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Transposable element activity captures human pluripotent cell states.

ABSTRACT: Transposable element activity captures human pluripotent cell states.

PROVIDER: PRJNA1135496 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29809715_1.fastq.gz	Fastqsanger.gz
	SRR29809715_2.fastq.gz	Fastqsanger.gz
	SRR29809716_1.fastq.gz	Fastqsanger.gz
	SRR29809716_2.fastq.gz	Fastqsanger.gz
	SRR29809717_1.fastq.gz	Fastqsanger.gz

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Project description:Human pluripotent stem cells (hPSCs) serve as powerful in vitro models to elucidate the molecular underpinnings of embryonic cell fate transitions. hPSCs can be maintained in two distinct states: a naïve state, corresponding to the pre-implantation epiblast, and a primed state, mirroring the post-implantation epiblast. Our research demonstrates that transposable elements act as sensitive indicators of these pluripotency states. We engineered hPSCs with fluorescent reporters that capture the temporal expression dynamics of two transposable elements, LTR5_Hs and MER51B. This dual reporter system facilitates real-time monitoring and isolation of stem cells as they transition from naïve to primed pluripotency and further towards differentiation. Unexpectedly, we identified a rare, metastable cell population within primed hPSCs, marked by transcripts associated with pre-implantation embryo development and triggered by DNA damage. Additionally, our system uncovered novel transcriptional regulators involved in pluripotency, naïve reprogramming, and differentiation. Our study provides key insights into the dynamic regulation of transposable elements during embryonic development and introduces a novel system for investigating and exploiting cellular plasticity.

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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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Project description: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. Some of these genes are influenced by neighboring transposable element fragments, while other genes are targeted by transposable element derived 21 nucleotide siRNAs. Conclusion: The regulation of the genic portion of the Arabidopsis genome is heavily influenced by the epigenetic regulation of transposable elements. The regulation of genes by transposable elements can occur through multiple mechanisms. Three biological replicates for two genotypes

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