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.

MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libraries, with matching Cap Analysis Gene Expression (CAGE) data, from 396 human and 47 mouse RNA samples. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species. We also found that primary and mature miRNA expression levels were correlated, allowing us to use the primary miRNA measurements as a proxy for mature miRNA levels in a total of 1,829 human and 1,029 mouse CAGE libraries. We thus provide a broad atlas of miRNA expression and promoters in primary mammalian cells, establishing a foundation for detailed analysis of miRNA expression patterns and transcriptional control regions.

In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.

We investigated the effect of water-soluble alcohols (glycerol, propylene glycol, and 1-propanol) on the surfactant aggregation and its structure by phase study, surface tension measurement, small-angle X-ray scattering (SAXS) measurement, and pulsed field gradient NMR self-diffusion measurement. The phase behavior in the (water + glycerol)/C12EO8 system as a function of the glycerol content in water at constant temperature is similar to that in the water/C12EO8 system as a function of temperature, and a phase separation (clouding phenomenon) takes place at a high glycerol content. The phase separation was not observed in the other alcohol systems. However, a hexagonal liquid crystal (H1) changes to an isotropic solution (Wm) in all the systems with increasing the alcohol content. The SAXS measurement for the H1 and the Wm phases, and the self-diffusion measurement for the Wm phase suggest that the dehydration of the ethylene oxide chain takes place and the aggregates tend to grow with increasing glycerol content. On the other hand, propylene glycol or 1-propanol molecules tend to penetrate into the palisade layer of the aggregates and the micelles are downsized, and eventually they are broken into monomers with increasing the alcohol content. The critical micelle concentration measurement also supports the difference in the alcohol effects on the phase behavior in the aqueous nonionic surfactant system.