Small RNAs from a Big Genome: The piRNA Pathway and Transposable Elements in the Salamander Species Desmognathus fuscus

2016 ◽  
Vol 83 (3-4) ◽  
pp. 126-136 ◽  
Author(s):  
M. J. Madison-Villar ◽  
Cheng Sun ◽  
Nelson C. Lau ◽  
Matthew L. Settles ◽  
Rachel Lockridge Mueller
Keyword(s):  
Transposable Elements ◽  
Small Rnas ◽  
Pirna Pathway ◽  
Salamander Species

Erratum to: Small RNAs from a Big Genome: The piRNA Pathway and Transposable Elements in the Salamander Species Desmognathus fuscus

2016 ◽  
Vol 84 (1) ◽  
pp. 67-67
Author(s):  
M. J. Madison-Villar ◽  
Cheng Sun ◽  
Nelson C. Lau ◽  
Matthew L. Settles ◽  
Rachel Lockridge Mueller
Keyword(s):  
Transposable Elements ◽  
Small Rnas ◽  
Pirna Pathway ◽  
Salamander Species

scholarly journals Intergenerational metabolic priming by sperm piRNAs

2021 ◽  
Author(s):  
Adelheid Lempradl ◽  
Unn Kugelberg ◽  
Mary Iconomou ◽  
Ian Beddows ◽  
Daniel Nätt ◽  
...  
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Target Gene ◽  
Epigenetic Inheritance ◽  
Mature Sperm ◽  
Transcriptional Reprogramming ◽  
Complementary Sequences ◽  
Specific Manner ◽  
Dietary Sugar ◽  
Pirna Pathway

Preconception parental environment can reproducibly program offspring phenotype without altering the DNA sequence, yet the mechanisms underpinning this epigenetic inheritance remains elusive. Here, we demonstrate the existence of an intact piRNA-pathway in mature Drosophila sperm and show that pathway modulation alters offspring gene transcription in a sequence-specific manner. We map a dynamic small RNA content in developing sperm and find that the mature sperm carry a highly distinct small RNA cargo. By biochemical pulldown, we identify a small RNA subset bound directly to piwi protein. And, we show that piRNA-pathway controlled sperm small RNAs are linked to target gene repression in offspring. Critically, we find that full piRNA-pathway dosage is necessary for the intergenerational metabolic and transcriptional reprogramming events triggered by high paternal dietary sugar. These data provide a direct link between regulation of endogenous mature sperm small RNAs and transcriptional programming of complementary sequences in offspring. Thus, we identify a novel mediator of paternal intergenerational epigenetic inheritance.

scholarly journals Diverse Defenses: A Perspective Comparing Dipteran Piwi-piRNA Pathways

Cells ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 2180
Author(s):  
Stephanie Gamez ◽  
Satyam Srivastav ◽  
Omar S. Akbari ◽  
Nelson C. Lau
Keyword(s):  
Innate Immune System ◽  
Small Rnas ◽  
Fruit Flies ◽  
Innate Immune ◽  
Virus Infections ◽  
Genome Composition ◽  
Chromatin Regulators ◽  
Open Questions ◽  
Pathogenic Viruses ◽  
Pirna Pathway

Animals face the dual threat of virus infections hijacking cellular function and transposons proliferating in germline genomes. For insects, the deeply conserved RNA interference (RNAi) pathways and other chromatin regulators provide an important line of defense against both viruses and transposons. For example, this innate immune system displays adaptiveness to new invasions by generating cognate small RNAs for targeting gene silencing measures against the viral and genomic intruders. However, within the Dipteran clade of insects, Drosophilid fruit flies and Culicids mosquitoes have evolved several unique mechanistic aspects of their RNAi defenses to combat invading transposons and viruses, with the Piwi-piRNA arm of the RNAi pathways showing the greatest degree of novel evolution. Whereas central features of Piwi-piRNA pathways are conserved between Drosophilids and Culicids, multiple lineage-specific innovations have arisen that may reflect distinct genome composition differences and specific ecological and physiological features dividing these two branches of Dipterans. This perspective review focuses on the most recent findings illuminating the Piwi/piRNA pathway distinctions between fruit flies and mosquitoes, and raises open questions that need to be addressed in order to ameliorate human diseases caused by pathogenic viruses that mosquitoes transmit as vectors.

scholarly journals Transposons, Genome Size, and Evolutionary Insights in Animals

2015 ◽  
Vol 147 (4) ◽  
pp. 217-239 ◽  
Author(s):  
Adriana Canapa ◽  
Marco Barucca ◽  
Maria A. Biscotti ◽  
Mariko Forconi ◽  
Ettore Olmo
Keyword(s):  
Natural Selection ◽  
Transposable Elements ◽  
Genome Size ◽  
Small Rnas ◽  
Evolutionary History ◽  
Animal Species ◽  
Current Situation ◽  
Environmental Stressors ◽  
Functional Parameters ◽  
The Relationship

The relationship between genome size and the percentage of transposons in 161 animal species evidenced that variations in genome size are linked to the amplification or the contraction of transposable elements. The activity of transposable elements could represent a response to environmental stressors. Indeed, although with different trends in protostomes and deuterostomes, comprehensive changes in genome size were recorded in concomitance with particular periods of evolutionary history or adaptations to specific environments. During evolution, genome size and the presence of transposable elements have influenced structural and functional parameters of genomes and cells. Changes of these parameters have had an impact on morphological and functional characteristics of the organism on which natural selection directly acts. Therefore, the current situation represents a balance between insertion and amplification of transposons and the mechanisms responsible for their deletion or for decreasing their activity. Among the latter, methylation and the silencing action of small RNAs likely represent the most frequent mechanisms.

scholarly journals The PIWI/piRNA response is relaxed in a rodent that lacks mobilizing transposable elements

2019 ◽  
Author(s):  
Michael W. Vandewege ◽  
Roy N. Patt ◽  
Dana K. Merriman ◽  
David A. Ray ◽  
Federico G. Hoffmann
Keyword(s):  
Transposable Elements ◽  
Ground Squirrel ◽  
Small Rnas ◽  
Oryctolagus Cuniculus ◽  
Genome Integrity ◽  
European Rabbit ◽  
Present Evidence ◽  
Major Threat ◽  
Crucial Difference ◽  
Mammalian Genomes

AbstractTransposable elements (TEs) have the capability to propagate throughout genomes. Mammalian genomes are typically dominated by LINE retrotransposons and their associated SINEs, and their mobilization in the germline is a challenge to genome integrity. There are genomic defenses against TE proliferation and the PIWI/piRNAs defense is among the most well understood. However, the PIWI/piRNA system has been investigated largely in animals with abundant and actively mobilizing TEs and it is unclear how the PIWI/piRNA system functions in the absence of mobilizing TEs. The thirteen-lined ground squirrel provides an excellent opportunity to examine PIWI/piRNA and TE dynamics within the context of minimal, and possibly nonexistent, TE accumulation. We sequenced RNA and small RNAs pools from the testis of juvenile and adult squirrels and compared results to TE and PIWI/piRNA dynamics in the European rabbit (Oryctolagus cuniculus) and house mouse (Mus musculus). Interestingly in squirrels, despite a lack of young insertions, TEs were still actively transcribed in comparable levels to mouse and rabbit. All three PIWI proteins were either not expressed, or only minimally expressed, prior to P8 in squirrel testis, moreover we also discovered that PIWIL4 is expressed all the way into adulthood in the squirrel. This is a crucial difference as PIWIL4 is understood to facilitate TE methylation. We present evidence the PIWI/piRNA system reduced TE expression in rabbit and mouse, but the squirrel PIWIs largely did not affect TE expression. These observations indicate that L1s do not represent a major threat to genome integrity in the squirrel genome, and therefore repression mechanisms have relaxed.

scholarly journals Heterogeneity of transposon expression and activation of the repressive network in human fetal germ cells

2018 ◽  
Author(s):  
Boris Reznik ◽  
Steven A. Cincotta ◽  
Rebecca G. Jaszczak ◽  
Leslie J. Mateo ◽  
Joel Shen ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Nuclear Localization ◽  
Germ Cells ◽  
Epigenetic Silencing ◽  
Epigenetic Marks ◽  
Fetal Testis ◽  
Pirna Pathway

AbstractEpigenetic resetting in germ cells during development leads to the de-repression of transposable elements (TEs). piRNAs protect fetal germ cells from potentially harmful TEs by targeted destruction of mRNA and deposition of repressive epigenetic marks. Here we provide the first evidence for an active piRNA pathway and TE repression in germ cells of human fetal testis. We identify pre-pachytene piRNAs with features of secondary amplification that map most abundantly to L1 family TEs. We find that L1-ORF1p expression is heterogeneous in fetal germ cells, peaks at mid-gestation and declines concomitantly with increasing levels of piRNAs and H3K9me3, as well as nuclear localization of HIWI2. Surprisingly, following this decline, the same cells with accumulation of L1-ORF1p display highest levels of HIWI2 and H3K9me3, whereas L1-ORF1p low cells are also low in HIWI2 and H3K9me3. Conversely, earlier in development, the germ cells lacking L1-ORF1p express high levels of the chaperone HSP90a. We propose that a subset of HSP90a-armed germ cells resists L1 expression, whereas only those vulnerable L1-expressing germ cells activate the PIWI-piRNA repression pathway which leads to epigenetic silencing of L1 via H3K9me3.

scholarly journals Diversification of small RNA amplification mechanisms for targeting transposon-related sequences in ciliates

2019 ◽  
Vol 116 (29) ◽  
pp. 14639-14644 ◽  
Author(s):  
Masatoshi Mutazono ◽  
Tomoko Noto ◽  
Kazufumi Mochizuki
Keyword(s):  
Transposable Elements ◽  
Small Rna ◽  
Signal Amplification ◽  
Small Rnas ◽  
Ciliated Protozoa ◽  
Rna Amplification ◽  
Somatic Nucleus ◽  
Dna Elimination ◽  
Internal Eliminated Sequences ◽  
Rna Biogenesis

The silencing of repetitive transposable elements (TEs) is ensured by signal amplification of the initial small RNA trigger, which occurs at distinct steps of TE silencing in different eukaryotes. How such a variety of secondary small RNA biogenesis mechanisms has evolved has not been thoroughly elucidated. Ciliated protozoa perform small RNA-directed programmed DNA elimination of thousands of TE-related internal eliminated sequences (IESs) in the newly developed somatic nucleus. In the ciliate Paramecium, secondary small RNAs are produced after the excision of IESs. In this study, we show that in another ciliate, Tetrahymena, secondary small RNAs accumulate at least a few hours before their derived IESs are excised. We also demonstrate that DNA excision is dispensable for their biogenesis in this ciliate. Therefore, unlike in Paramecium, small RNA amplification occurs before IES excision in Tetrahymena. This study reveals the remarkable diversity of secondary small RNA biogenesis mechanisms, even among ciliates with similar DNA elimination processes, and thus raises the possibility that the evolution of TE-targeting small RNA amplification can be traced by investigating the DNA elimination mechanisms of ciliates.

scholarly journals Small RNAs, DNA methylation and transposable elements in wheat

BMC Genomics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 408 ◽  
Author(s):  
Dario Cantu ◽  
Leonardo S Vanzetti ◽  
Adam Sumner ◽  
Martin Dubcovsky ◽  
Marta Matvienko ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Transposable Elements ◽  
Small Rnas
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