Cis-acting lnc-eRNA SEELA1/2 in leukemia progression
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ABSTRACT:
PROVIDER: PRJNA659934 | ENA |
REPOSITORIES: ENA
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Project description:Long non-coding enhancer RNAs (lnc-eRNAs) are a subset of stable eRNAs identified from the annotated lncRNAs. They might serve as enhancer activity-related therapeutic targets in cancer; however, the epigenetic activation mechanisms and the function of lnc-eRNAs in cancer initiation and progression remain largely unknown.Here, by genome-wide screening we firstly identified a set of lncRNAs as lnc-eRNAs according to the epigenetic signatures of enhancers.To demonstrate the functional roles of lnc-eRNAs, two newly identified lnc-eRNAs, SEELA1 and SEELA2, were chosen for further studies.Further studies showed that SEELA1/2-SERINC2 axis regulated cancer metabolism, such as sphingolipid synthesis, to affect the leukemia progression.
2020-08-29 | GSE157040 | GEO
Project description: Not available
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Project description:Primary piRNAs in Drosophila ovarian somatic cells arise from piRNA cluster transcripts and the 3′ UTRs of a subset of mRNAs, including Traffic jam (Tj) mRNA. However, it is unclear how these RNAs are determined as primary piRNA sources. Here, we identify a cis-acting 100-nt fragment in the Tj 3′ UTR that is sufficient for producing artificial piRNAs from unintegrated DNA. These artificial piRNAs were effective in endogenous gene transcriptional silencing. Yb, a core component of primary piRNA biogenesis center Yb bodies, directly bound the Tj-cis-element. Disruption of this interaction markedly reduced piRNA production. Thus, Yb is the trans-acting partner of the Tj-cis-element. Yb-CLIP revealed that Yb-binding correlated with somatic piRNA production but Tj-cis-element downstream sequences produced few artificial piRNAs. Thus, Yb determines primary piRNA sources by two modes of action; primary binding to cis-elements to specify substrates, and secondary binding to downstream regions to increase diversity in piRNA populations. HITS-CLIP of Yb in OSCs (Ovarian Somatic Cells) depleted for tj cis-element, and small RNA sequencing of Piwi-piRNAs in OSCs depleted for tj cis-element.
2015-06-05 | E-GEOD-69625 | biostudies-arrayexpress
Project description:Primary piRNAs in Drosophila ovarian somatic cells arise from piRNA cluster transcripts and the 3′ UTRs of a subset of mRNAs, including Traffic jam (Tj) mRNA. However, it is unclear how these RNAs are determined as primary piRNA sources. Here, we identify a cis-acting 100-nt fragment in the Tj 3′ UTR that is sufficient for producing artificial piRNAs from unintegrated DNA. These artificial piRNAs were effective in endogenous gene transcriptional silencing. Yb, a core component of primary piRNA biogenesis center Yb bodies, directly bound the Tj-cis-element. Disruption of this interaction markedly reduced piRNA production. Thus, Yb is the trans-acting partner of the Tj-cis-element. Yb-CLIP revealed that Yb-binding correlated with somatic piRNA production but Tj-cis-element downstream sequences produced few artificial piRNAs. Thus, Yb determines primary piRNA sources by two modes of action; primary binding to cis-elements to specify substrates, and secondary binding to downstream regions to increase diversity in piRNA populations.
2015-06-05 | GSE69625 | GEO
Project description:We assessed whether human transcripts expressed in an aneuploid mouse that carries human chromosome 21 (HsChr21) are spliced in a human-specific or mouse-specific fashion. In almost all cases, human-specific alternative splicing is maintained in the mouse nucleus. Species-specific splicing therefore appears to be primarily directed by cis-acting elements, rather than changes in the levels or activities of trans-acting factors. Approximately 485 million Illumina 50-nt sequence reads were generated for brain and liver tissues from normal human, Tc0 (wildtype) mouse and Tc1 mouse strains. Sequence reads were mapped to splice junctions and %in levels were estimated.
2012-12-01 | E-GEOD-31454 | biostudies-arrayexpress
Project description:We assessed whether human transcripts expressed in an aneuploid mouse that carries human chromosome 21 (HsChr21) are spliced in a human-specific or mouse-specific fashion. In almost all cases, human-specific alternative splicing is maintained in the mouse nucleus. Species-specific splicing therefore appears to be primarily directed by cis-acting elements, rather than changes in the levels or activities of trans-acting factors.
2012-12-01 | GSE31454 | GEO
Project description:Endogenous retroviruses (ERVs) are transposable elements that cause host genome instability and usually play deleterious roles such as tumorigenesis. Recent advances also suggest that this 'enemy within' may encode viral mimic to induce antiviral immune responses through viral sensors. Here, through whole genome RNA-seq we discovered a full-length ERV-derived long non-coding RNA (lncRNA), designated lnc-EPAV (ERV-derived lncRNA positively regulates antiviral responses), as a positive regulator of NF-κB signaling. Lnc-EPAV expression was rapidly up-regulated by viral RNA mimic or RNA viruses to facilitate the expression of RELA, an NF-κB subunit that plays a critical role in antiviral responses. In turn, RELA promoted the transcription of lnc-EPAV to form a positive feedback loop. Transcriptome analysis of lnc-EPAV-silenced macrophages, combined with gain- and loss-of-function experiments, showed that lnc-EPAV was critical for induction of type I interferon (IFN) and inflammatory cytokine expression by RNA viruses. Consistently, lnc-EPAV-deficient mice exhibited reduced expression of type I IFNs, and consequently increased viral loads and mortality following lethal RNA virus infection. Mechanistically, lnc-EPAV promoted expression of RELA by competitively binding to and displacing SFPQ, a transcriptional repressor of RELA. The binding between ERV-derived RNAs and SFPQ also existed in human cells. Altogether, our work demonstrates an alternative mechanism by which ERVs regulate antiviral immune responses.
2018-11-07 | PXD011577 | Pride
Project description:Many genes harbour multiple transcriptional enhancers that act concomitantly to achieve robust and precise spatial-temporal expression. In vertebrates, however, the mechanisms underlying cooperation between cis-acting elements are poorly documented. The mouse gene Krox20 encodes a transcription factor required for the specification of two segments (rhombomeres) of the developing hindbrain. In rhombomere 3, Krox20 is subject to positive feedback, governed by enhancer A, which is directly bound by the KROX20 protein, whereas another element, C, distant from 70 kb, was supposed to be only required for initiation of expression. Here, using both enhancer knock-outs and investigations of chromatin organisation, we show that element C possesses a dual activity: besides its classical enhancer function, it is also permanently required in cis to potentiate element A autoregulatory activity, by increasing its chromatin accessibility. This work uncovers a novel, asymmetrical, long-range mode of cooperation between cis-acting elements that might be essential to avoid promiscuous activation of positive autoregulatory elements.
2017-07-18 | GSE94715 | GEO
Project description:Many genes harbour multiple transcriptional enhancers that act concomitantly to achieve robust and precise spatial-temporal expression. In vertebrates, however, the mechanisms underlying cooperation between cis-acting elements are poorly documented. The mouse gene Krox20 encodes a transcription factor required for the specification of two segments (rhombomeres) of the developing hindbrain. In rhombomere 3, Krox20 is subject to positive feedback, governed by enhancer A, which is directly bound by the KROX20 protein, whereas another element, C, distant from 70 kb, was supposed to be only required for initiation of expression. Here, using both enhancer knock-outs and investigations of chromatin organisation, we show that element C possesses a dual activity: besides its classical enhancer function, it is also permanently required in cis to potentiate element A autoregulatory activity, by increasing its chromatin accessibility. This work uncovers a novel, asymmetrical, long-range mode of cooperation between cis-acting elements that might be essential to avoid promiscuous activation of positive autoregulatory elements.
2017-07-18 | GSE94131 | GEO
Project description:Many genes harbour multiple transcriptional enhancers that act concomitantly to achieve robust and precise spatial-temporal expression. In vertebrates, however, the mechanisms underlying cooperation between cis-acting elements are poorly documented. The mouse gene Krox20 encodes a transcription factor required for the specification of two segments (rhombomeres) of the developing hindbrain. In rhombomere 3, Krox20 is subject to positive feedback, governed by enhancer A, which is directly bound by the KROX20 protein, whereas another element, C, distant from 70 kb, was supposed to be only required for initiation of expression. Here, using both enhancer knock-outs and investigations of chromatin organisation, we show that element C possesses a dual activity: besides its classical enhancer function, it is also permanently required in cis to potentiate element A autoregulatory activity, by increasing its chromatin accessibility. This work uncovers a novel, asymmetrical, long-range mode of cooperation between cis-acting elements that might be essential to avoid promiscuous activation of positive autoregulatory elements.
2017-07-18 | GSE97102 | GEO