An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo
Abstract Enhancers are important cis-regulatory elements controlling cell-type specific expression patterns of genes. Furthermore, combinations of enhancers and minimal promoters are utilized to construct small, artificial promoters for gene delivery vectors. Large-scale functional screening methodo...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-04-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-33448-w |
| _version_ | 1827956768888586240 |
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| author | Ya-Chien Chan Eike Kienle Martin Oti Antonella Di Liddo Maria Mendez-Lago Dominik F. Aschauer Manuel Peter Michaela Pagani Cosmas Arnold Andreas Vonderheit Christian Schön Sebastian Kreuz Alexander Stark Simon Rumpel |
| author_facet | Ya-Chien Chan Eike Kienle Martin Oti Antonella Di Liddo Maria Mendez-Lago Dominik F. Aschauer Manuel Peter Michaela Pagani Cosmas Arnold Andreas Vonderheit Christian Schön Sebastian Kreuz Alexander Stark Simon Rumpel |
| author_sort | Ya-Chien Chan |
| collection | DOAJ |
| description | Abstract Enhancers are important cis-regulatory elements controlling cell-type specific expression patterns of genes. Furthermore, combinations of enhancers and minimal promoters are utilized to construct small, artificial promoters for gene delivery vectors. Large-scale functional screening methodology to construct genomic maps of enhancer activities has been successfully established in cultured cell lines, however, not yet applied to terminally differentiated cells and tissues in a living animal. Here, we transposed the Self-Transcribing Active Regulatory Region Sequencing (STARR-seq) technique to the mouse brain using adeno-associated-viruses (AAV) for the delivery of a highly complex screening library tiling entire genomic regions and covering in total 3 Mb of the mouse genome. We identified 483 sequences with enhancer activity, including sequences that were not predicted by DNA accessibility or histone marks. Characterizing the expression patterns of fluorescent reporters controlled by nine candidate sequences, we observed differential expression patterns also in sparse cell types. Together, our study provides an entry point for the unbiased study of enhancer activities in organisms during health and disease. |
| first_indexed | 2024-04-09T15:10:00Z |
| format | Article |
| id | doaj.art-affa02ed88a1427f95b54b6dbac3c570 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-09T15:10:00Z |
| publishDate | 2023-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-affa02ed88a1427f95b54b6dbac3c5702023-04-30T11:17:09ZengNature PortfolioScientific Reports2045-23222023-04-0113111910.1038/s41598-023-33448-wAn unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivoYa-Chien Chan0Eike Kienle1Martin Oti2Antonella Di Liddo3Maria Mendez-Lago4Dominik F. Aschauer5Manuel Peter6Michaela Pagani7Cosmas Arnold8Andreas Vonderheit9Christian Schön10Sebastian Kreuz11Alexander Stark12Simon Rumpel13Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University MainzInstitute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University MainzInstitute of Molecular Biology GmbH (IMB)Institute of Molecular Biology GmbH (IMB)Institute of Molecular Biology GmbH (IMB)Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University MainzResearch Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)Institute of Molecular Biology GmbH (IMB)Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KGResearch Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KGResearch Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University MainzAbstract Enhancers are important cis-regulatory elements controlling cell-type specific expression patterns of genes. Furthermore, combinations of enhancers and minimal promoters are utilized to construct small, artificial promoters for gene delivery vectors. Large-scale functional screening methodology to construct genomic maps of enhancer activities has been successfully established in cultured cell lines, however, not yet applied to terminally differentiated cells and tissues in a living animal. Here, we transposed the Self-Transcribing Active Regulatory Region Sequencing (STARR-seq) technique to the mouse brain using adeno-associated-viruses (AAV) for the delivery of a highly complex screening library tiling entire genomic regions and covering in total 3 Mb of the mouse genome. We identified 483 sequences with enhancer activity, including sequences that were not predicted by DNA accessibility or histone marks. Characterizing the expression patterns of fluorescent reporters controlled by nine candidate sequences, we observed differential expression patterns also in sparse cell types. Together, our study provides an entry point for the unbiased study of enhancer activities in organisms during health and disease.https://doi.org/10.1038/s41598-023-33448-w |
| spellingShingle | Ya-Chien Chan Eike Kienle Martin Oti Antonella Di Liddo Maria Mendez-Lago Dominik F. Aschauer Manuel Peter Michaela Pagani Cosmas Arnold Andreas Vonderheit Christian Schön Sebastian Kreuz Alexander Stark Simon Rumpel An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo Scientific Reports |
| title | An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo |
| title_full | An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo |
| title_fullStr | An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo |
| title_full_unstemmed | An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo |
| title_short | An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo |
| title_sort | unbiased aav starr seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo |
| url | https://doi.org/10.1038/s41598-023-33448-w |
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