snRNA and Heterochromatin Formation Are Involved in DNA Excision during Macronuclear Development in Stichotrichous Ciliates

Juranek, Stefan; Rupprecht, Sina; Postberg, Jan; Lipps, Hans J.

doi:10.1128/ec.4.11.1934-1941.2005

Cited by 37 publications

(44 citation statements)

References 30 publications

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“…However, some IESs in Stylonychia and Oxytricha are smaller than the observed 26–27 nt small RNAs [29], [32], which are also smaller than a nucleosome core particle. This poses a challenge, because small RNAs would be unable to mark such IESs precisely.…”

Section: Discussionmentioning

confidence: 70%

The Pathway to Detangle a Scrambled Gene

Möllenbeck¹,

Zhou

Cavalcanti

et al. 2008

PLoS ONE

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BackgroundProgrammed DNA elimination and reorganization frequently occur during cellular differentiation. Development of the somatic macronucleus in some ciliates presents an extreme case, involving excision of internal eliminated sequences (IESs) that interrupt coding DNA segments (macronuclear destined sequences, MDSs), as well as removal of transposon-like elements and extensive genome fragmentation, leading to 98% genome reduction in Stylonychia lemnae. Approximately 20–30% of the genes are estimated to be scrambled in the germline micronucleus, with coding segment order permuted and present in either orientation on micronuclear chromosomes. Massive genome rearrangements are therefore critical for development.Methodology/Principal FindingsTo understand the process of DNA deletion and reorganization during macronuclear development, we examined the population of DNA molecules during assembly of different scrambled genes in two related organisms in a developmental time-course by PCR. The data suggest that removal of conventional IESs usually occurs first, accompanied by a surprising level of error at this step. The complex events of inversion and translocation seem to occur after repair and excision of all conventional IESs and via multiple pathways.Conclusions/Significance This study reveals a temporal order of DNA rearrangements during the processing of a scrambled gene, with simpler events usually preceding more complex ones. The surprising observation of a hidden layer of errors, absent from the mature macronucleus but present during development, also underscores the need for repair or screening of incorrectly-assembled DNA molecules.

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Section: Discussionmentioning

confidence: 70%

The Pathway to Detangle a Scrambled Gene

Möllenbeck¹,

Zhou

Cavalcanti

et al. 2008

PLoS ONE

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“…Macronuclear development is slightly delayed during the first DNA amplification stage and is arrested in the polytene chromosome stage of the macronuclear anlage (Figure 1A). Upon TSA treatment, IES (internal eliminated sequence) excision is defective [31] and incubation of cells with the C646 inhibitor at the beginning of sexual reproduction largely prevents the accumulation of H3K9ac/K14ac at the 5′-end of this stage (Additional file 3). Furthermore, we observed that methylated cytosines at both nanochromosomes mdp1 and mdp2 remained present during macronuclear development, whereas after incubation with TSA the DNA remained unmethylated (Figure 4A, B).…”

Section: Resultsmentioning

confidence: 99%

A permissive chromatin structure is adopted prior to site-specific DNA demethylation of developmentally expressed genes involved in macronuclear differentiation

Bulic

Postberg

Fischer³

et al. 2013

Epigenetics & Chromatin

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BackgroundDNA methylation and demethylation are important epigenetic regulatory mechanisms in eukaryotic cells and, so far, only partially understood. We exploit the minimalistic biological ciliate system to understand the crosstalk between DNA modification and chromatin structure. In the macronucleus of these cells, the DNA is fragmented into individual short DNA molecules, each representing a functional expression and replication unit. Therefore, long range epigenomic interaction can be excluded in this system.ResultsIn the stichotrichous ciliate Stylonychia lemnae, cytosine methylation occurs in a small subset of macronuclear nanochromosomes expressed only during sexual reproduction. Methylation pattern shows similarity to that observed in fungi and Drosophila. Cytosine methylation correlates with gene activity and chromatin structure. Upon gene activation, cytosines become demethylated and a redistribution of histone post-translational modifications (PTMs) takes place. Evidence is presented that the formation of a permissive chromatin structure in the vicinity of the 5meCs precedes cytosine methylation and is probably a necessary prerequisite for their demethylation. Shortly after demethylation of cytosines occurs, the parental macronucleus degenerates, a new macronucleus is formed from a micronuclear derivative and the specific methylation pattern is transmitted from the germline micronucleus to the new macronucleus.ConclusionsWe show that very few, or even only one, discrete methylated cytosines are required to assign regulatory functions at a specific locus. Furthermore, evidence is provided that a permissive chromatin structure is probably a necessary prerequisite for the demethylation of specific cytosines. Our results allow us to propose a mechanistic model for the biological function of cytosine methylation in the ciliate cell and its regulation during the cell cycle.

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“…2], may discard close to 98% of its MIC DNA during MAC development (36). Yet an earlier paper suggested that its sRNAs are more consistent with the scan RNA model (88); however that inference was based only on hybridization, with no sequence analysis, and numerous other factors could have affected these early results.…”

Section: Bodymentioning

confidence: 99%

Programmed Genome Rearrangements in the Ciliate Oxytricha

Yerlici

Landweber

2014

Microbiol Spectr

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The ciliate Oxytricha is a microbial eukaryote with two genomes, one of which experiences extensive genome remodeling during development. Each round of conjugation initiates a cascade of events that construct a transcriptionally active somatic genome from a scrambled germline genome, with considerable help from both long and small noncoding RNAs. This process of genome remodeling entails massive DNA deletion and reshuffling of remaining DNA segments to form functional genes from their interrupted and scrambled germline precursors. The use of Oxytricha as a model system provides an opportunity to study an exaggerated form of programmed genome rearrangement. Furthermore, studying the mechanisms that maintain nuclear dimorphism and mediate genome rearrangement has demonstrated a surprising plasticity and diversity of non-coding RNA pathways, with new roles that go beyond conventional gene silencing. Another aspect of ciliate genetics is their unorthodox patterns of RNA-mediated, epigenetic inheritance, that rival Mendelian inheritance. This review takes the reader through the key experiments in a model eukaryote that led to fundamental discoveries in RNA biology and pushes the biological limits of DNA processing.

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snRNA and Heterochromatin Formation Are Involved in DNA Excision during Macronuclear Development in Stichotrichous Ciliates

Cited by 37 publications

References 30 publications

The Pathway to Detangle a Scrambled Gene

The Pathway to Detangle a Scrambled Gene

A permissive chromatin structure is adopted prior to site-specific DNA demethylation of developmentally expressed genes involved in macronuclear differentiation

Programmed Genome Rearrangements in the Ciliate Oxytricha

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