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Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE43801 | GEO | 2013/05/21

SECONDARY ACCESSION(S): PRJNA187456

REPOSITORIES: GEO

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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

2013-05-21 | E-GEOD-43801 | biostudies-arrayexpress

Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles.

Project description: Not available

| S-EPMC3749862 | biostudies-literature

Dissolution of RNA condensates by the embryonic stem cell protein L1TD1 [CLIP-seq]

Project description:L1TD1 is a cytoplasmic RNA-binding protein that is specifically expressed in pluripotent stem cells and, unlike its mouse paralogue, is essential for the maintenance of stemness in human cells. Although L1TD1 is the only known domesticated gene from a LINE-1 (L1) retroelement, the functional legacy from its ancestral protein, ORF1p of L1, and the novelty are so far unknown. Here, we determined RNAs associated with L1TD1 and found that, like ORF1p, L1TD1 binds L1 RNAs, localizes to high-density ribonucleoprotein (RNP) condensates, and increases L1 retrotransposition. Unexpectedly, L1TD1 enhanced the translation of a subset of mRNAs enriched in the condensates. In HeLa cells, ectopically expressed L1TD1 facilitated the dissolution of stress granules and granules formed by pathological mutations of TDP-43 and FUS. The glutamate-rich domain and the ORF1-homology domain facilitated dispersal of the RNPs and induced autophagy, respectively. These results provide insights into how L1TD1 regulates gene expression in pluripotent stem cells. We propose that the ability of L1TD1 to dissolve stress granules may provide novel opportunities for treatments of neurodegenerative diseases caused by disturbed stress granule dynamics.

2023-04-26 | GSE227855 | GEO

Dissolution of RNA condensates by the embryonic stem cell protein L1TD1 [RNA-seq]

2023-04-26 | GSE227854 | GEO

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.

2023-05-26 | PXD039425 | Pride

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.

2018-01-17 | PXD008542 | Pride

TDP-43 safeguards the embryo genome from L1 retrotransposition

Project description:We report that TAR DNA binding protein 43 (TDP-43), mutations in which constitute a major risk factor for amyotrophic lateral sclerosis (ALS), inhibits L1 retrotransposition in mouse embryonic stem cells (mESCs) and preimplantation embryos. Knockdown of TDP-43 resulted in massive genomic L1 expansion and impaired cell growth in preimplantation embryos and ESCs. Functional analysis demonstrated that TDP-43 interacts with L1 open reading frame 1 protein (L1 ORF1p) to mediate genomic protection, and loss of this interaction led to de-repression of L1 retrotransposition. Our results identify TDP-43 as a guardian of the embryonic genome by protecting it from massive L1 retrotransposition.

2023-01-04 | GSE199197 | GEO

Human LINE-1 ORF1p complex LC-MS/MS

Project description:Host proteins regulate LINE-1 (L1) retrotransposition. Here, we use immunoprecipitation followed by liquid chromatography-tandem mass spectrometry to identify proteins that associate with the L1 ORF1-encoded protein (ORF1p) in ribonucleoprotein particles.

2023-03-11 | PXD038851 | Pride

EGAS00001002907-2-sc-20190130 - samples

Project description:Variants and WGS data for Gardner et al. 2018 (biorxiv 471375). One VCF each for Alu, L1, and SVA. Flat text file and WGS for processed pseudogenes.

| EGAD00001004586 | EGA

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