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

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.Overall design: Datasets: 1) sRNAs from asexually growing O.trifallax cells from WT (mix of strain JRB310 and JRB510), dcl-123, dcl-141, rdrp13. 2) RNAseq from Poly(A) selected RNA from WT (strain JRB310), dcl-141, rdrp13. 3) Whole cell Genomic DNA from WT (strain JRB310), WT (F1 crossed between JRB310 and JRB510), dcl-141, rdrp13

Data type: Other

Sample scope: Multiisolate

Relevance: Other

Last updated: 2017-09-20