The pathway to detangle a scrambled gene

Background: Programmed DNA elimination and reorganization frequently occur during cellular differentiation. Development of the somatic macronucleus in some ciliates presents an extreme case, involving excision of internal eliminated sequences (IESs) that interupt cuding DNA segments (macronuclear destined sequences, MDSs), as well as removal of transposon-like elements and exrensive genome fragmentation, leading to 98% genome reduction in Stylonychia lemnae. Approximately 20-30% of the genes are estomated to be scrambled in the germline microbucleus, with coding segment order permuted and present in either orientation on micronuclear chromosomes. Massive genome rearrangement are therefore critical for development. Methology/Principal Findings: To understand the process of DNA deletion and reorganization during macronuclear development, we examined the population of DNA molecules during asembly of different scrambled genes in two related organisms in a developmental time course by PCR. The data suggest that removal of conventional IESs usually occurs first, accompanied by a surprising level of error at this step. The complex events of inversion and translocation seem to occur after repair and excision of all conventional IESs and via multiple pathways. Conclusions/Significance: This study reveals a temporal order of DNA rearrangements during the processing of a scrambled gene, with simpler events usually preceding more complex ones. The surprising observation of hidden layer of errors, absent from the mature macronucleus but present during development, also underscore the need for repair or screening of incorrectly-assembled DNA molecules.