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Large numbers of putative miRNAs originate from DNA transposons and are coincident with a large species radiation in bats.

ABSTRACT: Large numbers of putative miRNAs originate from DNA transposons and are coincident with a large species radiation in bats.

PROVIDER: PRJNA206437 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1179650.fastq.gz	Fastqsanger.gz
	SRR1205281.fastq.gz	Fastqsanger.gz
	SRR871530.fastq.gz	Fastqsanger.gz
	SRR871532.fastq.gz	Fastqsanger.gz

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Large numbers of putative miRNAs originate from DNA transposons and are coincident with a large species radiation in bats.

Project description:Vesper bats (family Vespertilionidae) experienced a rapid adaptive radiation beginning around 36 mya that resulted in the second most species rich mammalian family. Coincident with that radiation was an initial burst of DNA transposon activity that has continued into the present. Deep sequencing of small RNAs from the vespertilionid, Eptesicus fuscus, as well as dog and horse revealed that substantial numbers of novel bat miRNAs are derived from DNA transposons unique to vespertilionids. In fact, 35.9% of Eptesicus-specific miRNAs derive from DNA transposons compared to 2.2 and 5.9% of dog- and horse-specific miRNAs, respectively and targets of several miRNAs are identifiable. Timing of the DNA transposon expansion and the introduction of novel miRNAs coincides remarkably well with the rapid diversification of the family Vespertilionidae. We suggest that the rapid and repeated perturbation of regulatory networks by the introduction of many novel miRNA loci was a factor in the rapid radiation. A testicular tissue sample from dog, horse, and two different Eptesicus fuscus individuals. Four samples total.

2014-05-19 | E-GEOD-47593 | biostudies-arrayexpress

Large numbers of putative miRNAs originate from DNA transposons and are coincident with a large species radiation in bats.

2014-05-19 | GSE47593 | GEO

Nucleosome-depleted DNA transposons act as enhancers of meiotic recombination at Arabidopsis genes (RNA-seq)

Project description:To investigate the influence of heterochromatin on transposon transcription, we performed sequencing of RNA in wild type plant and met1 mutant which is defective in maintenance of CG context DNA methylation. The met1 mutant showed de-repression of centromeric transposons including Gypsy and EnSpm, which is coincident with increased meiotic DSBs and decreased nucleosome occupancy.

2017-06-05 | E-MTAB-5417 | biostudies-arrayexpress

SINE transposons

Project description:SINE transposons in multiple lepidopteran insects Raw sequence reads

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Maternally inherited piRNAs silence transposons during Drosophila embryogenesis

Project description:The piRNA pathway controls transposon expression in animal germ cells, thereby ensuring genome stability over generations. piRNAs are maternally deposited and required for proper transposon silencing in adult offspring. However, a long-standing question in the field is the precise function of maternally deposited piRNAs and its associated factors during embryogenesis. Here, we probe the spatio-temporal expression patterns of several piRNA pathway components during early stages of development. Amongst those, factors required for transcriptional gene silencing (TGS) showed ubiquitous abundance in somatic and pole cells throughout the first half of embryogenesis. We further analysed the transcriptomes of various embryo stages and correlated these with the presence of selected chromatin marks. We found that a number of transposon families show bursts of transcription during early embryonic stages. Transposons heavily targeted by maternally deposited piRNAs accumulated repressive chromatin marks following their spike in expression. Furthermore, depletion of maternally deposited Piwi protein in early embryos resulted in increased expression of transposons targeted by inherited piRNAs and was accompanied by a strong loss of repressive chromatin marks at coding sequences. Overall, our data suggests a pivotal role for the piRNA pathway in transposon defence during Drosophila embryogenesis in somatic cells.

2021-07-26 | PXD022409 | Pride

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Repeated horizontal transfers of four DNA transposons in invertebrates and bats.

Project description:BackgroundHorizontal transfer (HT) of transposable elements (TEs) into a new genome is considered as an important force to drive genome variation and biological innovation. However, most of the HT of DNA transposons previously described occurred between closely related species or insects.ResultsIn this study, we carried out a detailed analysis of four DNA transposons, which were found in the first sequenced twisted-wing parasite, Mengenilla moldrzyki. Through the homology-based strategy, these transposons were also identified in other insects, freshwater planarian, hydrozoans, and bats. The phylogenetic distribution of these transposons was discontinuous, and they showed extremely high sequence identities (>87%) over their entire length in spite of their hosts diverging more than 300 million years ago (Mya). Additionally, phylogenies and comparisons of transposons versus orthologous gene identities demonstrated that these transposons have transferred into their hosts by independent HTs.ConclusionsHere, we provided the first documented example of HT of CACTA transposons, which have been so far extensively studied in plants. Our results demonstrated that bats had continuously acquired new DNA elements via HT. This implies that predation on a large quantity of insects might increase bat exposure to HT. In addition, parasite-host interaction might facilitate exchanging of their genetic materials.

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Project description:Chromosome conformation capture (3C) techniques are crucial to understanding tissue-specific regulation of gene expression, but current methods generally require large numbers of cells. This hampers the investigation of chromatin structure in rare cell populations. We present two new low-input Capture-C protocols that generate high-quality, reproducible interaction profiles from fewer than 20,000 cells, and show that these are not biased by PCR amplification or the degree of formaldehyde fixation.

2017-11-20 | GSE99257 | GEO

Mobilization of Pack-CACTA transposons in Arabidopsis suggests the mechanism of gene shuffling

Project description:Pack-TYPE transposons are a unique class of potentially mobile non-autonomous elements that can capture, merge and relocate fragments of chromosomal DNA. It has been postulated that their activity accelerates the evolution of host genes. However, this important presumption is based only on the sequences of currently inactive Pack-TYPE transposons and the acquisition of chromosomal DNA has not been recorded in real time. Analysing the DNA copy number variation in hypomethylated Arabidopsis lines, we have now for the first time witnessed the mobilization of novel Pack-TYPE elements related to the CACTA transposon family, over several plant generations. Remarkably, these elements can insert into genes as closely spaced direct repeats and they frequently undergo incomplete excisions, resulting in the deletion of one of the end sequences. These properties suggest a mechanism of efficient acquisition of genic DNA residing between neighbouring Pack-TYPE transposons and its subsequent mobilization. Our work documents crucial steps in the formation of in vivo novel Pack-TYPE transposons, and thus the possible mechanism of gene shuffling mediated by this type of mobile element.

2018-11-22 | GSE120571 | GEO

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