New Software Boosts Genome Editing Accuracy for Genetic Therapies

A Ph.D. student in Biomolecular Engineering at the University of California, Santa Cruz, has developed software to improve the accuracy of genome editing. This is important for developing therapies for genetic disorders, including metabolic and blood conditions such as sickle-cell anemia.

Image Credit: Butusova Elena/Shutterstock.com

The tool, called CRISPRware, is named after CRISPR-Cas9, a widely used genome-editing system. Cas9 is a protein that binds to a short RNA sequence designed to match a specific region of DNA.

This RNA segment, called a guide RNA, directs Cas9 to the target location on the genome. Once there, Cas9 creates a double-strand break in the DNA. This allows researchers to introduce precise changes.

One limitation in CRISPR targeting is that Cas9 requires a specific short sequence, or motif, in the guide RNA to bind properly. While there are tools that help researchers find guide RNAs for well-studied protein-coding genes, these tools are less effective for unexplored or poorly understood regions of the genome.

To address this, Ph.D. candidate Eric Malekos developed CRISPRware. The software allows users to design guide RNAs for any region of the genome. It also supports multiple CRISPR systems, each with its own binding-site requirements. CRISPRware can scan an entire genome and identify all possible guide RNAs that meet the necessary constraints.

There was really no good tool for customizing which portions of the genome you want to target.

Eric Malekos, Ph.D. Student, University of California, Santa Cruz

Eric Malekos’s research focuses on small, uncharacterized peptides that come from large, unannotated regions of the genome.

Big Influence of Small Peptides

Although these peptides are short, they can have important biological functions. For example, glucagon-like peptide-1 is about 60 amino acids long and plays a role in regulating blood sugar, appetite, and digestion. This peptide, known as GLP-1, forms the basis of several type 2 diabetes treatments, including drugs like Ozempic and Wegovy, which are also used for weight loss.

Malekos studies how these small peptides may function in the innate immune system and inflammatory responses. He works in the lab of Susan Carpenter, professor of molecular, cell, and developmental biology at UC Santa Cruz. Carpenter described CRISPRware as a flexible tool. When linked to the widely used UCSC Genome Browser, it becomes more accessible to researchers who may not have a background in bioinformatics.

This year marks 25 years since the UCSC Genome Browser was launched. Tens of thousands of scientists use it daily to view, annotate, and analyze genomes from a wide range of species, including humans and viruses.

Eric’s tool helps democratize the use of CRISPR by greatly reducing the need for computational expertise.

Susan Carpenter, Professor, Molecular, Cell, and Developmental Biology, University of California, Santa Cruz

Carpenter noted that the recent case of a patient receiving the first personalized gene therapy using CRISPR—for carbamoyl phosphate synthetase 1 (CPS1) deficiency—demonstrates the type of application CRISPRware can support.

Leveraging a Popular Platform

Most current bioinformatics tools are not easily usable by non-specialists. By integrating CRISPRware into the UCSC Genome Browser, the software becomes accessible to a larger group of researchers who are already familiar with the platform. Without needing advanced programming skills, users can:

• 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 added, “This approach lowers the barrier to entry, helping spread CRISPR’s benefits across the entire life-sciences community. CRISPRware’s usability is definitely another major asset.”

The system also supports high-throughput CRISPR screening. Instead of analyzing one region at a time, researchers can test thousands of peptide candidates in parallel. This method is useful for identifying peptides that play roles in immunity and inflammation. It also contributes to mapping the "dark proteome"—the set of short, functional proteins that remain poorly characterized in genomic data.

Proven Across Model Species

Malekos validated 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 noted, “Whether you are working on C. elegans or a fruit fly, this ensures that researchers studying any of these organisms can quickly identify optimal guide RNAs for their experiments.”