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

Towards a better understanding of fashion clothing involvement

This study is concerned with consumer involvement in fashion clothing. Amidst the consumer objects that facilitate everyday life, fashion clothing is an important and meaningful object for many consumers. In the extant consumer literature few studies have attempted to examine fashion clothing involvement, particularly in terms of its causes and outcomes. This study then focuses on building a reliable nomological network to bring a greater understanding to this facet of consumer behaviour. To achieve this, materialism and gender are examined as drivers of fashionclothinginvolvement. Recreational shopper identity, ongoing information search, market mavenism, and purchase decision involvement are explored as outcomes of fashion clothing involvement. Data were gathered using an Australian Generation Y sample resulting in 200 completed questionnaires. The results support the study’s model and its hypotheses and show that materialism and gender are significant drivers of fashion clothing involvement. While also, recreational shopper identity, ongoing information search, market mavenism and purchase decision involvement are significant outcomes of fashion clothing involvement

The RgI2 (ion-pair states) van der Waals complexes

This paper is an overview of our recent experimental investigations of the RgI2 van der Waals complexes, Rg = He, Ar, Kr, performed by means of laser induced fluorescence spectroscopy, optical-optical double resonance and supersonic molecular beam techniques. Spectroscopic parameters of these complexes in the E0g+ ion-pair state, such as binding energies and several spectroscopic constants, have been determined. Most likely, the potential energy surfaces of the all RgI2(E) complexes under study present T-shaped minima. Vibrational and electronic predissociations of the RgI2(E) complexes were analyzed. Relative contributions of the different electronic predissociation channels and vibrational distributions of the decay products were determined. Possible mechanisms of the complexes decay are suggested and discussed

Standardizing Definitions of Hematopoietic Recovery, Graft Rejection, Graft Failure, Poor Graft Function, and Donor Chimerism in Allogeneic Hematopoietic Cell Transplantation : A Report on Behalf of the American Society for Transplantation and Cellular Therapy

Allogeneic hematopoietic cell transplantation (allo-HCT) is potentially curative for certain hematologic malignancies and nonmalignant diseases. The field of allo-HCT has witnessed significant advances, including broadening indications for transplantation, availability of alternative donor sources, less toxic preparative regimens, new cell manipulation techniques, and novel GVHD prevention methods, all of which have expanded the applicability of the procedure. These advances have led to clinical practice conundrums when applying traditional definitions of hematopoietic recovery, graft rejection, graft failure, poor graft function, and donor chimerism, because these may vary based on donor type, cell source, cell dose, primary disease, graft-versus-host disease (GVHD) prophylaxis, and conditioning intensity, among other variables. To address these contemporary challenges, we surveyed a panel of allo-HCT experts in an attempt to standardize these definitions. We analyzed survey responses from adult and pediatric transplantation physicians separately. Consensus was achieved for definitions of neutrophil and platelet recovery, graft rejection, graft failure, poor graft function, and donor chimerism, but not for delayed engraftment. Here we highlight the complexities associated with the management of mixed donor chimerism in malignant and nonmalignant hematologic diseases, which remains an area for future research. We recognize that there are multiple other specific, and at times complex, clinical scenarios for which clinical management must be individualized

A promoter-level mammalian expression atlas

Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly ‘housekeeping’, whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research

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

10.1038/s41467-021-23143-7Nature Communications121329