An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo.

Autor: Chan YC; Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany., Kienle E; Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany., Oti M; Institute of Molecular Biology GmbH (IMB), Mainz, Germany.; Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an Der Riß, Germany., Di Liddo A; Institute of Molecular Biology GmbH (IMB), Mainz, Germany., Mendez-Lago M; Institute of Molecular Biology GmbH (IMB), Mainz, Germany., Aschauer DF; Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany., Peter M; Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA., Pagani M; Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria., Arnold C; Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.; CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria., Vonderheit A; Institute of Molecular Biology GmbH (IMB), Mainz, Germany., Schön C; Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an Der Riß, Germany., Kreuz S; Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an Der Riß, Germany., Stark A; Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.; Medical University of Vienna, Vienna BioCenter (VBC), 1030, Vienna, Austria., Rumpel S; Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany. sirumpel@uni-mainz.de.
Jazyk: angličtina
Zdroj: Scientific reports [Sci Rep] 2023 Apr 25; Vol. 13 (1), pp. 6745. Date of Electronic Publication: 2023 Apr 25.
DOI: 10.1038/s41598-023-33448-w
Abstrakt: 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.
(© 2023. The Author(s).)
Databáze: MEDLINE
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