Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism

Better Bounds on the Accommodating Ratio for the Seat Reservation Problem

In a recent paper [J. Boyar and K.S. Larsen, The seat reservation problem, Algorithmica, 25(1999), 403--417], the seat reservation problem was investigated. It was shown that for the unit price problem, where all tickets have the same price, all "fair" algorithms are at least 1/2-accommodating, while no fair algorithm is more than (4/5 + O(1/k))-accommodating, where k is the number of stations the train travels. In this paper, we design a more dextrous adversary ..

Experimental analysis of some factors affecting parental expenditure and investment in Gasterosteus aculeatus (Gasterosteidae)

Parental investment is the cost of providing parental care. Parental investment was measured in the paternal stickleback, Gasterosteus aculeatus, by comparing future survival (measured indirectly as energy content of the body) and growth of parental and non-parental males. The time taken by parental males to renest was also measured. Male energy content was unaffected after a single parental cycle and no difference in growth rate was detected. Re-nesting was delayed. The effect of stressing parental males by exposing them to potential predators of their offspring and reducing their ration level, was also investigated. Stressed males had reduced energy contents in comparison with unstressed parental males. The time taken by stressed males to re-nest was unaffected. Males on low rations did not fan significantly less than well-fed males. Males exposed to brood predators did fan significantly less than parental males not exposed to brood predators, but the former did spend nearly 60% of their time attacking the predators when present.</p