Functional Consequences of Subunit Diversity in RNA Polymerases II and V
Cell Reports, 2012 Multisubunit RNA polymerases IV and V (Pol IV and Pol V) evolved as specialized forms of Pol II that mediate RNA-directed DNA methylation (RdDM) and transcriptional silencing of transposons, viruses, and endogenous repeats in plants.
Ek Han Tan +3 more
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The RNA silencing enzyme RNA polymerase v is required for plant immunity. [PDF]
PLoS Genetics, 2011 RNA-directed DNA methylation (RdDM) is an epigenetic control mechanism driven by small interfering RNAs (siRNAs) that influence gene function. In plants, little is known of the involvement of the RdDM pathway in regulating traits related to immune ...
Ana López +4 more
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Use of Site-Specifically Tethered Chemical Nucleases to Study Macromolecular Reactions
Biological Procedures Online, 2003 During a complex macromolecular reaction multiple changes in molecular conformation and interactions with ligands may occur. X-ray crystallography may provide only a limited set of snapshots of these changes.
Mukherjee Srabani, Sousa Rui
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Primer Extension Reactions for the PCR- based α- complementation Assay
Bio-Protocol, 2015 The PCR- based- α- complementation assay is an effective technique to measure the fidelity of polymerases, especially RNA-dependent RNA polymerases (RDRP) and Reverse Transcriptases (RT). It has been successfully employed to determine the fidelity of the
Vasudevan Achuthan, Jeffrey DeStefano
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Computational Investigations on Polymerase Actions in Gene Transcription and Replication Combining Physical Modeling and Atomistic Simulations [PDF]
Chin. Phys. B Vol. 25, No. 1 (2016) 018706, 2015 Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication fidelity through the non-equilibrium enzymatic cycles.
arxiv +1 more source
Cotranscriptional kinetic folding of RNA secondary structures including pseudoknots [PDF]
Journal of Computational Biology, 2021, 2020 Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence, however, has shown that RNA folds concurrently with its elongation.
arxiv +1 more source
Stochastic resetting in backtrack recovery by RNA polymerases [PDF]
Phys. Rev. E 93, 062411 (2016), 2016 Transcription is a key process in gene expression, in which RNA polymerases produce a complementary RNA copy from a DNA template. RNA polymerization is frequently interrupted by backtracking, a process in which polymerases perform a random walk along the DNA template.
arxiv +1 more source
Mechanical Properties of Transcription [PDF]
Phys. Rev. Lett. 118, 268101 (2017), 2016 Recently the physical characterization of a number of biological processes has proven indispensable for a full understanding of natural phenomena. One such example is the mechanical properties of transcription, which have been shown to have significant effects in gene expression.
arxiv +1 more source
PLoS Biology, 2015 Small RNA pathways act at the front line of defence against transposable elements across the Eukaryota. In animals, Piwi interacting small RNAs (piRNAs) are a crucial arm of this defence.
Peter Sarkies +14 more
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Uncovering the effect of RNA polymerase steric interactions on gene expression noise: analytical distributions of nascent and mature RNA numbers [PDF]
arXiv, 2023 The telegraph model is the standard model of stochastic gene expression, which can be solved exactly to obtain the distribution of mature RNA numbers per cell. A modification of this model also leads to an analytical distribution of the nascent RNA numbers. These solutions are routinely used for the analysis of single-cell data, including the inference
arxiv