Bioinformatics Analysis of Transcriptome Dynamics during Growth in Angus Cattle Longissimus Muscle
Transcriptome dynamics in the longissimus muscle (LM) of young Angus cattle were evaluated at 0, 60, 120, and 220 days from early-weaning. Bioinformatic analysis was performed using the dynamic impact approach (DIA) by means of Kyoto Encyclopedia of Genes and Genomes (KEGG) and Database for Annotati...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2013-01-01
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| Series: | Bioinformatics and Biology Insights |
| Online Access: | https://doi.org/10.4137/BBI.S12328 |
| _version_ | 1819046295863558144 |
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| author | Sonia J. Moisá Daniel W. Shike Daniel E. Graugnard Sandra L. Rodriguez-Zas Robin E. Everts Harris A. Lewin Dan B. Faulkner Larry L. Berger Juan J. Loor |
| author_facet | Sonia J. Moisá Daniel W. Shike Daniel E. Graugnard Sandra L. Rodriguez-Zas Robin E. Everts Harris A. Lewin Dan B. Faulkner Larry L. Berger Juan J. Loor |
| author_sort | Sonia J. Moisá |
| collection | DOAJ |
| description | Transcriptome dynamics in the longissimus muscle (LM) of young Angus cattle were evaluated at 0, 60, 120, and 220 days from early-weaning. Bioinformatic analysis was performed using the dynamic impact approach (DIA) by means of Kyoto Encyclopedia of Genes and Genomes (KEGG) and Database for Annotation, Visualization and Integrated Discovery (DAVID) databases. Between 0 to 120 days (growing phase) most of the highly-impacted pathways (eg, ascorbate and aldarate metabolism, drug metabolism, cytochrome P450 and Retinol metabolism) were inhibited. The phase between 120 to 220 days (finishing phase) was characterized by the most striking differences with 3,784 differentially expressed genes (DEGs). Analysis of those DEGs revealed that the most impacted KEGG canonical pathway was glycosylphosphatidylinositol (GPI)-anchor biosynthesis, which was inhibited. Furthermore, inhibition of calpastatin and activation of tyrosine aminotransferase ubiquitination at 220 days promotes proteasomal degradation, while the concurrent activation of ribosomal proteins promotes protein synthesis. Therefore, the balance of these processes likely results in a steady-state of protein turnover during the finishing phase. Results underscore the importance of transcriptome dynamics in LM during growth. |
| first_indexed | 2024-12-21T10:42:12Z |
| format | Article |
| id | doaj.art-ef9d44b6f0e1406ab126bde42b6957cf |
| institution | Directory Open Access Journal |
| issn | 1177-9322 |
| language | English |
| last_indexed | 2024-12-21T10:42:12Z |
| publishDate | 2013-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Bioinformatics and Biology Insights |
| spelling | doaj.art-ef9d44b6f0e1406ab126bde42b6957cf2022-12-21T19:06:54ZengSAGE PublishingBioinformatics and Biology Insights1177-93222013-01-01710.4137/BBI.S12328Bioinformatics Analysis of Transcriptome Dynamics during Growth in Angus Cattle Longissimus MuscleSonia J. Moisá0Daniel W. Shike1Daniel E. Graugnard2Sandra L. Rodriguez-Zas3Robin E. Everts4Harris A. Lewin5Dan B. Faulkner6Larry L. Berger7Juan J. Loor8Division of Nutritional Sciences, University of Illinois, Urbana, Illinois USA.Department of Animal Sciences, University of Illinois, Urbana, Illinois, USA.Division of Nutritional Sciences, University of Illinois, Urbana, Illinois USA.Department of Animal Sciences, University of Illinois, Urbana, Illinois, USA.Department of Animal Sciences, University of Illinois, Urbana, Illinois, USA.Department of Animal Sciences, University of Illinois, Urbana, Illinois, USA.Department of Animal Science, University of Arizona, Tucson, Arizona, USA.Department of Animal Science, University of Nebraska–Lincoln, Lincoln, USA.Department of Animal Sciences, University of Illinois, Urbana, Illinois, USA.Transcriptome dynamics in the longissimus muscle (LM) of young Angus cattle were evaluated at 0, 60, 120, and 220 days from early-weaning. Bioinformatic analysis was performed using the dynamic impact approach (DIA) by means of Kyoto Encyclopedia of Genes and Genomes (KEGG) and Database for Annotation, Visualization and Integrated Discovery (DAVID) databases. Between 0 to 120 days (growing phase) most of the highly-impacted pathways (eg, ascorbate and aldarate metabolism, drug metabolism, cytochrome P450 and Retinol metabolism) were inhibited. The phase between 120 to 220 days (finishing phase) was characterized by the most striking differences with 3,784 differentially expressed genes (DEGs). Analysis of those DEGs revealed that the most impacted KEGG canonical pathway was glycosylphosphatidylinositol (GPI)-anchor biosynthesis, which was inhibited. Furthermore, inhibition of calpastatin and activation of tyrosine aminotransferase ubiquitination at 220 days promotes proteasomal degradation, while the concurrent activation of ribosomal proteins promotes protein synthesis. Therefore, the balance of these processes likely results in a steady-state of protein turnover during the finishing phase. Results underscore the importance of transcriptome dynamics in LM during growth.https://doi.org/10.4137/BBI.S12328 |
| spellingShingle | Sonia J. Moisá Daniel W. Shike Daniel E. Graugnard Sandra L. Rodriguez-Zas Robin E. Everts Harris A. Lewin Dan B. Faulkner Larry L. Berger Juan J. Loor Bioinformatics Analysis of Transcriptome Dynamics during Growth in Angus Cattle Longissimus Muscle Bioinformatics and Biology Insights |
| title | Bioinformatics Analysis of Transcriptome Dynamics during Growth in Angus Cattle Longissimus Muscle |
| title_full | Bioinformatics Analysis of Transcriptome Dynamics during Growth in Angus Cattle Longissimus Muscle |
| title_fullStr | Bioinformatics Analysis of Transcriptome Dynamics during Growth in Angus Cattle Longissimus Muscle |
| title_full_unstemmed | Bioinformatics Analysis of Transcriptome Dynamics during Growth in Angus Cattle Longissimus Muscle |
| title_short | Bioinformatics Analysis of Transcriptome Dynamics during Growth in Angus Cattle Longissimus Muscle |
| title_sort | bioinformatics analysis of transcriptome dynamics during growth in angus cattle longissimus muscle |
| url | https://doi.org/10.4137/BBI.S12328 |
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