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

Posted: The Campaign Sign Landscape, Race, and Political Participation in Mississippi

Cultural landscapes offer potential insights into cultural processes. As a cultural/political landscape element, the domestic campaign sign is linked to a variety of socio-cultural and political processes. Examination of the geographical distribution of 2004 presidential election campaign signs posted throughout the town of Hattiesburg, Mississippi, illustrates that race is a factor in understanding who chooses to post signs. Historically, limitations on political participation in the South would have included use of landscape for communication, imposing a sort of metacommunicative landscape hegemony. Further, patterns of sign postings and voter turnout indicate that both activities are forms of political participation that are embraced differently by different social groups

Concise formulas for the standard errors of component loading estimates

asymptotic standard errors, principal component analysis, component loadings, rotation, information matrix, least squares,

Asymptotic biases in exploratory factor analysis and structural equation modeling

Asymptotic biases, structural equation modeling, asymptotic variances, nonnormal data, asymptotic robustness, factor analysis,