Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA248259 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Comparison of CoV 3'UTR cis-acting element interactome to link the cis-acting element to coronavirus replication by LC-MS/MS. The study is performed by in vitro-transcribed RNA followed by RNA-protein pull-down assay. In addition, the concluded results are decided by comparison between the biological processes derived from analysis of interactome and the replication efficiency.
2024-08-07 | MSV000095535 | MassIVE
Project description:Comparison of CoV 3'UTR cis-acting element interactome to link the cis-acting element to coronavirus replication by LC-MS/MS. The study is performed by in vitro-transcribed RNA followed by RNA-protein pull-down assay. In addition, the concluded results are decided by comparison between the biological processes derived from analysis of interactome and the replication efficiency.
2024-08-06 | MSV000095522 | MassIVE
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:Here, using ChIP-seq, we define the NF-κB cistrome which is comprised of 31,070 cis-acting binding sites responsive to LPS-induced signaling. In addition, we demonstrate that the transcriptional repressor B-cell lymphoma 6 (Bcl-6) regulates nearly a third of the Tlr4-regulated transcriptome and that 90% of the Bcl-6 cistrome is collapsed following Tlr4 activation. Bcl-6 deficient macrophages are acutely hypersensitive to lipopolysaccharide (LPS) and, using comparative ChIP-seq analyses, we find that the Bcl-6 and NF-κB cistromes intersect, within nucleosomal distance, at nearly half of Bcl-6 binding sites in stimulated macrophages to promote opposing epigenetic modifications of the local chromatin. These results reveal a genomic strategy for controlling the innate immune response in which repressive and inductive cistromes establish a dynamic balance between macrophage quiescence and activation via epigenetically marked cis-regulatory elements. keywords: Genome-wide location analysis Identification of BCL6 and NFkB binding sites in unstimulated and LPS-stimulated primary bone-marrow derived macrophages.
2010-11-24 | E-GEOD-16723 | biostudies-arrayexpress
Project description:By targeting disruption of SNF2, male gametocytes lost capacity for exflagellation completely, and transcripts of male-specific genes decreased significantly, whereas female gametocytes display normal phenotype. ChIP-seq analysis showed that gSNF2 molecules were divided into two groups according to motif sequences on the genome they were recruited: those recruited to female-specific cis-acting element, TGTRNNYACA, and those recruited to a five base motif, YGTCT, that exists on the upstream of male-specific genes. Studies using a male-specific dynein promoter demonstrated that the five-base motif is a male-specific cis-acting element. ATAC-seq analysis demonstrated that the disruption of gSNF prohibits creation of a nucleosome-free region (NFR) on the promoter of male-specific target genes, and the reduction rates of NFR correlated well with those of target gene expression. These results suggests that global changes of chromatin structure by gSNF2 occur in initial step of male development. The present study also suggested that male-specific gene expression is under the control of a single kind of male-specific cis-acting element thus a single sequence-specific TF. This is a first report genome-wide changes of nucleosome positioning by a remodeling complex play a role in stage conversion of this parasite.
2022-08-05 | GSE198587 | GEO
Project description:By targeting disruption of SNF2, male gametocytes lost capacity for exflagellation completely, and transcripts of male-specific genes decreased significantly, whereas female gametocytes display normal phenotype. ChIP-seq analysis showed that gSNF2 molecules were divided into two groups according to motif sequences on the genome they were recruited: those recruited to female-specific cis-acting element, TGTRNNYACA, and those recruited to a five base motif, YGTCT, that exists on the upstream of male-specific genes. Studies using a male-specific dynein promoter demonstrated that the five-base motif is a male-specific cis-acting element. ATAC-seq analysis demonstrated that the disruption of gSNF prohibits creation of a nucleosome-free region (NFR) on the promoter of male-specific target genes, and the reduction rates of NFR correlated well with those of target gene expression. These results suggests that global changes of chromatin structure by gSNF2 occur in initial step of male development. The present study also suggested that male-specific gene expression is under the control of a single kind of male-specific cis-acting element thus a single sequence-specific TF. This is a first report genome-wide changes of nucleosome positioning by a remodeling complex play a role in stage conversion of this parasite.
2022-08-05 | GSE198585 | GEO
Project description:By targeting disruption of SNF2, male gametocytes lost capacity for exflagellation completely, and transcripts of male-specific genes decreased significantly, whereas female gametocytes display normal phenotype. ChIP-seq analysis showed that gSNF2 molecules were divided into two groups according to motif sequences on the genome they were recruited: those recruited to female-specific cis-acting element, TGTRNNYACA, and those recruited to a five base motif, YGTCT, that exists on the upstream of male-specific genes. Studies using a male-specific dynein promoter demonstrated that the five-base motif is a male-specific cis-acting element. ATAC-seq analysis demonstrated that the disruption of gSNF prohibits creation of a nucleosome-free region (NFR) on the promoter of male-specific target genes, and the reduction rates of NFR correlated well with those of target gene expression. These results suggests that global changes of chromatin structure by gSNF2 occur in initial step of male development. The present study also suggested that male-specific gene expression is under the control of a single kind of male-specific cis-acting element thus a single sequence-specific TF. This is a first report genome-wide changes of nucleosome positioning by a remodeling complex play a role in stage conversion of this parasite.
2022-08-05 | GSE198586 | GEO