Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils
Neutrophils are vital components of the immune system for limiting the invasion and proliferation of pathogens in the body. Surprisingly, the functional annotation of porcine neutrophils is still limited. The transcriptomic and epigenetic assessment of porcine neutrophils from healthy pigs was perfo...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-05-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2023.1107462/full |
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| author | Juber Herrera-Uribe Kyu-Sang Lim Kyu-Sang Lim Kristen A. Byrne Lance Daharsh Haibo Liu Ryan J. Corbett Gianna Marco Martine Schroyen James E. Koltes Crystal L. Loving Christopher K. Tuggle |
| author_facet | Juber Herrera-Uribe Kyu-Sang Lim Kyu-Sang Lim Kristen A. Byrne Lance Daharsh Haibo Liu Ryan J. Corbett Gianna Marco Martine Schroyen James E. Koltes Crystal L. Loving Christopher K. Tuggle |
| author_sort | Juber Herrera-Uribe |
| collection | DOAJ |
| description | Neutrophils are vital components of the immune system for limiting the invasion and proliferation of pathogens in the body. Surprisingly, the functional annotation of porcine neutrophils is still limited. The transcriptomic and epigenetic assessment of porcine neutrophils from healthy pigs was performed by bulk RNA sequencing and transposase accessible chromatin sequencing (ATAC-seq). First, we sequenced and compared the transcriptome of porcine neutrophils with eight other immune cell transcriptomes to identify a neutrophil-enriched gene list within a detected neutrophil co-expression module. Second, we used ATAC-seq analysis to report for the first time the genome-wide chromatin accessible regions of porcine neutrophils. A combined analysis using both transcriptomic and chromatin accessibility data further defined the neutrophil co-expression network controlled by transcription factors likely important for neutrophil lineage commitment and function. We identified chromatin accessible regions around promoters of neutrophil-specific genes that were predicted to be bound by neutrophil-specific transcription factors. Additionally, published DNA methylation data from porcine immune cells including neutrophils were used to link low DNA methylation patterns to accessible chromatin regions and genes with highly enriched expression in porcine neutrophils. In summary, our data provides the first integrative analysis of the accessible chromatin regions and transcriptional status of porcine neutrophils, contributing to the Functional Annotation of Animal Genomes (FAANG) project, and demonstrates the utility of chromatin accessible regions to identify and enrich our understanding of transcriptional networks in a cell type such as neutrophils. |
| first_indexed | 2024-03-13T10:01:39Z |
| format | Article |
| id | doaj.art-cedb7edc21234d88b20d51e19310d1be |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-03-13T10:01:39Z |
| publishDate | 2023-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-cedb7edc21234d88b20d51e19310d1be2023-05-23T05:17:51ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-05-011410.3389/fgene.2023.11074621107462Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophilsJuber Herrera-Uribe0Kyu-Sang Lim1Kyu-Sang Lim2Kristen A. Byrne3Lance Daharsh4Haibo Liu5Ryan J. Corbett6Gianna Marco7Martine Schroyen8James E. Koltes9Crystal L. Loving10Christopher K. Tuggle11Department of Animal Science, Iowa State University, Ames, IA, United StatesDepartment of Animal Science, Iowa State University, Ames, IA, United StatesDepartment of Animal Resource Science, Kongju National University, Yesan, Republic of KoreaUSDA-Agriculture Research Service, National Animal Disease Center, Food Safety and Enteric Pathogens Research Unit, Ames, IA, United StatesDepartment of Animal Science, Iowa State University, Ames, IA, United StatesDepartment of Animal Science, Iowa State University, Ames, IA, United StatesDepartment of Animal Science, Iowa State University, Ames, IA, United StatesDepartment of Animal Science, Iowa State University, Ames, IA, United StatesDepartment of Animal Science, Iowa State University, Ames, IA, United StatesDepartment of Animal Science, Iowa State University, Ames, IA, United StatesUSDA-Agriculture Research Service, National Animal Disease Center, Food Safety and Enteric Pathogens Research Unit, Ames, IA, United StatesDepartment of Animal Science, Iowa State University, Ames, IA, United StatesNeutrophils are vital components of the immune system for limiting the invasion and proliferation of pathogens in the body. Surprisingly, the functional annotation of porcine neutrophils is still limited. The transcriptomic and epigenetic assessment of porcine neutrophils from healthy pigs was performed by bulk RNA sequencing and transposase accessible chromatin sequencing (ATAC-seq). First, we sequenced and compared the transcriptome of porcine neutrophils with eight other immune cell transcriptomes to identify a neutrophil-enriched gene list within a detected neutrophil co-expression module. Second, we used ATAC-seq analysis to report for the first time the genome-wide chromatin accessible regions of porcine neutrophils. A combined analysis using both transcriptomic and chromatin accessibility data further defined the neutrophil co-expression network controlled by transcription factors likely important for neutrophil lineage commitment and function. We identified chromatin accessible regions around promoters of neutrophil-specific genes that were predicted to be bound by neutrophil-specific transcription factors. Additionally, published DNA methylation data from porcine immune cells including neutrophils were used to link low DNA methylation patterns to accessible chromatin regions and genes with highly enriched expression in porcine neutrophils. In summary, our data provides the first integrative analysis of the accessible chromatin regions and transcriptional status of porcine neutrophils, contributing to the Functional Annotation of Animal Genomes (FAANG) project, and demonstrates the utility of chromatin accessible regions to identify and enrich our understanding of transcriptional networks in a cell type such as neutrophils.https://www.frontiersin.org/articles/10.3389/fgene.2023.1107462/fullpigtranscriptomebulk-RNA-seqco-expressed genestranscription factor (TF)gene regulation |
| spellingShingle | Juber Herrera-Uribe Kyu-Sang Lim Kyu-Sang Lim Kristen A. Byrne Lance Daharsh Haibo Liu Ryan J. Corbett Gianna Marco Martine Schroyen James E. Koltes Crystal L. Loving Christopher K. Tuggle Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils Frontiers in Genetics pig transcriptome bulk-RNA-seq co-expressed genes transcription factor (TF) gene regulation |
| title | Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils |
| title_full | Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils |
| title_fullStr | Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils |
| title_full_unstemmed | Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils |
| title_short | Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils |
| title_sort | integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils |
| topic | pig transcriptome bulk-RNA-seq co-expressed genes transcription factor (TF) gene regulation |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2023.1107462/full |
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