Revisiting the Relationship between Transposable Elements and the Eukaryotic Stress Response

Horváth, Vivien; Merenciano, Miriam; González, Josefa

doi:10.1016/j.tig.2017.08.007

Cited by 167 publications

(167 citation statements)

References 74 publications

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“…Of note, RNA expression from repeat regions (including transposable elements, TEs; and virus‐derived sequences) can be linked to particular cellular states. For instance, stem cells express TEs and retroviral sequences over a spectrum of pluripotency states, LINE‐1 (L1) elements are expressed during particular meiotic stages in the mammalian germ line and act as nuclear scaffolds for protein recruitment in embryonic stem cells, the de‐repression of TEs and viral sequences correlates with the de‐methylation of paternal genomes in the early zygote and often stress responses coincide with the expression of genomic repeat elements …”

Section: Which Biophysical Properties Of Rnas Could Affect Llps?mentioning

confidence: 99%

“…For instance, stem cells express TEs and retroviral sequences over a spectrum of pluripotency states, [71,72] LINE-1 (L1) elements are expressed during particular meiotic stages in the mammalian germ line [73] and act as nuclear scaffolds for protein recruitment in embryonic stem cells, [74] the de-repression of TEs and viral sequences correlates with the de-methylation of paternal genomes in the early zygote [75,76] and often stress responses coincide with the expression of genomic repeat elements. [77] In addition to long RNAs, smaller RNAs were also able to affect LLPS and BioMC formation. [48] Naturally occurring small RNAs such as snRNAs, small nucleolar RNAs (snoRNAs), or tRNAs are highly abundant and can selfassemble, making them suitable for additional functions without affecting their canonical roles.…”

Section: Rnas Encode Specific Sequence Information and Often Sequencementioning

confidence: 99%

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RNAs, Phase Separation, and Membrane‐Less Organelles: Are Post‐Transcriptional Modifications Modulating Organelle Dynamics?

Drino¹,

Schaefer²

2018

BioEssays

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Membranous organelles allow sub‐compartmentalization of biological processes. However, additional subcellular structures create dynamic reaction spaces without the need for membranes. Such membrane‐less organelles (MLOs) are physiologically relevant and impact development, gene expression regulation, and cellular stress responses. The phenomenon resulting in the formation of MLOs is called liquid–liquid phase separation (LLPS), and is primarily governed by the interactions of multi‐domain proteins or proteins harboring intrinsically disordered regions as well as RNA‐binding domains. Although the presence of RNAs affects the formation and dissolution of MLOs, it remains unclear how the properties of RNAs exactly contribute to these effects. Here, the authors review this emerging field, and explore how particular RNA properties can affect LLPS and the behavior of MLOs. It is suggested that post‐transcriptional RNA modification systems could be contributors for dynamically modulating the assembly and dissolution of MLOs.

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Section: Which Biophysical Properties Of Rnas Could Affect Llps?mentioning

confidence: 99%

Section: Rnas Encode Specific Sequence Information and Often Sequencementioning

confidence: 99%

RNAs, Phase Separation, and Membrane‐Less Organelles: Are Post‐Transcriptional Modifications Modulating Organelle Dynamics?

Drino¹,

Schaefer²

2018

BioEssays

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“…Transposable elements (TEs) are major genome components that can induce mutations and facilitate ectopic recombination, but transposons have also been co-opted for normal cellular functions, and transposon mobilization has rewired transcriptional networks to drive evolution (Ayarpadikannan and Kim, 2014;Hedges and Deininger, 2007;Horvath et al, 2017;Piacentini et al, 2014); (Chuong et al, 2017;Jangam et al, 2017). Species survival may therefore depend on a balance of transposon silencing and activation.…”

Section: Introductionmentioning

confidence: 99%

Adaptive evolution targets a piRNA precursor transcription network

Parhad

Zhang

et al. 2019

Preprint

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In Drosophila, transposon-silencing piRNAs are derived from heterochromatic clusters and a subset of euchromatic transposon insertions, which are transcribed from internal non-canonical initiation sites and flanking canonical promoters. Rhino binds to Deadlock, which recruits TRF2 to promote non-canonical transcription of these loci. Cuff co-localizes with Rhino and Del. The role of Cuff is less well understood, but the cuff gene shows hallmarks of adaptive evolution, which frequently targets functional interactions within host defense systems. We show that Drosophila simulans cuff is a dominant negative allele when expressed in Drosophila melanogaster, where it traps Deadlock, TRF2 and the transcriptional co-repressor CtBP in stable nuclear complexes. Cuff promotes Rhino and Deadlock localization, driving non-canonical transcription. CtBP, by contrast, suppresses canonical cluster and transposon transcription, which interferes with downstream non-canonical transcription and piRNA production. Cuff, TRF2 and CtBP thus form a network that balances canonical and non-canonical piRNA precursor transcription.

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“…However, the efficiency of TE silencing can be influenced by a number of factors, including environmental or cellular stressors. In some cases, the reactivation of TEs can be explained by the presence of stress-associated transcription factor binding sites in TE promoters (reviewed by Horváth et al, 2017). However, a more global impact of stress on the efficiency of TE-silencing mechanisms has also been suggested (TittelElmer et al, 2010).…”

Section: Transposition Burst and The Generation Of A High-effect Mutamentioning

confidence: 99%

The “Polyploid Hop”: Shifting Challenges and Opportunities Over the Evolutionary Lifespan of Genome Duplications

et al. 2018

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The duplication of an entire genome is no small affair. Whole genome duplication (WGD) is a dramatic mutation with long-lasting effects, yet it occurs repeatedly in all eukaryotic kingdoms. Plants are particularly rich in documented WGDs, with recent and ancient polyploidization events in all major extant lineages. However, challenges immediately following WGD, such as the maintenance of stable chromosome segregation or detrimental ecological interactions with diploid progenitors, commonly do not permit establishment of nascent polyploids. Despite these immediate issues some lineages nevertheless persist and thrive. In fact, ecological modeling commonly supports patterns of adaptive niche differentiation in polyploids, with young polyploids often invading new niches and leaving their diploid progenitors behind. In line with these observations of polyploid evolutionary success, recent work documents instant physiological consequences of WGD associated with increased dehydration stress tolerance in first-generation autotetraploids. Furthermore, population genetic theory predicts both short-and long-term benefits of polyploidy and new empirical data suggests that established polyploids may act as "sponges" accumulating adaptive allelic diversity. In addition to their increased genetic variability, introgression with other tetraploid lineages, diploid progenitors, or even other species, further increases the available pool of genetic variants to polyploids. Despite this, the evolutionary advantages of polyploidy are still questioned, and the debate over the idea of polyploidy as an evolutionary dead-end carries on. Here we broadly synthesize the newest empirical data moving this debate forward. Altogether, evidence suggests that if early barriers are overcome, WGD can offer instantaneous fitness advantages opening the way to a transformed fitness landscape by sampling a higher diversity of alleles, including some already preadapted to their local environment. This occurs in the context of intragenomic, population genomic, and physiological modifications that can, on occasion, offer an evolutionary edge. Yet in the long run, early advantages can turn into long-term hindrances, and without ecological drivers such as novel ecological niche availability or agricultural propagation, a restabilization of the genome via diploidization will begin the cycle anew.

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Revisiting the Relationship between Transposable Elements and the Eukaryotic Stress Response

Cited by 167 publications

References 74 publications

RNAs, Phase Separation, and Membrane‐Less Organelles: Are Post‐Transcriptional Modifications Modulating Organelle Dynamics?

RNAs, Phase Separation, and Membrane‐Less Organelles: Are Post‐Transcriptional Modifications Modulating Organelle Dynamics?

Adaptive evolution targets a piRNA precursor transcription network

The “Polyploid Hop”: Shifting Challenges and Opportunities Over the Evolutionary Lifespan of Genome Duplications

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