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Characterization of the RNA present in L1 ORF1p macromolecular complexes from Mael-/- mouse testes

ABSTRACT: Characterization of the RNA present in L1 ORF1p macromolecular complexes from Mael-/- mouse testes

PROVIDER: PRJNA922048 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23021829.fastq.gz	Fastqsanger.gz
	SRR23021830.fastq.gz	Fastqsanger.gz
	SRR23021831.fastq.gz	Fastqsanger.gz
	SRR23021832.fastq.gz	Fastqsanger.gz
	SRR23021833.fastq.gz	Fastqsanger.gz

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Characterization of the RNA present in L1 ORF1p macromolecular complexes from Mael-/- mouse testes

Project description:piRNA-deficient Maelstrom (Mael) null mice are characterized by a strong upregulation of LINE-1 (L1) retrotransposon in meiotic spermatocytes. This defect turns out in the accumulation of L1 RNA and ORF1p in their cytoplasm and the formation of prominent ribonucleoprotein aggregates. We used 3-months-old Mael-/- male mice to characterize the RNA present in those ORF1p aggregates. To favor the isolation of complexed versus free ORF1p protein, we first fractionated Mael-/- testis extracts (that we refer to as TOTAL) by sucrose gradient ultracentrifugation, in the presence of EDTA. We then pooled the sucrose fractions where ORF1p macromolecular complexes sediment (fractions 5-8) and used this pool as the INPUT for an anti-ORF1p co-immunoprecipitation (IP) followed by RNA-seq.

2023-05-25 | GSE222416 | GEO

Characterization of L1 ORF1p macromolecular complexes from Mael-/- mouse testes

Project description:piRNA-deficient Maelstrom (Mael) null mice are characterized by a strong upregulation of retrotransposon LINE-1 (L1) in meiotic spermatocytes. This defect turns out in the accumulation of L1 RNA and ORF1p in their cytoplasm and the formation of prominent ribonucleoprotein aggregates. We used 3-months-old Mael-/- male mice to characterize the protein composition of those ORF1p aggregates.

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Dissection of affinity captured LINE-1 macromolecular complexes

Project description:Long Interspersed Nuclear Element-1 (LINE-1, L1) is a mobile genetic element active in human genomes. L1-encoded ORF1 and ORF2 proteins bind L1 RNAs, forming ribonucleoproteins (RNPs). These RNPs interact with diverse host proteins, some repressive and others required for the L1 lifecycle. Using differential affinity purifications, quantitative mass spectrometry, and next generation RNA sequencing, we have characterized the proteins and nucleic acids associated with distinctive, enzymatically active L1 macromolecular complexes. Among them, we describe a cytoplasmic intermediate that we hypothesize to be the canonical ORF1p/ORF2p/L1-RNA-containing RNP, and we describe a nuclear population containing ORF2p, but lacking ORF1p, which likely contains host factors participating in target-primed reverse transcription.

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Lysosomal damage-induced secretion of macromolecular complexes in HeLa cells by label-free proteomics

Project description:HeLa cells were treated with LLOMe to induce lysosomal membrane permeabilization. Conditioned media were collected, and secreted macromolecular complexes were enriched by ultracentrifugation at 100,000 × g. The protein content was analyzed by label-free, non-quantitative LC-MS/MS to identify components of stress-induced extracellular protein assemblies.

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Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles

Project description:We explored the RNA binding properties of LINE-1 ORF1p, both free and in the L1 RNP, using a recently developed photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation technique (PAR-CLIP) to comprehensively identify ORF1p binding sites in the transcriptome of human cells (HEK293T). Our results show that ORF1p binds to a wide range of cellular mRNAs, with an enrichment for binding at the 3’ UTR. Our data also show that ORF1p binds very strongly with retrotransposable RNA, i.e., L1, Alu and SVA. PAR-CLIP analysis of L1 RNPs and free ORF1p RNA binding profiles, comparison to HuR RNA binding profile

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Project description:Dynamic regulation of epigenetic states relies on complex macromolecular interactions such as at the protein-protein and protein-DNA level. It remains an unsolved question how H3K27me3, the hallmark histone modification for facultative heterochromatin, and its writer Polycomb repressive complex 2 (PRC2) are spatiotemporally regulated during development. Here we engineered separation-of-function mutants to surgically dissect the roles of individual macromolecular interactions required for PRC2 function. We show that Polycomb-mediated silencing is precisely regulated by the dynamic interactions among the PRC2 core complex, its accessory proteins, DNA sequences, and other histone modifications. Combining CRISPR-mediated engineering of separation-of-function mutants, human stem cell differentiation models, next-generation sequencing approaches, and reconstituted biochemical assays, we identified distinct regulatory functions of these macromolecular interactions on epigenetic repression in human pluripotent stem cells and cardiac differentiation. Disruption of key interactions led to distinct and opposing effects on cardiomyocyte differentiation, suggesting their highly specified roles in cell fate determination. Together, these results reveal the importance of individual macromolecular interactions at the center of PRC2 controlling epigenetic repression.

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