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.

This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.

Antisense transcription (transcription from the opposite strand to a protein-coding or sense strand) has been ascribed roles in gene regulation involving degradation of the corresponding sense transcripts (RNA interference), as well as gene silencing at the chromatin level. Global transcriptome analysis provides evidence that a large proportion of the genome can produce transcripts from both strands, and that antisense transcripts commonly link neighboring "genes" in complex loci into chains of linked transcriptional units. Expression profiling reveals frequent concordant regulation of sense/antisense pairs. We present experimental evidence that perturbation of an antisense RNA can alter the expression of sense messenger RNAs, suggesting that antisense transcription contributes to control of transcriptional outputs in mammals.

Peptidyl-prolyl cis-trans isomerase (PPIase) catalyses the cis-trans isomerization of proline imidic peptide bonds in oligopeptides and has been shown to accelerate the refolding of several proteins in vitro. Its activity has been detected in yeast, insects and Escherichia coli as well as in mammals, and it is though to be essential for protein folding during protein synthesis in the cell. We purified PPIase from pig kidney and found that its amino-acid sequence is identical to that reported for bovine cyclophilin, a protein known to bind the immunosuppressive drug, cyclosporin A (ref. 5). To investigate the functional relationship between PPIase and cyclophilin we examined the effect of cyclosporin A on PPIase activity and found that it was inhibitory. Thus we propose that the peptidyl-prolyl cis-trans isomerizing activity of PPIase may be involved in events, such as those occurring early in T-cell activation, that are suppressed by cyclosporin A.

We have isolated a novel liver-specific organic anion transporter, LST-1, that is expressed exclusively in the human, rat, and mouse liver. LST-1 is a new gene family located between the organic anion transporter family and prostaglandin transporter. LST-1 transports taurocholate (K m ‫؍‬ 13.6 M) in a sodium-independent manner. LST-1 also shows broad substrate specificity. It transports conjugated steroids (dehydroepiandrosterone sulfate, estradiol-17␤-glucuronide, and estrone-3-sulfate), eicosanoids (prostaglandin E 2 , thromboxane B 2 , leukotriene C 4 , leukotriene E 4 ), and thyroid hormones (thyroxine, K m ‫؍‬ 3.0 M and triiodothyronine, K m ‫؍‬ 2.7 M), reflecting hepatic multispecificity.LST-1 is probably the most important transporter in human liver for clearance of bile acids and organic anions because hepatic levels of another organic anion transporter, OATP, is very low. This is also the first report of the human molecule that transports thyroid hormones.One of the major function of the liver is the removal of various endogenous and exogenous compounds from the circulation (1, 2). This clearance process involves basolateral membrane transport systems that mediate the hepatocellular uptake of bile acids, organic anions, and organic cations (3, 4). One well studied class of substrates are the bile acids. The uptake of taurocholate is mainly mediated by the Na ϩ /taurocholate cotransporting polypeptide (ntcp) in a Na ϩ -dependent manner (5). The uptake of other bile acids (e.g. cholate) occurs predominantly via a Na ϩ -independent mechanism (2, 4). Some amount of taurocholate is also transported by the Na ϩ -independent mechanism. This Na ϩ -independent carrier system further shows a broad substrate specificity transporting conjugated steroids, cardiac glycosides, and other xenobiotics (4).Initially, the organic anion transporter (oatp) 1 family (oatp1, oatp2, oatp3) was considered to represent the Na ϩ -independent transporting mechanisms in the liver (6 -8). Subsequently, a human cDNA, termed OATP, was isolated (9). However, significant differences were found between human OATP and rat oatp family. First, although the substrate specificities were qualitatively similar, significant differences were found between human OATP-and rat oatp family-mediated initial uptake rates and apparent K m values (10, 11). Second, Northern blot analysis of the human OATP showed considerably high expression in the brain, a pattern that is different from any of the oatp family members. These findings strongly suggest the existence of a different group of organic anion transporters in human liver.Here we report the isolation of a novel human organic anion transporter, termed LST-1, which is expressed exclusively in the liver. When expressed in Xenopus oocytes, many of the functional characteristics of LST-1 were identical to the multispecific transporting mechanisms of human liver. These results suggest that LST-1 is the predominant clearance mechanism of several endogenous and exogenous substrates in human liver. MATERIALS ...