Genome-scale analysis of programmed DNA elimination sites in tetrahymena thermophila

Joseph N. Fass, Nikhil A. Joshi, Mary T. Couvillion, Josephine Bowen, Martin A. Gorovsky, Eileen P. Hamilton, Eduardo Orias, Kyungah Hong, Robert S. Coyne, Jonathan A. Eisen, Douglas L. Chalker, Dawei Lin, Kathleen Collins

Research output: Contribution to journalArticlepeer-review

60 Scopus citations


Genetically programmed DNA rearrangements can regulate mRNA expression at an individual locus or, for some organisms, on a genome-wide scale. Ciliates rely on a remarkable process of whole-genome remodeling by DNA elimination to differentiate an expressed macronucleus (MAC) from a copy of the germline micronucleus (MIC) in each cycle of sexual reproduction. Here we describe results from the first highthroughput sequencing effort to investigate ciliate genome restructuring, comparing Sanger long-read sequences from a Tetrahymena thermophila MIC genome library to the MAC genome assembly. With almost 25% coverage of the unique-sequence MAC genome by MIC genome sequence reads, we created a resource for positional analysis of MIC-specific DNA removal that pinpoints MAC genome sites of DNA elimination at nucleotide resolution. The widespread distribution of internal eliminated sequences (IES) in promoter regions and introns suggests that MAC genome restructuring is essential not only for what it removes (for example, active transposons) but also for what it creates (for example, splicing-competent introns). Consistent with the heterogeneous boundaries and epigenetically modulated efficiency of individual IES deletions studied to date, we find that IES sites are dramatically under-represented in the 25% of theMAC genome encoding exons. As an exception to this general rule, we discovered a previously unknown class of small (<500 bp) IES with precise elimination boundaries that can contribute the 39 exon of an mRNA expressed during genome restructuring, providing a new mechanism for expanding mRNA complexity in a developmentally regulated manner.

Original languageEnglish
Pages (from-to)515-522
Number of pages8
JournalG3: Genes, Genomes, Genetics
Issue number6
StatePublished - Nov 2011


  • Ciliate nuclear dualism
  • Community sequencing project
  • DNA breakage and joining
  • Genome rearrangement
  • Tetrahymena


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