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CapTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements

ABSTRACT: capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements

PROVIDER: PRJNA848389 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19632512_1.fastq.gz	Fastqsanger.gz
	SRR19632513_1.fastq.gz	Fastqsanger.gz
	SRR19632514_1.fastq.gz	Fastqsanger.gz
	SRR19632515_1.fastq.gz	Fastqsanger.gz
	SRR19632516_1.fastq.gz	Fastqsanger.gz

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capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements

Project description:Transposable elements (TEs) serve as both insertional mutagens and regulatory elements in cells, and their aberrant activity is increasingly being revealed to contribute to diseases and cancers. However, measuring the transcriptional consequences of nonreference and young TEs at individual loci remains challenging with current methods, primarily due to technical limitations, including short read lengths generated and insufficient coverage in target regions. Here, we introduce a long-read targeted RNA sequencing method, Cas9-assisted profiling TE expression sequencing (capTEs), for quantitative analysis of transcriptional outputs for individual TEs, including transcribed nonreference insertions, noncanonical transcripts from various transcription patterns and their correlations with expression changes in related genes. This method selectively identified TE-containing transcripts and outputted data with up to 90% TE reads, maintaining a comparable data yield to whole-transcriptome sequencing. We applied capTEs to human cancer cells and found that internal and inserted Alu elements may employ distinct regulatory mechanisms to upregulate gene expression.

2023-08-31 | GSE205935 | GEO

capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements.

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Exogenous Transposable Elements Circumvent Homology Permitting the Dissection of Expression Dependent Silencing

Project description:The propagation of epigenetic marks has received a great deal of attention, yet the initiation of epigenetic silencing on a new transgene, virus, or transposable element remains incompletely characterized. The overlapping function of multiple silencing mechanisms has obscured this area of investigation. Here, we have revealed two broad mechanisms that are both able to initiate silencing independently: homology-based silencing and expression-dependent silencing. By transforming exogenous transposable elements into Arabidopsis, we circumvented homology-based silencing allowing us to isolate and investigate the molecular mechanism of expression-dependent silencing. We found that several small RNA-generating mechanisms all trigger de novo expression-dependent RNA-directed DNA methylation (RdDM) through RNA Polymerase V. In addition, the silencing of transposable elements fragments stalls at the RdDM phase, while full-length elements quickly progress through RdDM to maintenance methylation and heterochromatin formation. We found that there is a narrow window of time for the transition to a fully silenced state. Transformation into a mutant genotype followed by introgression into wild-type does not result in the same level of silencing as direct transformation into wild-type. This demonstrates that the genotype of transposable element insertion or transgene transformation is key for establishing the transgenerational extent of epigenetic silencing.

2017-08-25 | GSE86787 | GEO

Small RNA accumulation in Transposable Element-silent and Transposable Element-active epigenomes

Project description: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-silenced and Transposable Element-active epigenome backgrounds. Results: We found that Transposable Elements generate large amounts of 21-22nt siRNAs only when they are transcriptionally active. These 21-22nt siRNAs are incorporated into the AGO6 protein. Conclusion: Ago6 is the key protein that bridges the post-transcriptional degradation of Transposable Element mRNAs and the establishment of DNA methylation. Examination of flower bud small RNAs from wild type and 5 single or double mutant combinations, many of which have biological replicates. In addition, IP purification of the AGO6 protein (and mock no-antigen controls) followed by sequencing of the incorporated small RNAs. Replicate A for Col and ddm1 are submitted in GSE41755

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The Oscillating miRNA 959-964 cluster impacts Drosophila feeding time and other circadian outputs.

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Locus-specific chromatin profiling of evolutionarily young transposable elements

Project description:Locus-specific chromatin profiling of evolutionarily young transposable elements

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Large-Scale CRISPR Screening in Primary Human 3D Gastric Organoids Enables Comprehensive Dissection of Gene-Drug Interactions

Project description:Large-Scale CRISPR Screening in Primary Human 3D Gastric Organoids Enables Comprehensive Dissection of Gene-Drug Interactions

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Incorporation of transposable element small RNAs into the Arabidopsis AGO1 protein

Project description: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 siRNAs when transposable elements are epigenetically activated and transcribed. The incorporation of transposable element siRNAs is at the expense of the most abundant microRNAs. These transposable element siRNAs can act as tasiRNAs, regulating genes that they have partial complementarity to. Conclusion: Transposable element small RNAs are more dynamic than previously thought. They can be incorporated into AGO1 and regulate genes. Three biological replicates of small RNA sequencing from two genotypes

2014-04-07 | E-GEOD-45990 | biostudies-arrayexpress

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2014-11-14 | GSE57191 | GEO

Locus-specific chromatin profiling of evolutionarily young transposable elements [HiChIP]

Project description:Locus-specific chromatin profiling of evolutionarily young transposable elements [HiChIP]

| PRJNA755722 | ENA