Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes
Abstract Fluorescent in situ hybridization (FISH) is a powerful method for the targeted visualization of nucleic acids in their native contexts. Recent technological advances have leveraged computationally designed oligonucleotide (oligo) probes to interrogate > 100 distinct targets in the same s...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-02-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-45385-x |
| _version_ | 1797273864833597440 |
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| author | Robin Aguilar Conor K. Camplisson Qiaoyi Lin Karen H. Miga William S. Noble Brian J. Beliveau |
| author_facet | Robin Aguilar Conor K. Camplisson Qiaoyi Lin Karen H. Miga William S. Noble Brian J. Beliveau |
| author_sort | Robin Aguilar |
| collection | DOAJ |
| description | Abstract Fluorescent in situ hybridization (FISH) is a powerful method for the targeted visualization of nucleic acids in their native contexts. Recent technological advances have leveraged computationally designed oligonucleotide (oligo) probes to interrogate > 100 distinct targets in the same sample, pushing the boundaries of FISH-based assays. However, even in the most highly multiplexed experiments, repetitive DNA regions are typically not included as targets, as the computational design of specific probes against such regions presents significant technical challenges. Consequently, many open questions remain about the organization and function of highly repetitive sequences. Here, we introduce Tigerfish, a software tool for the genome-scale design of oligo probes against repetitive DNA intervals. We showcase Tigerfish by designing a panel of 24 interval-specific repeat probes specific to each of the 24 human chromosomes and imaging this panel on metaphase spreads and in interphase nuclei. Tigerfish extends the powerful toolkit of oligo-based FISH to highly repetitive DNA. |
| first_indexed | 2024-03-07T14:50:15Z |
| format | Article |
| id | doaj.art-11b986022f7646e6b02f240607074f00 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-07T14:50:15Z |
| publishDate | 2024-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-11b986022f7646e6b02f240607074f002024-03-05T19:42:58ZengNature PortfolioNature Communications2041-17232024-02-0115111410.1038/s41467-024-45385-xTigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomesRobin Aguilar0Conor K. Camplisson1Qiaoyi Lin2Karen H. Miga3William S. Noble4Brian J. Beliveau5Department of Genome Sciences, University of WashingtonDepartment of Genome Sciences, University of WashingtonDepartment of Genome Sciences, University of WashingtonDepartment of Biomolecular Engineering, University of California Santa CruzDepartment of Genome Sciences, University of WashingtonDepartment of Genome Sciences, University of WashingtonAbstract Fluorescent in situ hybridization (FISH) is a powerful method for the targeted visualization of nucleic acids in their native contexts. Recent technological advances have leveraged computationally designed oligonucleotide (oligo) probes to interrogate > 100 distinct targets in the same sample, pushing the boundaries of FISH-based assays. However, even in the most highly multiplexed experiments, repetitive DNA regions are typically not included as targets, as the computational design of specific probes against such regions presents significant technical challenges. Consequently, many open questions remain about the organization and function of highly repetitive sequences. Here, we introduce Tigerfish, a software tool for the genome-scale design of oligo probes against repetitive DNA intervals. We showcase Tigerfish by designing a panel of 24 interval-specific repeat probes specific to each of the 24 human chromosomes and imaging this panel on metaphase spreads and in interphase nuclei. Tigerfish extends the powerful toolkit of oligo-based FISH to highly repetitive DNA.https://doi.org/10.1038/s41467-024-45385-x |
| spellingShingle | Robin Aguilar Conor K. Camplisson Qiaoyi Lin Karen H. Miga William S. Noble Brian J. Beliveau Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes Nature Communications |
| title | Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes |
| title_full | Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes |
| title_fullStr | Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes |
| title_full_unstemmed | Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes |
| title_short | Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes |
| title_sort | tigerfish designs oligonucleotide based in situ hybridization probes targeting intervals of highly repetitive dna at the scale of genomes |
| url | https://doi.org/10.1038/s41467-024-45385-x |
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