Summary Eukaryotic cells make many types of primary and processed RNAs that are found either in specific sub-cellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic sub-cellular localizations are also poorly understood. Since RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell’s regulatory capabilities are focused on its synthesis, processing, transport, modifications and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations taken together prompt to a redefinition of the concept of a gene.

Abstract. Vertical and horizontal transport mechanisms for marine oil spills are investigated using numerical model simulations. To realistically resolve the 3-D development of a spill on the ocean surface and in the water column, recently published parameterizations for the vertical mixing of oil spills are implemented in the open-source trajectory framework OpenDrift (https://doi.org/10.5281/zenodo.1300358, last access: 7 April 2018). The parameterizations include the wave entrainment of oil, two alternative formulations for the droplet size spectra, and turbulent mixing. The performance of the integrated oil spill model is evaluated by comparing model simulations with airborne observations of an oil slick. The results show that an accurate description of a chain of physical processes, in particular vertical mixing and oil weathering, is needed to represent the horizontal spreading of the oil spill. Using ensembles of simulations of hypothetic oil spills, the general drift behavior of an oil spill during the first 10 days after initial spillage is evaluated in relation to how vertical processes control the horizontal transport. Transport of oil between the surface slick and the water column is identified as a crucial component affecting the horizontal transport of oil spills. The vertical processes are shown to control differences in the drift of various types of oil and in various weather conditions.

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Abortive transcription initiation can be rate-limiting for promoter escape and therefore represents a barrier to productive gene expression. The mechanism for abortive initiation is unknown, but the amount of abortive transcript is known to vary with the composition of the initial transcribed sequence (ITS). Here, we used a thermodynamic model of translocation combined with experimental validation to investigate the relationship between ITS and promoter escape on a set of phage T5 N25 promoters. We found a strong, negative correlation between RNAP's propensity to occupy the pretranslocated state during initial transcription and the efficiency of promoter escape (r = -0.67; p < 10(-6)). This correlation was almost entirely caused by free energy changes due to variation in the RNA 3' dinucleotide sequence at each step, implying that this sequence element controls the disposition of initial transcribing complexes. We tested our model experimentally by constructing a set of novel N25-ITS promoter variants; quantitative transcription analysis again showed a strong correlation (r = -0.81; p < 10(-6)). Our results support a model in which sequence-directed bias for the pretranslocated state during scrunching results in increased backtracking, which limits the efficiency of promoter escape. This provides an answer to the long-standing issue of how sequence composition of the ITS affects promoter escape efficiency.