Exp Eye Res. By utilizing a rod photoreceptor-specific chromatin signature, and the RefSeq database of established transcription start sites, we have identified essentially all known rod photoreceptor genes as well as a group of novel genes that have a high probability of being expressed in rod photoreceptors. Dive into the research topics of 'Identification and prediction of alternative transcription start sites that generate rod photoreceptor-specific transcripts from ubiquitously expressed genes'. With the aim to improve the computational prediction accuracy, we … This suggests that, during retina development, some genes use ATSS to regulate cell type and temporal specificity, effectively generating a rod transcript from otherwise ubiquitously expressed genes. The frequency of CpG islands is much higher than the background frequency of this dinucleotide. By utilizing a rod photoreceptor-specific chromatin signature, and the RefSeq database of established transcription start sites, we have identified essentially all known rod photoreceptor genes as well as a group of novel genes that have a high probability of being expressed in rod photoreceptors. Computitional prediction of transcription-factor binding site locations. Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq. Identification and prediction of alternative transcription start sites that generate rod photoreceptor-specific transcripts from ubiquitously expressed genes. Prediction of a transcription start site is one of the many active research areas in bioinformatics. This suggests that, during retina development, some genes use ATSS to regulate cell type and temporal specificity, effectively generating a rod transcript from otherwise ubiquitously expressed genes. Prevention and treatment information (HHS). 5.4. Identification and prediction of alternative transcription start sites that generate rod photoreceptor-specific transcripts from ubiquitously expressed genes By Evgenya Y. Popova, Anna C. Salzberg, Chen Yang, Samuel Shao-Min Zhang and Colin J. Barnstable The ASTD alternative transcript collection is built through three successive stages of transcript-to-genome mapping corresponding to splicing (AltSplice), polyadenylation (AltTrans and AltPAS) and transcriptional start site (AltTSS) variant prediction. Biological conformation of the use of some of these TSS suggests that this method will be valuable for exploring the range of transcriptional complexity in many tissues. Confirmation of relationship between epigenetic signatures and gene expression. H3K4me2 epigenetic signature predicts tissue and cell specificity of TSS. Helps also to find alternative transcription start sites. doi: Zhang X, Chen MH, Wu X, Kodani A, Fan J, Doan R, et al. Comparison of mouse and human genome-wide data indicates that most of these alternate TSS appear to be present in both species, indicating that our approach can be useful for identification of regulatory regions that might play a role in human retinal disease. Fig 5. Evidence for such a mechanism is supported by mouse transgenic experiments in which ablation of binding sites for the ubiquitous transcription factor Sp1 was shown to facilitate de novo methylation of the APRT promoter CGI [44] , [45] . 2C) . While good performance was achieved by the method on Escherichia coli and Clostridium thermocellum, … Mali RS, Zhang X, Hoerauf W, Doyle D, Devitt J, Loffreda-Wren J, Mitton KP. in DOAJ. Confirmation of relationship between epigenetic…. Fig 8. Would you like email updates of new search results? Alternative transcription start (ATS) and alternative polyadenylation (APA) create alternative RNA isoforms and modulate many aspects of RNA expression and protein production. 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