Large transgene arrays cause aberrant transcription and synthetic molting defects.

Multicopy transgene arrays remain widely used in Caenorhabditis elegans research. It is usually assumed that they behave neutrally, not impacting the phenotype under investigation. Here, we reveal that a previously reported heterochronic extra-molt phenotype associated with myrf-1(mg412) depends on the presence of the integrated molting reporter mgIs49. Nanopore long-read sequencing shows that mgIs49 is a massive 8.8-Mb insertion - around 50% of the size of its host chromosome - which disrupts the prmt-9 gene. Both mgIs49 and another array, maIs105, cause dysregulation of the transcriptome and accumulation of reads mapping in sense-direction to transgene promoter sequences. We identify additional arrays exceeding 4 Mb and show that variable molting defects occur across different transgenic lines when combined with myrf-1(mg412), implicating array size or composition in the synthetic phenotype. Our results underscore the necessity of replacing multicopy reporters in developmental studies with single-copy insertions or endogenous tagging whenever possible.