Transcribed germline-limited coding sequences inOxytricha trifallax

Richard V Miller,Laura F Landweber,Jaspreet S Khurana,Derek M Clay,Michael W Lu,Jananan S Pathmanathan,V Talya Yerlici,Rafik Neme,T Hughes

doi:10.1093/g3journal/jkab092

Richard V Miller, Laura F Landweber + Show 7 more

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https://doi.org/10.1093/g3journal/jkab092

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Abstract

The germline-soma divide is a fundamental distinction in developmental biology, and different genes are expressed in germline and somatic cells throughout metazoan life cycles. Ciliates, a group of microbial eukaryotes, exhibit germline-somatic nuclear dimorphism within a single cell with two different genomes. The ciliate Oxytricha trifallax undergoes massive RNA-guided DNA elimination and genome rearrangement to produce a new somatic macronucleus (MAC) from a copy of the germline micronucleus (MIC). This process eliminates noncoding DNA sequences that interrupt genes and also deletes hundreds of germline-limited open reading frames (ORFs) that are transcribed during genome rearrangement. Here, we update the set of transcribed germline-limited ORFs (TGLOs) in O. trifallax. We show that TGLOs tend to be expressed during nuclear development and then are absent from the somatic MAC. We also demonstrate that exposure to synthetic RNA can reprogram TGLO retention in the somatic MAC and that TGLO retention leads to transcription outside the normal developmental program. These data suggest that TGLOs represent a group of developmentally regulated protein-coding sequences whose gene expression is terminated by DNA elimination.

Highlights

Ciliates are a lineage of microbial eukaryotes characterized by functional nuclear differentiation
Like the previous set of germline-limited genes, we show that transcribed germline-limited ORFs (TGLOs) contain several predicted functions and conserved domains that could be involved in Oxytricha development
To set read mapping thresholds appropriate for the variable sequencing depth of individual RNA and DNA libraries, we used a Monte Carlo approach in which the predicted 217,805 candidate loci were randomly shuffled 100 times throughout the germline-limited portion of the MIC genome, while recording the distribution of the number of DNA and RNA reads mapped to the random loci

Summary

Introduction

Ciliates are a lineage of microbial eukaryotes characterized by functional nuclear differentiation. Each ciliate cell has one or more somatic macronuclei (MAC) and one or more germline micronuclei (MIC). Previous studies have shown that Oxytricha’s sexual rearrangement cycle is guided by several noncoding RNA pathways. In the early stages of the sexual life cycle, bidirectional transcription across the length of nanochromosomes produce thousands of long template RNAs from the parental MAC (Lindblad et al 2017). These transcripts guide the rearrangement of macronuclear destined sequences (MDSs) during development, and previous experiments showed that injection of synthetic template RNAs could program aberrant rearrangements (Nowacki et al 2008; Bracht et al 2017; Nowacki et al 2011).

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