# Two paralogous PHD finger proteins participate in natural genome editing in Paramecium tetraurelia

## TL;DR

This study shows that two PHD finger proteins, DevPF1 and DevPF2, are essential for precise DNA excision during genome reorganization in the ciliate Paramecium.

## Contribution

The paper identifies distinct roles for paralogous PHD finger proteins in regulating genome editing during Paramecium development.

## Key findings

- DevPF1 and DevPF2 are both involved in internal eliminated sequence excision during new MAC genome formation.
- DevPF2 knockdown leads to preferential retention of long IESs and reduced late-expressed small RNAs.
- Both proteins influence the expression of genes critical for genome reorganization in the new MAC.

## Abstract

The unicellular eukaryote Paramecium tetraurelia contains functionally distinct nuclei: germline micronuclei (MICs) and a somatic macronucleus (MAC). During sex, the MIC genome is reorganized into a new MAC genome and the old MAC is lost. Almost 45,000 unique internal eliminated sequences (IESs) distributed throughout the genome require precise excision to guarantee a functional new MAC genome. Here, we characterize a pair of paralogous PHD finger proteins involved in DNA elimination. DevPF1, the early-expressed paralog, is present in only some of the gametic and post-zygotic nuclei during meiosis. Both DevPF1 and DevPF2 localize in the new developing MACs, where IES excision occurs. Upon DevPF2 knockdown (KD), long IESs are preferentially retained and late-expressed small RNAs decrease; no length preference for retained IESs was observed in DevPF1-KD and development-specific small RNAs were abolished. The expression of at least two genes from the new MAC with roles in genome reorganization seems to be influenced by DevPF1- and DevPF2-KD. Thus, both PHD fingers are crucial for new MAC genome development, with distinct functions, potentially via regulation of non-coding and coding transcription in the MICs and new MACs.

Summary: Investigation of the PHD finger proteins DevPF1 and DevPF2 indicates that they play crucial roles in genome reorganization in the ciliate Paramecium, potentially by regulating the coding and non-coding transcription during development.