Modeling the Cascade of Genome Rearrangements in the ciliate Oxytricha trifallax

Genome rearrangement is a widespread process in development and evolution that includes translocations, inversions, deletions, and duplications. Organisms can benefit from developmental genome rearrangement processes, which enable access to otherwise inaccessible regions of the genetic landscape and allow for combinatorial variation. However, rearrangement can also introduce genetic errors that impair normal gene function and lead to genome instability and diseases such as cancer. The ciliate Oxytricha trifallax is an excellent model organism for studying mechanisms and fidelity of programmed DNA rearrangement because of its complex genomic structure. Its transcriptionally active genome is massively reorganized from a scrambled germline template during development, requiring the precise deletion, inversion, and translocation of tens of thousands of sequence segments. This project leverages a first-of-its-kind, time-resolved, long-read sequencing dataset that captures genome-wide rearrangement intermediates across development. In Aim 1, I will develop quantitative summaries of rearrangement progression and use unsupervised learning to uncover how sequence complexity and regulatory features shape timing and pathway dynamics. In Aim 2, I will construct and test competing stochastic and deterministic models to identify the principles governing rearrangement order and timing. In Aim 3, I will identify and classify naturally occurring rearrangement errors, validate key intermediates with PCR/qPCR, and explore sequence features that may explain error susceptibility. This research will define generalizable rules for accurate genome reassembly, providing a model for understanding how genomes self-organize with high fidelity. It also lays a foundation for future comparative work on the evolutionary origins of genome scrambling and may inform broader principles of genome regulation, editing, and stability in both health and disease. Project Number: 1F32GM159408-01A1 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of General Medical Sciences (NIGMS) | Principal Investigator: Amanda Wilson | Institution: COLUMBIA UNIVERSITY HEALTH SCIENCES, NEW YORK, NY | Award Amount: $76,300 | Activity Code: F32 | Study Section: Special Emphasis Panel[ZRG1 F08-L (20)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11324083