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

ESTABLISHMENT OF IMMORTALIZED HUMAN HEPATIC STELLATE SCAVENGER CELLS TO DEVELOP BIOARTIFICIAL LIVERS

BACKGROUND: Maintenance of liver-specific functions has been shown to be stabilized by co-cultivation of hepatocytes with hepatic stellate cells (HSC). Because the limited lifespan of human HSC is a major hurdle to their use, the authors report here the amplification of human HSC populations in vitro by retroviral transfer of human telomerase reverse transcriptase (hTERT). METHODS: Human HSC strain LI 90 cells were transduced with a retroviral vector SSR#197 expressing hTERT and green fluorescent protein (GFP) cDNA flanked by a pair of loxP. TWNT-1, one of SSR#197-immortalized HSC, was characterized. Differentiated liver functions were evaluated in an immortalized human hepatocyte NKNT-3-TWNT-1 co-culture system. RESULTS: TWNT-1 cells showed differential functions of HSC, including uptake of acetylated low-density lipoproteins and synthesis of collagen type I and hepatocyte growth factor. Efficient excision of the retrovirally transferred hTERT and GFP cDNAs was achieved by TAT-mediated expression of the Cre recombinase and subsequent GFP-negative cell sorting. When co-cultured with TWNT-1 cells, NKNT-3 increased protein expression of the detoxifying cytochrome P450-associated protein isoenzymes 3A4 and 2C9 and urea synthesis. CONCLUSIONS: TWNT-1 cells could be valuable in the study of integrated liver functions and contribute to the optimization of liver cell therapies and bioartificial livers

Space environment of an asteroid preserved on micrograins returned by the Hayabusa spacecraft

Records of micrometeorite collisions at down to submicron scales were discovered on dust grains recovered from near-Earth asteroid 25143 (Itokawa). Because the grains were sampled from very near the surface of the asteroid, by the Hayabusa spacecraft, their surfaces reflect the low-gravity space environment influencing the physical nature of the asteroid exterior. The space environment was examined by description of grain surfaces and asteroidal scenes were reconstructed. Chemical and O isotope compositions of five lithic grains, with diameters near 50 μm, indicate that the uppermost layer of the rubble-pile-textured Itokawa is largely composed of equilibrated LL-ordinary-chondrite-like material with superimposed effects of collisions. The surfaces of the grains are dominated by fractures, and the fracture planes contain not only sub-μm-sized craters but also a large number of sub-μm- to several-μm-sized adhered particles, some of the latter composed of glass. The size distribution and chemical compositions of the adhered particles, together with the occurrences of the sub-μm-sized craters, suggest formation by hypervelocity collisions of micrometeorites at down to nm scales, a process expected in the physically hostile environment at an asteroid’s surface. We describe impact-related phenomena, ranging in scale from 10-9 to 104 meters, demonstrating the central role played by impact processes in the long-term evolution of planetary bodies. Impact appears to be an important process shaping the exteriors of not only large planetary bodies, such as the moon, but also low-gravity bodies such as asteroids