RNA-mediated transgenerational inheritance in ciliates and plants

Zachary T Neeb,Mariusz Nowacki

doi:10.1007/s00412-017-0655-4

Abstract

In the age of next-generation sequencing (NGS) and with the availability of whole sequenced genomes and epigenomes, some attention has shifted from purely sequence-based studies to those of heritable epigenetic modifications. Transgenerational inheritance can be defined as heritable changes to the state of DNA that may be passed on to subsequent generations without alterations to the underlying DNA sequence. Although this phenomenon has been extensively studied in many systems, studies of transgenerational inheritance in mammals and other higher-level eukaryotes may be complicated by the fact that many epigenetic marks are reprogrammed during sexual reproduction. This, by definition, may obscure our interpretation of what is in fact truly transgenerational. Therefore, in this mini review, we discuss what is currently known in the field about transgenerational epigenetic inheritance in ciliates and plants, with a particular emphasis on RNA-mediated processes and changes in chromatin states.

Highlights

CiliatesIn recent years, there has been much focus on the subject of epigenetic inheritance and how heritable changes in chromatin states may be transmitted to subsequent generations
Small non-coding RNAs have been implicated in many of these processes and likely mediate transgenerational inheritance across eukaryotic species, since they can induce changes in chromatin dynamics and guide histone modifications. While these phenomena have been described in mammals and extensive work has been performed to elucidate mechanisms, this review will focus primarily on RNA-mediated transgenerational inheritance in ciliated protozoans and plants
Oxytricha has additional largest and second largest Pol II subunit paralogs (RPB1b and RPB2b) that are highly upregulated during macronuclear development and likely play roles in the transcription of either small RNA precursors or the guide RNAs described in the process of gene unscrambling (Khurana et al 2014; Neeb et al 2017)

Summary

Introduction

There has been much focus on the subject of epigenetic inheritance and how heritable changes in chromatin states may be transmitted to subsequent generations. During the early stages of the sexual life cycle of these ciliates, the entire micronuclear genome is transcribed bidirectionally to produce long double-stranded RNAs (Chalker and Yao 2001; Mochizuki and Gorovsky 2004b) These double-stranded RNA precursors are processed by Dicer-like enzymes, DCL2/3 in Paramecium and Dcl1p in Tetrahymena, to produce a class of small RNAs called scan RNAs (scnRNAs) (25 nt and 26–31 nt, respectively) (Chalker et al 2005; Malone et al 2005; Mochizuki and Gorovsky 2004a, 2005; Sandoval et al 2014). In both Paramecium and Tetrahymena, this elimination relies on repressive heterochromatin marks, namely histone H3 lysine 9 and lysine 27 methylation

Targeting and Excision of all remaining IESs

Pol V

Findings

Conclusion