A Non-Long Terminal Repeat Retrotransposon Family Is Restricted to the Germ Line Micronucleus of the Ciliated Protozoan Tetrahymena thermophila

Abstract

The ciliated protozoan Tetrahymena thermophila undergoes extensive programmed DNA rearrangements during the development of a somatic macronucleus from the germ line micronucleus in its sexual cycle. To investigate the relationship between programmed DNA rearrangements and transposable elements, we identified several members of a family of non-long terminal repeat (LTR) retrotransposons (retroposons) in T. thermophila, the first characterized in the ciliated protozoa. This multiple-copy retrotransposon family is restricted to the micronucleus of T. thermophila. The REP (Tetrahymena non-LTR retroposon) elements encode an ORF2 typical of non-LTR elements that contains apurinic/apyrimidinic endonuclease (APE) and reverse transcriptase (RT) domains. Phylogenetic analysis of the RT and APE domains indicates that the element forms a deep-branching clade within the non-LTR retrotransposon family. Northern analysis with a probe to the conserved RT domain indicates that transcripts from the element are small and heterogeneous in length during early macronuclear development. The presence of a repeated transposable element in the genome is consistent with the model that programmed DNA deletion in T. thermophila evolved as a method of eliminating deleterious transposons from the somatic macronucleus.Developmentally programmed DNA rearrangements occur in a wide variety of organisms (reviewed in reference 5). Functions such as altering gene dosage or directly regulating gene expression have been assigned to many but not all examples of programmed DNA rearrangements. A clinically important example of a programmed DNA rearrangement is V(D)J recombination (2). In addition, a variety of mammalian parasites use programmed DNA rearrangements to vary their surface antigens to avoid host immune response (4). The function of other programmed DNA rearrangements is not as clear. The extensive genome rearrangements that occur during nuclear development in the ciliated protozoa provide an example of programmed DNA rearrangements with poorly understood function.Like all ciliated protozoa, the oligohymenopheran Tetrahymena thermophila displays nuclear dimorphism with a mostly transcriptionally silent diploid germ line nucleus (micronucleus) and a polyploid and transcriptionally active somatic nucleus (macronucleus) within the same cell. The macronucleus develops from a mitotic product of the micronucleus during conjugation. When two cells of different mating types conjugate, the micronucleus in each divides meiotically and mitotically to generate a haploid gametic nucleus that is reciprocally exchanged and fuses with that of its partner to form a zygotic nucleus. This zygotic nucleus divides and from one of the products develops a new macronucleus, while the old macronucleus is concurrently degraded. In T. thermophila, macronuclear development involves extensive programmed DNA rearrangements, including chromosome fragmentation, DNA amplification, and site-specific interstitial DNA deletion (12). Interstitial DNA deletion is responsible for t...

Biased transcription and selective degradation of small RNAs shape the pattern of DNA elimination in Tetrahymena

“…The IES-biased production of scnRNAs may be caused by preferential production of scnRNAs from repeated sequences in the genome because some IESs are related to transposon-derived sequences and are repeated in the Mic genome (Yao and Gorovsky 1974;Wuitschick et al 2002;Fillingham et al 2004), and scnRNAs are processed from dsRNA precursors (Malone et al 2005;Mochizuki and Gorovsky 2005;Noto et al 2010), which can be more frequently formed by hybridization of transcripts from repeated sequences. To evaluate this possibility, we classified the annotated Mic genome sequences into three classes according to their repetitiveness.…”

“…IESs in Tetrahymena vary in size (;0.5-20 kb) and sequence, and recent Mic genome sequencing indicates that they account for about one-third of the Mic genome (Tetrahymena Comparative Sequencing Project, Broad Institute of Harverd and Massachussetts Institute of Technology [http:// www.broadinstutute.org]). Some IESs are moderately repeated in the Mic genome (Yao and Gorovsky 1974) and are related to transposable elements (Wuitschick et al 2002;Fillingham et al 2004). IESs are primarily located in nongenic regions, although some are located in genic regions (Fass et al 2011).…”

Dynamic distributions of long double-stranded RNA in Tetrahymena during nuclear development and genome rearrangements

“…The development of new MACs triggers drastic genome rearrangements including fragmentation and amplification of the chromosomes and extensive internal deletion of one-third of the genome (Yao et al, 2014). The deleted sequences (referred to as internal eliminated sequences, IESs) largely comprise repetitive sequences and transposon-derived elements (Wuitschick et al, 2002;Fillingham et al, 2004). Removal of these elements from MACs can be considered an ultimate gene silencing mechanism.…”

LIA4 Encodes a Chromoshadow Domain Protein Required for Genomewide DNA Rearrangements in Tetrahymena thermophila

“…In addition, DNA segments of various sizes, called internal eliminated sequences (IESs), are eliminated from thousands of loci dispersed throughout the genome (17). These sequences include transposons and other repetitive elements (18,19) Unlike the conserved chromosomal breakage sequence, there is no conserved sequence that identifies an IES. Instead, these diverse loci are recognized by homologous small RNAs and targeted for removal from the genome by RNA-guided heterochromatin formation (20).…”