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Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax.

ABSTRACT: We report the existence of both methylcytosine and hydroxymethylcytosine in the genomic DNA of the ciliate Oxytricha trifallax during its genome rearrangement process. These modifications are dynamically added, de novo, to sequences targeted for elimination and are not present after the rearrangement process (in vegetative cells). We performed methyl-DNA immunoprecipitation-sequencing (meDIP-seq) with antibodies against methylcytosine and hydroxymethylcytosine.

ORGANISM(S): Oxytricha trifallax

PROVIDER: GSE41060 | GEO | 2012/09/26

SECONDARY ACCESSION(S): PRJNA175642

REPOSITORIES: GEO

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Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax.

Project description:We report the existence of both methylcytosine and hydroxymethylcytosine in the genomic DNA of the ciliate Oxytricha trifallax during its genome rearrangement process. These modifications are dynamically added, de novo, to sequences targeted for elimination and are not present after the rearrangement process (in vegetative cells). We performed methyl-DNA immunoprecipitation-sequencing (meDIP-seq) with antibodies against methylcytosine and hydroxymethylcytosine. We performed methyl-DNA immunoprecipitation-sequencing (meDIP-seq) with antibodies against methylcytosine and hydroxymethylcytosine, and used an IgG control for nonspecific immunoprecpitation. Immunoprecipitation was performed on both vegetative (negative control) and 46h cells (with methylation). The data were normalized to RPKM, then the number of vegetative reads was subtracted from the number of 46h reads, giving excess reads at 46h, which we denote as the methylation/hydroxymethylation "signal". Those data are reported in the tab-deliminated data files included with this dataset.

2012-09-26 | E-GEOD-41060 | biostudies-arrayexpress

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Project description:Ciliate protist Oxytricha trifallax

| PRJNA12856 | ENA

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| PRJNA12857 | ENA

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Project description:Oxytricha trifallax developmental life cycle

| PRJNA665991 | ENA

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Project description:Long-read sequencing of the Oxytricha trifallax macronuclear genome

| PRJNA352762 | ENA

Oxytricha trifallax strain:JRB310

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Role of small RNAs in gene dosage regulation in the ciliate Oxytricha trifallax

Project description:Dicer-dependent small non-coding RNAs play important roles in gene regulation in a wide variety of organisms. Endogenous small interfering RNAs (siRNAs) are part of an ancient pathway of transposon control in plants and animals. The ciliate, Oxytricha trifallax, has approximately 16,000 gene-sized chromosomes in its somatic nucleus. Long non-coding RNAs establish high ploidy levels at the onset of sexual development, but the factors that regulate chromosome copy numbers during cell division and growth have been a mystery. We report a novel function of a class of Dicer (Dcl-1)– and RNA-dependent RNA polymerase (RdRP)– dependent endogenous small RNAs in regulating chromosome copy number and gene dosage in O. trifallax. Asexually growing populations express an abundant class of 21nt sRNAs that map to both coding and non-coding regions of most chromosomes. These sRNAs are bound to chromatin and their levels surprisingly do not correlate with mRNA levels. Instead, the levels of these small RNAs correlate with genomic DNA copy number. Reduced sRNA levels in dcl-1 or rdrp mutants lead to concomitant reduction in chromosome copy number. Furthermore, these cells show no signs of transposon activation, but instead display irregular nuclear architecture and signs of replication stress. In conclusion, Oxytricha Dcl-1 and RdRP-dependent small RNAs that derive from the somatic nucleus contribute to the maintenance of gene dosage, possibly via a role in DNA replication, offering a novel role for these small RNAs in eukaryotes.

2017-09-21 | GSE104078 | GEO

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