Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development

Abstract

The ciliate Oxytricha trifallax maintains two genomes: a germline genome that is active only during sexual conjugation and a transcriptionally active, somatic genome that derives from the germline via extensive sequence reduction and rearrangement. Previously, we found that long noncoding (lnc) RNA "templates"-telomere-containing, RNA-cached copies of mature chromosomes-provide the information to program the rearrangement process. Here we used a modified RNA-seq approach to conduct the first genome-wide search for endogenous, telomere-to-telomere RNA transcripts. We find that during development, Oxytricha produces long noncoding RNA copies for over 10,000 of its 16,000 somatic chromosomes, consistent with a model in which Oxytricha transmits an RNA-cached copy of its somatic genome to the sexual progeny. Both the primary sequence and expression profile of a somatic chromosome influence the temporal distribution and abundance of individual template RNAs. This suggests that Oxytricha may undergo multiple rounds of DNA rearrangement during development. These observations implicate a complex set of thousands of long RNA molecules in the wiring and maintenance of a highly elaborate somatic genome architecture.

Small RNA-mediated regulation of DNA dosage in the ciliate Oxytricha

“…During the sexual phase of the life cycle, genome-wide transcription of the somatic chromosomes from the parental macronucleus produces long noncoding template RNAs that guide DNA rearrangements (Nowacki et al 2008;Khurana et al 2014;Lindblad et al 2017) and also regulate chromosome copy number in the progeny (Nowacki et al 2010); however, the mechanism is unclear. The new class of sRNAs reported in this manuscript could derive from these Small RNAs and DNA copy-number regulation www.rnajournal.org 25 maternal template RNAs that appear post fertilization.…”

“…The macronucleus (MAC) contains the somatic genome, responsible for gene transcription during asexual growth, while the micronucleus (MIC) is the zygotic nucleus, which supplies both an archival germline nucleus and a duplicate copy that develops into the new macronucleus. An arsenal of noncoding RNAs, ranging from long telomere-containing transcripts (Nowacki et al 2008;Lindblad et al 2017) to 27-nt piRNAs (Fang et al 2012) regulates the whole process of genome rearrangement to produce a new somatic genome during post-zygotic development.…”

Evolutionary origins and impacts of genome architecture in ciliates

“…For example, in Oxytricha piRNAs, two types of RNAs are involved in forming a faithful reproduction of the old parental genome. Small piRNAs protect MDSs from elimination, which presumably then use RNA copies of whole chromosomes that guide accurate rearrangement of these protected MDSs, regardless their orientation in the germline …”

“…and B) . In these taxa, small RNAs from the parental genome aid in demarcating portions of the germ‐line genome that ought to be retained, as in Paramecium and Tetrahymena , but full chromosomes (i.e., long template RNAs) are transcribed to ensure the correct rearrangement order …”

“…These data clearly demonstrate how genome unscrambling can generate novel genetic diversity upon which selection can act. So long as these alternatively processed chromosomes do not negatively impact the cell's fitness, these rearranged chromosomes provide the template for unscrambling the respective germ‐line loci during the next sexual event …”