UC Santa Cruz Scientist Unveils Groundbreaking CRISPRware Software

Advancements in Gene Editing with CRISPRware

A Ph.D. graduate student in biomolecular engineering at the University of California, Santa Cruz, has developed an innovative software program called CRISPRware. This tool streamlines the gene-editing process for researchers working on treatments for genetic conditions such as sickle cell disease and cystic fibrosis. The software was introduced in a recently published paper in "BMC Genomics," co-authored by the software’s creator, Eric Malekos, alongside fellow Ph.D. student Christy Montano from the Molecular, Cell and Developmental Biology Department, and under the guidance of Professor Susan Carpenter from the Carpenter Lab.

Understanding RNA and Its Role in Immune Responses

“I am an immunologist by training,” said Carpenter. “I’ve been studying all the molecular pathways involved in driving inflammation, particularly acute and chronic inflammation related to autoinflammatory diseases. My lab initially focused on the role that RNA plays in regulating these responses.”

RNA, or ribonucleic acid, is similar to DNA but typically exists as a single strand rather than a double helix. While some RNA acts as a messenger between DNA and ribosomes, which produce proteins, others do not code for proteins. These are known as long non-coding RNAs (lncRNAs).

“When I was training, RNA sequencing became a hot technique, and we discovered many RNA genes that change after inflammatory responses or infections, but they don’t code for proteins,” explained Carpenter. “There are about 36,000 lncRNA genes identified in the human genome, which greatly outnumber protein-coding genes. However, we know very little about their functions. My lab focuses on understanding how these lncRNAs regulate immune responses.”

How CRISPR Works and the Limitations It Faces

CRISPR, or Clustered Regularly Interspaced Short Palindromic Repeats, is a gene-editing tool used to target specific regions of the genome. The process involves a protein called Cas9, which is guided by a short RNA sequence to snip the genome at a precise location.

“The key aspect of CRISPR is its ability to target specific parts of the genome,” said Malekos. “The guide RNA contains about 20 nucleotides, allowing it to match a specific sequence in the genome. This level of specificity makes it possible to target distinct regions of the genome.”

However, existing tools only provided guide RNA for the approximately 20,000 known protein-coding genes, leaving other regions unexplored. CRISPRware addresses this gap by scanning entire genomes and identifying potential guide RNAs for any region.

Expanding the Scope of CRISPR Research

Malekos tested CRISPRware on the genomes of six model species: human, rat, mouse, zebrafish, fruit fly, and Caenorhabditis elegans. The software generated comprehensive guide RNA catalogs for each species, which were then uploaded into the UCSC Genome Browser.

“This feature is really powerful,” said Carpenter. “If you’re working on a fruit fly and want to target a gene but have never used CRISPR before, you can figure out the right guide within a day. It significantly speeds up the process of using CRISPR in these organisms.”

Future Applications of CRISPRware

Looking ahead, Malekos envisions CRISPRware being adapted to study more complex genomes, such as those of cancer cells and plants. Cancer cells often have abnormal chromosomes, and plants can have hundreds of chromosomes, which current versions of CRISPRware are not designed to handle.

“Cancer genomes are quite different from normal human cells, with extra chromosomes and unusual structures,” said Malekos. “CRISPRware currently works with two sets of chromosomes, so future work could involve adapting it to handle more complex genomic structures.”

Concerns About Science Funding

Despite these advancements, both Carpenter and Malekos are concerned about the future of scientific research due to recent funding challenges. As a National Institute of Health predoctoral fellow, Malekos understands the importance of sustained support for scientific progress.

“Science funding is crucial,” said Carpenter. “We’re excited about our research and believe it’s important for people to continue exploring these areas. We understand what’s at stake and the potential losses if funding decreases.”