Publications

Prime editing enables precise modifications to DNA without introducing double-strand breaks, offering exciting opportunities for genome engineering. However, editing efficiency can vary considerably depending on the type of modification and genomic location. What determines these differences, and can they be overcome?

In a new study published in The CRISPR Journal, research assistant Iryna Vykhlyantseva from the Genome Engineering and Measurement Lab (GEML), together with colleagues from the Corn Lab and the Rossi Group  (IUF Düsseldorf), investigated how DNA repair pathways influence prime editing outcomes, identifying PARP1 as an important regulator of insertion efficiency.

By screening 569 compounds targeting DNA damage and repair pathways, we found that inhibiting PARP activity could more than double prime editing-mediated insertions at a specific genomic locus, without a comparable effect on substitutions or deletions. Gene knockout experiments confirmed that PARP1 was primarily responsible for this effect. Importantly, the improvement extended across different prime editing configurations, insertion sizes, and cell types, including primary human T cells, without increasing unwanted editing byproducts.

However, the effect depended on the genomic location and the design of the reverse transcription template, highlighting the importance of cellular and sequence context in determining editing outcomes.

These findings identify PARP1 as a context-dependent barrier to precise DNA insertions and suggest that targeting PARP activity could provide a strategy for improving prime editing-mediated insertions in suitable contexts.

Read the paper in The CRISPR Journal.

X Close

CRISPR technologies have transformed biomedical research, opening new possibilities for understanding, diagnosing, and treating cancer. But how close are we to translating these advances into clinical practice?

 In a new Review published in Nature Reviews Clinical Oncology, Postdoc Carolyn Shembrey together with Samuel Grigg and Joshua Casan (University of Melbourne and Peter MacCallum Cancer Centre, Australia) explore the rapidly expanding applications of CRISPR technologies in oncology and discuss the opportunities and challenges associated with their clinical translation.

CRISPR-based functional genomics screens are uncovering cancer-specific dependencies, mechanisms of drug resistance, and synthetic lethal interactions, opening new opportunities for targeted therapies. Beyond target discovery, CRISPR-based diagnostic approaches offer promising strategies for rapid and precise detection of cancer-associated mutations, with potential applications in liquid biopsies and disease monitoring.

The Review also discusses the growing clinical potential of CRISPR-based therapeutics, particularly through the engineering of immune cells to improve their ability to recognize and eliminate cancer. Other emerging strategies aim to directly target cancer-associated genetic alterations, potentially expanding treatment options beyond conventional approaches.

Despite these advances, important challenges remain. Ensuring editing safety, achieving efficient delivery, and navigating regulatory requirements will be essential for translating CRISPR technologies into broadly accessible cancer diagnostics and treatments.

Congratulations to all co-authors on this comprehensive Review!

Read the Review in  Nature Reviews Clinical Oncology.

X Close

The genome-editing toolbox is rapidly expanding, offering increasingly diverse ways to make precise changes to DNA. But with so many emerging technologies, how do we choose the right tool for a particular application—and where does homology-directed repair (HDR) fit within this changing landscape?

In a new Comment published in Nature Reviews Molecular Cell Biology, Postdoc Eric Aird and Jacob discuss the current and future role of Cas-induced HDR alongside emerging genome-editing technologies.

New technologies are increasingly specialized for different types and sizes of genetic modification. Base, prime and DNA polymerase editors are particularly well suited to small sequence changes, while emerging approaches such as prime assembly, CASTs, large serine recombinases and bridge recombinases are opening possibilities for much larger modifications. HDR, however, occupies a particularly broad space in this toolbox, enabling precise modifications ranging from individual base pairs to kilobase-scale sequences.

No single editing technology is likely to be optimal for every application. Choosing an approach requires balancing not only the desired modification and its size, but also precision and outcome purity, cell type, design complexity, delivery, time, cost and ease of use. As newer technologies continue to mature, HDR therefore remains an important and versatile option rather than simply being replaced by the latest generation of editors.

The Comment provides a perspective on how these complementary technologies may shape the future of precise genome editing and emphasizes an increasingly important question for the field: not simply whether we can make a particular edit, but which tool is best suited to make it.

Check out the Comment in Nature Reviews Molecular Cell Biology!

X Close

How does a cell find the right DNA template to accurately repair a DNA double-strand break?

When DNA breaks, cells can repair the damage through homologous recombination, a process that relies on RAD51 to search the genome for a matching DNA sequence from which missing genetic information can be copied. Despite its central role in maintaining genome stability, how RAD51 carries out this search within the complex three-dimensional environment of the human genome has remained difficult to study.

In our new work published in Cell Reports, Charles Yeh developed RAD51 proximity identification sequencing (RaPID-seq), a new approach that captures transient interactions made by RAD51 during the homology search. Together with colleagues, Charles used RaPID-seq to map where RAD51 searches for matching sequences following a DNA double-strand break in human cells.

The study reveals that homology search in humans is strongly constrained by spatial proximity: DNA regions that are physically close to the break are almost exclusively explored, highlighting an important role for the three-dimensional organization of chromatin in DNA repair. In contrast, homology search in yeast eventually expands globally to encompass the whole genome. This difference highlights a potential mechanism preventing erroneous recombination in humans between highly homologous, but spatially separated genes. We also found that externally introduced DNA repair templates, such as used in genome editing, can overcome these spatial constraints to efficiently participate in the repair process. Notably, these external DNA repair templates even interfere with native search and repair processes.

These findings provide a new view of how cells navigate the genome to accurately repair damaged DNA. Beyond improving our understanding of genome maintenance, the work may also help inform strategies to make homology-directed genome editing more efficient, predictable, and safe.

Congratulations to Charles and all collaborators on this exciting work!

For more info, read the paper in Cell Reports.

X Close

Programmable nucleases have transformed genome editing, enabling precise DNA modification for both research and therapeutic applications. However, ensuring that these tools cut only at their intended target—and not elsewhere in the genome—remains a key challenge, particularly for clinically relevant platforms where accurate off-target detection is essential.

In our latest collaboration with the Genome Engineering and Measurement Lab (GEML) and Allogene Therapeutics, we introduce DisTAL-Seq, a method that enables genome-wide detection of TALEN-induced DNA double strand breaks directly in human cells. The experimental work was led by research technician Lena Kobel. This approach builds on the principles of DISCOVER-Seq and incorporates analysis logic tailored to TALEN binding architecture, including variable repeat specificity, cleavage offset, and dimerization behavior.

Using DisTAL-Seq, we identified and validated editing sites across different TALEN designs and primary human T-cell donors, providing a systematic view of TALEN specificity in clinically relevant contexts.

These results expand the genome-wide profiling approaches developed at GEML and provide a framework for evaluating the safety and performance of genome editing nucleases as they move towards therapeutic applications.

For more detail, check out our paper in Molecular Therapy: Nucleic Acids.

X Close

Stimulation of the innate immune system by foreign RNA triggers a strong interferon response that helps cells defend against infection. However, this powerful defense mechanism can also lead to cell death if not properly controlled. How do cells maintain this delicate balance?

Our latest breakthrough was led by postdoc Eric Aird in collaboration with the Hale Lab (University of Zurich), Recher Lab (University of Basel, University Hospital Basel), Jackson Lab (UCAM) and University of Kuwait.

Using genome-wide CRISPR screens and follow-up cellular biochemistry experiments, we discovered that speckled protein 110 (SP110) functions as a key safeguard against cell death triggered by interferon signaling.

Mechanistically, the study revealed that SP110 interacts with the nuclear body protein SP100 to regulate the disassembly of nuclear promyelocytic leukemia (PML) bodies. Loss of SP110 made cells highly sensitive to interferon stimulation, led to mitotic retention of SP100 and PML bodies, which associated with and perturb segregating chromosomes, leading to micronucleus formation, DNA damage and genotoxic cell death. Conversely, restoring SP110 protected cells from this lethal response. The SP100-SP110 axis is molecularly achieved by newly described functions for the SP100 and SP110 CARD domains that mediate assembly and disassembly of SP100 oligomers. By controlling this process, SP110 helps maintain a balance between effective immune signaling and cell survival.

These findings highlight regulated disassembly of phase-separated biomolecular bodies as essential for cell health and that its failure may contribute to diverse human diseases.

For more details, please visit Nature Cell Biology!

X Close

The DNA damage response (DDR) protects the genome from myriad insults. Indeed, because endogenous damage is an existential and continual threat, cells achieve robustness by engaging multiple overlapping pathways to deal with it. In the context of cancer, these relationships can present therapeutic opportunities because DDR-deficient tumors often rely on backup repair mechanisms for survival. However, addressing this complexity is a daunting challenge because gene functions in essential DNA repair processes can be masked and overlooked when pathways use completely different mechanisms to complement one another. But which DDR gene interactions are essential for cell survival during normal homeostasis? Our latest CRISPR interference (CRISPRi) screen has the answers!

In our latest paper, we performed the most systematic genetic interaction investigation of the human DDR to date. This exciting new work was driven by postdoc John Fielden and PhD student Sebastian Siegner in collaboration with the Jackson  (UCAM), Cejka (USI) and Jost  (HMS) labs.

We tested 150,000 genetic interactions, asking which DDR genes have synthetic lethal interactions with each other. We uncovered previously unknown connections between DNA repair factors as well as interactions that may be clinically exploitable. All these interactions can be browsed on our user-friendly website, SPIDRweb.

 For deep mechanistic studies, we prioritized two of the strongest novel synthetic interactions: WDR48:LIG1/FEN1 and FANCM:SMARCAL1. First, we found that WDR48 partners with USP1 to prevent PCNA degradation in cells lacking either FEN1 or LIG1, two enzymes which ordinarily prevent the accumulation of DNA nicks, gaps, and single-strand breaks. Second, we revealed that FANCM and SMARCAL1, two well-known but previously unconnected DNA translocases, have overlapping roles in unwinding DNA secondary structures that form at TA-rich repeats. In doing so, they effectively shield the genome from catastrophic fragmentation by the ERCC1-ERCC4 nuclease complex.

From a clinical perspective, our data suggest that already existing USP1 inhibitors may synergize with chemotherapies that induce DNA gaps, such as ATR and WEE1 inhibitors. Moreover, FANCM and SMARCAL1 are mutated in breast cancers and glioblastomas, respectively, pinpointing them as promising targets for drug development.

Overall, our work reveals new aspects of DDR biology and suggests multiple targets for synthetic lethality-based cancer therapy. We anticipate that our genetic interaction map will reveal further insights into fundamental DDR biology as well as cancer cell-specific vulnerabilities and candidate drug targets.

For more info check out our new paper in Nature!

X Close

Proteins are essential building blocks of life, but they can become toxic to our cells if damaged, for example under oxidative stress. In turn, human cells selectively remove damaged proteins to maintain a healthy proteome. But how can cells identify individual damaged proteins among thousands of intact ones? An old hypothesis states that cells scan the proteome for chemical modifications that occur, for example, when proteins break. Are you interested in learning more about how cells combat chemical protein damage?

Have a look at our newest research breakthrough, led by postdoc Matthias Muhar in a collaboration with Jakob Farnung from the Bode group (D-CHAB) as well as with Jessberger group (UZH), Jinek group (UZH), Mann group (Max Plank Institute of Biochemistry) Germany   and Schulman group (Max Plank Institute of Biochemistry, Germany).

In this study, using a semi-synthetic chemical biology approach coupled to cellular assays, we found that C-terminal amide-bearing proteins (CTAPs) are rapidly cleared from human cells.

To identify the cellular machinery underlying CTAP clearance, we utilized a genome-wide CRISPR screen for genes that are responsible for specific degradation of C-terminally amidated proteins. We identified SCF–FBXO31 ubiquitin ligase as a key reader of C-terminal amides, marking CTAPs for proteasomal degradation. With a conserved binding pocket, FBXO31 exhibits remarkable selectivity, binding C-terminal peptides with amides while excluding non-modified proteins. This mechanism allows cell to remove CTAPs, which form when proteins break under under oxidative stress. Intriguingly, a human mutation linked to neurodevelopmental disorders alters FBXO31’s substrate recognition, leading to toxicity. These findings suggest CTAPs may represent a new class of modified amino acid degrons (MAADs) that mark proteins for removal by reader proteins and downstream effectors, offering insights into selective surveillance of chemically damaged proteins.

In conclusion, this research uncovered new signals for protein clearance and advanced our understanding of cellular protein quality control.

For more info check out our new paper in Nature!

X Close

Genome editing creates double-strand breaks (DSBs) that can be repaired through either non-homologous end joining (NHEJ), microhomology-mediated end joining or homology-directed repair (HDR). While NHEJ is quick but error-prone, HDR uses a DNA template for precise edits, allowing targeted changes from single-nucleotide fixes to large gene insertions, greatly benefiting biomedical research and therapies. However, HDR is a relatively inefficient process, and ongoing efforts aim to improve its efficiency, including the use of small molecule inhibitors targeting DNA repair. One such highly potent inhibitor, AZD7648, selectively targets DNA-PKcs, redirecting DNA repair from the error-prone NHEJ pathway to the more precise HDR pathway in both transformed cell lines and primary human cells. However, the potential unintended consequences of its use in genome editing remain largely unexplored.

Are you curious to find out more?

Check out our recent advancement, led by postdoc Grégoire Cullot in a collaboration with the Gehart group (IMHS), Cathomen group (University of Freiburg, Germany) and the Gene Therapy research group of CSL Behring.

This work demonstrated that genome editing with a single Cas9-induced DSB in combination with AZD7648 leads to an increase in HDR, but this was accompanied by Cas9-induced genomic instability at on-target sites, where small-scale NHEJ outcomes were transformed into larger genetic alterations that cannot be detected by short-read sequencing.

Through the use of long-read sequencing, droplet digital PCR (ddPCR) for copy number analysis, single-cell RNA sequencing, and unbiased translocation detection, we discovered that AZD7648 significantly amplifies the frequency of kilobase-scale deletions, chromosome arm loss, and translocations across various cell types.

More broadly, genome editing-induced large-scale genomic alterations might still be largely underestimated. Indeed, these large-scale genomic alterations evade classical genome editing detection assays, typically short-read next-generation sequencing (NGS) and necessitate specific techniques that are not currently commonly used in the genome editing field. This means that clinical genome editing groups might be unaware of potential induced genomic instability and safety risks. Of note, AZD7648 is being tested by many clinical genome editing groups, however our results urge caution when deploying it during genome editing and reinforce the need to investigate genetic outcomes beyond those accessible to short-read target amplicon next-generation sequencing.

For more info check out our new paper in Nature Biotechnology!

X Close

Cells constantly experience DNA damage throughout their lifespan due to a variety of endogenous and exogenous factors. Among the different types of DNA damage, double-stranded breaks (DSBs) are particularly severe and can be detrimental if left unrepaired. Eukaryotes have developed mechanisms to detect and repair such damage, known as the DNA damage response (DDR), which involves hundreds of key players and supporting factors. Are you curious to discover more about DDR? Have a look at latest breakthrough,  led by postdoc Erman Karasu in a collaboration with the Jonas group (IMBB) and Zavolan group (University of Basel).

By utilizing a CRISPR screening system to assay about 18,000 gene knockdowns, we identified new players influencing homology-directed repair (HDR). Among these, we focused on CCAR1, an enigmatic gene whose role in the DDR was not well understood. We found that reducing CCAR1 levels impaired both HDR and the repair of interstrand crosslinks, similar to what occurs when the Fanconi anemia (FA) pathway is inactivated. Interestingly, CCAR1 deficiency leads to FANCA protein depletion without affecting FANCA mRNA or other FA gene mRNAs levels. Instead, CCAR1 ensures FANCA mRNA splicing by suppressing a poison exon inclusion. CCAR1 binds to U2-type spliceosome and acts on multiple splicing sites. This demonstrates that CCAR1 is crucial for proper mRNA splicing. Further analysis showed that CCAR1’s role in mRNA splicing extends beyond FANCA, affecting many genes and ensuring that their mRNAs are correctly processed in both mouse and human cells. Our work highlights CCAR1’s unexpected role in maintaining accurate mRNA splicing, which is essential for proper protein function.

For more info check out our new paper in Molecular Cell!

X Close