A microarray analysis of developmentally regulated genes during macronuclear differentiation in the stichotrichous ciliate Stylonychia lemnae

Paschka, Adrian G.; Horejschi, Volker; Jönsson, Franziska; Lindecke, Antje; Weier, Gero; Kaltschmidt, Christian; Lipps, Hans J.

doi:10.1016/j.gene.2005.06.024

Cited by 9 publications

(13 citation statements)

References 23 publications

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“…It is therefore interesting to see whether in O. trifallax such a correlation also exists. The expression levels of MDP 2 and PIWI were excluded because their expression is known to be conjugation specific in S. lemnae (Paschka et al, 2005). In fact, we detected very minimal expression from both of these two genes during vegetative growth in Oxytricha (0.001 and 0.03 respectively, compared to 1 for HSP 70).…”

Section: Correlation Between Copy Number and Gene Expressionmentioning

confidence: 82%

“…The most abundant chromosome we quantified was the PIWI gene at 15.72× 10 4 copies per cell, while the lowest was the MDP 2 gene at 0.77 × 10 4 copies per cell, or a twenty fold difference. Interestingly, both genes were found to be conjugation-specific, only highly expressed during conjugation, but not during vegetative growth in Stylonychia lemnae (Paschka et al, 2005). Also noteworthy, while TEBP α and TEBP β proteins are both prominent and required in equimolar amounts in spirotrichs for protecting and maintaining telomeres (Gottschling and Zakian, 1986;Paeschke et al, 2005;Price and Cech, 1987), the copy number of TEBP β was nearly twice that of TEBP α (pb 0.05).…”

Section: Copy Numbers Of 9 Genes In O Trifallaxmentioning

confidence: 98%

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Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax

Doak

Lipps

et al. 2012

Gene

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Section: Correlation Between Copy Number and Gene Expressionmentioning

confidence: 82%

Section: Copy Numbers Of 9 Genes In O Trifallaxmentioning

confidence: 98%

Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax

Doak

Lipps

et al. 2012

Gene

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“…We were able to find mRNA sequences corresponding to each of the divergent histone variants in a cDNA library created by subtraction of vegetative cDNA from cDNA from Stylonychia cells 10 h postconjugation (Paschka et al 2005). From quantitative polymerase chain reaction data Stylonychia ’s histone H3.7 was also shown to be the most highly expressed H3 variant during the development of the new MAC, and was upregulated approximately 7 or 8 orders of magnitude compared with its vegetative expression (Forcob et al 2014).…”

Section: Resultsmentioning

confidence: 99%

The Draft Assembly of the Radically Organized Stylonychia lemnae Macronuclear Genome

Aeschlimann¹,

Jönsson²,

Postberg³

et al. 2014

Genome Biology and Evolution

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Stylonychia lemnae is a classical model single-celled eukaryote, and a quintessential ciliate typified by dimorphic nuclei: A small, germline micronucleus and a massive, vegetative macronucleus. The genome within Stylonychia’s macronucleus has a very unusual architecture, comprised variably and highly amplified “nanochromosomes,” each usually encoding a single gene with a minimal amount of surrounding noncoding DNA. As only a tiny fraction of the Stylonychia genes has been sequenced, and to promote research using this organism, we sequenced its macronuclear genome. We report the analysis of the 50.2-Mb draft S. lemnae macronuclear genome assembly, containing in excess of 16,000 complete nanochromosomes, assembled as less than 20,000 contigs. We found considerable conservation of fundamental genomic properties between S. lemnae and its close relative, Oxytricha trifallax, including nanochromosomal gene synteny, alternative fragmentation, and copy number. Protein domain searches in Stylonychia revealed two new telomere-binding protein homologs and the presence of linker histones. Among the diverse histone variants of S. lemnae and O. trifallax, we found divergent, coexpressed variants corresponding to four of the five core nucleosomal proteins (H1.2, H2A.6, H2B.4, and H3.7) suggesting that these ciliates may possess specialized nucleosomes involved in genome processing during nuclear differentiation. The assembly of the S. lemnae macronuclear genome demonstrates that largely complete, well-assembled highly fragmented genomes of similar size and complexity may be produced from one library and lane of Illumina HiSeq 2000 shotgun sequencing. The provision of the S. lemnae macronuclear genome sets the stage for future detailed experimental studies of chromatin-mediated, RNA-guided developmental genome rearrangements.

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“…This suggests that the cell executes gross rearrangements, usually by inversion and/or translocation, often after excision and possible repair of all conventional IES junctions, indicating the presence of preferred steps in the gene assembly process. These steps could be associated with the expression onset of specific proteins or factors responsible for different types of reactions during DNA rearrangement [40]. This particular cascade of events both shortens and substantially simplifies the precursor DNA molecule in preparation for the later events of unscrambling, dynamically reducing the complexity of the descrambling problem and opportunity for error.…”

Section: Resultsmentioning

confidence: 99%

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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A microarray analysis of developmentally regulated genes during macronuclear differentiation in the stichotrichous ciliate Stylonychia lemnae

Cited by 9 publications

References 23 publications

Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax

Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax

The Draft Assembly of the Radically Organized Stylonychia lemnae Macronuclear Genome

The Pathway to Detangle a Scrambled Gene

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