Epigenetics of Ciliates

Chalker, Douglas L.; Meyer, Éric; Mochizuki, Kazufumi

doi:10.1101/cshperspect.a017764

Cited by 102 publications

(117 citation statements)

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“…tions leading directly to the cell phenotype (Chalker et al, 2013). MIC is diploid and transcriptionally silent except during sexual development (conjugation), whereas MAC is polyploidy (about 45×) and transcriptionally active during vegetative growth (Karrer, 2012).…”

Section: Introductionmentioning

confidence: 99%

Enzymatic and chemical mapping of nucleosome distribution in purified micro- and macronuclei of the ciliated model organism, Tetrahymena thermophila

Chen

Gao

Liu

et al. 2016

Sci. China Life Sci.

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Genomic distribution of the nucleosome, the basic unit of chromatin, contains important epigenetic information. To map nucleosome distribution in structurally and functionally differentiated micronucleus (MIC) and macronucleus (MAC) of the ciliate Tetrahymena thermophila, we have purified MIC and MAC and performed micrococcal nuclease (MNase) digestion as well as hydroxyl radical cleavage. Different factors that may affect MNase digestion were examined, to optimize mono-nucleosome production. Mono-nucleosome purity was further improved by ultracentrifugation in a sucrose gradient. As MNase concentration increased, nucleosomal DNA sizes in MIC and MAC converged on 147 bp, as expected for the nucleosome core particle. Both MNase digestion and hydroxyl radical cleavage consistently showed a nucleosome repeat length of ~200 bp in MAC of Tetrahymena, supporting ~50 bp of linker DNA. Our work has systematically tested methods currently available for mapping nucleosome distribution in Tetrahymena, and provided a solid foundation for future epigenetic studies in this ciliated model organism.

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Section: Introductionmentioning

confidence: 99%

Enzymatic and chemical mapping of nucleosome distribution in purified micro- and macronuclei of the ciliated model organism, Tetrahymena thermophila

Chen

Gao

Liu

et al. 2016

Sci. China Life Sci.

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“…One intriguing aspect is in the government of genome integrity. For example, noncoding RNA plays key roles in the silencing of transposons in many organisms (van Wolfswinkel and Ketting, 2010) and the elimination of foreign DNAs in bacteria (Bhaya et al, 2011) and ciliated protozoa (Chalker and Yao, 2011;Chalker et al, 2013;Yao et al, 2014). This property affects genome structures both within an organism and through evolution.…”

Section: Introductionmentioning

confidence: 99%

Dynamic distributions of long double-stranded RNA in Tetrahymena during nuclear development and genome rearrangements

Woo

Chao

Yao

2016

Journal of Cell Science

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Bi-directional non-coding transcripts and their ∼29-nt small RNA products are known to guide DNA deletion in Tetrahymena, leading to the removal of one-third of the genome from developing somatic nuclei. Using an antibody specific for long double-stranded RNAs (dsRNAs), we determined the dynamic subcellular distributions of these RNAs. Conjugation-specific dsRNAs were found and show sequential appearances in parental germline, parental somatic nuclei and finally in new somatic nuclei of progeny. The dsRNAs in germline nuclei and new somatic nuclei are likely transcribed from the sequences destined for deletion; however, the dsRNAs in parental somatic nuclei are unexpected, and PCR analyses suggested that they were transcribed in this nucleus. Deficiency in the RNA interference (RNAi) pathway led to abnormal aggregations of dsRNA in both the parental and new somatic nuclei, whereas accumulation of dsRNAs in the germline nuclei was only seen in the Dicer-like gene mutant. In addition, RNAi mutants displayed an early loss of dsRNAs from developing somatic nuclei. Thus, long dsRNAs are made in multiple nuclear compartments and some are linked to small RNA production whereas others might participate in their regulations.

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“…Nanney was often explicit about the role of the cytoplasm in epigenetics. The differentiation of ciliate germline and somatic nuclei from genetically identical anlagen is asexually inherited, and is now known to serve as the basis for a vast range of epigenetic phenomena in ciliates (Chalker et al 2013). Nanney also experimentally showed the existence of a cytoplasmic polarity that is required for the correct differentiation of the two types of nuclei in Tetrahymena.…”

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confidence: 99%