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Cell. 2014 Aug 28;158(5):1187-1198. doi: 10.1016/j.cell.2014.07.034.

The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development.

Author information

1
Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
2
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
3
Department of Mathematics and Statistics, University of South Florida, Tampa, FL 33620, USA.
4
Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland.
5
Collaborative Proteomics and Mass Spectrometry Center, Molecular Biology Department and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
6
Department of Biology, University of Indiana, Bloomington, IN 47405, USA.
7
Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA.
8
Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
9
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA. Electronic address: lfl@princeton.edu.

Abstract

Programmed DNA rearrangements in the single-celled eukaryote Oxytricha trifallax completely rewire its germline into a somatic nucleus during development. This elaborate, RNA-mediated pathway eliminates noncoding DNA sequences that interrupt gene loci and reorganizes the remaining fragments by inversions and permutations to produce functional genes. Here, we report the Oxytricha germline genome and compare it to the somatic genome to present a global view of its massive scale of genome rearrangements. The remarkably encrypted genome architecture contains >3,500 scrambled genes, as well as >800 predicted germline-limited genes expressed, and some posttranslationally modified, during genome rearrangements. Gene segments for different somatic loci often interweave with each other. Single gene segments can contribute to multiple, distinct somatic loci. Terminal precursor segments from neighboring somatic loci map extremely close to each other, often overlapping. This genome assembly provides a draft of a scrambled genome and a powerful model for studies of genome rearrangement.

PMID:
25171416
PMCID:
PMC4199391
DOI:
10.1016/j.cell.2014.07.034
[Indexed for MEDLINE]
Free PMC Article

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