Local Effect of Enhancer of Zeste-Like Reveals Cooperation of Epigenetic and cis-Acting Determinants for Zygotic Genome Rearrangements

Hagen

Vitali

2020

Preprint

Section: Resultsmentioning

confidence: 99%

“…The datasets of Internal Eliminated Sequences (IESs) for the control stocks were obtained from (Arnaiz et al 2012) (stock d4-2), (Lhuillier-Akakpo et al 2014) (stock 51, cultured at 27°C) and (Vitali et al 2019) (stock d12, F0 line cultured at 25°C). The IES datasets for the MA lines were extracted with ParTIES (Denby Wilkes et al 2016) .…”

Section: Methodsmentioning

confidence: 99%

Prolonged exposure to constant environmental conditions prompts nonrandom genetic variation

Hagen

Vitali

2020

Preprint

“…These spliced sequences are known as internal eliminated sequences (IESs) . IES excision in ciliates is particularly well studied in Paramecium, Tetrahymena, and Oxytricha . Here, we will focus on the process of IES excision in the best‐studied species of Paramecium, Paramecium tetraurelia .…”

Section: Dna‐level Splicingmentioning

confidence: 99%

“…In essence, the scnRNAs that are able to pair with maternal long noncoding RNAs are inactivated, whereas the germline‐specific (IES‐matching) scnRNAs remain unpaired and intact. Third, these unpaired scnRNAs are transported to the developing MAC, where they facilitate IES excision by PiggyMac via mechanisms involving chromatin modifications . An addendum to this model has been recently proposed after a distinct class of small RNAs—termed iesRNAs—has been found to participate in the development of the Paramecium macronuclear genome .…”

Section: Dna‐level Splicingmentioning

confidence: 99%

On the path to genetic novelties: insights from programmed DNA elimination and RNA splicing

Schmitz

2015

WIREs RNA

Understanding how genetic novelties arise is a central goal of evolutionary biology. To this end, programmed DNA elimination and RNA splicing deserve special consideration. While programmed DNA elimination reshapes genomes by eliminating chromatin during organismal development, RNA splicing rearranges genetic messages by removing intronic regions during transcription. Small RNAs help to mediate this class of sequence reorganization, which is not error-free. It is this imperfection that makes programmed DNA elimination and RNA splicing excellent candidates for generating evolutionary novelties. Leveraging a number of these two processes' mechanistic and evolutionary properties, which have been uncovered over the past years, we present recently proposed models and empirical evidence for how splicing can shape the structure of protein-coding genes in eukaryotes. We also chronicle a number of intriguing similarities between the processes of programmed DNA elimination and RNA splicing, and highlight the role that the variation in the population-genetic environment may play in shaping their target sequences.

“…Conventional approaches may fail to classify these highly retained IESs as Dcl2/3-dependent because the shifts between pre-and post-KD levels of IES retention might be negligible. Leveraging the IRSs obtained by previous Dcl2/3 KD experiments (Lhuillier-Akakpo et al 2014; Sandoval et al 2014) we identified 236 IESs that despite having particularly elevated IRSs in these KD experiments (IRS > 0.3) were not recorded as influenced by the scnRNA machinery. Around 68% of these IESs (n=160) are found in our 4-way-shared set.…”

Section: Resultsmentioning

confidence: 80%

Enhanced plasticity of programmed DNA elimination boosts adaptive potential in suboptimal environments

Vitali

Hagen

2018

Preprint

19The impact of ecological changes on the development of new somatic genomes has 20 thus far been neglected. This oversight yields an incomplete understanding of the 21 mechanisms that underlie environmental adaptation and can be tackled leveraging the 22 biological properties of ciliates. When Paramecium reproduces sexually, its polyploid 23 somatic genome regenerates from the germline genome via a developmental process, 24 Programmed DNA elimination (PDE), that involves the removal of thousands of ORF-25 interrupting germline sequences. Here, we demonstrate that exposure to sub-optimal 26 temperatures impacts PDE efficiency, prompting the emergence of hundreds of 27 alternative DNA splicing variants that dually embody cryptic (germline) variation and 28 de novo induced (somatic) mutations. In contrast to trivial biological errors, many of 29 these alternative DNA isoforms display a patterned genomic topography, are 30 epigenetically controlled, inherited trans-somatically, and under purifying selection. 31Developmental thermoplasticity in Paramecium is a likely source of evolutionary 32 innovation. 33 34 Developmental plasticity-the environmentally induced phenotypic variance 35 associated with alternative developmental trajectories-has been proposed to fuel 36 adaptive evolution by initiating phenotypic changes (West-Eberhard 2005; Uller et al. 37 2018). Exploring the molecular mechanisms that underlie developmental plasticity can 38 reveal a direct link between environmental changes and phenotypic differentiation, 39 shedding light on how variation can surface from a single genotype in a stressful 40 environment. This knowledge has important consequences for current understanding 41 of evolutionary processes and human health (Lea et al. 2017b; Lea et al. 2017a). 42 Previous studies in flies, plants, fungi, and vertebrates suggest that 43 environmental changes that alter the molecular chaperone Hsp90's buffering capacity 44 during development can unlock cryptic genetic variation and boost phenotypic 45 diversification (Rutherford and Lindquist 1998; Queitsch et al. 2002; Yeyati et al. 46 2007; Jarosz and Lindquist 2010; Rohner et al. 2013). These observations 47 substantiate an evolutionary model where cryptic developmental variation, which is 48 revealed in response to environmental stress, might become genetically assimilated 49 (Waddington 1953). An alternative mechanism that links genetic and phenotypic 50 variation via environmental stress has also been proposed. Recent studies in flies 51 suggest that environmental stress, rather than exposing cryptic variation, may induce 52 de novo mutations, DNA deletions and transposon insertions (Fanti et al. 2017), 53 which can result from the disruption of a class of germline-specific small RNAs known 54 as Piwi-interacting RNAs (Specchia et al. 2010; Gangaraju et al. 2011). Following 55 stress-induced epigenetic changes, transposon activation or DNA deletions would 56 generate somatic changes, which might ultimately become heritable via de novo 57 germline ...