A promoter-level mammalian expression atlas.

Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly 'housekeeping', whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research.

Correction to: Relatively frequent switching of transcription start sites during cerebellar development.

CORRECTION: The authors of the original article [1] would like to recognize the critical contribution of core members of the FANTOM5 Consortium, who played the critical role of HeliScopeCAGE sequencing experiments, quality control of tag reads and processing of the raw sequencing data.

Relatively frequent switching of transcription start sites during cerebellar development.

BACKGROUND: Alternative transcription start site (TSS) usage plays important roles in transcriptional control of mammalian gene expression. The growing interest in alternative TSSs and their role in genome diversification spawned many single-gene studies on differential usages of tissue-specific or temporal-specific alternative TSSs. However, exploration of the switching usage of alternative TSS usage on a genomic level, especially in the central nervous system, is largely lacking. RESULTS: In this study, We have prepared a unique set of time-course data for the developing cerebellum, as part of the FANTOM5 consortium ( http://fantom.gsc.riken.jp/5/ ) that uses their innovative capturing of 5' ends of all transcripts followed by Helicos next generation sequencing. We analyzed the usage of all transcription start sites (TSSs) at each time point during cerebellar development that provided information on multiple RNA isoforms that emerged from the same gene. We developed a mathematical method that systematically compares the expression of different TSSs of a gene to identify temporal crossover and non-crossover switching events. We identified 48,489 novel TSS switching events in 5433 genes during cerebellar development. This includes 9767 crossover TSS switching events in 1511 genes, where the dominant TSS shifts over time. CONCLUSIONS: We observed a relatively high prevalence of TSS switching in cerebellar development where the resulting temporally-specific gene transcripts and protein products can play important regulatory and functional roles.

edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test.

Next-generation sequencing platforms for measuring digital expression such as RNA-Seq are displacing traditional microarray-based methods in biological experiments. The detection of differentially expressed genes between groups of biological conditions has led to the development of numerous bioinformatics tools, but so far, few exploit the expanded dynamic range afforded by the new technologies. We present edgeRun, an R package that implements an unconditional exact test that is a more powerful version of the exact test in edgeR. This increase in power is especially pronounced for experiments with as few as two replicates per condition, for genes with low total expression and with large biological coefficient of variation. In comparison with a panel of other tools, edgeRun consistently captures functionally similar differentially expressed genes.

CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments.

Alternate promoter usage is an important molecular mechanism for generating RNA and protein diversity. Cap Analysis Gene Expression (CAGE) is a powerful approach for revealing the multiplicity of transcription start site (TSS) events across experiments and conditions. An understanding of the dynamics of TSS choice across these conditions requires both sensitive quantification and comparative visualization. We have developed CAGExploreR, an R package to detect and visualize changes in the use of specific TSS in wider promoter regions in the context of changes in overall gene expression when comparing different CAGE samples. These changes provide insight into the modification of transcript isoform generation and regulatory network alterations associated with cell types and conditions. CAGExploreR is based on the FANTOM5 and MPromDb promoter set definitions but can also work with user-supplied regions. The package compares multiple CAGE libraries simultaneously. Supplementary Materials describe methods in detail, and a vignette demonstrates a workflow with a real data example. AVAILABILITY AND IMPLEMENTATION: The package is freely available under the MIT license from CRAN (http://cran.r-project.org/web/packages/CAGExploreR). CONTACT: edimont@mail.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online.

The lateral brow: position in relation to age, gender, and ethnicity.

PURPOSE: Despite multiple studies regarding modes of eyebrow measurement and movement over time, the lateral aspect of the brow has been relatively ignored in the literature. Therefore, we arranged a study of the most lateral aspect of the eyebrow; in doing so, we hoped to ascertain the most practical line or angle of measurement. METHODS: In this cross-sectional study, adults age 18 years and older with no history of congenital or acquired periorbital or orbital pathology or surgery, brow tattooing or heavy plucking, phthisis, or strabismus were measured using a combination of in-office metrics and computer analysis. Subjects were asked to identify their ethnicity and country of origin. Models of age, gender, and ethnicity were created. RESULTS: One thousand twenty-four subjects were included (1,944 eyes). Measurements of nasal ala to lateral brow (NALB), lateral brow plumb line (LBPL; the vertical line between the tail of the brow and a horizontal line extending from the lateral canthus), and angle from the midbrow to the lateral brow tail showed statistically significant decline over time. The angle and LBPL varied mostly by ethnicity. The angle narrowed approximately 3° per 20 years, while the LBPL fell approximately 2.5 mm per 20 years. The NALB varied most by age and fell approximately 3 mm per 20 years. CONCLUSIONS: The lateral tail of the brow descends with age. Measurements of its location and rate of change vary between genders and within ethnic groups. Two easily measured values-NALB and LBPL-can be used for preoperative planning and postoperative documentation.

Gateways to the FANTOM5 promoter level mammalian expression atlas.

The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE. Based on manual curation of sample information and development of an ontology for sample classification, we assemble the resulting data into a centralized data resource (http://fantom.gsc.riken.jp/5/). This resource contains web-based tools and data-access points for the research community to search and extract data related to samples, genes, promoter activities, transcription factors and enhancers across the FANTOM5 atlas.

Urinary benzene biomarkers and DNA methylation in Bulgarian petrochemical workers: study findings and comparison of linear and beta regression models.

Chronic occupational exposure to benzene is associated with an increased risk of hematological malignancies such as acute myeloid leukemia (AML), but the underlying mechanisms are still unclear. The main objective of this study was to investigate the association between benzene exposure and DNA methylation, both in repeated elements and candidate genes, in a population of 158 Bulgarian petrochemical workers and 50 unexposed office workers. Exposure assessment included personal monitoring of airborne benzene at work and urinary biomarkers of benzene metabolism (S-phenylmercapturic acid [SPMA] and trans,trans-muconic acid [t,t-MA]) at the end of the work-shift. The median levels of airborne benzene, SPMA and t,t-MA in workers were 0.46 ppm, 15.5 µg/L and 711 µg/L respectively, and exposure levels were significantly lower in the controls. Repeated-element DNA methylation was measured in Alu and LINE-1, and gene-specific methylation in MAGE and p15. DNA methylation levels were not significantly different between exposed workers and controls (P>0.05). Both ordinary least squares (OLS) and beta-regression models were used to estimate benzene-methylation associations. Beta-regression showed better model specification, as reflected in improved coefficient of determination (pseudo R(2)) and Akaike's information criterion (AIC). In beta-regression, we found statistically significant reductions in LINE-1 (-0.15%, P<0.01) and p15 (-0.096%, P<0.01) mean methylation levels with each interquartile range (IQR) increase in SPMA. This study showed statistically significant but weak associations of LINE-1 and p15 hypomethylation with SPMA in Bulgarian petrochemical workers. We showed that beta-regression is more appropriate than OLS regression for fitting methylation data.