DataSheet1_Analysis of cis-regulatory changes underlying phenotype divergence shaped by domestication in pigs.ZIP
Background<p>Cis-regulatory elements (CREs) are regions of DNA that regulate the expression of nearby genes. Changes in these elements can lead to phenotypic variations and adaptations in different populations. However, the regulatory dynamics underlying the local adaptation of traits remain p...
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2024
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| _version_ | 1852025336481447936 |
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| author | Chunpeng Liu (20143734) |
| author2 | Na Ao (14555513) Yuwen Liang (19834947) Tingting Ma (228102) Qishan Wang (102904) Zhen Wang (72451) Fen Wu (210935) Zhenyang Zhang (9183830) Yifei Fang (10717932) Minghui Wang (15418) Yuchun Pan (102909) Jing Fu (177892) |
| author2_role | author author author author author author author author author author author |
| author_facet | Chunpeng Liu (20143734) Na Ao (14555513) Yuwen Liang (19834947) Tingting Ma (228102) Qishan Wang (102904) Zhen Wang (72451) Fen Wu (210935) Zhenyang Zhang (9183830) Yifei Fang (10717932) Minghui Wang (15418) Yuchun Pan (102909) Jing Fu (177892) |
| author_role | author |
| dc.creator.none.fl_str_mv | Chunpeng Liu (20143734) Na Ao (14555513) Yuwen Liang (19834947) Tingting Ma (228102) Qishan Wang (102904) Zhen Wang (72451) Fen Wu (210935) Zhenyang Zhang (9183830) Yifei Fang (10717932) Minghui Wang (15418) Yuchun Pan (102909) Jing Fu (177892) |
| dc.date.none.fl_str_mv | 2024-11-08T04:08:17Z |
| dc.identifier.none.fl_str_mv | 10.3389/fgene.2024.1421859.s001 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/dataset/DataSheet1_Analysis_of_cis-regulatory_changes_underlying_phenotype_divergence_shaped_by_domestication_in_pigs_ZIP/27634380 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy ATAC-seq chromatin accessibility cis-regulatory element allelic frequency pig |
| dc.title.none.fl_str_mv | DataSheet1_Analysis of cis-regulatory changes underlying phenotype divergence shaped by domestication in pigs.ZIP |
| dc.type.none.fl_str_mv | Dataset info:eu-repo/semantics/publishedVersion dataset |
| description | Background<p>Cis-regulatory elements (CREs) are regions of DNA that regulate the expression of nearby genes. Changes in these elements can lead to phenotypic variations and adaptations in different populations. However, the regulatory dynamics underlying the local adaptation of traits remain poorly understood in Chinese and Western pigs. By comparing the chromatin accessibility profiles of skeletal muscle, liver, and fat between these two pig populations, we aimed to identify key regulatory elements that could explain phenotypic differences observed between the two groups.</p>Results<p>Our results revealed that the genome-wide chromatin accessibility profiles were largely similar at a qualitative level within tissues. However, we also identified local regions that exhibited quantitative differences, most of which occurred in liver tissue. Interestingly, we found that most of the increased chromatin accessibility in the livers of Chinese pigs was associated with tissue-specific openness. Furthermore, we observed a positive correlation between the ATAC-seq signal at the transcript start site (TSS) and the expression levels of nearby genes. Motif enrichment analysis revealed NR2F1 as a key regulator in Chinese pigs. Differentially expressed genes (DEGs) in Chinese pigs showed enrichment for NR2F1 response targets. One of the genes regulated by NR2F1 in Chinese pigs, NPC1, harbored a high alternative allelic frequency in the intron region.</p>Conclusion<p>Overall, our study provides valuable insights into the regulatory dynamics underlying phenotypic variation in pigs. By elucidating the role of CREs in driving phenotypic variation, we can better understand the genetic basis of complex traits and potentially identify targets for genetic improvement in livestock breeding programs.</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_4bf4e5d0da0258beef38ddeabdc5585c |
| identifier_str_mv | 10.3389/fgene.2024.1421859.s001 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/27634380 |
| publishDate | 2024 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | DataSheet1_Analysis of cis-regulatory changes underlying phenotype divergence shaped by domestication in pigs.ZIPChunpeng Liu (20143734)Na Ao (14555513)Yuwen Liang (19834947)Tingting Ma (228102)Qishan Wang (102904)Zhen Wang (72451)Fen Wu (210935)Zhenyang Zhang (9183830)Yifei Fang (10717932)Minghui Wang (15418)Yuchun Pan (102909)Jing Fu (177892)GeneticsGenetic EngineeringBiomarkersDevelopmental Genetics (incl. Sex Determination)Epigenetics (incl. Genome Methylation and Epigenomics)Gene Expression (incl. Microarray and other genome-wide approaches)Genome Structure and RegulationGenomicsGenetically Modified AnimalsLivestock CloningGene and Molecular TherapyATAC-seqchromatin accessibilitycis-regulatory elementallelic frequencypigBackground<p>Cis-regulatory elements (CREs) are regions of DNA that regulate the expression of nearby genes. Changes in these elements can lead to phenotypic variations and adaptations in different populations. However, the regulatory dynamics underlying the local adaptation of traits remain poorly understood in Chinese and Western pigs. By comparing the chromatin accessibility profiles of skeletal muscle, liver, and fat between these two pig populations, we aimed to identify key regulatory elements that could explain phenotypic differences observed between the two groups.</p>Results<p>Our results revealed that the genome-wide chromatin accessibility profiles were largely similar at a qualitative level within tissues. However, we also identified local regions that exhibited quantitative differences, most of which occurred in liver tissue. Interestingly, we found that most of the increased chromatin accessibility in the livers of Chinese pigs was associated with tissue-specific openness. Furthermore, we observed a positive correlation between the ATAC-seq signal at the transcript start site (TSS) and the expression levels of nearby genes. Motif enrichment analysis revealed NR2F1 as a key regulator in Chinese pigs. Differentially expressed genes (DEGs) in Chinese pigs showed enrichment for NR2F1 response targets. One of the genes regulated by NR2F1 in Chinese pigs, NPC1, harbored a high alternative allelic frequency in the intron region.</p>Conclusion<p>Overall, our study provides valuable insights into the regulatory dynamics underlying phenotypic variation in pigs. By elucidating the role of CREs in driving phenotypic variation, we can better understand the genetic basis of complex traits and potentially identify targets for genetic improvement in livestock breeding programs.</p>2024-11-08T04:08:17ZDatasetinfo:eu-repo/semantics/publishedVersiondataset10.3389/fgene.2024.1421859.s001https://figshare.com/articles/dataset/DataSheet1_Analysis_of_cis-regulatory_changes_underlying_phenotype_divergence_shaped_by_domestication_in_pigs_ZIP/27634380CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/276343802024-11-08T04:08:17Z |
| spellingShingle | DataSheet1_Analysis of cis-regulatory changes underlying phenotype divergence shaped by domestication in pigs.ZIP Chunpeng Liu (20143734) Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy ATAC-seq chromatin accessibility cis-regulatory element allelic frequency pig |
| status_str | publishedVersion |
| title | DataSheet1_Analysis of cis-regulatory changes underlying phenotype divergence shaped by domestication in pigs.ZIP |
| title_full | DataSheet1_Analysis of cis-regulatory changes underlying phenotype divergence shaped by domestication in pigs.ZIP |
| title_fullStr | DataSheet1_Analysis of cis-regulatory changes underlying phenotype divergence shaped by domestication in pigs.ZIP |
| title_full_unstemmed | DataSheet1_Analysis of cis-regulatory changes underlying phenotype divergence shaped by domestication in pigs.ZIP |
| title_short | DataSheet1_Analysis of cis-regulatory changes underlying phenotype divergence shaped by domestication in pigs.ZIP |
| title_sort | DataSheet1_Analysis of cis-regulatory changes underlying phenotype divergence shaped by domestication in pigs.ZIP |
| topic | Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy ATAC-seq chromatin accessibility cis-regulatory element allelic frequency pig |