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Falo-Sanjuan J, Diaz-Tirado Y, Turner MA, Davis J, Medrano C, Haines J, McKenna J, Eisen MB, Garcia HG. Targeted mutagenesis of specific genomic DNA sequences in animals for the in vivo generation of variant libraries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598328. [PMID: 38915503 PMCID: PMC11195090 DOI: 10.1101/2024.06.10.598328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Understanding how the number, placement and affinity of transcription factor binding sites dictates gene regulatory programs remains a major unsolved challenge in biology, particularly in the context of multicellular organisms. To uncover these rules, it is first necessary to find the binding sites within a regulatory region with high precision, and then to systematically modulate this binding site arrangement while simultaneously measuring the effect of this modulation on output gene expression. Massively parallel reporter assays (MPRAs), where the gene expression stemming from 10,000s of in vitro-generated regulatory sequences is measured, have made this feat possible in high-throughput in single cells in culture. However, because of lack of technologies to incorporate DNA libraries, MPRAs are limited in whole organisms. To enable MPRAs in multicellular organisms, we generated tools to create a high degree of mutagenesis in specific genomic loci in vivo using base editing. Targeting GFP integrated in genome of Drosophila cell culture and whole animals as a case study, we show that the base editor AIDevoCDA1 stemming from sea lamprey fused to nCas9 is highly mutagenic. Surprisingly, longer gRNAs increase mutation efficiency and expand the mutating window, which can allow the introduction of mutations in previously untargetable sequences. Finally, we demonstrate arrays of >20 gRNAs that can efficiently introduce mutations along a 200bp sequence, making it a promising tool to test enhancer function in vivo in a high throughput manner.
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Affiliation(s)
- Julia Falo-Sanjuan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Yuliana Diaz-Tirado
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Meghan A. Turner
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
| | - Julian Davis
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Claudia Medrano
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Jenna Haines
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Joey McKenna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Michael B. Eisen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Integrative Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Hernan G. Garcia
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Physics, University of California, Berkeley, CA, USA
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, CA, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA, USA
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
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Witzenberger M, Schwartz S. Directing RNA-modifying machineries towards endogenous RNAs: opportunities and challenges. Trends Genet 2024; 40:313-325. [PMID: 38350740 DOI: 10.1016/j.tig.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 02/15/2024]
Abstract
Over 170 chemical modifications can be naturally installed on RNA, all of which are catalyzed by dedicated machineries. These modifications can alter RNA sequence structure, stability, and translation as well as serving as quality control marks that record aspects of RNA processing. The diverse roles played by RNAs within cells has motivated endeavors to exogenously introduce RNA modifications at target sites for diverse purposes ranging from recording RNA:protein interactions to therapeutic applications. Here, we discuss these applications and the approaches that have been employed to engineer RNA-modifying machineries, and highlight persisting challenges and perspectives.
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Affiliation(s)
- Monika Witzenberger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel.
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel.
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Thakkar N, Hejzlarova A, Brabec V, Dolezel D. Germline Editing of Drosophila Using CRISPR-Cas9-Based Cytosine and Adenine Base Editors. CRISPR J 2023; 6:557-569. [PMID: 37917075 DOI: 10.1089/crispr.2023.0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Target-AID, BE3, and ABE7.10 base editors fused to the catalytically modified Cas9 and xCas9(3.7) were tested for germline editing of the fruit fly Drosophila melanogaster. We developed a guide RNA-expressing construct, white-4gRNA, targeting splice sites in the white gene, an X-chromosome located gene. Using white-4gRNA flies and transgenic lines expressing Target-AID, BE3, and ABE7.10 base editors, we tested the efficiency of stable germline gene editing at three different temperatures. Classical Cas9 generating insertions/deletions by non-homologous end joining served as a reference. Our data indicate that gene editing is most efficient at 28°C, the highest temperature suitable for fruit flies. Finally, we created a new allele of the core circadian clock gene timeless using Target-AID. This base edited mutant allele timSS308-9FL had a disrupted circadian clock with a period of ∼29 h. The white-4gRNA expressing fly can be used to test new generations of base editors for future applications in Drosophila.
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Affiliation(s)
- Nirav Thakkar
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Adela Hejzlarova
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - Vaclav Brabec
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - David Dolezel
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
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Abruzzi KC, Ratner C, Rosbash M. Comparison of TRIBE and STAMP for identifying targets of RNA binding proteins in human and Drosophila cells. RNA (NEW YORK, N.Y.) 2023; 29:1230-1242. [PMID: 37169395 PMCID: PMC10351885 DOI: 10.1261/rna.079608.123] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/28/2023] [Indexed: 05/13/2023]
Abstract
RNA binding proteins (RBPs) perform a myriad of functions and are implicated in numerous neurological diseases. To identify the targets of RBPs in small numbers of cells, we developed TRIBE, in which the catalytic domain of the RNA editing enzyme ADAR (ADARcd) is fused to an RBP. When the RBP binds to an mRNA, ADAR catalyzes A to G modifications in the target mRNA that can be easily identified in standard RNA sequencing. In STAMP, the concept is the same except the ADARcd is replaced by the RNA editing enzyme APOBEC. Here we compared TRIBE and STAMP side-by-side in human and Drosophila cells. The goal is to learn the pros and cons of each method so that researchers can choose the method best suited to their RBP and system. In human cells, TRIBE and STAMP were performed using the RBP TDP-43. Although they both identified TDP-43 target mRNAs, combining the two methods more successfully identified high-confidence targets. In Drosophila cells, RBP-APOBEC fusions generated only low numbers of editing sites, comparable to the level of control editing. This was true for two different RBPs, Hrp48 and Thor (Drosophila EIF4E-BP), indicating that STAMP does not work well in Drosophila.
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Affiliation(s)
- Katharine C Abruzzi
- Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Corrie Ratner
- Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA
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