TATA and paused promoters active in differentiated tissues have distinct expression characteristics
Abstract Core promoter types differ in the extent to which RNA polymerase II (Pol II) pauses after initiation, but how this affects their tissue‐specific gene expression characteristics is not well understood. While promoters with Pol II pausing elements are active throughout development, TATA promo...
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| Format: | Article |
| Language: | English |
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Springer Nature
2021-02-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.15252/msb.20209866 |
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| author | Vivekanandan Ramalingam Malini Natarajan Jeff Johnston Julia Zeitlinger |
| author_facet | Vivekanandan Ramalingam Malini Natarajan Jeff Johnston Julia Zeitlinger |
| author_sort | Vivekanandan Ramalingam |
| collection | DOAJ |
| description | Abstract Core promoter types differ in the extent to which RNA polymerase II (Pol II) pauses after initiation, but how this affects their tissue‐specific gene expression characteristics is not well understood. While promoters with Pol II pausing elements are active throughout development, TATA promoters are highly active in differentiated tissues. We therefore used a genomics approach on late‐stage Drosophila embryos to analyze the properties of promoter types. Using tissue‐specific Pol II ChIP‐seq, we found that paused promoters have high levels of paused Pol II throughout the embryo, even in tissues where the gene is not expressed, while TATA promoters only show Pol II occupancy when the gene is active. The promoter types are associated with different chromatin accessibility in ATAC‐seq data and have different expression characteristics in single‐cell RNA‐seq data. The two promoter types may therefore be optimized for different properties: paused promoters show more consistent expression when active, while TATA promoters have lower background expression when inactive. We propose that tissue‐specific genes have evolved to use two different strategies for their differential expression across tissues. |
| format | Article |
| id | doaj-art-f26a8cfb54b147fd97bbef5f3d2ae438 |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2021-02-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-f26a8cfb54b147fd97bbef5f3d2ae4382025-08-20T03:46:37ZengSpringer NatureMolecular Systems Biology1744-42922021-02-0117211210.15252/msb.20209866TATA and paused promoters active in differentiated tissues have distinct expression characteristicsVivekanandan Ramalingam0Malini Natarajan1Jeff Johnston2Julia Zeitlinger3Stowers Institute for Medical ResearchStowers Institute for Medical ResearchStowers Institute for Medical ResearchStowers Institute for Medical ResearchAbstract Core promoter types differ in the extent to which RNA polymerase II (Pol II) pauses after initiation, but how this affects their tissue‐specific gene expression characteristics is not well understood. While promoters with Pol II pausing elements are active throughout development, TATA promoters are highly active in differentiated tissues. We therefore used a genomics approach on late‐stage Drosophila embryos to analyze the properties of promoter types. Using tissue‐specific Pol II ChIP‐seq, we found that paused promoters have high levels of paused Pol II throughout the embryo, even in tissues where the gene is not expressed, while TATA promoters only show Pol II occupancy when the gene is active. The promoter types are associated with different chromatin accessibility in ATAC‐seq data and have different expression characteristics in single‐cell RNA‐seq data. The two promoter types may therefore be optimized for different properties: paused promoters show more consistent expression when active, while TATA promoters have lower background expression when inactive. We propose that tissue‐specific genes have evolved to use two different strategies for their differential expression across tissues.https://doi.org/10.15252/msb.20209866effector genesgene expression noisePol II pausingscRNA‐seqTATA promoter |
| spellingShingle | Vivekanandan Ramalingam Malini Natarajan Jeff Johnston Julia Zeitlinger TATA and paused promoters active in differentiated tissues have distinct expression characteristics Molecular Systems Biology effector genes gene expression noise Pol II pausing scRNA‐seq TATA promoter |
| title | TATA and paused promoters active in differentiated tissues have distinct expression characteristics |
| title_full | TATA and paused promoters active in differentiated tissues have distinct expression characteristics |
| title_fullStr | TATA and paused promoters active in differentiated tissues have distinct expression characteristics |
| title_full_unstemmed | TATA and paused promoters active in differentiated tissues have distinct expression characteristics |
| title_short | TATA and paused promoters active in differentiated tissues have distinct expression characteristics |
| title_sort | tata and paused promoters active in differentiated tissues have distinct expression characteristics |
| topic | effector genes gene expression noise Pol II pausing scRNA‐seq TATA promoter |
| url | https://doi.org/10.15252/msb.20209866 |
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