Open AccessDissertation
G-quadruplexes and gene expression in Arabidopsis thaliana
TLDR
A novel method for identifying G4s is introduced, which uses a machine learning approach trained on datasets derived from the high throughput sequencing of G4 structures, to study the prevalence of PG4s in the genome of Arabidopsis thaliana, the model plant.Abstract:
G-Quadruplexes (G4s) are four stranded DNA structures which form in regions with high GC content and high GC skew. Because of the dependence of G4 structure on specific sequences, it is possible to predict putative G4s (PG4s) throughout genomic sequence. PG4s are non-uniformly distributed in genomes, with higher densities within various genic features, particularly promoters, 5’ untranslated regions (UTRs) and coding sequences (CDSs). When they form G4s, these sequences can have a variety of implications for biological processes including replication, transcription, translation and splicing. Here, we introduce a novel method for identifying PG4s, which uses a machine learning approach trained on datasets derived from the high throughput sequencing of G4 structures. We apply this and other techniques, to study the prevalence of PG4s in the genome of Arabidopsis thaliana, the model plant. Finally, we study the effect of G4 stabilisation on gene expression in Arabidopsis, using the GQuadruplex binding agent N-methyl mesoporphyrin (NMM). We identify a family of genes which are strongly downregulated by NMM, and find that they contain large numbers of PG4s in their CDSs.read more
Citations
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References
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Overexpression of RNase H partially complements the growth defect of an Escherichia coli delta topA mutant: R-loop formation is a major problem in the absence of DNA topoisomerase I.
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Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila
Yevgenia L. Khodor,Joseph Rodriguez,Katharine C. Abruzzi,Chih-Hang Anthony Tang,Michael T. Marr,Michael Rosbash +5 more
TL;DR: Intons with low cotranscriptional splicing efficiencies are present in the same primary transcript with efficiently spliced introns, indicating that splicing is intron-specific.
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Localization of a putative transcriptional regulator (atrx) at pericentromeric heterochromatin and the short arms of acrocentric chromosomes
T. L. McDowell,Richard J. Gibbons,Heidi G. Sutherland,Delia O'Rourke,Wendy A. Bickmore,Ana Pombo,H. Turley,K. Gatter,David J. Picketts,Veronica J. Buckle,Lynda Chapman,Daniela Rhodes,Douglas R. Higgs +12 more
TL;DR: The unexpected association of a putative transcriptional regulator with highly repetitive DNA provides a potential explanation for the variability in phenotype of patients with identical mutations in the ATRX gene.
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Python: the tutorial
TL;DR: Over the years, programming languages have grown more powerful, but correspondingly more complex; and while that complexity is fine and appropriate for professional programmers, it hinders and discourages beginning Computer Science students.