Sequence features that drive human promoter function and tissue specificity.

Promoters are important regulatory elements that contain the necessary sequence features for cells to initiate transcription. To functionally characterize a large set of human promoters, we measured the transcriptional activities of 4575 putative promoters across eight cell lines using transient transfection reporter assays. In parallel, we measured gene expression in the same cell lines and observed a significant correlation between promoter activity and endogenous gene expression (r = 0.43). As transient transfection assays directly measure the promoting effect of a defined fragment of DNA sequence, decoupled from epigenetic, chromatin, or long-range regulatory effects, we sought to predict whether a promoter was active using sequence features alone. CG dinucleotide content was highly predictive of ubiquitous promoter activity, necessitating the separation of promoters into two groups: high CG promoters, mostly ubiquitously active, and low CG promoters, mostly cell line-specific. Computational models trained on the binding potential of transcriptional factor (TF) binding motifs could predict promoter activities in both high and low CG groups: average area under the receiver operating characteristic curve (AUC) of the models was 91% and exceeded the AUC of CG content by an average of 23%. Known relationships, for example, between HNF4A and hepatocytes, were recapitulated in the corresponding cell lines, in this case the liver-derived cell line HepG2. Half of the associations between tissue-specific TFs and cell line-specific promoters were new. Our study underscores the importance of collecting functional information from complementary assays and conditions to understand biology in a systematic framework.

The DNA sequence and comparative analysis of human chromosome 5.

Chromosome 5 is one of the largest human chromosomes and contains numerous intrachromosomal duplications, yet it has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding conservation with non-mammalian vertebrates, suggesting that they are functionally constrained. In total, we compiled 177.7 million base pairs of highly accurate finished sequence containing 923 manually curated protein-coding genes including the protocadherin and interleukin gene families. We also completely sequenced versions of the large chromosome-5-specific internal duplications. These duplications are very recent evolutionary events and probably have a mechanistic role in human physiological variation, as deletions in these regions are the cause of debilitating disorders including spinal muscular atrophy.

Reducing Risks for Older Adults With an Interprofessional Community-Academic Partnership: A Case Study.

As the older adult population in the United States increases and diversifies, understanding and reducing risks for hospitalization and institutionalization can reduce burdens for this vulnerable population. Using evidence-based assessment tools to understand medical, psychosocial, pharmacologic, and functional status can aid an interprofessional team to best evaluate older adults at risk. By providing culturally competent care for a diversifying older adult demographic, attention to social determinants can improve health equity for this population. This article describes in a case study exemplar, how one such interprofessional collaborative practice program, Geriatric Outreach and Training with Care (GOT Care!) provides a comprehensive assessment for high-risk older adults, identifies and documents these risks, and shares recommendations and rationale with the primary care provider toward risk reduction and improvement of outcomes.

Suicide attempts among adolescent Mexican American students enrolled in special education classes.

Suicide is the second leading cause of death among school-aged students between the ages of 15 and 19. There is an increasing frequency of suicide and other self-destructive behaviors among Mexican American youth and students in special education classrooms for emotional and behavioral disabilities. Recognizing Mexican American youth in special education classes as a separate risk group, this study (a) identifies factors that contribute to suicide, (b) reviews the signs and characteristics associated with these factors, (c) interviews Mexican American students in special education who have either exhibited various characteristics of suicidal thoughts and/or have attempted suicide, (d) explores effective prevention programs, and (e) provides suggestions for school personnel. Interviews with five adolescent Mexican American special education students support previous research findings that depression, substance abuse, social and interpersonal conflict, family distress, and school stress are primary characteristics related to suicidal minority youth.

Political power and health inequalities in Vieques, Puerto Rico.

The relationship between political power and the various pathways to health inequalities in Vieques, Puerto Rico, is explored. The U.S. Navy used the island for 62 years for bombing and other military exercises. The article focuses on the resulting changes to the island's socioeconomic positioning and the health inequalities over six decades. Secondary data analysis of census data using a revised World Health Organization model is used to examine the relationships of political power, labor markets, employment, material deprivation, social and family networks, and health inequalities. Findings are interpreted through a social justice lens and implications suggest the use of political advocacy for social change.

An alternate HIV preventive strategy: sex scripts in media for women of color.

New cases of HIV/AIDS among women of color in the United States highlight the continuing need for the public and private sectors to develop alternate preventive strategies. The author discusses the conceptual basis for using television sex scripts to incorporate women of color relational needs (trust, romance, sexual pressure) to promote HIV risk-reduction messages through a process of association with the television storyline. Sex scripts are a source of implicit knowledge about how to behave in situations that involve sexual intimacy. The article suggests that sexual scripts prevention messages build on the agency of women through the use of power theory-that is supporting woman's self-power by participating in sexual behavioral change. Implications for sexual equality in media programming are discussed.

Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver.

To investigate the role of DNA methylation during human development, we developed Methyl-seq, a method that assays DNA methylation at more than 90,000 regions throughout the genome. Performing Methyl-seq on human embryonic stem cells (hESCs), their derivatives, and human tissues allowed us to identify several trends during hESC and in vivo liver differentiation. First, differentiation results in DNA methylation changes at a minimal number of assayed regions, both in vitro and in vivo (2%-11%). Second, in vitro hESC differentiation is characterized by both de novo methylation and demethylation, whereas in vivo fetal liver development is characterized predominantly by demethylation. Third, hESC differentiation is uniquely characterized by methylation changes specifically at H3K27me3-occupied regions, bivalent domains, and low density CpG promoters (LCPs), suggesting that these regions are more likely to be involved in transcriptional regulation during hESC differentiation. Although both H3K27me3-occupied domains and LCPs are also regions of high variability in DNA methylation state during human liver development, these regions become highly unmethylated, which is a distinct trend from that observed in hESCs. Taken together, our results indicate that hESC differentiation has a unique DNA methylation signature that may not be indicative of in vivo differentiation.

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.

Molecular interactions between protein complexes and DNA mediate essential gene-regulatory functions. Uncovering such interactions by chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-Seq) has recently become the focus of intense interest. We here introduce quantitative enrichment of sequence tags (QuEST), a powerful statistical framework based on the kernel density estimation approach, which uses ChIP-Seq data to determine positions where protein complexes contact DNA. Using QuEST, we discovered several thousand binding sites for the human transcription factors SRF, GABP and NRSF at an average resolution of about 20 base pairs. MEME motif-discovery tool-based analyses of the QuEST-identified sequences revealed DNA binding by cofactors of SRF, providing evidence that cofactor binding specificity can be obtained from ChIP-Seq data. By combining QuEST analyses with Gene Ontology (GO) annotations and expression data, we illustrate how general functions of transcription factors can be inferred.