Intercepting noncoding messages between germline and soma: Figure 1.

Gao, Shan; Liu, Yifan

doi:10.1101/gad.199992.112

Cited by 12 publications

(6 citation statements)

References 44 publications

(89 reference statements)

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“…Several earlier studies offered partial support, although they were not conclusive (40,43,70). With the release of the micronuclear genome sequence, high-throughput sequence analysis of sRNA become possible and has now been reported (71). The result of this comprehensive analysis is not in total agreement with the scanning model.…”

Section: Role Of Parental Macronuclei and The Rna Scanning Modelcontrasting

confidence: 33%

Programmed Genome Rearrangements in Tetrahymena

2014

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Ciliates are champions in programmed genome rearrangements. They carry out extensive restructuring during differentiation to drastically alter the complexity, relative copy number, and arrangement of sequences in the somatic genome. This chapter focuses on the model ciliate Tetrahymena, perhaps the simplest and best-understood ciliate studied. It summarizes past studies on various genome rearrangement processes and describes in detail the remarkable progress made in the past decade on the understanding of DNA deletion and other processes. The process occurs at thousands of specific sites to remove defined DNA segments that comprise roughly one-third of the genome including all transposons. Interestingly, this DNA rearranging process is a special form of RNA interference. It involves the production of double-stranded RNA and small RNA that guides the formation of heterochromatin. A domesticated piggyBac transposase is believed to cut off the marked chromatin, and the retained sequences are joined together through nonhomologous end-joining processes. Many of the proteins and DNA players involved have been analyzed and are described. This link provides possible explanations for the evolution, mechanism, and functional roles of the process. The article also discusses the interactions between parental and progeny somatic nuclei that affect the selection of sequences for deletion, and how the specific deletion boundaries are determined after heterochromatin marking.

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Section: Role Of Parental Macronuclei and The Rna Scanning Modelcontrasting

confidence: 33%

Programmed Genome Rearrangements in Tetrahymena

2014

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“…In the meiotic MIC, lack of key cotranscriptional processing machineries entails the exclusive production of ncRNA. Indeed, regulating the accessibility of cotranscriptional processing machineries or utilizing alternative transcriptional machineries may be a recurring theme for TE silencing during meiosis, which has also been implicated in the biogenesis of piRNA (Le Thomas et al 2014;Mohn et al 2014;Zhang et al 2014;Senti et al 2015;Andersen et al 2017)-the metazoan equivalent of scnRNA (Gao and Liu 2012;Mochizuki 2012). In the developing MAC, the RNAi machinery targets nascent RNA transcripts and disrupts mRNA production, possibly by cleavage with the slicer activity of TWI1 (Noto et al 2010) or interference with mRNA processing (Perales and Bentley 2009).…”

Section: Discussionmentioning

confidence: 99%

RNAi-dependent Polycomb repression controls transposable elements in Tetrahymena

et al. 2019

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RNAi and Polycomb repression play evolutionarily conserved and often coordinated roles in transcriptional silencing. Here, we show that, in the protozoan Tetrahymena thermophila, germline-specific internally eliminated sequences (IESs)-many related to transposable elements (TEs)-become transcriptionally activated in mutants deficient in the RNAi-dependent Polycomb repression pathway. Germline TE mobilization also dramatically increases in these mutants. The transition from noncoding RNA (ncRNA) to mRNA production accompanies transcriptional activation of TE-related sequences and vice versa for transcriptional silencing. The balance between ncRNA and mRNA production is potentially affected by cotranscriptional processing as well as RNAi and Polycomb repression. We posit that interplay between RNAi and Polycomb repression is a widely conserved phenomenon, whose ancestral role is epigenetic silencing of TEs.

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“…The above observations suggest that HEN1's recruitment in eukaryotes was followed by its deployment in modifying small RNAs from different limbs of the RNAi system in different eukaryotic lineages. However, given the role of both animal piRNAs and ciliate scnRNA in suppressing gene disruption via transposons or selfish DNA, it is conceivable that modification by HEN1 is a fairly ancient aspect of RNAi‐dependent protection of genes from selfish elements (Figure ). Nsun2 is an additional methyltransferase containing the same fold as Hen1 recently observed in position‐specific methylation of vRNA as a prerequisite for svRNA generation .…”

Section: Evolution Of Protein Components In Rnai Pathways In Relationmentioning

confidence: 99%

New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing

2013

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Our understanding of the pervasive involvement of small RNAs in regulating diverse biological processes has been greatly augmented by recent application of deep-sequencing technologies to small RNA across diverse eukaryotes. We review the currently-known small RNA classes and place them in context of the reconstructed evolutionary history of the RNAi protein machinery. This synthesis indicates the earliest versions of eukaryotic RNAi systems likely utilized small RNA processed from three types of precursors: 1) sense-antisense transcriptional products, 2) genome-encoded, imperfectly-complementary hairpin sequences, and 3) larger non-coding RNA precursor sequences. Structural dissection of PIWI proteins along with recent discovery of novel families (including Med13 of the Mediator complex) suggest that emergence of a distinct architecture with the N-terminal domains (also occurring separately fused to endoDNases in prokaryotes) formed via duplication of an ancestral unit was key to their recruitment as primary RNAi effectors and use of small RNAs of certain preferred lengths. Prokaryotic PIWI proteins are typically components of several RNA-directed DNA restriction or CRISPR/Cas systems. However, eukaryotic versions appear to have emerged from a subset that evolved RNA-directed RNA interference. They were recruited alongside RNaseIII domains and RdRP domains, also from prokaryotic systems, to form the core eukaryotic RNAi system. Like certain regulatory systems, RNAi diversified into two distinct but linked arms concomitant with eukaryotic nucleo-cytoplasmic compartmentalization. Subsequent elaboration of RNAi proceeded via diversification of the core protein machinery through lineage-specific expansions and recruitment of new components from prokaryotes (nucleases and small RNA-modifying enzymes), allowing for diversification of associating small RNAs.

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Intercepting noncoding messages between germline and soma: Figure 1.

Cited by 12 publications

References 44 publications

Programmed Genome Rearrangements in Tetrahymena

Programmed Genome Rearrangements in Tetrahymena

RNAi-dependent Polycomb repression controls transposable elements in Tetrahymena

New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing

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