 10.1093/nar/gkab366] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/12/2021] [Accepted: 05/04/2021] [Indexed: 12/12/2022] Open
Abstract
Transcriptome profiling is essential for gene regulation studies in development and disease. Current web-based tools enable functional characterization of transcriptome data, but most are restricted to applying gene-list-based methods to single datasets, inefficient in leveraging up-to-date and species-specific information, and limited in their visualization options. Additionally, there is no systematic way to explore data stored in the largest transcriptome repository, NCBI GEO. To fill these gaps, we have developed eVITTA (easy Visualization and Inference Toolbox for Transcriptome Analysis; https://tau.cmmt.ubc.ca/eVITTA/). eVITTA provides modules for analysis and exploration of studies published in NCBI GEO (easyGEO), detailed molecular- and systems-level functional profiling (easyGSEA), and customizable comparisons among experimental groups (easyVizR). We tested eVITTA on transcriptomes of SARS-CoV-2 infected human nasopharyngeal swab samples, and identified a downregulation of olfactory signal transducers, in line with the clinical presentation of anosmia in COVID-19 patients. We also analyzed transcriptomes of Caenorhabditis elegans worms with disrupted S-adenosylmethionine metabolism, confirming activation of innate immune responses and feedback induction of one-carbon cycle genes. Collectively, eVITTA streamlines complex computational workflows into an accessible interface, thus filling the gap of an end-to-end platform capable of capturing both broad and granular changes in human and model organism transcriptomes.
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Affiliation(s)
- Xuanjin Cheng
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada.,British Columbia Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Junran Yan
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada.,British Columbia Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada.,Graduate Program for Cell and Developmental Biology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Yongxing Liu
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada.,British Columbia Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jiahe Wang
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada.,British Columbia Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Stefan Taubert
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada.,British Columbia Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada.,Graduate Program for Cell and Developmental Biology, The University of British Columbia, Vancouver, British Columbia, Canada
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