109 research outputs found
Unbiased, Genome-Wide In Vivo Mapping of Transcriptional Regulatory Elements Reveals Sex Differences in Chromatin Structure Associated with Sex-Specific Liver Gene Expression
No full textWe have used a simple and efficient method to identify condition-specific transcriptional regulatory sites in vivo to help elucidate the molecular basis of sex-related differences in transcription, which are widespread in mammalian tissues and affect normal physiology, drug response, inflammation, and disease. To systematically uncover transcriptional regulators responsible for these differences, we used DNase hypersensitivity analysis coupled with high-throughput sequencing to produce condition-specific maps of regulatory sites in male and female mouse livers and in livers of male mice feminized by continuous infusion of growth hormone (GH). We identified 71,264 hypersensitive sites, with 1,284 showing robust sex-related differences. Continuous GH infusion suppressed the vast majority of male-specific sites and induced a subset of female-specific sites in male livers. We also identified broad genomic regions (up to ~100 kb) showing sex-dependent hypersensitivity and similar patterns of GH responses. We found a strong association of sex-specific sites with sex-specific transcription; however, a majority of sex-specific sites were >100 kb from sex-specific genes. By analyzing sequence motifs within regulatory regions, we identified two known regulators of liver sexual dimorphism and several new candidates for further investigation. This approach can readily be applied to mapping condition-specific regulatory sites in mammalian tissues under a wide variety of physiological conditions.National Institutes of Health (U.S) ( DK33765)National Institutes of Health (U.S) (grant 577 5 P42 ES07381
Polyglutamine Expanded Huntingtin Dramatically Alters the Genome-Wide Binding of HSF1
Get PDFIn Huntington's disease (HD), polyglutamine expansions in the huntingtin (Htt) protein cause subtle changes in cellular functions that, over-time, lead to neurodegeneration and death. Studies have indicated that activation of the heat shock response can reduce many of the effects of mutant Htt in disease models, suggesting that the heat shock response is impaired in the disease. To understand the basis for this impairment, we have used genome-wide chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) to examine the effects of mutant Htt on the master regulator of the heat shock response, HSF1. We find that, under normal conditions, HSF1 function is highly similar in cells carrying either wild-type or mutant Htt. However, polyQ-expanded Htt severely blunts the HSF1-mediated stress response. Surprisingly, we find that the HSF1 targets most affected upon stress are not directly associated with proteostasis, but with cytoskeletal binding, focal adhesion and GTPase activity. Our data raise the intriguing hypothesis that the accumulated damage from life-long impairment in these stress responses may contribute significantly to the etiology of Huntington's disease.National Institutes of Health (U.S.) (Grant R24 DK-090963)National Institutes of Health (U.S.) (Grant R01-GM089903)National Institutes of Health (U.S.) (Grant P30-ES002109)National Science Foundation (U.S.) (Award DB1-0821391
Isolated hydramnios at term gestation and the occurrence of peripartum complications
No full textObjective: To determine if hydramnios at term gestation is an independent risk factor for poor pregnancy outcome and perinatal death. Study design: The study population consisted of 60 702 patients with singleton gestation who delivered at term (>37 weeks). Patients were classified into two groups according to the presence or the absence of hydramnios. Hydramnios was diagnosed in the presence of an amniotic fluid index greater than 25 cm or of a maximum vertical pocket of amniotic fluid of at least 8 cm or by subjective assessment. Logistic regression analysis was used to evaluate the unique contribution of hydramnios to fetal death and to perinatal and maternal morbidity. Results: The prevalence of hydramnios was 1211/60702 (2%). Patients with hydramnios had a higher incidence of complications than those with a normal amount of amniotic fluid: cesarean section (22.8 vs. 8.5%, P<0.01), antepartum death (0.6 vs. 0.2%, P<0.005), postpartum death (2.8 vs. 0.4%, P<0.01), abruptio placenta (0.9 vs, 0.3%, P<0.001), fetal distress (6.1 vs. 3.65%, P<0.0015), meconium-stained amniotic fluid (17.8 vs. 15%, P<0.001), low Apgar score at 5 min (2.95 vs. 1%, P<0.01), malpresentation (6.8 vs. 2.9%, P<0.01), clinical chorioamnionitis (0.3 vs. 0.1%, P<0.05), prolapse of cord (2.2 vs. 0.3%, P<0.01), and large-for- gestational-age infant (LGA) (23.8 vs. 8.1%, P<0.01). When adjusted for confounding variables, the presence of hydramnios remained strongly associated with perinatal mortality (odds ratio 5.5 (95% Cl 3.2-9.3)) and neonatal and maternal morbidity (odds ratios 2.1 (Cl 1.1-3.7) and 2.3 (Cl 1.9-2.7), respectively). Conclusions: (1) Hydramnios at term is an independent risk factor for perinatal death; (2) Fetal surveillance is warranted in patients with hydramnios even in the absence of other known risk factors for adverse pregnancy outcome
Recommended from our members
Evolution of low-grade glioma through intratumoral heterogeneity of the genome and epigenome
Get PDFLow-grade glioma (LGG) is a diffuse and infiltrative adult brain tumor. Due to the invasive nature of the tumor, surgical resection is rarely curative. LGG often undergo malignant progression and recur as a high-grade glioblastoma (GBM). The genomic and epigenomic landscapes of these tumors, particularly at recurrence, are understudied yet clinically important. Recurrent tumors may be driven by a distinct set of genetic and epigenetic alterations than their initial tumors, yet therapeutic decisions are often made based on profiling of initial malignancies. Here we comprehensively profiled 33 LGGs and their patient-matched recurrences, including cases with 2-6 intratumoral samples, with exome sequencing to identify somatic mutations, with the Infinium 450K array to investigate DNA methylation changes, and with RNA sequencing to measure gene expression changes. We found a wide range in the degree of evolution from initial to recurrence, in terms of both somatic mutations and DNA methylation changes. Tumors treated with the alkylating chemotherapy temozolomide (TMZ) often recurred with a hypermutation phenotype that was suggestive of therapy-driven malignant progression to GBM. Therapy-associated mutational activation of the AKT-mTOR pathway was a consistent feature of these hypermutated recurrences, which promoted a new clinical trial combining the anti-tumor activity of TMZ with an mTOR inhibitor. Recurrence as GBM was associated with aberrations to cell cycle genes through convergence of both genetic and epigenetic mechanisms. Moreover, we found that the evolutionary history of a tumor is similar whether inferred from genetic or epigenetic data, suggesting co-evolution of the genome and epigenome. Finally, we identified cases in which mutations in IDH1, which are the earliest known alteration in LGG and drive gliomagenesis, were either deleted or amplified at recurrence. Mutant IDH1 reprograms the epigenome and these recurrences showed partial reversion of these epigenomic alterations. Together, these findings highlight the heterogeneity and continual evolution of LGG and emphasize the importance of studying recurrent tumors for a more complete understanding of tumor evolution and to make more informed treatment decisions
A quantitative model of transcriptional regulation reveals the influence binding location on expression
No full textUnderstanding the mechanistic basis of transcriptional regulation has been a central focus of molecular biology since its inception. New high-throughput chromatin immunoprecipitation experiments have revealed that most regulatory proteins bind thousands of sites in mammalian genomes. However, the functional significance of these binding sites remains unclear. We present a quantitative model of transcriptional regulation that suggests the contribution of each binding site to tissue-specific gene expression depends strongly on its position relative to the transcription start site. For three cell types, we show that, by considering binding position, it is possible to predict relative expression levels between cell types with an accuracy approaching the level of agreement between different experimental platforms. Our model suggests that, for the transcription factors profiled in these cell types, a regulatory site's influence on expression falls off almost linearly with distance from the transcription start site in a 10 kilobase range. Binding to both evolutionarily conserved and non-conserved sequences contributes significantly to transcriptional regulation. Our approach also reveals the quantitative, tissue-specific role of individual proteins in activating or repressing transcription. These results suggest that regulator binding position plays a previously unappreciated role in influencing expression and blurs the classical distinction between proximal promoter and distal binding events
Direct Recruitment of Polycomb Repressive Complex 1 to Chromatin by Core Binding Transcription Factors
No full textPolycomb repressive complexes (PRCs) play key roles in developmental epigenetic regulation. Yet the mechanisms that target PRCs to specific loci in mammalian cells remain incompletely understood. In this study we show that Bmi1, a core component of Polycomb Repressive Complex 1 (PRC1), binds directly to the Runx1/CBFβ transcription factor complex. Genome-wide studies in megakaryocytic cells demonstrate significant chromatin occupancy overlap between the PRC1 core component Ring1b and Runx1/CBFβ and functional regulation of a considerable fraction of commonly bound genes. Bmi1/Ring1b and Runx1/CBFβ deficiencies generate partial phenocopies of one another in vivo. We also show that Ring1b occupies key Runx1 binding sites in primary murine thymocytes and that this occurs via PRC2-independent mechanisms. Genetic depletion of Runx1 results in reduced Ring1b binding at these sites in vivo. These findings provide evidence for site-specific PRC1 chromatin recruitment by core binding transcription factors in mammalian cells.National Institutes of Health (U.S.) (Grant U54-CA112967)National Institutes of Health (U.S.) (Grant R01-GM089903)National Science Foundation (U.S.) (Award DB1-0821391)National Institutes of Health (U.S.) (P30-ES002109
Intratumoral Heterogeneity of the Epigenome
Get PDFInvestigation into intratumoral heterogeneity (ITH) of the epigenome is in a formative stage. The patterns of tumor evolution inferred from epigenetic ITH and genetic ITH are remarkably similar, suggesting widespread co-dependency of these disparate mechanisms. The biological and clinical relevance of epigenetic ITH are becoming more apparent. Rare tumor cells with unique and reversible epigenetic states may drive drug resistance, and the degree of epigenetic ITH at diagnosis may predict patient outcome. This perspective presents these current concepts and clinical implications of epigenetic ITH, and the experimental and computational techniques at the forefront of ITH exploration
- …
