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

Socio-demographic and epidemiological characteristics associated with human immunodeficiency virus type I (HIV-1) infection in HIV-1-explosed but uninfected individuals, and in HIV-1-infected patients from a southern brasilian population Características sociodemográficas e epidemiológicas associadas com a infecção pelo vírus da imunodeficiência humana tipo 1 (HIV-1) em indivíduos expostos ao HIV-1 mas não infectados e em pacientes infectados pelo HIV-1, provenientes da população da região Sul do Brasil

The ability to control human immunodeficiency virus type 1 (HIV-1) infection and progression of the disease is regulated by host and viral factors. This cross-sectional study describes the socio-demographic and epidemiological characteristics associated with HIV-1 infection in 1,061 subjects attended in Londrina and region, south of Brazil: 136 healthy individuals (Group 1), 147 HIV-1-exposed but uninfected individuals (Group 2), 161 HIV-1-infected asymptomatic patients (Group 3), and 617 patients with AIDS (Group 4). Data were obtained by a standardized questionnaire and serological tests. The age of the individuals ranged from 15.1 to 79.5 years, 54.0% and 56.1% of the Groups 3 and 4 patients, respectively, were men. The major features of groups 2, 3, and 4 were a predominance of education level up to secondary school (55.8%, 60.2% and 62.4%, respectively), sexual route of exposure (88.4%, 87.0% and 82.0%, respectively), heterosexual behavior (91.8%, 75.2% and 83.7%, respectively), and previous sexually transmitted diseases (20.4%, 32.5%, and 38.1%, respectively). The patients with AIDS showed the highest rates of seropositivity for syphilis (25.6%), of anti-HCV (22.3%), and anti-HTLV I/II obtained by two serological screening tests (6.2% and 6.8%, respectively). The results documenting the predominant characteristics for HIV-1 infection among residents of Londrina and region, could be useful for the improvement of current HIV-1 prevention, monitoring and therapeutic programs targeted at this population.<br>Este estudo transversal descreve as principais características sociodemográficas e epidemiológicas associadas com a infecção pelo HIV-1 em 1.061 indivíduos atendidos em Londrina e região, Sul do Brasil: 136 indivíduos saudáveis (Grupo 1), 147 indivíduos expostos ao HIV-1 mas não infectados (Grupo 2), 161 pacientes infectados pelo HIV-1 assintomáticos (Grupo 3) e 617 pacientes com aids (Grupo 4). Os dados foram obtidos pela aplicação de um questionário padronizado e realização de testes sorológicos. A idade dos indivíduos variou de 15,1 a 79,5 anos; 54,0% e 56,1% dos pacientes dos Grupos 3 e 4, respectivamente, eram homens. As principais características dos indivíduos dos Grupos 2, 3 e 4 foram o predomínio do nível educacional com até oito anos de escolaridade (58,8%, 60,2% e 62,4%, respectivamente), a via sexual de transmissão (88,4%, 87,0% e 82,0%, respectivamente), o comportamento heterossexual (91,8%, 75,2% e 83,7%, respectivamente) e antecedentes de doenças sexualmente transmissíveis (20,4%, 32,5% e 38,1%, respectivamente). Os pacientes com aids apresentaram os valores mais elevados de soropositividade para sífilis (25,6%), anti-HCV (22,3%) e anti-HTLV I/II em dois testes de triagem sorológica (6,2% e 6,8%, respectivamente). Os resultados documentando as características predominantes associadas com a infecção pelo HIV-1 observada nos indivíduos de Londrina e região, poderá ser útil na melhoria dos atuais programas de prevenção, monitoramento e de tratamento da infecção pelo HIV-1 dirigidos a esta população

Ultraestructura de los acinos sudoríparos de las glándulas pelvianas de Chaetophractus villosus (Mammalia, Dasypodidae) Ultrastructure of sudoriparous acini of pelvian glands of Chaetophractus villosus (Mammalia, Dasypodidae)

<abstract language="eng">The acini of pelvian glands of Chaetophractus villosus (Desmarest, 1804) consisted of an inner layer of secretory cells and an outer layer of myoepithelial cells. Secretory cells have numerous secretory vacuoles. The secretion is released by exocytosis. Myoepithelial cells have numerous myofilaments that occupy much of the cytoplasm. There is a third cell type with an extremely electron-lucent cytoplasm