Subtraction by addition: domesticated transposases in programmed DNA elimination: Figure 1.

Motl, Jason A.; Chalker, Douglas L.

doi:10.1101/gad.1864609

Cited by 4 publications

(3 citation statements)

References 44 publications

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“…The strain might be a highly proliferative variant, with distinct cell cycle control or which undergoes macronuclear differentiation involving heightened gene amplification, above that found in other variants. Although recent studies have shed light on the mechanisms of macronuclear development in ciliate species (Nowacki et al 2008, Motl & Chalker 2009, there are currently no reported studies of the mechanisms that operate during macronucleus formation in M. rubra. Exploration of the nuclear dualism of M. rubra might provide clues to the highly proliferative nature of the bloom-forming variants of M. rubra.…”

Section: Discussionmentioning

confidence: 99%

Myrionecta rubra population genetic diversity and its cryptophyte chloroplast specificity in recurrent red tides in the Columbia River estuary

Herfort

Peterson²,

McCue

et al. 2011

Aquat. Microb. Ecol.

105

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For several decades, annually recurring blooms of the photosynthetic ciliate Myrionecta rubra have been observed in the Columbia River estuary in late summer. In an effort to understand the dynamics of these blooms, we investigated the genetic variability of M. rubra and its cryptophyte plastids within 3 large estuarine blooms formed in consecutive years (2007 to 2009), and conducted a broader spatial survey along the coasts of Oregon and Washington. Analysis of the '18S-28S' sequences specific for Mesodiniidae uncovered at least 5 variants of M. rubra within the Columbia River coastal margin in spring and summer, but only one of these M. rubra variants was implicated in estuary bloom formation. Using a multigene approach, we show that the bloom-forming variant of M. rubra appears to harbor the same cryptophyte chloroplast in recurring blooms. Analyses of chloroplast 16S rRNA, cryptophyte RuBisCO and Photosystem II D2 genes together suggest that the plastid is derived from Teleaulax amphioxeia. Free-living cells of this species and of other cryptophytes were practically absent from the bloom patches in the estuary main channels based on 18S rDNA sequence analyses. The respectively low and high proportions of T. amphioxeia nuclei and chloroplast signals found in the M. rubra bloom of the Columbia River estuary in successive years supports the notion of an association (either endosymbiosis or kleptoplastidy) between T. amphioxeia and the bloom-forming M. rubra variant, with loss of cryptophyte nuclei. The genetic variability of M. rubra uncovered here is relevant to the controversy in the literature regarding the cryptophyte/M. rubra association.

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Section: Discussionmentioning

confidence: 99%

Myrionecta rubra population genetic diversity and its cryptophyte chloroplast specificity in recurrent red tides in the Columbia River estuary

Herfort

Peterson²,

McCue

et al. 2011

Aquat. Microb. Ecol.

105

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“…A key feature differentiating HO from true homing endonucleases is that it does not propagate its own DNA sequence – in other words, it does not home. HO has become a normal cellular gene, and is one of the many known examples of a mobile genetic element that has been domesticated to take on a new role (Volff, 2006; Kaiser et al, 2009; Motl and Chalker, 2009; McDowell and Meyers, 2013; Chiruvella et al, 2016; Huang et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

The yeast mating-type switching endonuclease HO is a domesticated member of an unorthodox homing genetic element family

Coughlan

Lombardi

Braun‐Galleani

et al. 2020

Preprint

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SummaryThe mating-type switching endonuclease HO plays a central role in the natural life cycle of Saccharomyces cerevisiae, but its evolutionary origin is unknown. HO is a recent addition to yeast genomes, present in only a few genera. It resembles a degenerated intein fused to a zinc finger domain. Here we show that HO is structurally and phylogenetically related to a family of unorthodox homing genetic elements found in Torulaspora and Lachancea yeasts. These WHO elements integrate into the aldolase gene FBA1, replacing its 3’ end each time. Their structural organization is different from all known classes of homing elements. We show that a WHO protein cleaves Torulaspora delbrueckii FBA1 efficiently and in an allele-specific manner, leading to DNA repair by gene conversion or NHEJ. The DNA rearrangement steps during WHO element homing are very similar to those during mating-type switching, and indicate that HO is a domesticated WHO-like element.

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“…A reasonable prediction as to which sequences may be more amenable to SGV could first consider (retro)transposons, then elements such as LINEs and SINEs, especially those sequences known or suspected to assume anomalous non-B conformations [ 44 , 48 ]. It has been reported that, in the spectrum of the events responsible for human genome variations, deletions are more frequent than insertions or other rearrangements [ 49 ]: this is reasonable and may reflect a compensatory removal of sequences following synthetic (retro)transpositions otherwise responsible of an unbearable overgrowth of the genome size [ 50 ]. Relevant to this is the observation that during development: “The set of genes deleted is not random in the (human) genome; there is a clear association with segmental duplications among larger deletion events.…”

Section: State Of the Artmentioning

confidence: 99%

Are we Genomic Mosaics? Variations of the Genome of Somatic Cells can Contribute to Diversify our Phenotypes

Astolfi

Salamini²,

Sgaramella³

2010

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Theoretical and experimental evidences support the hypothesis that the genomes and the epigenomes may be different in the somatic cells of complex organisms. In the genome, the differences range from single base substitutions to chromosome number; in the epigenome, they entail multiple postsynthetic modifications of the chromatin. Somatic genome variations (SGV) may accumulate during development in response both to genetic programs, which may differ from tissue to tissue, and to environmental stimuli, which are often undetected and generally irreproducible. SGV may jeopardize physiological cellular functions, but also create novel coding and regulatory sequences, to be exposed to intraorganismal Darwinian selection. Genomes acknowledged as comparatively poor in genes, such as humans’, could thus increase their pristine informational endowment. A better understanding of SGV will contribute to basic issues such as the “nature vs nurture” dualism and the inheritance of acquired characters. On the applied side, they may explain the low yield of cloning via somatic cell nuclear transfer, provide clues to some of the problems associated with transdifferentiation, and interfere with individual DNA analysis. SGV may be unique in the different cells types and in the different developmental stages, and thus explain the several hundred gaps persisting in the human genomes “completed” so far. They may compound the variations associated to our epigenomes and make of each of us an “(epi)genomic” mosaic. An ensuing paradigm is the possibility that a single genome (the ephemeral one assembled at fertilization) has the capacity to generate several different brains in response to different environments.

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Subtraction by addition: domesticated transposases in programmed DNA elimination: Figure 1.

Cited by 4 publications

References 44 publications

Myrionecta rubra population genetic diversity and its cryptophyte chloroplast specificity in recurrent red tides in the Columbia River estuary

Myrionecta rubra population genetic diversity and its cryptophyte chloroplast specificity in recurrent red tides in the Columbia River estuary

The yeast mating-type switching endonuclease HO is a domesticated member of an unorthodox homing genetic element family

Are we Genomic Mosaics? Variations of the Genome of Somatic Cells can Contribute to Diversify our Phenotypes

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