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TranscriptomicsGene expression in Arabidopsis ddm1 mutants with high levels of Transposable Element activity
Background: Transposable elements are known to influence the regulation of some genes. We aimed to determine which genes show altered gene expression when transposable elements are epigenetically activated. Results: We find over 2000 genes with altered steady-state expression levels in ddm1 mutants....
ORGANISM(S): Arabidopsis thaliana 
2014-04-07 | E-GEOD-46050 | biostudies-arrayexpress
TranscriptomicsIncorporation of transposable element small RNAs into the Arabidopsis AGO1 protein
Background: Transposable element 24 nucleotide small RNAs are not efficiently incorporated into the AGO1 protein, which is involved in endogenous RNAi and gene regulation through the microRNA and tasiRNA pathways. Results: The AGO1 protein incorporates large quantities of transposable element siRNA...
ORGANISM(S): Arabidopsis thaliana 
2014-04-07 | E-GEOD-45990 | biostudies-arrayexpress
TranscriptomicsTransposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata
This SuperSeries is composed of the following subset Series: GSE24571: Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata [RNA-Seq] GSE38109: Natural variation in Arabidopsis thaliana transcriptomes Refer to individual Se...
ORGANISM(S): Arabidopsis thaliana 
2012-05-21 | E-GEOD-38113 | biostudies-arrayexpress
TranscriptomicsExtensive demethylation of repetitive elements during seed development underlies gene imprinting
DNA methylation is an epigenetic mark associated with transposable element silencing and gene imprinting in flowering plants and mammals. In plants, imprinting occurs in the endosperm, which nourishes the embryo during seed development. We have profiled Arabidopsis DNA methylation genome-wide in the...
ORGANISM(S): Arabidopsis thaliana 
2009-06-12 | E-GEOD-14570 | biostudies-arrayexpress
GenomicsTransposable elements study for Fritillaria imperialis
Transposable elements study for Fritillaria imperialis
PRJEB104641 | ENA
TranscriptomicsSmall RNA accumulation in Transposable Element-silent and Transposable Element-active epigenomes
Background: The small RNAs that Transposable Elements generate are vastly different when they are transcriptionally silenced compared to when they are transcriptionally activated. We performed the deep sequencing of small RNAs in a number of small RNA biogenesis mutants in both Transposable Element-...
ORGANISM(S): Arabidopsis thaliana 
2014-11-14 | E-GEOD-57191 | biostudies-arrayexpress
TranscriptomicsThe transposable element composition of human lincRNAs reveals a role for HERVH elements to promote stem cell specific expression of lincRNAs
Numerous studies over the past decade have elucidated a substantial set of long intergenic noncoding RNAs (lincRNAs). It has since become clear that lincRNAs constitute an important layer of genome regulation across a wide spectrum of species. Yet, the factors governing their evolution and origins r...
ORGANISM(S): Homo sapiens 
2013-01-22 | E-GEOD-38993 | biostudies-arrayexpress
TranscriptomicsMLL2 facilitates long-range gene regulation through LINE1 elements [Micro-C]
Transcriptional regulation is tightly linked to chromatin organization, with H3K4me3 commonly marking both active and bivalent promoters. In embryonic stem cells (ESC), MLL2 is essential for H3K4me3 deposition at bivalent promoters, which has been proposed to facilitate the induction of major develo...
ORGANISM(S): Mus musculus 
2025-10-23 | E-MTAB-15688 | biostudies-arrayexpress
TranscriptomicsMLL2 facilitates long-range gene regulation through LINE1 elements [scRNA-seq]
Transcriptional regulation is tightly linked to chromatin organization, with H3K4me3 commonly marking both active and bivalent promoters. In embryonic stem cells (ESC), MLL2 is essential for H3K4me3 deposition at bivalent promoters, which has been proposed to facilitate the induction of major develo...
ORGANISM(S): Mus musculus 
2026-07-12 | E-MTAB-17228 | biostudies-arrayexpress
UnknownRetrotransposons and their recognition of pol II promoters: a comprehensive survey of the transposable elements from the complete genome sequence of Schizosaccharomyces pombe.
Not available
S-EPMC403668 | biostudies-literature
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