The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development. Chen, X., Bracht, J., R., Goldman, A., D., Dolzhenko, E., Clay, D., M., Swart, E., C., Perlman, D., H., Doak, T., G., Stuart, A., Amemiya, C., T., Sebra, R., P., & Landweber, L., F. Cell, 158(5):1187-1198, Cell Press, 2014.
The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development [link]Website  abstract   bibtex   
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. © 2014 Elsevier Inc.
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 title = {The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development},
 type = {article},
 year = {2014},
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 keywords = {Cell Nucleus; Chromosomes; Gene Rearrangement; Ge,Protozoan; Molecular Sequence Data; Oxytricha,article; chromosome; development; DNA sequence; DN,development and aging; metabolism; molecular gene},
 pages = {1187-1198},
 volume = {158},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84907350409&doi=10.1016%2Fj.cell.2014.07.034&partnerID=40&md5=686c2e1d011edce98709b7410dc154f4},
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 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. © 2014 Elsevier Inc.},
 bibtype = {article},
 author = {Chen, X and Bracht, J R and Goldman, A D and Dolzhenko, E and Clay, D M and Swart, E C and Perlman, D H and Doak, T G and Stuart, A and Amemiya, C T and Sebra, R P and Landweber, L F},
 journal = {Cell},
 number = {5}
}

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