Investigation of promoter regions, motifs, and CpG islands in the regulation of gene expression in Trametes hirsuta strain 072
Abstract Background In silico analysis of transcription start sites, promoter regions, transcription factors and their binding sites, and CpG islands for the Trametes hirsuta strain 072 genome were performed to understand the regulation mechanisms of gene expression and its genetic variations in the...
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| Format: | Article |
| Language: | English |
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Elsevier
2021-10-01
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| Series: | Journal of Genetic Engineering and Biotechnology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s43141-021-00261-9 |
| _version_ | 1797204343218241536 |
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| author | Dinku Senbeta Mulugeta Kebede |
| author_facet | Dinku Senbeta Mulugeta Kebede |
| author_sort | Dinku Senbeta |
| collection | DOAJ |
| description | Abstract Background In silico analysis of transcription start sites, promoter regions, transcription factors and their binding sites, and CpG islands for the Trametes hirsuta strain 072 genome were performed to understand the regulation mechanisms of gene expression and its genetic variations in the genomes. Therefore, a computational survey was carried out for the Trametes hirsuta strain 072 genome with the open reading frames from the National Center for Biotechnology Information database. Seventeen functional sequences were used to analyze promoter regions and their regulatory elements. Result The present study revealed that 94% of Trametes hirsuta strain 072 genes contained more than two TSSs. Among these identified TSSs, a TSS with the highest predictive score was considered to determine a promoter region of the genes. Moreover, a total of five common candidate motifs such as MotI, MotII, MotIII, MotIV, and MotV were identified. Among these motifs, motif IV was investigated as the common promoter motif for 41.17% of genes that serve as binding sites for transcription factors (TFs) involved in the expression regulation of Trametes hirsuta strain 072 genes. Motif IV was also compared to registered motifs in publically available databases to see if they are similar to known regulatory motifs for TF using TOMTOM web server. Hence, it was revealed that MotIV might serve as the binding site mainly for the leucine zipper TF gene family to regulate a gene expression of Trametes hirsuta strain 072. Regarding CpG island determination, it was concluded that there is no CpG island in both promoter and gene body regions of the Trametes hirsuta strain 072 genome. Conclusions This study provides a better insight into further molecular characterization which aimed to efficiently exploit a white rot fungus, Trametes hirsuta strain 072, for several biotechnological applications aimed to revitalize a severely contaminated environment. |
| first_indexed | 2024-04-24T08:33:43Z |
| format | Article |
| id | doaj.art-a1994b2bbc974328b95ac067112f1f24 |
| institution | Directory Open Access Journal |
| issn | 2090-5920 |
| language | English |
| last_indexed | 2024-04-24T08:33:43Z |
| publishDate | 2021-10-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Genetic Engineering and Biotechnology |
| spelling | doaj.art-a1994b2bbc974328b95ac067112f1f242024-04-16T18:22:51ZengElsevierJournal of Genetic Engineering and Biotechnology2090-59202021-10-0119111010.1186/s43141-021-00261-9Investigation of promoter regions, motifs, and CpG islands in the regulation of gene expression in Trametes hirsuta strain 072Dinku Senbeta0Mulugeta Kebede1Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology UniversityDepartment of Applied Biology, School of Applied Natural Science, Adama Science and Technology UniversityAbstract Background In silico analysis of transcription start sites, promoter regions, transcription factors and their binding sites, and CpG islands for the Trametes hirsuta strain 072 genome were performed to understand the regulation mechanisms of gene expression and its genetic variations in the genomes. Therefore, a computational survey was carried out for the Trametes hirsuta strain 072 genome with the open reading frames from the National Center for Biotechnology Information database. Seventeen functional sequences were used to analyze promoter regions and their regulatory elements. Result The present study revealed that 94% of Trametes hirsuta strain 072 genes contained more than two TSSs. Among these identified TSSs, a TSS with the highest predictive score was considered to determine a promoter region of the genes. Moreover, a total of five common candidate motifs such as MotI, MotII, MotIII, MotIV, and MotV were identified. Among these motifs, motif IV was investigated as the common promoter motif for 41.17% of genes that serve as binding sites for transcription factors (TFs) involved in the expression regulation of Trametes hirsuta strain 072 genes. Motif IV was also compared to registered motifs in publically available databases to see if they are similar to known regulatory motifs for TF using TOMTOM web server. Hence, it was revealed that MotIV might serve as the binding site mainly for the leucine zipper TF gene family to regulate a gene expression of Trametes hirsuta strain 072. Regarding CpG island determination, it was concluded that there is no CpG island in both promoter and gene body regions of the Trametes hirsuta strain 072 genome. Conclusions This study provides a better insight into further molecular characterization which aimed to efficiently exploit a white rot fungus, Trametes hirsuta strain 072, for several biotechnological applications aimed to revitalize a severely contaminated environment.https://doi.org/10.1186/s43141-021-00261-9Trametes hirsuta strain 072Promoter regionMotifCpG island |
| spellingShingle | Dinku Senbeta Mulugeta Kebede Investigation of promoter regions, motifs, and CpG islands in the regulation of gene expression in Trametes hirsuta strain 072 Journal of Genetic Engineering and Biotechnology Trametes hirsuta strain 072 Promoter region Motif CpG island |
| title | Investigation of promoter regions, motifs, and CpG islands in the regulation of gene expression in Trametes hirsuta strain 072 |
| title_full | Investigation of promoter regions, motifs, and CpG islands in the regulation of gene expression in Trametes hirsuta strain 072 |
| title_fullStr | Investigation of promoter regions, motifs, and CpG islands in the regulation of gene expression in Trametes hirsuta strain 072 |
| title_full_unstemmed | Investigation of promoter regions, motifs, and CpG islands in the regulation of gene expression in Trametes hirsuta strain 072 |
| title_short | Investigation of promoter regions, motifs, and CpG islands in the regulation of gene expression in Trametes hirsuta strain 072 |
| title_sort | investigation of promoter regions motifs and cpg islands in the regulation of gene expression in trametes hirsuta strain 072 |
| topic | Trametes hirsuta strain 072 Promoter region Motif CpG island |
| url | https://doi.org/10.1186/s43141-021-00261-9 |
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