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56 results for “repetitive elements”
Repetitive elements of Erebia and Carex and their genomic proportions
<p>Datasets of repetitive elements in the genomes of <em>Erebia </em>and <em>Carex</em>, detected and annotated using RepeatExplorer2 (Novák et al., 2010, 2020) using low-coverage (0.1X) short read sequencing data. Data from the article "Holocentric repeat landscapes: from microevolutionary patterns to macroevolutionary associations with karyotype evolution":</p> <p>Cornet, C., Mora, P., Augustijnen, H., Nguyen, P., Escudero, M., & Lucek, K. (2023). Holocentric repeat landscapes: From micro-evolutionary patterns to macro-evolutionary associations with karyotype evolution. Molecular Ecology, 00, 1–19. <a href="https://doi.org/10.1111/ mec.17100">https://doi.org/10.1111/ mec.17100</a></p> <p>47 <em>Erebia </em>and 14 <em>Carex </em>species were analysed in genus-level analyses ("Erebia" and "Carex" folders).<br> In addition, individuals of 4 <em>Erebia </em>species ("Erebia cassioides", "Erebia tyndarus", "Erebia nivalis" and "Erebia pronoe" folders) from different populations were analysed in species-level analyses. </p> <p>Subfolders "Individuals" and "Comparative" represent the two modes in which RepeatExplorer2 was run: the individual mode identifies repeats in each sample separately, and the comparative mode identifies repeats in all samples simultaneously, allowing comparisons between individuals and species. </p> <p>Files named "CLUSTER_TABLE..." are the raw output of RepeatExplorer2 and represent the overall number of reads in each cluster of repetitive element, and their annotation.<br> Files named "COMPARATIVE_ANALYSIS_COUNTS..." are the raw output of RepeatExplorer2 in comparative mode, representing the number of reads in each cluster for each sample included in the analysis. <br> Files named "Genome_proportion..." are the genomic proportion of each repeat annotation, calculated as the proportion of reads with the same annotation.</p> <p>Refer to Cornet et al. (2023) in Molecular Ecology for more details on how the data was generated, the downstream analyses and the sample names (see Tables S1, S2 and S3). </p> <p>References:</p> <p>Novák, P., Neumann, P., & Macas, J. (2010). Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics, 11(1), 378. https://doi.org/10.1186/1471-2105-11-378</p> <p>Novák, P., Neumann, P., & Macas, J. (2020). Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2. Nature Protocols, 15(11), Article 11. https://doi.org/10.1038/s41596-020-0400-y</p>
Data from: Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements
Cytosine DNA methylation (mC) is a genome modification that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of mC in response to environmental cues. Using whole genome bisulfite sequencing to assess the spatio-temporal dynamics of mC in rice grown under phosphate starvation and recovery conditions, we identified widespread phosphate starvation-induced changes in mC, preferentially localized in transposable elements (TEs) close to highly induced genes. These changes in mC occurred after changes in nearby gene transcription, were mostly DCL3a-independent, could partially be propagated through mitosis, however no evidence of meiotic transmission was observed. Similar analyses performed in Arabidopsis revealed a very limited effect of phosphate starvation on mC, suggesting a species-specific mechanism. Overall, this suggests that TEs in proximity to environmentally induced genes are silenced via hypermethylation, and establishes the temporal hierarchy of transcriptional and epigenomic changes in response to stress.
Data from: Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among vesper bats
The repetitive landscapes of mammalian genomes typically display high Class I (retrotransposon) transposable element (TE) content, usually around half of the genome. In contrast, the Class II (DNA transposon) contribution is typically small (<3% in model mammals). Most mammalian genomes also exhibit a precipitous decline in Class II activity beginning roughly 40 million years ago (Ma). The first signs of more recently active mammalian Class II TEs were obtained from the little brown bat, Myotis lucifugus and are reflected by higher genome content (~5%). To aid in determining taxonomic limits and potential impacts of this elevated Class II activity, we performed 454 survey sequencing of a second Myotis species as well as four additional taxa within the family Vespertilionidae and an outgroup species from Phyllostomidae. Graph-based clustering methods were used to reconstruct the major repeat families present in each species and novel elements were identified in several taxa. Retrotransposons remained the dominant group with regard to overall genome mass. Elevated Class II TE composition (3-4%) was observed in all five vesper bats while less than 0.5% of the phyllostomid reads were identified as Class II derived. Differences in satellite DNA and Class I TE content are also described among vespertilionid taxa. These analyses present the first cohesive description of TE evolution across closely related mammals, revealing genome-scale differences in TE content within a single family.
Supplementary material 5 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Table 5 : Data type: Table
Supplementary material 4 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Table 4 : Data type: Table
Supplementary material 1 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Table 1 : Data type: Table
Supplementary material 3 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Table 3 : Data type: Table
Supplementary material 7 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Figure 2 : Data type: Image
Supplementary material 2 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Table 2 : Data type: Table
Supplementary material 6 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Figure 1 : Data type: Image
Data from: Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements
Open the record for dataset details and reuse information.
Data from: Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among vesper bats
Open the record for dataset details and reuse information.
Extensive demethylation of repetitive elements during seed development underlies gene imprinting
GEO Series GSE14570. Arabidopsis thaliana. 10 samples. Type: Methylation profiling by genome tiling array; Methylation profiling by high throughput sequencing.
Epigenetic therapies in ovarian cancer alter repetitive element expression in a TP53-dependent manner: OC Line RNAseq
GEO Series GSE182119. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
The DAXX/ATRX Complex Protects Tandem Repetitive Elements in the Absence of DNA Methylation by Promoting H3K9 Trimethylation [RNA-Seq]
GEO Series GSE70849. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Competition for H2A.Z underlies the developmental impacts of repetitive element de-repression
GEO Series GSE237095. Danio rerio. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Aggressive PDACs show hypomethylation of repetitive elements and the execution of an intrinsic IFN program linked to a ductal cell-of-origin. [Activation of stellate cells by tumor conditioned medium]
GEO Series GSE134093. Homo sapiens. 6 samples. Type: Expression profiling by array.
Splenic CD43- B cells exhibit DNA hypomethylation specifically at repetitive elements compared to CD43+ cells
GEO Series GSE229684. Mus musculus. 12 samples. Type: Methylation profiling by array.
Epigenetic therapies in ovarian cancer alter repetitive element expression in a TP53-dependent manner: ChIPseq
GEO Series GSE182114. Homo sapiens. 9 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Aggressive PDACs show hypomethylation of repetitive elements and the execution of an intrinsic IFN program linked to a ductal cell-of-origin
GEO Series GSE161956. Homo sapiens. 13 samples. Type: Methylation profiling by high throughput sequencing.
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