The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences

Abstract

Insertions of parasitic DNA within coding sequences are usually deleterious and are generally counter-selected during evolution. Thanks to nuclear dimorphism, ciliates provide unique models to study the fate of such insertions. Their germline genome undergoes extensive rearrangements during development of a new somatic macronucleus from the germline micronucleus following sexual events. In Paramecium, these rearrangements include precise excision of unique-copy Internal Eliminated Sequences (IES) from the somatic DNA, requiring the activity of a domesticated piggyBac transposase, PiggyMac. We have sequenced Paramecium tetraurelia germline DNA, establishing a genome-wide catalogue of ∼45,000 IESs, in order to gain insight into their evolutionary origin and excision mechanism. We obtained direct evidence that PiggyMac is required for excision of all IESs. Homology with known P. tetraurelia Tc1/mariner transposons, described here, indicates that at least a fraction of IESs derive from these elements. Most IES insertions occurred before a recent whole-genome duplication that preceded diversification of the P. aurelia species complex, but IES invasion of the Paramecium genome appears to be an ongoing process. Once inserted, IESs decay rapidly by accumulation of deletions and point substitutions. Over 90% of the IESs are shorter than 150 bp and present a remarkable size distribution with a ∼10 bp periodicity, corresponding to the helical repeat of double-stranded DNA and suggesting DNA loop formation during assembly of a transpososome-like excision complex. IESs are equally frequent within and between coding sequences; however, excision is not 100% efficient and there is selective pressure against IES insertions, in particular within highly expressed genes. We discuss the possibility that ancient domestication of a piggyBac transposase favored subsequent propagation of transposons throughout the germline by allowing insertions in coding sequences, a fraction of the genome in which parasitic DNA is not usually tolerated.

Local Effect of Enhancer of Zeste-Like Reveals Cooperation of Epigenetic and cis-Acting Determinants for Zygotic Genome Rearrangements

“…S4). The low amount of H3K27me3 detected by Western blot appears to be compatible with the fact that IESs cover 3.2 Mb and thus represent about 3% of the sequence complexity of the MIC genome [2]. Yet we cannot formally exclude the possibility that the Ezl1 protein has an additional role in DNA elimination independently of histone H3 methylation.…”

“…We also performed a qualitative evaluation of Sardine retention by mapping reads from each dataset to the known cloned copies of this transposable element [2](Fig. S9).…”

Epigenetics of Ciliates

“…This class of IESs is short ( 25 -900 bp in Paramecium), single-copy, noncoding DNA segments. There are .45,000 such IESs per haploid genome of Paramecium; they are abundant within coding sequences, but also distributed throughout intergenic or intronic regions of germline chromosomes (reviewed in Jahn and Klobutcher 2002;Arnaiz et al 2012). These precisely excised IESs, the so-called "TA" IESs are identified as having invariable 5 ′ -TA-3 ′ repeat at each boundary, one copy of which remains within the macronuclear locus after excision (see Betermier 2004).…”

Insights into Three Whole-Genome Duplications Gleaned from theParamecium caudatumGenome Sequence

“…Later work provided fundamental insights into major issues in biology, including mutagenesis (Igarashi 1966), molecular and developmental genetics (Sonneborn 1947), symbiosis (Beale et al 1969), mitochondrial genetics (Adoutte and Beisson 1972), aging (Siegel 1967), nuclear differentiation (Berger 1937), and gene regulation (Allen and Gibson 1972). More recently, Paramecium has been used to study maternal inheritance (Nowacki et al 2005), programmed genome rearrangements and transposon domestication (Arnaiz et al 2012), epigenetic inheritance (Singh et al 2014), and whole-genome duplication (Aury et al 2006;Lynn McGrath, Jean-Francois Gout, Parul Johri, Thomas Graeme Doak, and Michael Lynch, unpublished results). Although not as well-studied as the P. aurelia complex of species, P. caudatum also has a long history of research (Calkins 1902;Sonneborn 1933).…”