Table_2_Transcriptional Programs Underlying Cold Acclimation of Common Carp (Cyprinus carpio L.).XLSX
<p>Properly regulated transcriptional responses to environmental perturbations are critical for the fitness of fish. Although gene expression profiles in the tissues of common carp upon cold stress were previously characterized, the transcriptional programs underlying cold acclimation are stil...
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2020
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| _version_ | 1851598431985860608 |
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| author | Yong Long (138508) |
| author2 | Xixi Li (5482247) Fengyang Li (9335144) Guodong Ge (9213185) Ran Liu (303585) Guili Song (138501) Qing Li (84975) Zhigang Qiao (6730748) Zongbin Cui (138513) |
| author2_role | author author author author author author author author |
| author_facet | Yong Long (138508) Xixi Li (5482247) Fengyang Li (9335144) Guodong Ge (9213185) Ran Liu (303585) Guili Song (138501) Qing Li (84975) Zhigang Qiao (6730748) Zongbin Cui (138513) |
| author_role | author |
| dc.creator.none.fl_str_mv | Yong Long (138508) Xixi Li (5482247) Fengyang Li (9335144) Guodong Ge (9213185) Ran Liu (303585) Guili Song (138501) Qing Li (84975) Zhigang Qiao (6730748) Zongbin Cui (138513) |
| dc.date.none.fl_str_mv | 2020-09-23T04:14:58Z |
| dc.identifier.none.fl_str_mv | 10.3389/fgene.2020.556418.s006 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/dataset/Table_2_Transcriptional_Programs_Underlying_Cold_Acclimation_of_Common_Carp_Cyprinus_carpio_L_XLSX/12992399 |
| 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 cold acclimation common carp stress response transcriptional program gene expression genetic diversity alternative splicing |
| dc.title.none.fl_str_mv | Table_2_Transcriptional Programs Underlying Cold Acclimation of Common Carp (Cyprinus carpio L.).XLSX |
| dc.type.none.fl_str_mv | Dataset info:eu-repo/semantics/publishedVersion dataset |
| description | <p>Properly regulated transcriptional responses to environmental perturbations are critical for the fitness of fish. Although gene expression profiles in the tissues of common carp upon cold stress were previously characterized, the transcriptional programs underlying cold acclimation are still not well known. In this study, the ability of three common carp strains including Hebao red carp (HB), Songpu mirror carp (SPM) and Yellow river carp (YR) to establish cold resistance after acclimation to a mild hypothermia stress at 18°C for 24 h was confirmed by measurements of the critical thermal minimums (CTMin). The gene expression profiles of the brain and the heart from these strains under both control and cold-acclimated conditions were characterized with RNA-sequencing. The data of the three common carp strains with different genetic background were combined in the differential gene expression analyses to balance the effects of genetic diversity on gene expression. Marked effects of tissue origins on the cold-induced transcriptional responses were revealed by comparing the differentially expressed gene (DEG) lists of the two tissues. Functional categories including spliceosome and RNA splicing were highly enriched in the DEGs of both tissues. However, steroid biosynthesis was specifically enriched in DEGs of the brain and response to unfolded protein was solely enriched in DEGs of the heart. Consistent with the up-regulation of the genes involved in cholesterol biosynthesis, total cholesterol content of the brain was significantly increased upon cold stress. Moreover, cold-induced alternative splicing (AS) events were explored and AS of the rbmx (RNA-binding motif protein, X chromosome) gene was confirmed by real-time quantitative PCR. Finally, a core set of cold responsive genes (CRGs) were defined by comparative transcriptomic analyses. Our data provide insights into the transcriptional programs underlying cold acclimation of common carp and offer valuable clues for further investigating the genetic determinants for cold resistance of farmed fish.</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_867d9a8e17e6a0f0b51a61255e5519de |
| identifier_str_mv | 10.3389/fgene.2020.556418.s006 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/12992399 |
| publishDate | 2020 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Table_2_Transcriptional Programs Underlying Cold Acclimation of Common Carp (Cyprinus carpio L.).XLSXYong Long (138508)Xixi Li (5482247)Fengyang Li (9335144)Guodong Ge (9213185)Ran Liu (303585)Guili Song (138501)Qing Li (84975)Zhigang Qiao (6730748)Zongbin Cui (138513)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 Therapycold acclimationcommon carpstress responsetranscriptional programgene expressiongenetic diversityalternative splicing<p>Properly regulated transcriptional responses to environmental perturbations are critical for the fitness of fish. Although gene expression profiles in the tissues of common carp upon cold stress were previously characterized, the transcriptional programs underlying cold acclimation are still not well known. In this study, the ability of three common carp strains including Hebao red carp (HB), Songpu mirror carp (SPM) and Yellow river carp (YR) to establish cold resistance after acclimation to a mild hypothermia stress at 18°C for 24 h was confirmed by measurements of the critical thermal minimums (CTMin). The gene expression profiles of the brain and the heart from these strains under both control and cold-acclimated conditions were characterized with RNA-sequencing. The data of the three common carp strains with different genetic background were combined in the differential gene expression analyses to balance the effects of genetic diversity on gene expression. Marked effects of tissue origins on the cold-induced transcriptional responses were revealed by comparing the differentially expressed gene (DEG) lists of the two tissues. Functional categories including spliceosome and RNA splicing were highly enriched in the DEGs of both tissues. However, steroid biosynthesis was specifically enriched in DEGs of the brain and response to unfolded protein was solely enriched in DEGs of the heart. Consistent with the up-regulation of the genes involved in cholesterol biosynthesis, total cholesterol content of the brain was significantly increased upon cold stress. Moreover, cold-induced alternative splicing (AS) events were explored and AS of the rbmx (RNA-binding motif protein, X chromosome) gene was confirmed by real-time quantitative PCR. Finally, a core set of cold responsive genes (CRGs) were defined by comparative transcriptomic analyses. Our data provide insights into the transcriptional programs underlying cold acclimation of common carp and offer valuable clues for further investigating the genetic determinants for cold resistance of farmed fish.</p>2020-09-23T04:14:58ZDatasetinfo:eu-repo/semantics/publishedVersiondataset10.3389/fgene.2020.556418.s006https://figshare.com/articles/dataset/Table_2_Transcriptional_Programs_Underlying_Cold_Acclimation_of_Common_Carp_Cyprinus_carpio_L_XLSX/12992399CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/129923992020-09-23T04:14:58Z |
| spellingShingle | Table_2_Transcriptional Programs Underlying Cold Acclimation of Common Carp (Cyprinus carpio L.).XLSX Yong Long (138508) 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 cold acclimation common carp stress response transcriptional program gene expression genetic diversity alternative splicing |
| status_str | publishedVersion |
| title | Table_2_Transcriptional Programs Underlying Cold Acclimation of Common Carp (Cyprinus carpio L.).XLSX |
| title_full | Table_2_Transcriptional Programs Underlying Cold Acclimation of Common Carp (Cyprinus carpio L.).XLSX |
| title_fullStr | Table_2_Transcriptional Programs Underlying Cold Acclimation of Common Carp (Cyprinus carpio L.).XLSX |
| title_full_unstemmed | Table_2_Transcriptional Programs Underlying Cold Acclimation of Common Carp (Cyprinus carpio L.).XLSX |
| title_short | Table_2_Transcriptional Programs Underlying Cold Acclimation of Common Carp (Cyprinus carpio L.).XLSX |
| title_sort | Table_2_Transcriptional Programs Underlying Cold Acclimation of Common Carp (Cyprinus carpio L.).XLSX |
| 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 cold acclimation common carp stress response transcriptional program gene expression genetic diversity alternative splicing |