Ontology highlight
ABSTRACT:
PROVIDER: PRJNA476145 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Targeted enrichment of ultraconserved elements and exons from suboscine passerines
| PRJNA655842 | ENA
Project description:Although long non-coding RNAs (lncRNAs) encounter weaker evolutionary constraints and exhibit lower sequences conservation than coding genes, lncRNAs can conserve their features at different aspects. Here, we employed multiple approaches to systemically evaluate the conservation between human and mouse lncRNAs from various dimensions including sequences, promoter, global synteny, and local synteny, which led to the identification of 1731 conserved lncRNAs with 427 ultraconserved ones meeting multiple criteria. The conserved lncRNAs, in comparison with non-conserved ones, in generally have longer gene bodies, higher numbers of exons and transcripts, closer connections with human diseases, and are more abundant and widespread across different tissues. The transcriptional factor profile analysis revealed a significant enrichment of TF types and numbers in the promoters of conserved lncRNAs. We further identified a set of TFs that preferentially bind to conserved lncRNAs and exert stronger impacts on their expression than non-conserved lncRNAs’ expression. Thus, our study has revealed a new set of transcriptional “codes” that rules the expression of the conserved lncRNAs.
2023-03-19 | GSE156270 | GEO
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:Gene expression differences are shaped by selective pressures and contribute to phenotypic differences between species. We identified 964 copy number differences (CNDs) of conserved sequences across 3 primate species and examined their potential effects on gene expression profiles. Samples with copy number different genes had significantly different expression than samples with neutral copy number. Genes encoding regulatory molecules differed in copy number and were associated with significant expression differences. Additionally, we identified 127 CNDs which were processed pseudogenes and some of which were expressed. Furthermore, there were copy number different regulatory regions such as ultraconserved elements and long intergenic noncoding RNAs with the potential to affect expression. We postulate that CNDs of these conserved sequences fine-tune developmental pathways by altering the levels of RNA.
2012-08-01 | GSE33960 | GEO
Project description:Comparing ultraconserved elements and exons for phylogenomic analyses of Middle American cichlids: when data agree to disagree
| PRJNA690533 | ENA