Similar Datasets
Project description:Long non-coding RNAs (lncRNAs) are diverse transcription products emanating from thousands of loci in mammalian genomes, implicated in a wide array of cellular processes including transcriptional regulation, differentiation, cellular reprogramming, and many others. While a large majority of functional lncRNAs have been proposed to act in cis to their sites of transcription, an in-depth understanding of the functional features within such lncRNA loci, as well as their mechanisms of action, is currently lacking. Further insights are hindered by the heavy dependencies of observed phenotypes on the perturbation techniques employed. Here, we study Meteor, a lncRNA transcribed nearby the gene encoding for Eomes, a pleiotropic transcription factor with highly regulated spatiotemporal expression patterns throughout early development and in adult tissues. Using a wide array of perturbation techniques, we show that transcription elongation through the Meteor locus is required for Eomes activation in naive mouse embryonic stem cells (mESCs), with Meteor repression linked to a reduction in cells potentiated to differentiate to the mesoderm lineage. We further demonstrate that a distinct functional feature of the locus – namely, the underlying DNA element – is required for suppressing Eomes expression following neuronal differentiation of mESCs. Our results demonstrate the complex regulation that can be conferred by a single lncRNA locus, and emphasize the importance of careful selection of perturbation techniques for the study of lncRNA loci.
2023-04-23 | GSE223451 | GEO
Project description:Long non-coding RNAs (lncRNAs) are diverse transcription products emanating from thousands of loci in mammalian genomes, implicated in a wide array of cellular processes including transcriptional regulation, differentiation, cellular reprogramming, and many others. While a large majority of functional lncRNAs have been proposed to act in cis to their sites of transcription, an in-depth understanding of the functional features within such lncRNA loci, as well as their mechanisms of action, is currently lacking. Further insights are hindered by the heavy dependencies of observed phenotypes on the perturbation techniques employed. Here, we study Meteor, a lncRNA transcribed nearby the gene encoding for Eomes, a pleiotropic transcription factor with highly regulated spatiotemporal expression patterns throughout early development and in adult tissues. Using a wide array of perturbation techniques, we show that transcription elongation through the Meteor locus is required for Eomes activation in naive mouse embryonic stem cells (mESCs), with Meteor repression linked to a reduction in cells potentiated to differentiate to the mesoderm lineage. We further demonstrate that a distinct functional feature of the locus – namely, the underlying DNA element – is required for suppressing Eomes expression following neuronal differentiation of mESCs. Our results demonstrate the complex regulation that can be conferred by a single lncRNA locus, and emphasize the importance of careful selection of perturbation techniques for the study of lncRNA loci.
2023-04-21 | GSE223445 | GEO
Project description:Long non-coding RNAs (lncRNAs) are diverse transcription products emanating from thousands of loci in mammalian genomes, implicated in a wide array of cellular processes including transcriptional regulation, differentiation, cellular reprogramming, and many others. While a large majority of functional lncRNAs have been proposed to act in cis to their sites of transcription, an in-depth understanding of the functional features within such lncRNA loci, as well as their mechanisms of action, is currently lacking. Further insights are hindered by the heavy dependencies of observed phenotypes on the perturbation techniques employed. Here, we study Meteor, a lncRNA transcribed nearby the gene encoding for Eomes, a pleiotropic transcription factor with highly regulated spatiotemporal expression patterns throughout early development and in adult tissues. Using a wide array of perturbation techniques, we show that transcription elongation through the Meteor locus is required for Eomes activation in naive mouse embryonic stem cells (mESCs), with Meteor repression linked to a reduction in cells potentiated to differentiate to the mesoderm lineage. We further demonstrate that a distinct functional feature of the locus – namely, the underlying DNA element – is required for suppressing Eomes expression following neuronal differentiation of mESCs. Our results demonstrate the complex regulation that can be conferred by a single lncRNA locus, and emphasize the importance of careful selection of perturbation techniques for the study of lncRNA loci.
2023-04-23 | GSE223452 | GEO
Project description:Long non-coding RNAs (lncRNAs) are diverse transcription products emanating from thousands of loci in mammalian genomes, implicated in a wide array of cellular processes including transcriptional regulation, differentiation, cellular reprogramming, and many others. While a large majority of functional lncRNAs have been proposed to act in cis to their sites of transcription, an in-depth understanding of the functional features within such lncRNA loci, as well as their mechanisms of action, is currently lacking. Further insights are hindered by the heavy dependencies of observed phenotypes on the perturbation techniques employed. Here, we study Meteor, a lncRNA transcribed nearby the gene encoding for Eomes, a pleiotropic transcription factor with highly regulated spatiotemporal expression patterns throughout early development and in adult tissues. Using a wide array of perturbation techniques, we show that transcription elongation through the Meteor locus is required for Eomes activation in naive mouse embryonic stem cells (mESCs), with Meteor repression linked to a reduction in cells potentiated to differentiate to the mesoderm lineage. We further demonstrate that a distinct functional feature of the locus – namely, the underlying DNA element – is required for suppressing Eomes expression following neuronal differentiation of mESCs. Our results demonstrate the complex regulation that can be conferred by a single lncRNA locus, and emphasize the importance of careful selection of perturbation techniques for the study of lncRNA loci.
2023-04-23 | GSE223448 | GEO
Project description:Long non-coding RNAs (lncRNAs) are diverse transcription products emanating from thousands of loci in mammalian genomes, implicated in a wide array of cellular processes including transcriptional regulation, differentiation, cellular reprogramming, and many others. While a large majority of functional lncRNAs have been proposed to act in cis to their sites of transcription, an in-depth understanding of the functional features within such lncRNA loci, as well as their mechanisms of action, is currently lacking. Further insights are hindered by the heavy dependencies of observed phenotypes on the perturbation techniques employed. Here, we study Meteor, a lncRNA transcribed nearby the gene encoding for Eomes, a pleiotropic transcription factor with highly regulated spatiotemporal expression patterns throughout early development and in adult tissues. Using a wide array of perturbation techniques, we show that transcription elongation through the Meteor locus is required for Eomes activation in naive mouse embryonic stem cells (mESCs), with Meteor repression linked to a reduction in cells potentiated to differentiate to the mesoderm lineage. We further demonstrate that a distinct functional feature of the locus – namely, the underlying DNA element – is required for suppressing Eomes expression following neuronal differentiation of mESCs. Our results demonstrate the complex regulation that can be conferred by a single lncRNA locus, and emphasize the importance of careful selection of perturbation techniques for the study of lncRNA loci.
2023-04-23 | GSE223447 | GEO
Project description:Long non-coding RNAs (lncRNAs) are diverse transcription products emanating from thousands of loci in mammalian genomes, implicated in a wide array of cellular processes including transcriptional regulation, differentiation, cellular reprogramming, and many others. While a large majority of functional lncRNAs have been proposed to act in cis to their sites of transcription, an in-depth understanding of the functional features within such lncRNA loci, as well as their mechanisms of action, is currently lacking. Further insights are hindered by the heavy dependencies of observed phenotypes on the perturbation techniques employed. Here, we study Meteor, a lncRNA transcribed nearby the gene encoding for Eomes, a pleiotropic transcription factor with highly regulated spatiotemporal expression patterns throughout early development and in adult tissues. Using a wide array of perturbation techniques, we show that transcription elongation through the Meteor locus is required for Eomes activation in naive mouse embryonic stem cells (mESCs), with Meteor repression linked to a reduction in cells potentiated to differentiate to the mesoderm lineage. We further demonstrate that a distinct functional feature of the locus – namely, the underlying DNA element – is required for suppressing Eomes expression following neuronal differentiation of mESCs. Our results demonstrate the complex regulation that can be conferred by a single lncRNA locus, and emphasize the importance of careful selection of perturbation techniques for the study of lncRNA loci.
2023-04-23 | GSE223449 | GEO
Project description: Not available
| S-EPMC5769859 | biostudies-literature
Project description: Not available
| S-EPMC3488231 | biostudies-literature
Project description: Not available
| S-EPMC4830298 | biostudies-literature
Project description:The chronological lifespan (CLS) of Saccharomyces cerevisiae is defined as the number days that non-dividing cells remain viable, typically in stationary phase cultures or in water. CLS is extended by restricting glucose in the starting cultures, and is considered a form of caloric restriction (CR). Through a previous genetic screen our lab determined that deleting components of the de novo purine biosynthesis pathway also significantly increased CLS. Significant similarities in gene expression profiles between calorie restricted WT cells and a non-restricted ade4M-bM-^HM-^F mutant suggested the possibility of common gene expression biomarkers of all chronologically long lived cells that could also provide insights into general mechanisms of lifespan extension. We have identified additional growth conditions that extend CLS of WT cells, including supplementation of the media with isonicotinamide (INAM), a known sirtuin activator, or by supplementation with a concentrate collected from the expired media of a calorie restricted yeast culture, presumably due to an as yet unidentified longevity factor. Using these varied methods to extend CLS, we compared gene expression profiles in the aging cells (at day 8) to identify functionally relevant biomarkers of longevity. Nineteen genes were differentially regulated in all 4 of the long-lived populations relative to wild type. Of these 19 genes, viable haploid deletion mutants were available for 16 of them, and 12 were found to have a significant impact on CLS. Duplicate cultures were grown to saturation in SC media cultures, aged, and then harvested on day 8. The deletion mutant ade4M-bM-^HM-^F as well as WT cells treated with 25 mM isonicotinamide, calorie restricted (0.5% glucose), or treated with expired media concentrate from previously calorie restricted cultures. These 4 conditions were then compared to a wild-type (WT) strain. Total RNA was isolated and used for microarray hybridizations onto Affymetrix Yeast 2.0 Gene arrrays.
2014-09-12 | E-GEOD-61341 | biostudies-arrayexpress