The past few years have witnessed an exciting increase in the richness and complexity of rna-mediated regulatory circuitries, including new types of rna-rna interaction that underlie key steps in gene expression contr...
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The past few years have witnessed an exciting increase in the richness and complexity of rna-mediated regulatory circuitries, including new types of rna-rna interaction that underlie key steps in gene expression control in an organized and probably hierarchic system to dictate final protein output. Both small (especially mirnas) and long coding (lc) and noncoding (nc) rnas contain structural domains that can sense and bind other rnas via complementary base pairing. The versatility of the interaction confers multiple roles to rna-rna hybrids, from control of rna biogenesis to competition for common targets. Here, we focus on the emerging evidence around rna networks and their impact on gene expression regulation in light of recent breakthroughs around the crosstalk between coding rnas and ncrnas.
Human embryo implantation involves a complex network of molecular signaling that is modulated by endocrine and paracrine pathways. Here, we performed studies using a unique and recently developed three-dimensional (3D...
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Human embryo implantation involves a complex network of molecular signaling that is modulated by endocrine and paracrine pathways. Here, we performed studies using a unique and recently developed three-dimensional (3D) implantation model, characterized by an endometrium-like 3D culture system and Jar cell-derived spheroids mimicking the embryo/trophoblast. The aims were to investigate the effects of 17 beta estradiol (E-2) and medroxyprogesterone acetate (MPA) on (1) the interaction between epithelial and stromal cells, and (2) the attachment and invasion of trophoblast cells. We observed that epithelial and stromal cells in the 3D culture were ER alpha(+), ER beta(+), and PR+. Decidualization was confirmed by enhanced prolactin gene expression on day 7 of E2 plus MPA treatment. An effect of epithelial cells on the decidualization of stromal cells was indicated by significantly higher levels of prolactin mrna expression in the 3D culture compared to stromal cells grown within the fibrin-agarose gel matrix. On the other hand, the relative gene expressions of E-cadherin and IL-1 beta in epithelial cells of the 3D culture under decidualization conditions significantly differed from those in epithelial cells grown over the fibrin-agarose gel matrix without stromal cells, pointing to regulation of epithelial cells by the stroma. The attachment rate of Jar spheroids to the 3D was significantly increased by E-2 plus MPA treatment. Analyses of Z-stack confocal and stained optic microscopic images demonstrated that Jar spheroids breached the epithelial cell monolayer, invaded, and were embedded into the 3D matrix in response to decidualization signals. In summary, the newly bioengineered system provides a unique model for studying interactions between the different endometrial cell compartments, via soluble-paracrine signals as well as cell-to-cell interactions, and is a useful tool to study early embryonic implantation events.
The statistics about the open reading frames, the base compositions and the properties of the predicted secondary structures have potential to address the problem of discriminating coding and noncoding transcripts. Ag...
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The statistics about the open reading frames, the base compositions and the properties of the predicted secondary structures have potential to address the problem of discriminating coding and noncoding transcripts. Again, the Next Generation Sequencing platform, rna-seq, provides us bounty of data from which expression profiles of the transcripts can be extracted which urged us adding a new set of dimension in this classification task. In this paper, we proposed CNCTDiscriminator - a coding and noncoding transcript discriminating system where we applied the integration of these four categories of features about the transcripts. The feature integration was done using both hypothesis learning and feature specific ensemble learning approaches. The CNCTDiscriminator model which was trained with composition and ORF features outperforms (precision 83.86%, recall 82.01%) other three popular methods - CPC (precision 98.31%, recall 25.95%), CPAT (precision 97.74%, recall 52.50%) and PORTRAIT (precision 84.37%, recall 73.2%) when applied to an independent benchmark dataset. However, the CNCTDiscriminator model that was trained using the ensemble approach shows comparable performance (precision 89.85%, recall 71.08%).
Genome analysis has identified a number of putative non-protein-coding transcripts that do not contain ORFs longer than 100 codons. Although evidence strongly suggests that non-coding rnas are important in a variety o...
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Genome analysis has identified a number of putative non-protein-coding transcripts that do not contain ORFs longer than 100 codons. Although evidence strongly suggests that non-coding rnas are important in a variety of biological phenomena, the discovery of small peptide-coding mrnas confirms that some transcripts that have been assumed to be non-coding actually have coding potential. Their abundance and importance in biological phenomena makes the sorting of non-coding rnas from small peptide-coding mrnas a key issue in functional genomics. However, validating the coding potential of small peptide-coding rnas is complicated, because their ORF sequences are usually too short for computational analysis. In this review, we discuss computational and experimental methods for validating the translatability of these non-coding rnas. (C) 2011 Elsevier Masson SAS. All rights reserved.
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