Key takeaways
- CRISPRware is a new tool scientists can use to design the best guide RNAs to edit genes in many organisms, without the need for deep bioinformatics expertise.
- By making gene editing more precise and accessible, CRISPRware supports the development of personalized gene therapies like those already helping people with genetic diseases.
A Ph.D. student in biomolecular engineering at the University of California, Santa Cruz, has built a software program designed to facilitate the kind of precision genome editing involved in the development of cutting-edge therapeutics for genetic conditions such as certain metabolic or blood disorders, like sickle-cell anemia.
The new tool, CRISPRware, takes its name from CRISPR-Cas9, the workhorse of modern genome editing. At its core, Cas9 is a protein that binds with a short RNA sequence designed to be complementary to a specific region of the genome. This short sequence, called guide RNA, effectively acts as a homing device, directing Cas9 to a precise spot on the DNA. Once there, Cas9 makes a double-strand break that enables researchers to introduce precise changes.
However, a major constraint in CRISPR targeting is a short sequence motif in guide RNA that Cas9 requires for binding. And while many tools exist to help researchers locate guide RNAs for the roughly 20,000 well-annotated protein-coding genes in the human genome, they aren’t as useful for researching novel or less-characterized coding regions.
To address this, Ph.D candidate Eric Malekos developed CRISPRware, allowing users to design guide RNAs for any region of the genome, accommodating different CRISPR systems and their unique binding-site requirements. The software can scan an entire genome and identify all possible guide RNAs that meet those constraints.
“There was really no good tool for customizing which portions of the genome you want to target,” said Malekos, whose research focuses on small uncharacterized peptides produced from the vast unannotated portions of the genome.
Big influence of small peptides
Despite their small size, these peptides can be highly functional. For example, glucagon-like peptide-1 is only about 60 amino acids long, but it plays a crucial role in regulating blood sugar levels, appetite, and digestion. That peptide is now familiar to many by its abbreviated name, GLP-1, the basis for a class of medications for treating type 2 diabetes that have become widely popular as weight-loss drugs like Ozempic and Wegovy.
Malekos studies these small peptides for their possible roles in the innate immune system and inflammatory responses. He conducts his research in the lab of Susan Carpenter, professor of molecular, cell, and developmental biology at UC Santa Cruz. She said CRISPRware is a highly versatile tool that, by integrating it into the widely used UCSC Genome Browser, makes the program more accessible to researchers without bioinformatics expertise.
Celebrating the 25th anniversary of its launch this year, the UCSC Genome Browser is now accessed by tens of thousands of researchers a day to visualize, annotate, and study genomes of thousands of different species from humans to viruses. “Eric’s tool helps democratize the use of CRISPR by greatly reducing the need for computational expertise,” Carpenter said.
The recent milestone of the first human to successfully receive a CRISPR-based personalized gene-therapy treatment—for a rare and incurable genetic disease called carbamoyl phosphate synthetase 1 (CPS1) deficiency—is a powerful example of the type of breakthrough CRISPRware can play a role in enabling, Carpenter added.
Leveraging a popular platform
Most current bioinformatics tools remain inaccessible to non-specialists. But by integrating CRISPRware’s outputs directly into the UCSC Genome Browser—a platform already familiar to many researchers—the tool becomes approachable to many more. Scientists without deep computational skills can:
- quickly browse entire libraries of precomputed guide RNAs for six model organisms
- zoom in on their gene or region of interest
- select optimal guides without needing to write code or set up complex software
“This approach lowers the barrier to entry, helping spread CRISPR’s benefits across the entire life-sciences community,” Malekos said. “CRISPRware’s usability is definitely another major asset.”
In addition, the tool enables high-throughput CRISPR-based screening. Rather than testing one region at a time, researchers can systematically screen thousands of candidate peptides to discover those that matter in key contexts such as immunity. This kind of large-scale approach is critical for mapping the so-called “dark proteome”—the previously unseen world of short functional proteins hidden in our genome.
Proven across model species
To validate the CRISPRware, Malekos ran the tool on the entire genomes of six model species: human, rat, mouse, zebrafish, fruit fly and the roundworm Caenorhabditis elegans (C. elegans). For each organism, CRISPRware generated comprehensive catalogs of guide RNAs targeting coding regions—offering the research community a robust, accessible resource.
“Whether you’re 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,” Carpenter said.
The tool is presented in a paper titled “CRISPRware: a software package for contextual gRNA library design,” published on July 1 in BMC Genomics. CRISPRware’s development was supported by a prestigious F31 fellowship from the National Institute of Allergy and Infectious Diseases (NIAID)—a recognition of the project’s potential to advance biomedical science.
Additional support came from an R35 MIRA grant awarded by National Institute of General Medical Sciences (NIGMS), further underscoring the national investment in cutting-edge precision-medicine-enabling research.