Transposable Element ‘<i>roo</i>’ Attaches to Nuclear Matrix of the<i>Drosophila melanogaster</i>

Mamillapalli, Anitha; Pathak, Rashmi U.; Garapati, Hita Sony; Mishra, Rakesh K.

doi:10.1673/031.013.11101

Cited by 11 publications

(11 citation statements)

References 39 publications

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“…We identified TFBSs using the JASPAR database (see Material and Methods ). We also specifically looked for conservation of the regulatory regions previously described in the roo family [ 8 , 30 ], and for conserved core promoter motifs [ 1 ] ( Fig 3A and S2A Table ). Overall, there was very little diversity among the nine solo-LTRs ( S3A Fig ).…”

Section: Resultsmentioning

confidence: 99%

“…These roo elements differ in the insertion site and in their orientation. On the other hand, all elements have the same size and show high sequence conservation: all cis-regulatory elements previously described in roo LTRs are highly conserved [ 8 , 30 ]. We further investigated whether these different insertions were functionally equivalent by performing 5’-RACE, gene expression, and phenotypic analyses.…”

Section: Introductionmentioning

confidence: 99%

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Multiple Independent Retroelement Insertions in the Promoter of a Stress Response Gene Have Variable Molecular and Functional Effects in Drosophila

et al. 2016

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Promoters are structurally and functionally diverse gene regulatory regions. The presence or absence of sequence motifs and the spacing between the motifs defines the properties of promoters. Recent alternative promoter usage analyses in Drosophila melanogaster revealed that transposable elements significantly contribute to promote diversity. In this work, we analyzed in detail one of the transposable element insertions, named FBti0019985, that has been co-opted to drive expression of CG18446, a candidate stress response gene. We analyzed strains from different natural populations and we found that besides FBti0019985, there are another eight independent transposable elements inserted in the proximal promoter region of CG18446. All nine insertions are solo-LTRs that belong to the roo family. We analyzed the sequence of the nine roo insertions and we investigated whether the different insertions were functionally equivalent by performing 5’-RACE, gene expression, and cold-stress survival experiments. We found that different insertions have different molecular and functional consequences. The exact position where the transposable elements are inserted matters, as they all showed highly conserved sequences but only two of the analyzed insertions provided alternative transcription start sites, and only the FBti0019985 insertion consistently affects CG18446 expression. The phenotypic consequences of the different insertions also vary: only FBti0019985 was associated with cold-stress tolerance. Interestingly, the only previous report of transposable elements inserting repeatedly and independently in a promoter region in D. melanogaster, were also located upstream of a stress response gene. Our results suggest that functional validation of individual structural variants is needed to resolve the complexity of insertion clusters.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Multiple Independent Retroelement Insertions in the Promoter of a Stress Response Gene Have Variable Molecular and Functional Effects in Drosophila

et al. 2016

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“…Early research demonstrated that active transposons exist in germline cells (Bucheton, 1990). Transposons can move in the genome by insertion and transcription and thus interrupt the normal expression of genes (Kazazian, 2004;Mamillapalli et al, 2013). The main function of piRNA is the silencing of transposable elements (Senti and Brennecke, 2010;Weick and Miska, 2014).…”

Section: Discussionmentioning

confidence: 99%

Tudor knockdown disrupts ovary development in Bactrocera dorsalis

Xie

Shang

Ding

et al. 2018

Insect Molecular Biology

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One of the main functions of the piwi-interacting RNA pathway is the post-transcriptional silencing of transposable elements in the germline of many species. In insects, proteins belonging to the Tudor superfamily proteins belonging to the Tudor superfamily play an important role in to play an important role in this mechanism. In this study, we identified the tudor gene in the oriental fruit fly, Bactrocera dorsalis, investigated the spatiotemporal expressional profile of the gene, and performed a functional analysis using RNA interference. We identified one transcript for a tudor homologue in the B. dorsalis transcriptome, which encodes a protein containing the typical 10 Tudor domains and an Adenosine triphosphate (ATP) synthase delta subunit signature. Phylogenetic analysis confirmed the identity of this transcript as a tudor homologue in this species. The expression profile indicated a much higher expression in the adult and pupal stages compared to the larval stages (up to a 60-fold increase), and that the gene was mostly expressed in the ovaries, Malpighian tubules and fat body. Finally, gene knockdown of tudor in B. dorsalis led to clearly underdeveloped ovaries in the female adult and reductions in copulation rate and amount of oviposition, indicating its important role in reproduction. The results of this study shed more light on the role of tudor in ovary development and reproduction.

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“…Notably, the same gypsy sub-sequence that contains the insulator/silencer function (described above), also functions as MAR/SAR (matrix attachment region/scaffold attachment region), connecting a transcriptional role to a structural role of the gypsy retrotransposon [69]. A sequence displaying MAR function was also identified and characterized in the roo element [70]. Although this aspect is not deeply investigated, these results highlight a cis-structural role of TEs, whose importance is comparable to the role of TEs in centromeres and telomeres.…”

Section: Structural Role Of Cis-operating Sequences Within Tesmentioning

confidence: 99%

“What You Need, Baby, I Got It”: Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila

Moschetti

Palazzo

Lorusso

et al. 2020

Biology

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Transposable elements (TEs) are constitutive components of both eukaryotic and prokaryotic genomes. The role of TEs in the evolution of genes and genomes has been widely assessed over the past years in a variety of model and non-model organisms. Drosophila is undoubtedly among the most powerful model organisms used for the purpose of studying the role of transposons and their effects on the stability and evolution of genes and genomes. Besides their most intuitive role as insertional mutagens, TEs can modify the transcriptional pattern of host genes by juxtaposing new cis-regulatory sequences. A key element of TE biology is that they carry transcriptional control elements that fine-tune the transcription of their own genes, but that can also perturb the transcriptional activity of neighboring host genes. From this perspective, the transposition-mediated modulation of gene expression is an important issue for the short-term adaptation of physiological functions to the environmental changes, and for long-term evolutionary changes. Here, we review the current literature concerning the regulatory and structural elements operating in cis provided by TEs in Drosophila. Furthermore, we highlight that, besides their influence on both TEs and host genes expression, they can affect the chromatin structure and epigenetic status as well as both the chromosome's structure and stability. It emerges that Drosophila is a good model organism to study the effect of TE-linked regulatory sequences, and it could help future studies on TE-host interactions in any complex eukaryotic genome.

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Transposable Element ‘roo’ Attaches to Nuclear Matrix of theDrosophila melanogaster

Cited by 11 publications

References 39 publications

Multiple Independent Retroelement Insertions in the Promoter of a Stress Response Gene Have Variable Molecular and Functional Effects in Drosophila

Multiple Independent Retroelement Insertions in the Promoter of a Stress Response Gene Have Variable Molecular and Functional Effects in Drosophila

Tudor knockdown disrupts ovary development in Bactrocera dorsalis

“What You Need, Baby, I Got It”: Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila

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