DNA Specificity Determinants Associate with Distinct Transcription Factor Functions

To elucidate how genomic sequences build transcriptional control networks, we need to understand the connection between DNA sequence and transcription factor binding and function. Binding predictions based solely on consensus predictions are limited, because a single factor can use degenerate sequence motifs and because related transcription factors often prefer identical sequences. The ETS family transcription factor, ETS1, exemplifies these challenges. Unexpected, redundant occupancy of ETS1 and other ETS proteins is observed at promoters of housekeeping genes in T cells due to common sequence preferences and the presence of strong consensus motifs. However, ETS1 exhibits a specific function in T cell activation; thus, unique transcriptional targets are predicted. To uncover the sequence motifs that mediate specific functions of ETS1, a genome-wide approach, chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq), identified both promoter and enhancer binding events in Jurkat T cells. A comparison with DNase I sensitivity both validated the dataset and also improved accuracy. Redundant occupancy of ETS1 with the ETS protein GABPA occurred primarily in promoters of housekeeping genes, whereas ETS1 specific occupancy occurred in the enhancers of T cell–specific genes. Two routes to ETS1 specificity were identified: an intrinsic preference of ETS1 for a variant of the ETS family consensus sequence and the presence of a composite sequence that can support cooperative binding with a RUNX transcription factor. Genome-wide occupancy of RUNX factors corroborated the importance of this partnership. Furthermore, genome-wide occupancy of co-activator CBP indicated tight co-localization with ETS1 at specific enhancers, but not redundant promoters. The distinct sequences associated with redundant versus specific ETS1 occupancy were predictive of promoter or enhancer location and the ontology of nearby genes. These findings demonstrate that diversity of DNA binding motifs may enable variable transcription factor function at different genomic sites

Local perspectives of the ability of HIA stakeholder engagement to capture and reflect factors that impact Alaska Native health

Background: Health impact assessment (HIA) is a process used to inform planning and decision making in a range of sectors by identifying potential positive and negative health effects of proposed projects, programs, or policies. Stakeholder engagement is an integral component of HIA and requires careful consideration of participant diversity and appropriate methodologies. Ensuring that the engagement process is able to capture and address Indigenous worldviews and definitions of health is important where Indigenous populations are impacted, particularly in northern regions experiencing increases in natural resource development activities on Indigenous lands. Objective: Investigate local participant perspectives of an HIA of a proposed Alaska coal mine, with a focus on the ability of the HIA process to capture, reflect, and address health concerns communicated by Alaska Native participants. Design: A qualitative approach guided by semi-structured interviews with purposeful sampling to select key informants who participated in the coal mine HIA stakeholder engagement process. Results: Qualitative data identified three key themes as important from the perspective of Alaska Native participants in the Alaska coal mine HIA stakeholder engagement process: (i) the inability of the engagement process to recognize an Indigenous way of sharing or gathering information; (ii) the lack of recognizing traditional knowledge and its use for identifying health impacts and status; and (iii) the inability of the engagement process to register the relationship Indigenous people have with the environment in which they live. Issues of trust in the HIA process and of the HIA findings were expressed within each theme. Conclusions: Recommendations derived from the research identify the need to acknowledge and incorporate the history of colonialism and assimilation policies in an HIA when assessing health impacts of resource development on or near Indigenous lands. These historical contexts must be included in baseline conditions to understand particular vulnerabilities and potential health risks and impacts. Further, HIA practitioners should recognize the range of definitions for “health” and demonstrate this recognition throughout the stakeholder engagement process, as well as in the HIA recommendations and suggested mitigations

Seroprevalence of Trypanosoma cruzi infection in three rural communities in Guatemala Seroprevalencia de infección por Trypanosoma cruzi en tres comunidades rurales de Guatemala

A systematic, house-based serological survey for Trypanosoma cruzi seroreactivity was conducted in three contiguous communities in Olopa municipality, Chiquimula Department, Guatemala. Blood samples from a total of 292 individuals in 63 households were examined by enzyme-linked immunosorbent assay. The seropositive rate ranged from 0% to 20.8% for the three communities, with a mean of 15.1%. Log-linear models showed that seroprevalence was significantly related to age (P < 0.005) but not to sex. However, when the age group with the lowest prevalence (1-9 years) was excluded from the analysis, age was not a significant factor (P = 0.55). Data from a stratified sample collected at the same time were combined with those of the systematic sample to analyze the relationship between seropositivity and possible explanatory variables. Log-linear models, based on 586 individuals in 129 households from the two surveys, revealed a significant positive association between seropositivity and thatched roofs (P = 0.01).<br>Una encuesta serológica sistemática y domiciliaria para detectar serorreactividad a Trypanosoma cruzi se llevó a cabo en tres comunidades contiguas de la municipalidad de Olapa, en el departamento de Chiquimula, Guatemala. Se examinaron mediante inmunoadsorción enzimática muestras de sangre obtenidas de un total de 292 habitantes que residían en 63 viviendas. La tasa de seropositividad varió de 0 a 20,8% en las tres comunidades y tuvo una media de 15,1%. Los modelos logarítmico-lineales mostraron una asociación significativa entre la seroprevalencia y la edad (P < 0,05), pero no entre aquella y el sexo. No obstante, cuando el grupo de edad que tuvo la seroprevalencia más baja (el de 1 a 9 años) se excluyó del análisis, la edad dejó de ser un factor significativo (P = 0,55). Datos obtenidos de una muestra estratificada recogida simultáneamente se combinaron con los de la muestra sistemática con el fin de analizar la relación entre la seropositividad y algunas variables que podrían ser explicativas. Los modelos logarítmico-lineales, aplicados en 586 habitantes de 129 viviendas incluidas en ambas encuestas, revelaron una asociación positiva significativa entre la seropositividad y la presencia de techo de paja (P = 0,01)

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function