Alessandro Vindigni, Ph.D.

Professor
Biochemistry and Molecular Biology


Research

Studies on DNA replication stress, genome stability, and human disease.

Research Highlights

Replication Fork Reversal PARP PARylation activity is not required to form reversed forks, but it promotes the accumulation of regressed forks by inhibiting RECQ1 fork restoration activity, thus preventing premature restart of regressed forks.
PARP PARylation activity is not required to form reversed forks, but it promotes the accumulation of regressed forks by inhibiting RECQ1 fork restoration activity, thus preventing premature restart of regressed forks.

Replication fork reversal is rapidly emerging as a pivotal mechanism of replication stress response to cancer chemotherapeutics. This work identifies the first molecular mechanism required to restart replication forks that have reversed upon treatment with DNA topoisomerase I inhibitors. It also provides a new rationale to improve current chemotherapeutic modalities based on the use of DNA replication inhibitors. This article was rated as a “must read” by the Faculty of 1000.

Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition. Berti M, et.al., Nat. Struct. Mol. Biol. 20(3):347-354, 2013. (PMID 23396353).

Replication Stress Response

Electron micrograph of a partially single-stranded (left) and entirely double-stranded (right) reversed fork observed on genomic DNA upon HU-treatment. The black arrow points to the ssDNA region on the reversed arm.  D, daughter strand; P, parental strand; R, reversed arm.
Electron micrograph of a partially single-stranded (left) and entirely double-stranded (right) reversed fork observed on genomic DNA upon HU-treatment. The black arrow points to the ssDNA region on the reversed arm. D, daughter strand; P, parental strand; R, reversed arm.

This work defines new important roles for different human nucleases in replication stress response to cancer chemotherapeutics and opens new avenues to study the link between nucleolytic processing of stalled replication intermediates and chemotherapeutic sensitivity.

DNA2 drives processing and restart of reversed replication forks in human cells. Thangavel S, et.al., . Cell Biol. 208(5):545-562, 2015 (PMID 25733713).

RECQ1 Helicase Structure

Overall structure of the RECQ1/DNA complex and trajectory of the ssDNA tail. Perpendicular view of isolated monomer/DNA showing the trajectory of DNA. The top and bottom strands of the tailed duplex are colored black and orange, respectively. A third ssDNA strand from an adjacent complex in the crystal, which base-pairs at the separation junction, is colored cyan.
Overall structure of the RECQ1/DNA complex and trajectory of the ssDNA tail. Perpendicular view of isolated monomer/DNA showing the trajectory of DNA. The top and bottom strands of the tailed duplex are colored black and orange, respectively. A third ssDNA strand from an adjacent complex in the crystal, which base-pairs at the separation junction, is colored cyan.

This work determines the first DNA complex structures of the human RECQ1 helicase. These structures provide new insight into the RecQ helicase mechanism of DNA tracking, strand separation, and Holliday junction branch migration. This work helps clarify how different RecQ enzymes are uniquely adapted to process potentially recombinogenic DNA structures that arise upon replication stress.

Human RECQ1 helicase-driven DNA unwinding, annealing, and branch migration: insights from DNA complex structures. Pike AC, et.al., Proc. Natl. Acad. Sci. USA. 112(14):4286-4291, 2015. (PMID 25831490).

Research Interests

Our laboratory focuses on the mechanisms of DNA replication and repair, and on the possible strategies to target these mechanisms for cancer treatment. Aberrant DNA replication is one of the leading causes of mutations and chromosome rearrangements associated with several cancer related pathologies. At the same time, agents that stall or damage DNA replication forks are widely used for chemotherapy, in the attempt to selectively target highly proliferating cancer cells. Our work provides a new rationale to design novel molecularly-guided treatments targeting the pathways of replication stress response to cancer chemotherapeutics.

Publications

Human Ribonuclease H1 resolves R loops and thereby enables progression of the DNA replication fork
Parajuli S, Tealsey DC, Murali B, Jackson J, Vindigni A and Stewart SA
Pubmed | J. Biol. Chem.

DNA Fiber Analysis: Mind the Gap!
Quinet A, Carvajal-Maldonado D, Lemacon D and Vindigni A
Pubmed | Meth. Enzymol.

Special issue: “At the Intersection of DNA Replication and Genome Maintenance: from Mechanisms to Therapy”
Vindigni A
Pubmed | Biophys. Chem.

Combining electron microscopy with single molecule DNA fiber approaches to study DNA replication dynamics
Vindigni A and Lopes M
Pubmed | Biophys. Chem.

The Architectural Chromatin Factor High Mobility Group A1 Enhances DNA Ligase IV Activity Influencing DNA Repair
Pellarin I, Arnoldo L, Costantini S, Pegoraro S, Ros G, Penzo C, Triolo G, Demarchi F, Sgarra R, Vindigni A and Manfioletti G
Pubmed | PLoS ONE