1. Insertion of Alu elements impacts sequence-mediated nucleosome positioning
- Author
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Barbier, Jérémy, Sassolas, Fabien, Vaillant, Cédric, Volff, Jean-Nicolas, Brunet, Frédéric G., Audit, Benjamin, Laboratoire de Physique de l'ENS Lyon (Phys-ENS), École normale supérieure de Lyon (ENS de Lyon)-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
- Subjects
DNA sequence-encoded nucleosome ordering ,[SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] ,chromatin evolution ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,nucleosome depleted regions ,Alu elements - Abstract
International audience; A physical model for the formation of nucleosomes revealed that the DNA sequence codes for regions inhibiting the formation of nucleosomes. More than 1.6 million nucleosome inhibiting energy barriers (NIEBs) were delineated in the human genome and corroborated as in vivo nucleosome depleted regions (NDRs) in experimental nucleosome occupancy profiles. NIEBs are bordered on each side by compact arrays of 2-3 nucleosomes; one third of the human is covered by this intrinsic nucleosomal organization. Mutation profiles and GC content at NIEB loci presented modulations phased with the compact nucleosomal arrays and the comparison between interspecies and intraspecies divergence rates suggested that nucleosome positioning around these intrinsic NDRs was under selection. In all vertebrates analyzed, similar sequence properties were observed indicating that NIEBs with compacted neighboring nucleosomes are in fact ubiquitous. These results suggest the existence of evolutionary mechanisms linked to the intrinsic nucleosomal organization. We propose an evolutionary scenario in human and chimpanzee where the insertion of Alu transposable elements give rise to new NIEBs based on the observation that (i) a majority of Alu elements are inserted at NIEB borders, (ii) the most recently inserted Alu elements are the closest to the NIEBs, (iii) human insertion sites of polymorphic Alu elements show no preferential positioning regarding NIEBs and (iv) the species-specific Alu elements are mainly positioned at the borders of species-specific NIEBs. We identify transposable elements (TEs) in mouse and pig that are good candidates to follow a similar model of NIEB creation by insertion of TEs. The dynamics of transposition would thus be a general mechanism of chromatin evolution that could explain the evolutionary success of some TE families. This work allows to better apprehend the evolutionary mechanisms responsible for the genome-wide intrinsic nucleosomal organization.
- Published
- 2022