Advancements in Genome Editing with CRISPRware
A Ph.D. student at the University of California, Santa Cruz, has created a groundbreaking software tool that enhances the precision of genome editing. This innovation holds significant promise for developing treatments for genetic disorders, including conditions such as sickle-cell anemia and other metabolic or blood-related diseases.
The software, named CRISPRware, draws its name from the widely used CRISPR-Cas9 genome-editing system. Cas9 is a protein that binds to a short RNA sequence, known as guide RNA, which is designed to match a specific DNA region. This guide RNA directs Cas9 to the target location on the genome, where it creates a double-strand break. This break allows scientists to introduce precise modifications to the DNA.
One of the challenges in using CRISPR technology is that Cas9 requires a specific short sequence, or motif, in the guide RNA to function correctly. While there are existing tools for identifying guide RNAs in well-studied genes, they often fall short when dealing with less understood regions of the genome. To tackle this issue, Eric Malekos, a Ph.D. candidate, developed CRISPRware. The software enables users to design guide RNAs for any part of the genome and supports multiple CRISPR systems, each with unique binding-site requirements. It can scan entire genomes and identify all potential guide RNAs that meet the necessary criteria.
Malekos’s research focuses on small, uncharacterized peptides found in large, unannotated regions of the genome. These peptides, though short, can have critical biological functions. For example, glucagon-like peptide-1 (GLP-1), which is about 60 amino acids long, plays a key role in regulating blood sugar, appetite, and digestion. GLP-1 forms the basis of several diabetes treatments, such as Ozempic and Wegovy, which are also used for weight loss.
Malekos investigates how these small peptides might function within the innate immune system and inflammatory responses. He works in the lab of Susan Carpenter, a professor of molecular, cell, and developmental biology at UC Santa Cruz. Carpenter describes CRISPRware as a flexible tool. When linked to the UCSC Genome Browser, it becomes more accessible to researchers who may not have a background in bioinformatics.
This year marks the 25th anniversary of the UCSC Genome Browser, a platform used by tens of thousands of scientists daily to view, annotate, and analyze genomes from various species, including humans and viruses. Carpenter highlights that CRISPRware helps democratize the use of CRISPR by significantly reducing the need for computational expertise.
Carpenter also points out that the recent case of a patient receiving the first personalized gene therapy using CRISPR for carbamoyl phosphate synthetase 1 (CPS1) deficiency demonstrates the kind of application CRISPRware can support.
Integration with a Popular Platform
Most current bioinformatics tools are not user-friendly for non-specialists. By integrating CRISPRware into the UCSC Genome Browser, the software becomes accessible to a broader group of researchers already familiar with the platform. Users can now:
- Browse precomputed libraries of guide RNAs for six model species
- Focus on specific genes or genomic regions
- Select optimal guide RNAs without writing code or configuring software
Malekos emphasizes that this approach lowers the barrier to entry, helping spread the benefits of CRISPR across the life-sciences community. He adds that usability is a major asset of CRISPRware.
The system also supports high-throughput CRISPR screening, allowing researchers to test thousands of peptide candidates simultaneously. This method is valuable for identifying peptides involved in immunity and inflammation and contributes to mapping the “dark proteome”—the set of short, functional proteins that remain poorly characterized in genomic data.
Validation Across Model Species
Malekos tested CRISPRware using complete genomes from six model organisms: Caenorhabditis elegans (roundworm), zebrafish, fruit fly, rat, mouse, and human. The tool generated comprehensive sets of guide RNAs targeting coding regions in each species. These catalogs provide the research community with a consistent and accessible resource.
Carpenter notes that whether researchers are working on C. elegans or a fruit fly, this ensures that scientists studying any of these organisms can quickly find optimal guide RNAs for their experiments.
