UC Berkeley UC Berkeley Previously Published Works Title Genome-Scale Analysis of Programmed DNA Elimination Sites in Tetrahymena thermophila. Permalink https://escholarship.org/uc/item/8kc8r38p Journal G3 (Bethesda, Md.), 1(6) ISSN 2160-1836 Authors Fass, Joseph N Joshi, Nikhil A Couvillion, Mary T et al. Publication Date 2011-11-01 DOI 10.1534/g3.111.000927 Peer reviewed eScholarship.org Powered by the California Digital Library University of California INVESTIGATION 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,* and Kathleen Collins†,1 *Bioinformatics Core and ††Genome Center, University of California, Davis, California 95616, †Department of Molecular § and Cell Biology, University of California, Berkeley, California 94720, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106, ‡Department of Biology, University of Rochester, Rochester, New York 14627, **J. Craig Venter Institute, Rockville, Maryland 20850, and ‡‡Department of Biology, Washington University, St. Louis, Missouri 63130 ABSTRACT Genetically programmed DNA rearrangements can regulate mRNA expression at an individual KEYWORDS locus or, for some organisms, on a genome-wide scale. Ciliates rely on a remarkable process of whole-genome Tetrahymena remodeling by DNA elimination to differentiate an expressed macronucleus (MAC) from a copy of the germline ciliate nuclear micronucleus (MIC) in each cycle of sexual reproduction. Here we describe results from the first high- dualism throughput sequencing effort to investigate ciliate genome restructuring, comparing Sanger long-read community sequences from a Tetrahymena thermophila MIC genome library to the MAC genome assembly. With almost sequencing 25% coverage of the unique-sequence MAC genome by MIC genome sequence reads, we created a resource project for positional analysis of MIC-specific DNA removal that pinpoints MAC genome sites of DNA elimination at genome nucleotide resolution. The widespread distribution of internal eliminated sequences (IES) in promoter regions rearrangement and introns suggests that MAC genome restructuring is essential not only for what it removes (for example, DNA breakage active transposons) but also for what it creates (for example, splicing-competent introns). Consistent with the and joining 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 the MAC 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. Regulated genome rearrangements are an evolutionarily widespread Copyright © 2011 Fass et al. mechanism for affecting changes in gene expression, for example, doi: 10.1534/g3.111.000927 switching cell mating type, alternating surface protein presentation, Manuscript received August 21, 2011; accepted for publication September 30, 2011 or expanding the repertoire of antibody production (Rusche and Rine This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/ 2010). More extreme cases of genome remodeling by large-scale chro- by/3.0/), which permits unrestricted use, distribution, and reproduction in any matin diminution have been demonstrated in diverse eukaryotes, in- medium, provided the original work is properly cited. cluding ciliated protozoa, parasitic nematodes, and hagfish (Kloc and Supporting information is available online at http://www.g3journal.org/lookup/ Zagrodzinska 2001). In the entire phylum Ciliata, a transcriptionally suppl/doi:10.1534/g3.111.000927/-/DC1 active MAC is differentiated from a copy of the germline MIC by Paired-end Sanger reads from the JGI Community Sequencing Project for the Tetrahymena thermophila micronuclear genome: NCBI trace archives Project ID elimination of repetitive DNA (Karrer 2000; Duharcourt et al. 2009). 32845. Open-access UCSC-format genome browser display of annotated This process is proposed to accomplish a defense of the phenotypi- micronuclear genome read alignments to a size-ranked concatenation of cally expressed genome from the influence of foreign DNA. Consis- macronuclear genome scaffolds and gene predictions: gb.genomecenter. tent with this hypothesis, repetitive DNA elimination in ciliates ucdavis.edu, clade Alveolata, genome T. thermophila. 1Corresponding author: Department of Molecular and Cell Biology, 335 Life involves the same process of RNA-guided heterochromatin formation Sciences Addition, University of California at Berkeley, Berkeley, CA 94720-3200. required for transposon silencing in other eukaryotes (Mochizuki and E-mail: [email protected] Gorovsky 2004; Yao and Chao 2005; Chalker 2008). Knowledge of Volume 1 | November 2011 | 515 how the MAC and MIC differ is fundamental to understanding the average qualities at least Q20 and aligned using BWA-SW default evolutionarily success of ciliates as well as for enabling studies of the settings (bio-bwa.sourceforge.net). Read segments were designated chromosome structures that support meiosis and mitosis (MIC chro- by alignment order as aln1, aln2, etc. If more than 10 bp did not align mosomes) or chromosome segregation without classic heterochroma- from one side of the read only, the alignment was segregated to tin (MAC chromosomes). a separate browser track as a candidate indicator of IES position. Fully Among the ciliates, Tetrahymena thermophila has been a favorable mapping and one-sided-mapping reads that could align at more than model organism for discoveries of fundamental eukaryotic biology one MAC genome location were segregated to a separate set of multi- (Collins and Gorovsky 2005). The 104 Mbp MAC genome of mapper browser tracks. T. thermophila has been sequenced and annotated, revealing a com- plexity of gene families comparable to that in multicellular organisms Browser reference genome design and annotations (Eisen et al. 2006; Coyne et al. 2008). Genome-scale analysis of a ciliate MIC library reads were aligned to a concatenation of MAC genome MIC has not yet been described. Reassociation kinetics and quantita- contigs ordered by decreasing size. This reference genome contains tive DNA staining methods estimate T. thermophila MIC genome com- 103,002,206 bp of T. thermophila MAC genome project sequence with plexity as 10–20% greater than that of the MAC (Yao and Gorovsky 10 kbp blocks of N added between contigs, for a total of 114,482,206 1974; Gorovsky 1980), but only a handful of MIC-specificelements, bp. Browser track annotation of candidate IES sites allowed no more known as IES, have been characterized. IES are removed from the than 9 bp of overlap between the MAC-matching portions of conver- genome of the developing MAC en masse in a period of only a few gent L and R reads (described below). The mapped sequence reads, hours during the sexual process of conjugation (Yao and Chao 2005; IES annotations, previously predicted T. thermophila genes (indicated Chalker 2008). Extrapolation from the frequency of IES detection by by TTHERM number), and their individual predicted exons (Coyne differential restriction fragment mobility of MIC vs. MAC DNA, based et al. 2008) are aligned in an open-access community resource with on Southern blots of a few randomly selected genome regions (Yao the UCSC genome browser format (gb.genomecenter.ucdavis.edu, et al. 1984), suggests a number of 6,000 MAC genome sites of IES clade Alveolata, genome T. thermophila, Sep 2009 assembly). removal. Many sequenced IES appear to be noncoding, whereas others carry ORFs related to transposon-encoded genes (Yao and Chao 2005; RESULTS AND DISCUSSION Chalker 2008). No known T. thermophila IES interrupts a protein- coding open reading frame (ORF), although the much shorter IES of Library construction and read alignments Paramecium tetraurelia that lack epigenetic modulation of excision Previous shotgun sequencing and assembly of the T. thermophila frequently do (Duret et al. 2008). MAC used paired-end Sanger reads from 2–6 kbp DNA fragment Enabled by a Joint Genome Institute (JGI) Community Sequencing libraries (Eisen et al. 2006). In pilot Sanger sequencing trials of MIC Project, we used high-throughput T. thermophila MIC genome se- genome libraries, an 8 kbp insert DNA library was the maximal quencing to initiate the genome-scale investigation of nuclear differ- insert size to give a high yield of validated reads. However, high- entiation from MIC to MAC. By aligning MIC genome Sanger throughput sequencing of this MIC genome library did not yield sequence reads to the set of assembled MAC contigs in a manner the expected genome coverage of high-quality sequence reads, sug- refined for pinpointing positions of DNA elimination, we created gesting some destabilization of the 8 kbp insert library from the 75% a community resource for IES investigation. Although IES are dra- AT bias of the T. thermophila genomes (Yao and Gorovsky 1974). matically depleted in the 25% of