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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...

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Autores principales: Herrera-Uribe, Juber, Lim, Kyu-Sang, Byrne, Kristen A., Daharsh, Lance, Liu, Haibo, Corbett, Ryan J., Marco, Gianna, Schroyen, Martine, Koltes, James E., Loving, Crystal L., Tuggle, Christopher K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10242145/
https://www.ncbi.nlm.nih.gov/pubmed/37287538
http://dx.doi.org/10.3389/fgene.2023.1107462
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author Herrera-Uribe, Juber
Lim, Kyu-Sang
Byrne, Kristen A.
Daharsh, Lance
Liu, Haibo
Corbett, Ryan J.
Marco, Gianna
Schroyen, Martine
Koltes, James E.
Loving, Crystal L.
Tuggle, Christopher K.
author_facet Herrera-Uribe, Juber
Lim, Kyu-Sang
Byrne, Kristen A.
Daharsh, Lance
Liu, Haibo
Corbett, Ryan J.
Marco, Gianna
Schroyen, Martine
Koltes, James E.
Loving, Crystal L.
Tuggle, Christopher K.
author_sort Herrera-Uribe, Juber
collection PubMed
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.
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spelling pubmed-102421452023-06-07 Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils Herrera-Uribe, Juber Lim, Kyu-Sang Byrne, Kristen A. Daharsh, Lance Liu, Haibo Corbett, Ryan J. Marco, Gianna Schroyen, Martine Koltes, James E. Loving, Crystal L. Tuggle, Christopher K. Front Genet Genetics 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. Frontiers Media S.A. 2023-05-23 /pmc/articles/PMC10242145/ /pubmed/37287538 http://dx.doi.org/10.3389/fgene.2023.1107462 Text en Copyright © 2023 Herrera-Uribe, Lim, Byrne, Daharsh, Liu, Corbett, Marco, Schroyen, Koltes, Loving and Tuggle. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Herrera-Uribe, Juber
Lim, Kyu-Sang
Byrne, Kristen A.
Daharsh, Lance
Liu, Haibo
Corbett, Ryan J.
Marco, Gianna
Schroyen, Martine
Koltes, James E.
Loving, Crystal L.
Tuggle, Christopher K.
Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils
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 Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10242145/
https://www.ncbi.nlm.nih.gov/pubmed/37287538
http://dx.doi.org/10.3389/fgene.2023.1107462
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