Inter-generational nuclear crosstalk links the control of gene expression to programmed genome rearrangements during theParameciumsexual cycle

Abstract

Multinucleate cells are found in many eukaryotes, but how multiple nuclei coordinate their functions is still poorly understood. In the cytoplasm of the ciliateParamecium tetraurelia, two micronuclei (MIC) serving sexual reproduction coexist with a somatic macronucleus (MAC) dedicated to gene expression. During sexual processes, the MAC is progressively destroyed while still ensuring transcription and new MACs develop from copies of the zygotic MIC. Several gene clusters are successively induced and switched off before vegetative growth resumes. Concomitantly, programmed genome rearrangements (PGR) remove transposons and their relics from the new MACs. Development of the new MACs is controlled by the old MAC, since the latter expresses genes involved in PGR, including thePGMgene encoding the essential PiggyMac endonuclease that cleaves the ends of eliminated sequences. Using RNA deep sequencing and transcriptome analysis, we show that impairing PGR up-deregulates key PGR genes, together with ~600 other genes possibly also involved in PGR. Among these genes, 42% are no longer induced when no new MACs are formed, including 180 genes that are co-expressed withPGMunder all tested conditions. We propose that bi-directional crosstalk between the two coexisting generations of MACs links gene expression to the progression of MAC development.

ISWI1 complex proteins facilitate developmental genome editing inParamecium

“…Along with strong inhibition of iesRNAs, PTIWI10/11 expression was abolished by the ICOP KDs. As these genes are transcribed in the developing MAC, the loss of PTIWI10/11 expression could either be due to the retention of an IES in their promoter region or to nonsense-mediated decay (NMD) of mRNA triggered by IES retention in the CDS (Bazin-Gélis et al 2023;Sandoval et al 2014;Furrer et al 2017). sRNA sequencing also revealed that the MAC-specific scnRNAs are elevated in ICOP1/2-KD compared to the control (Fig 6H).…”

The nuclear PIWI-interacting protein Gtsf1 controls the selective degradation of small RNAs inParamecium

“…We found that these genes are indeed deregulated upon GTSF1 KD (Figure S2). Focusing on the 628 developmental genes that are up-regulated upon KD of the elimination machinery (Pgm, Ku80 and Xrcc4) (Bazin-Gélis et al, 2023), we found that depletion of either Gtsf1 or Ezl1 also affects the expression of these genes (Figure S2). Thus, Gtsf1 depletion, as that of other proteins essential for DNA elimination, results in the deregulation of a subset of developmental genes, and this is likely a response to defective IES excision in the new MAC.…”

Two paralogous PHD finger proteins participate inParamecium tetraurelia’s natural genome editing

“…At the subsequent stages, DevPF1 - and DevPF2 -KD affected similar genes. Either, the changes are nonspecific to the DevPF -KDs and result from the proposed nuclear crosstalk to adjust transcription levels to accommodate for failed IES excision (Bazin-Gélis et al, 2023) or they are specific to the DevPF -KDs and both paralogs exhibit similar functions in the regulation of gene expression. Interestingly, differential expression was observed at the “early” time point (Fig.…”