Micronuclear Genome Organization in <i>Euplotes crassus</i>: a Transposonlike Element Is Removed during Macronuclear Development

Baird, Scott Everet; Fino, Gina M.; Tausta, S Lori; Klobutcher, Lawrence A.

doi:10.1128/mcb.9.9.3793-3807.1989

Cited by 6 publications

(2 citation statements)

References 50 publications

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“…E. crassus has also been reported to have an abundant transposon family called Tec elements ( T ransposon of E uplotes c rassus ). Like TBEs, each Tec consists of three ORFs, and ORF1 also encodes a transposase from the Tc1/ mariner family ( Baird et al, 1989 ; Krikau and Jahn, 1991 ; Jahn et al, 1993 ; Jahn et al, 1989 ; Klobutcher and Herrick, 1997 ). The ~57 kD ORF2 encodes a tyrosine-type recombinase ( Doak et al, 2003 ), and the 20kD ORF3 has unknown function ( Jahn et al, 1993 ).…”

Section: Resultsmentioning

confidence: 99%

Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes

Feng

Neme

Beh

et al. 2022

eLife

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Ciliates are microbial eukaryotes that undergo extensive programmed genome rearrangement, a natural genome editing process that converts long germline chromosomes into smaller gene-rich somatic chromosomes. Three well-studied ciliates include Oxytricha trifallax, Tetrahymena thermophila and Paramecium tetraurelia, but only the Oxytricha lineage has a massively scrambled genome, whose assembly during development requires hundreds of thousands of precise programmed DNA joining events, representing the most complex genome dynamics of any known organism. Here we study the emergence of such complex genomes by examining the origin and evolution of discontinuous and scrambled genes in the Oxytricha lineage. This study compares six genomes from three species, the germline and somatic genomes for Euplotes woodruffi, Tetmemena sp., and the model ciliate Oxytricha trifallax. To complement existing data, we sequenced, assembled and annotated the germline and somatic genomes of Euplotes woodruffi, which provides an outgroup, and the germline genome of Tetmemena sp.. We find that the germline genome of Tetmemena is as massively scrambled and interrupted as Oxytricha's : 13.6% of its gene loci require programmed translocations and/or inversions, with some genes requiring hundreds of precise gene editing events during development. This study revealed that the earlier-diverged spirotrich, E. woodruffi, also has a scrambled genome, but only roughly half as many loci (7.3%) are scrambled. Furthermore, its scrambled genes are less complex, together supporting the position of Euplotes as a possible evolutionary intermediate in this lineage, in the process of accumulating complex evolutionary genome rearrangements, all of which require extensive repair to assemble functional coding regions. Comparative analysis also reveals that scrambled loci are often associated with local duplications, supporting a gradual model for the origin of complex, scrambled genomes via many small events of DNA duplication and decay.

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Section: Resultsmentioning

confidence: 99%

Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes

Feng

Neme

Beh

et al. 2022

eLife

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show abstract

“…Euplotes crassus has also been reported to have an abundant transposon family called Tec elements ( T ransposon of E uplotes c rassus ). Like TBEs, each Tec consists of three ORFs, and ORF1 also encodes a transposase from the Tc1/ mariner family (44, 45, 46, 47, 48). Using the three ORFs of Tec1 and Tec2 as queries for search, we identified 74 complete Tec elements in E. woodruffi .…”

Section: Resultsmentioning

confidence: 99%

Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes

Feng

Neme

Beh

et al. 2022

Preprint

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SummaryCiliates are microbial eukaryotes that undergo extensive programmed genome rearrangement that converts long germline chromosomes into smaller gene-rich somatic chromosomes. Three well-studied ciliates include Oxytricha trifallax, Tetrahymena thermophila and Paramecium tetraurelia, but only the Oxytricha lineage has a massively scrambled genome whose assembly requires hundreds of thousands of precise DNA joining events. Here we study the emergence of genome complexity by examining the origin and evolution of discontinuous and scrambled genes in the Oxytricha lineage.We sequenced, assembled and annotated the germline and somatic genomes of Euplotes woodruffi and the germline genome of Tetmemena sp., and compared their genome rearrangement features to that of the model ciliate Oxytricha trifallax. The germline genome of Tetmemena is as massively scrambled and interrupted as Oxytricha’s: 13.6% of its gene loci rearrange via translocations and/or inversions. This study revealed that the earlier-diverged spirotrich, E. woodruffi, also has a scrambled genome, but approximately half as many loci (7.3%) are scrambled, supporting its position as a possible evolutionary intermediate in this lineage, in the process of accumulating complex genome rearrangements. Scrambled loci are more often associated with local duplications, supporting a simple model for the origin of scrambled genes via DNA duplication and decay.

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An unusual histone H3 specific for early macronuclear development in Euplotes crassus

Jahn

Zhong

Tebeau

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

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Characterization of the histone H3 genes of the ciliated protozoan Euplotes crassus indicates that one gene functions only during the sexual phase of the life cycle. Maximum expression of this gene, as judged by transcript accumulation, correlates with DNA replications leading to polytenization of the micronuclear chromosomes before massive DNA elimination, which produces a transcriptionally active macronucleus. Transcripts of the other gene accumulate primarily during vegetative growth and in the sexual phase of the life cycle during replication phases not related to polytenization. Although both histone H3 genes encode proteins that are fairly divergent in sequence at the amino terminus, the meiotic/polytene-specific histone H3 contains two insertions in the amino terminus that increase the size of the protein by 15 amino acids. Analysis of micrococcal nuclease digests of chromatin using hybridization probes specific for micronuclear vs. macronuclear sequences indicates that a change in nucleosomal spacing correlates with the maximal expression of the meiotic/polytene-specific histone H3 gene. Thus, we surmise that this unusual histone H3 may play a key role in targeting DNA sequences for either transcriptional activation and retention in the macronucleus or heterochromatization and elimination.

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Micronuclear Genome Organization in Euplotes crassus: a Transposonlike Element Is Removed during Macronuclear Development

Cited by 6 publications

References 50 publications

Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes

Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes

Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes

An unusual histone H3 specific for early macronuclear development in Euplotes crassus

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