A. The biology level. Mutant phenotypes and DNA modifications can be analyzed at systems-, tissue-, cell-, subcellular-, and molecular levels. B. The DNA level. DNA modifications can be performed at genome-, chromosome-, subchromosome-, chromatin-, or nucleotide-levels. C. Methods to perform genome engineering at the different DNA levels. Currently, engineering technologies to manipulate genomes or chromosomes in toto are unavailable for Drosophila melanogaster or any other multicellular eukaryotic organism. On the other hand, numerous methods are available to precisely engineer chromosomal sections, gene environments, and gene properties. Note: Drawings for panel B were acquired by modifying free vector templates available from www.vector.me.