Throwing away DNA: programmed downsizing in somatic nuclei. Issue 5 (May 2022)

• Record Type: Journal Article
• Authors: Drotos, Katherine H.I.; Zagoskin, Maxim V.; Kess, Tony; Gregory, T. Ryan; Wyngaard, Grace A.
• Is Part Of: Trends in genetics. Volume 38:Issue 5(2022)
• Page Start: 483
• Page End: 500
• Publication Date: 2022-05
• Subjects: programmed DNA elimination -- transposable elements -- genome architecture -- genome stability -- germline–soma differentiation -- genome defense; Genetics -- Periodicals; 576.5
• DOI: 10.1016/j.tig.2022.02.003
• Languages: English
• ISSNs: 0168-9525

Abstract

Abstract : Programmed elimination of DNA during development yields somatic cell nuclei with dramatically different DNA sequence and content relative to germline nuclei, profoundly influencing genome architecture and stability. Whole-genome sequencing has significantly expanded the list of taxa known to exhibit this trait and has revealed the identity of excised genes and transposable elements (TEs) in certain taxa. Here, we compare the diverse mechanisms employed by ciliates, nematodes, copepods, and lamprey to downsize their genomes during development and propose tests of hypotheses about the evolution and/or maintenance of this trait. We explore possible functional roles that programmed DNA elimination (PDE) could play in genomic defense (especially against TEs), regulation of development, sex determination, co-option, and modulating nucleotypic effects, which together argue for a place in the mainstream investigation of genome evolution. Highlights: Organisms that possess programmed DNA elimination (PDE) inherently possess modular genomes. Whole-genome sequencing has expanded the number of taxa known to possess PDE and thus PDE may be more widespread than commonly acknowledged. Genome defense against the eliminated DNA is a commonly hypothesized role, but the eliminated DNA may also have been co-opted for beneficial roles that remain unexplored with respect to their possible adaptive significance. The amount and nature of excised DNA and the mechanisms to execute the DNA elimination are diverse, providing a wealth of biological systems ripe for evolutionary studies.