Genome-Wide Phylogenetic Analysis, Expression Pattern, and Transcriptional Regulatory Network of the Pig C/EBP Gene Family
The CCAAT/enhancer binding protein (C/EBP) transcription factors (TFs) regulate many important biological processes, such as energy metabolism, inflammation, cell proliferation etc. A genome-wide gene identification revealed the presence of a total of 99 C/EBP genes in pig and 19 eukaryote genomes....
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
SAGE Publishing
2021-08-01
|
| Series: | Evolutionary Bioinformatics |
| Online Access: | https://doi.org/10.1177/11769343211041382 |
| _version_ | 1818690124375916544 |
|---|---|
| author | Chaoxin Zhang Tao Wang Tongyan Cui Shengwei Liu Bing Zhang Xue Li Jian Tang Peng Wang Yuanyuan Guo Zhipeng Wang |
| author_facet | Chaoxin Zhang Tao Wang Tongyan Cui Shengwei Liu Bing Zhang Xue Li Jian Tang Peng Wang Yuanyuan Guo Zhipeng Wang |
| author_sort | Chaoxin Zhang |
| collection | DOAJ |
| description | The CCAAT/enhancer binding protein (C/EBP) transcription factors (TFs) regulate many important biological processes, such as energy metabolism, inflammation, cell proliferation etc. A genome-wide gene identification revealed the presence of a total of 99 C/EBP genes in pig and 19 eukaryote genomes. Phylogenetic analysis showed that all C/EBP TFs were classified into 6 subgroups named C/EBPα, C/EBPβ, C/EBPδ, C/EBPε, C/EBPγ , and C/EBPζ . Gene expression analysis showed that the C/EBPα, C/EBPβ, C/EBPδ, C/EBPγ , and C/EBPζ genes were expressed ubiquitously with inconsistent expression patterns in various pig tissues. Moreover, a pig C/EBP regulatory network was constructed, including C/EBP genes, TFs and miRNAs. A total of 27 feed-forward loop (FFL) motifs were detected in the pig C/EBP regulatory network. Based on the RNA-seq data, gene expression patterns related to FFL sub-network were analyzed in 27 adult pig tissues. Certain FFL motifs may be tissue specific. Functional enrichment analysis indicated that C/EBP and its target genes are involved in many important biological pathways. These results provide valuable information that clarifies the evolutionary relationships of the C/EBP family and contributes to the understanding of the biological function of C/EBP genes. |
| first_indexed | 2024-12-17T12:21:01Z |
| format | Article |
| id | doaj.art-f7fe2c1eb90b445f9a3dc2132ebee72c |
| institution | Directory Open Access Journal |
| issn | 1176-9343 |
| language | English |
| last_indexed | 2024-12-17T12:21:01Z |
| publishDate | 2021-08-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Evolutionary Bioinformatics |
| spelling | doaj.art-f7fe2c1eb90b445f9a3dc2132ebee72c2022-12-21T21:48:58ZengSAGE PublishingEvolutionary Bioinformatics1176-93432021-08-011710.1177/11769343211041382Genome-Wide Phylogenetic Analysis, Expression Pattern, and Transcriptional Regulatory Network of the Pig C/EBP Gene FamilyChaoxin Zhang0Tao Wang1Tongyan Cui2Shengwei Liu3Bing Zhang4Xue Li5Jian Tang6Peng Wang7Yuanyuan Guo8Zhipeng Wang9Bioinformatics Center, Northeast Agricultural University, Harbin, ChinaBioinformatics Center, Northeast Agricultural University, Harbin, ChinaBioinformatics Center, Northeast Agricultural University, Harbin, ChinaBioinformatics Center, Northeast Agricultural University, Harbin, ChinaBioinformatics Center, Northeast Agricultural University, Harbin, ChinaBioinformatics Center, Northeast Agricultural University, Harbin, ChinaBioinformatics Center, Northeast Agricultural University, Harbin, ChinaHeiLongJiang provincial Husbandry Dapartment, Harbin, ChinaBioinformatics Center, Northeast Agricultural University, Harbin, ChinaDaBeiNong Group, Beijing, ChinaThe CCAAT/enhancer binding protein (C/EBP) transcription factors (TFs) regulate many important biological processes, such as energy metabolism, inflammation, cell proliferation etc. A genome-wide gene identification revealed the presence of a total of 99 C/EBP genes in pig and 19 eukaryote genomes. Phylogenetic analysis showed that all C/EBP TFs were classified into 6 subgroups named C/EBPα, C/EBPβ, C/EBPδ, C/EBPε, C/EBPγ , and C/EBPζ . Gene expression analysis showed that the C/EBPα, C/EBPβ, C/EBPδ, C/EBPγ , and C/EBPζ genes were expressed ubiquitously with inconsistent expression patterns in various pig tissues. Moreover, a pig C/EBP regulatory network was constructed, including C/EBP genes, TFs and miRNAs. A total of 27 feed-forward loop (FFL) motifs were detected in the pig C/EBP regulatory network. Based on the RNA-seq data, gene expression patterns related to FFL sub-network were analyzed in 27 adult pig tissues. Certain FFL motifs may be tissue specific. Functional enrichment analysis indicated that C/EBP and its target genes are involved in many important biological pathways. These results provide valuable information that clarifies the evolutionary relationships of the C/EBP family and contributes to the understanding of the biological function of C/EBP genes.https://doi.org/10.1177/11769343211041382 |
| spellingShingle | Chaoxin Zhang Tao Wang Tongyan Cui Shengwei Liu Bing Zhang Xue Li Jian Tang Peng Wang Yuanyuan Guo Zhipeng Wang Genome-Wide Phylogenetic Analysis, Expression Pattern, and Transcriptional Regulatory Network of the Pig C/EBP Gene Family Evolutionary Bioinformatics |
| title | Genome-Wide Phylogenetic Analysis, Expression Pattern, and Transcriptional Regulatory Network of the Pig C/EBP Gene Family |
| title_full | Genome-Wide Phylogenetic Analysis, Expression Pattern, and Transcriptional Regulatory Network of the Pig C/EBP Gene Family |
| title_fullStr | Genome-Wide Phylogenetic Analysis, Expression Pattern, and Transcriptional Regulatory Network of the Pig C/EBP Gene Family |
| title_full_unstemmed | Genome-Wide Phylogenetic Analysis, Expression Pattern, and Transcriptional Regulatory Network of the Pig C/EBP Gene Family |
| title_short | Genome-Wide Phylogenetic Analysis, Expression Pattern, and Transcriptional Regulatory Network of the Pig C/EBP Gene Family |
| title_sort | genome wide phylogenetic analysis expression pattern and transcriptional regulatory network of the pig c ebp gene family |
| url | https://doi.org/10.1177/11769343211041382 |
| work_keys_str_mv | AT chaoxinzhang genomewidephylogeneticanalysisexpressionpatternandtranscriptionalregulatorynetworkofthepigcebpgenefamily AT taowang genomewidephylogeneticanalysisexpressionpatternandtranscriptionalregulatorynetworkofthepigcebpgenefamily AT tongyancui genomewidephylogeneticanalysisexpressionpatternandtranscriptionalregulatorynetworkofthepigcebpgenefamily AT shengweiliu genomewidephylogeneticanalysisexpressionpatternandtranscriptionalregulatorynetworkofthepigcebpgenefamily AT bingzhang genomewidephylogeneticanalysisexpressionpatternandtranscriptionalregulatorynetworkofthepigcebpgenefamily AT xueli genomewidephylogeneticanalysisexpressionpatternandtranscriptionalregulatorynetworkofthepigcebpgenefamily AT jiantang genomewidephylogeneticanalysisexpressionpatternandtranscriptionalregulatorynetworkofthepigcebpgenefamily AT pengwang genomewidephylogeneticanalysisexpressionpatternandtranscriptionalregulatorynetworkofthepigcebpgenefamily AT yuanyuanguo genomewidephylogeneticanalysisexpressionpatternandtranscriptionalregulatorynetworkofthepigcebpgenefamily AT zhipengwang genomewidephylogeneticanalysisexpressionpatternandtranscriptionalregulatorynetworkofthepigcebpgenefamily |