Ultraconserved elements in Rhabditidae and Panagrolaimidae
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PROVIDER: PRJEB90354 | ENA |
REPOSITORIES: ENA
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Project description:The manuscript by D. Licastro and colleagues “Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved sequence elements” presents an overview of experimental and computational approaches employed by the authors to perform a multi-facet characterization of ultraconserved elements (UCEs). The authors present an interesting analysis where they investigate the transcription of UCEs in mouse development at different stages by conductin an microarray experiment. Some of these results are further verified by RT-PCR. 12 Samples, 4 groups 3 samples per group.
2010-06-16 | E-GEOD-19371 | biostudies-arrayexpress
Project description:The manuscript by D. Licastro and colleagues “Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved sequence elements” presents an overview of experimental and computational approaches employed by the authors to perform a multi-facet characterization of ultraconserved elements (UCEs). The authors present an interesting analysis where they investigate the transcription of UCEs in mouse development at different stages by conductin an microarray experiment. Some of these results are further verified by RT-PCR.
2010-06-16 | GSE19371 | GEO
Project description:Non-coding ultraconserved regions showing hundreds of consecutive bases of perfect evolutionary sequence conservation across mammalian genomes have intrigued biologists in the decade since they were first described. While many of these sequences are known to represent distant-acting enhancers, initial deletion studies in mice showed that their loss had no obvious impact on viability or fertility. To explore the discrepancy between extraordinary evolutionary constraint and an apparent lack of phenotypes when deleted in vivo, we used genome editing to create an expanded series of knockout mice lacking individual or combinations of ultraconserved brain enhancers near the essential neuronal transcription factor Arx. While the loss of any single or pair of ultraconserved enhancers resulted in viable and fertile mice, detailed phenotyping revealed neurological or growth abnormalities in nearly all cases, including substantial alterations of neuron populations and abnormalities of the dentate gyrus. Our results demonstrate the functional importance of ultraconserved enhancers and highlight that extreme sequence conservation may result from evolutionary selection against fitness deficits that appear subtle in a laboratory setting.
2018-01-17 | GSE100384 | GEO
Project description:Analysis of the transcriptional changes in the forebrain resulting from the loss of ultraconserved enhancers near Arx gene.
2018-01-17 | GSE97321 | GEO
Project description:In this study, we identified the dysregulated ultraconserved regions (UCRs) in Non-small-Cell Lung Cancer patients. We measured the expression profile of UCRs in 18 paired frozen tumor and adjacent non-tumor lung, by microarray analysis. This analysis is performed to identify the most significant dysregulated T-UCRs in tumor compared to the near non-cancerous lung tissue.
2021-12-07 | E-MTAB-11010 | biostudies-arrayexpress
Project description: Not available
| S-EPMC2596485 | biostudies-literature
Project description:Introns have expanded dramatically during evolution, in which ultraconserved RNA motifs may play essential regulatory roles. Sharing the sequence with the actual 5' splice sites (5'SSs), pseudo-5'SSs are widespread in introns but never spliced. We searched homologous introns and identified eight ultraconserved pseudo-5'SSs (UCP-5'SSs). The most conserved one resides in the animal ENOX1/Enox genes that are involved in plasma electron transport and cell enlargement. In vivo deletion of this 9-nt UCP-5'SS in Drosophila results in a significantly enlarged ovary and increased fecundity. We demonstrate that this UCP-5'SS is a silencer for alternative splicing (AS) regulation of an upstream ultraconserved essential exon through interaction with the U1 snRNP-core proteins. The AS changes are observed in all the tested Drosophila mutants from the dTOR and Insulin-like pathways. Remarkably, loss of this UCP-5'SS significantly mitigates the changes. Conservatively, multiple-source human cells treated with the mTOR/Insulin pathway inhibitors also change the AS and specifically increase the translation of U1-70K. This study reveals an ultraconserved regulatory network in which a short intronic RNA motif functions as a sensor of TOR-related pathways during ovarian development.
2025-12-31 | GSE270522 | GEO
Project description:We investigate the role of a long ncRNA transcribed from an ultraconserved region (T-UCR) in the control of post-transcriptional pri-miRNA processing. The regulation is based on complementarity between the lower stem region in pri-miR-195 transcript and the ultraconserved sequence in Uc.283+A, which prevents pri-miRNA cleavage by Drosha. Mutation of the site in either RNA molecule uncouples regulation in vivo and in vitro. We propose a model in which lower-stem strand invasion by Uc.283+A impairs microprocessor recognition and efficient pri-miRNA cropping. In this work, we characterize a new role for Uc.283+A as a direct interactor and regulator of pri-miRNA-195 maturation at the level of Drosha processing. We combine cellular assays with in vitro biochemical analyses to reveal the first case of RNA-directed downregulation of miRNA biogenesis by a T-UCR
2014-05-01 | GSE56841 | GEO
Project description:Ultraconserved regions (UCRs) are segments of the human genome located in both intragenic and intergenic regions that are highly conserved in orthologous regions of the human, rat, and mouse genomes. Their transcriptional products, called T-UCRs, compose a new category of long noncoding RNA (lncRNAs). Most importantly, recent data suggests that T-UCRs are altered at the transcriptional level in human tumorigenesis and the aberrant T-UCRs expression profiles can be used to differentiate human cancer types. MicroRNAs and other types of non-codingRNAs have been shown to greatly contribute at biological function of cancer and are increasingly being used to help prognosticate patients with bladder cancer, this is not yet the case for T-UCRs. The presence and the roles for T-UCRs across different species is largely unknown rendering their investigation particularly important in our understanding the biology of cancer. Using genome-wide profiling, we identified 293 T-UCRs that were dysregulated in bladder tumor (n = 24) but not normal bladder tissues (n = 17) samples. The greatest change in expression was for the ultraconserved element 8 (uc.8+), whose expression significantly increased (6.7 fold; P = 0.001) in bladder cancer tissues. Dysregulated expression was validated for several T-UCRs in 60 patients and 16 healthy donors. We found that T-UCR 8+ acts as a natural decoy RNA for miR-596 in patients and bladder cancer cells. As a result, expression of matrix metallopeptidase 9, a direct target of this microRNA, was upregulated, thereby promoting cancer cell growth, migration, and invasion. We also observed that mir-596 mediated a network of interactions among uc.8+, uc.339+, uc.195+, and uc.388+, which appeared to be dysregulated in bladder tumors. Transcribed ultraconserved ncRNAs provide an evolutionarily-conserved regulatory layer that modulates miRNA levels, and opens up the possibility for the development of useful markers for diagnosis and prognosis, as well as for the development of new RNA-based cancer therapies.
2016-03-23 | GSE68594 | GEO