High coverage single cell RNA-Seq of pooled MCF7 and HEK293-ZRT cells to discover expression patterns of the LINE1 retrotransposon
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ABSTRACT:
PROVIDER: PRJNA812019 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18230168.fastq.gz | Fastqsanger.gz |
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Project description:We performed high coverage scRNA-Seq on a pool of MCF7 and HEK293-ZRT cells in a 9:1 ratio, respectively, using a total of 853 cells in this experiment. Detection of mobile element expression at the locus-specific level requires high sequencing depth. Here, MCF7 and HEK293-ZRT single cells have been sequenced to a sufficient level to quanitfy LINE1 expression in single cells and compare expression differences between individual cells. Single-cell RNA sequencing was carried out on individual cells using the 10X Genomics Chromium™ Single Cell 3’ Library & Gel Bead Kit v3 and 150 cycle kit. 750 cells were targeted for sequencing.
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Project description:Transposable elements make up nearly half of mammalian genomes, yet are generally described as ‘junk DNA’ or genome parasites. The LINE1 retrotransposon is the most abundant class and is thought to be deleterious for cells, but it is paradoxically expressed at high levels during early development. Here, we report that LINE1 plays essential roles in mouse embryonic stem (ES) cells and pre-implantation embryos. In ES cells, LINE1 acts as a nuclear RNA scaffold that recruits Nucleolin and Kap1/Trim28 to repress Dux, the master activator of a gene expression program specific to the 2-cell stage. In parallel, LINE1 RNA mediates binding of Nucleolin and Kap1 to rDNA, thereby promoting rRNA synthesis and ES cell self-renewal. In embryos, LINE1 RNA is required for silencing of Dux, proper synthesis of rRNA and exit from the 2-cell stage. These results reveal an essential partnership between nuclear LINE1 RNA and chromatin factors in the regulation of transcription, developmental potency and ES cell self-renewal.
2018-06-30 | GSE100938 | GEO
Project description:Transposable elements make up nearly half of mammalian genomes, yet are generally described as ‘junk DNA’ or genome parasites. The LINE1 retrotransposon is the most abundant class and is thought to be deleterious for cells, but it is paradoxically expressed at high levels during early development. Here, we report that LINE1 plays essential roles in mouse embryonic stem (ES) cells and pre-implantation embryos. In ES cells, LINE1 acts as a nuclear RNA scaffold that recruits Nucleolin and Kap1/Trim28 to repress Dux, the master activator of a gene expression program specific to the 2-cell stage. In parallel, LINE1 RNA mediates binding of Nucleolin and Kap1 to rDNA, thereby promoting rRNA synthesis and ES cell self-renewal. In embryos, LINE1 RNA is required for silencing of Dux, proper synthesis of rRNA and exit from the 2-cell stage. These results reveal an essential partnership between nuclear LINE1 RNA and chromatin factors in the regulation of transcription, developmental potency and ES cell self-renewal.
2018-06-30 | GSE100937 | GEO
Project description:Transposable elements make up nearly half of mammalian genomes, yet are generally described as ‘junk DNA’ or genome parasites. The LINE1 retrotransposon is the most abundant class and is thought to be deleterious for cells, but it is paradoxically expressed at high levels during early development. Here, we report that LINE1 plays essential roles in mouse embryonic stem (ES) cells and pre-implantation embryos. In ES cells, LINE1 acts as a nuclear RNA scaffold that recruits Nucleolin and Kap1/Trim28 to repress Dux, the master activator of a gene expression program specific to the 2-cell stage. In parallel, LINE1 RNA mediates binding of Nucleolin and Kap1 to rDNA, thereby promoting rRNA synthesis and ES cell self-renewal. In embryos, LINE1 RNA is required for silencing of Dux, proper synthesis of rRNA and exit from the 2-cell stage. These results reveal an essential partnership between nuclear LINE1 RNA and chromatin factors in the regulation of transcription, developmental potency and ES cell self-renewal.
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Project description:RNAseq analysis of Hep3B cells upon overexpression of LINE1 retrotransposon encoded protein L1orf1p
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Project description:The nuclear exosome targeting (NEXT) complex is responsible for recruiting RNA exosomes to degrade specific nuclear RNAs in mammalian cells. However, its function in mammalian development remains unknown. Here, we found that the depletion of a central factor of the NEXT complex, Zcchc8, resulted in mouse developmental defects, a shortened life span and infertility. Zcchc8-deficient embryonic stem cells (ESCs) exhibited proliferation abnormalities and reduced developmental potencies. Interestingly, we found that retrotransposon elements, especially LINE1 RNAs, are targeted and degraded by Zcchc8 in ESCs. We subsequently demonstrated that Zcchc8-depleted oocytes show defects in meiotic maturation and early embryo development. Moreover, the sustained expression of higher levels of LINE1 RNA was also detected in maternal Zcchc8-depleted oocytes and Zcchc8-deficient embryos, which can further increase chromatin accessibility. Collectively, our study uncovers the important role of Zcchc8 in the degradation of LINE1 transcripts in early embryos and ESCs at the posttranscriptional level.
2019-11-07 | GSE127790 | GEO
Project description:Transposable elements (TEs) are mobile sequences that engender widespread mutations and thus are a major hazard that must be silenced. The most abundant active class of TEs in mammalian genomes is long interspersed element class 1 (LINE1). Here, we report that LINE1 transposition is suppressed in the male germline by transcription factors encoded by a rapidly evolving X-linked homeobox gene cluster. LINE1 transposition is repressed by many members of this RHOX transcription factor family, including those with different patterns of expression during spermatogenesis. One family member—RHOX10—suppresses LINE1 transposition during fetal development in vivo when the germline would otherwise be susceptible to LINE1 activation because of epigenetic reprogramming. We provide evidence that RHOX10 suppresses LINE transposition by inducing Piwil2, which encodes a key component in the Piwi-interacting (pi) RNA pathway that protects against TEs. The ability of RHOX transcription factors to suppress LINE1 is conserved in humans, but is lost in RHOXF2 mutants from several infertile human patients, raising the possibility that loss of RHOXF2 causes human infertility by allowing uncontrolled LINE1 expression in the germline. Together, our results support a model in which the Rhox gene cluster is in an evolutionary arms race with TEs, resulting in expansion of the Rhox gene cluster to suppress TEs in different biological contexts.
2021-05-20 | GSE160600 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE32180: MIWI catalysis is required for piRNA amplification-independent LINE1 transposon silencing [microarray] GSE32184: MIWI catalysis is required for piRNA amplification-independent LINE1 transposon silencing [deep sequencing] Refer to individual Series
2011-11-30 | E-GEOD-32183 | biostudies-arrayexpress
Project description:N6-methyladenosine (m6A) is the most abundant internal modification on mammalian messenger RNA (mRNA). It is installed by a writer complex and can be reversed by erasers such as the fat mass and obesity-associated protein (FTO). Despite extensive research, the primary physiological substrates of FTO in mammalian tissues and development remain elusive. Here, we show that FTO mediates m6A demethylation of long-interspersed element-1 (LINE1) RNA in mouse embryonic stem cells (mESCs), regulating LINE1 RNA abundance and the local chromatin state, which in turn modulates transcription of LINE1-containing genes. FTO-mediated LINE1 RNA m6A demethylation also plays regulatory roles in shaping chromatin state and gene expression during mouse oocyte and embryonic development. Our results suggest broad effects of LINE1 RNA m6A demethylation by FTO in mammals.
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Project description:DiSCoVer-PIWet-Campylobacter
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