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.

Although it is generally accepted that cellular differentiation requires changes to transcriptional networks, dynamic regulation of promoters and enhancers at specific sets of genes has not been previously studied en masse. Exploiting the fact that active promoters and enhancers are transcribed, we simultaneously measured their activity in 19 human and 14 mouse time courses covering a wide range of cell types and biological stimuli. Enhancer RNAs, then messenger RNAs encoding transcription factors, dominated the earliest responses. Binding sites for key lineage transcription factors were simultaneously overrepresented in enhancers and promoters active in each cellular system. Our data support a highly generalizable model in which enhancer transcription is the earliest event in successive waves of transcriptional change during cellular differentiation or activation.

Autophagy is an intracellular process for vacuolar bulk degradation of cytoplasmic components. The molecular machinery responsible for yeast and mammalian autophagy has recently begun to be elucidated at the cellular level, but the role that autophagy plays at the organismal level has yet to be determined. In this study, a genome-wide search revealed significant conservation between yeast and plant autophagy genes. Twenty-five plant genes that are homologous to 12 yeast genes essential for autophagy were discovered. We identified an Arabidopsis mutant carrying a T-DNA insertion within AtAPG9, which is the only ortholog of yeast Apg9 in Arabidopsis (atapg9-1). AtAPG9 is transcribed in every wild-type organ tested but not in the atapg9-1 mutant. Under nitrogen or carbon-starvation conditions, chlorosis was observed earlier in atapg9-1 cotyledons and rosette leaves compared with wild-type plants. Furthermore, atapg9-1 exhibited a reduction in seed set when nitrogen starved. Even under nutrient growth conditions, bolting and natural leaf senescence were accelerated in atapg9-1 plants. Senescence-associated genes SEN1 and YSL4 were up-regulated in atapg9-1 before induction of senescence, unlike in wild type. All of these phenotypes were complemented by the expression of wild-type AtAPG9 in atapg9-1 plants. These results imply that autophagy is required for maintenance of the cellular viability under nutrient-limited conditions and for efficient nutrient use as a whole plant.Protein degradation is an important process in almost every facet of plant physiology and development. In plants, three major degradation pathways have been described: the ubiquitin-dependent pathway and the chloroplast and the vacuolar degradation pathways (for review, see Vierstra, 1996). Among these pathways, vacuolar degradation is assumed to be involved in bulk protein degradation by virtue of the resident proteases in the vacuole. Two types of vacuoles have been described in plants: the storage vacuole and the lytic central vacuole (for review, see Marty, 1999). However, there may be additional vacuole types that await discovery. Protein storage vacuoles are often found in seed tissues and accumulate proteins that are mobilized and used as the main nutrient resource for germination. Most cells in vegetative tissues have a large central vacuole, containing a wide range of proteases in an acidic environment. Substrate proteins must be transported and sequestered into this vacuole for degradation.Autophagy, a ubiquitous eukaryotic process, is responsible for this sequestration. Two types of autophagy have been described, namely macroautophagy and microautophagy (for review, see Klionsky and Ohsumi, 1999). In yeast macroautophagy, a portion of the cytoplasm is first enclosed by a doublemembrane structure, the autophagosome. The outer membrane of the autophagosome then fuses to the vacuolar membrane, so that its inner membrane structure, the autophagic body, is delivered into the vacuolar lumen. The contents of the autophagic body are then digest...

Blood vessels and nerves are complex, branched structures that share a high degree of anatomical similarity. Guidance of vessels and nerves has to be exquisitely regulated to ensure proper wiring of both systems. Several regulators of axon guidance have been identified and some of these are also expressed in endothelial cells; however, the extent to which their guidance functions are conserved in the vascular system is still incompletely understood. We show here that the repulsive netrin receptor UNC5B is expressed by endothelial tip cells of the vascular system. Disruption of the Unc5b gene in mice, or of Unc5b or netrin-1a in zebrafish, leads to aberrant extension of endothelial tip cell filopodia, excessive vessel branching and abnormal navigation. Netrin-1 causes endothelial filopodial retraction, but only when UNC5B is present. Thus, UNC5B functions as a repulsive netrin receptor in endothelial cells controlling morphogenesis of the vascular system.

IntroductionMultipotential mesenchymal stem/progenitor cells (MSCs) can be induced to differentiate into bone, adipose, cartilage, muscle, and endothelium if these cells are cultured under specific permissive conditions [1,2]. In rodents, a specific type of MSC (termed multipotent adult progenitor cell) can be isolated from bone marrow (BM) and contributes to most somatic cell types when injected into early blastocysts at the single-cell level [3] , kidney, lung, and liver). These cells are also present in the fetal environment (e.g., blood, liver, BM, and kidney). However, MSCs are a rare population in these tissues. Here we tried to identify cells with MSC-like potency in human placenta. We isolated adherent cells from trypsin-digested term placentas and established two clones by limiting dilution. We examined these cells for morphology, surface markers, gene expression patterns, and differentiation potential and found that they expressed several stem cell markers, hematopoietic/ endothelial cell-related genes, and organ-specific genes, as determined by reverse transcription-polymerase chain reaction and fluorescence-activated cell sorter analysis. They also showed osteogenic and adipogenic differentiation potentials under appropriate conditions. We suggest that placenta-derived cells have multilineage differentiation potential similar to MSCs in terms of morphology, cell-surface antigen expression, and gene expression patterns. The placenta may prove to be a useful source of MSCs.

In contrast to other cereals, typical barley cultivars have caryopses with adhering hulls at maturity, known as covered (hulled) barley. However, a few barley cultivars are a free-threshing variant called naked (hulless) barley. The covered/naked caryopsis is controlled by a single locus (nud) on chromosome arm 7HL. On the basis of positional cloning, we concluded that an ethylene response factor (ERF) family transcription factor gene controls the covered/naked caryopsis phenotype. This conclusion was validated by (i) fixation of the 17-kb deletion harboring the ERF gene among all 100 naked cultivars studied; (ii) two x-ray-induced nud alleles with a DNA lesion at a different site, each affecting the putative functional motif; and (iii) gene expression strictly localized to the testa. Available results indicate the monophyletic origin of naked barley. The Nud gene has homology to the Arabidopsis WIN1/SHN1 transcription factor gene, whose deduced function is control of a lipid biosynthesis pathway. Staining with a lipophilic dye (Sudan black B) detected a lipid layer on the pericarp epidermis only in covered barley. We infer that, in covered barley, the contact of the caryopsis surface, overlaid with lipids to the inner side of the hull, generates organ adhesion.caryopsis ͉ domestication ͉ epidermis ͉ ethylene response factor ͉ grass B arley (Hordeum vulgare L.) is the world's fourth most important cereal crop behind wheat, rice, and maize. A particular botanical feature of domesticated barley is that most cultivars have covered (hulled) caryopses in which the hull (outer lemma and inner palea) is firmly adherent to the pericarp epidermis at maturity; but a few cultivars are of a free-threshing variant called naked (hulless) barley (Fig. 1). No other Poaceae (grass) family crops show such hull-caryopsis adhesion. Both caryopsis types of barley have agronomic value and are used for different purposes. Covered barley is mainly used as an animal feed and for brewing. The hull of covered barley protects embryos from damage during mechanical harvest, and it also provides a filtration medium in separation of fermentable extract (wort) during malt processing (1). In contrast, naked barley is preferred for human food, because extensive pearling to remove the hull is unnecessary. Now that healthy effects of the soluble-fiber-rich barley products have been officially approved (2, 3), consumers' current interest in nutrition might boost the status of barley as human food.Easy processing of edible part can be a primary character of selection during domestication of a food crop (4, 5). Consequently, the naked caryopsis is considered a key domestication character in barley (5-8). The wild progenitor of barley, H. vulgare subsp. spontaneum, has covered grains. The covered grain is therefore considered adaptive in the wild: the hulls protect the caryopses from various biotic and abiotic stresses, and the awn attached to the distal end of the lemma facilitates seed dispersal and burial (9). According to archeological evidence (4)...

Because androgen function is regulated by its receptors, androgen-androgen receptor signaling is crucial for regulating spermatogenesis. Androgen is mainly testosterone secreted by testis. Based on the results of early studies in goats, the administration of melatonin over an extended period of time increases steroid production, but the underlying mechanism remains unclear. Here, we report the expression of the melatonin membrane receptors MT1 and MT2 and the retinoic acid receptor-related orphan receptor-alpha (RORα) in the goat testis. An in vitro differentiation system using spermatogonial stem cells (SSCs) cultured in the presence of testicular somatic cells was able to support the formation of sperm-like cells with a single flagellum. The addition of 10-7 M melatonin to the in vitro culture system increased RORα expression and considerably improved the efficiency of haploid cell differentiation, and the addition of the RORα agonist CGP52608 significantly increased the testosterone concentration and expression of GATA binding factor 4 (GATA-4). Furthermore, inhibitors of melatonin membrane receptors and a RORα antagonist (T0901317) also led to a considerable reduction in the efficiency of haploid spermatid formation, which was coupled with the suppression of GATA-4 expression. Based on these results, RORα may play a crucial role in enhancing melatonin-regulated GATA-4 transcription and steroid hormone synthesis in the goat spermatogonial stem cell differentiation culture system.

Brassinosteroids (BRs) play important roles throughout plant growth and development. Despite the importance of clarifying the mechanism of BR-related growth regulation in cereal crops, BR-related cereal mutants have been identified only in rice (Oryza sativa). We previously found that semidwarf barley (Hordeum vulgare) accessions carrying the "uzu" gene, called "uzu" barley in Japan, are non-responding for brassinolide (BL). We then performed chemical and molecular analyses to clarify the mechanisms of uzu dwarfism using isogenic line pairs of uzu gene. The response of the uzu line to BL was significantly lower than that of its corresponding normal line. Measurement of BRs showed that the uzu line accumulates BRs, similar to known BR-insensitive mutants. The marker synteny of rice and barley chromosomes suggests that the uzu gene may be homologous to rice D61, a rice homolog of Arabidopsis BR-insensitive 1 (BRI1), encoding a BR-receptor protein.A barley homolog of BRI1, HvBRI1, was isolated by using degenerate primers. A comparison of HvBRI1 sequences in uzu and normal barley varieties showed that the uzu phenotype is correlated with a single nucleotide substitution. This substitution results in an amino acid change at a highly conserved residue in the kinase domain of the BR-receptor protein.These results may indicate that uzu dwarfism is caused by the missense mutation in HvBRI1. The uzu gene is being introduced into all hull-less barley cultivars in Japan as an effective dwarf gene for practical use, and this is the first report about an agronomically important mutation related to BRs.Brassinolide (BL) is a firstly identified plant steroid hormone, isolated from rape (Brassica napus) pollen (Grove et al., 1979). Diverse plant species have been found to contain BL and a variety of structural analogs, called brassinosteroids (BRs). With their characteristic physiological effect on plant growth and development, BRs should be included as essential plant hormones, along with GAs, auxins, cytokinins (CKs), abscisic acid (ABA), and ethylene. The effect of BRs on germination, elongation growth, flowering, and sex expressions of plants have been reported, and various application techniques have been tested in the greenhouse and in the field (Yokota, 1999). BR applications have often increased grain and vegetable yields. Plants treated with BRs also acquired resistance to or tolerance against such stresses as cold, drought, salt, disease, and herbicide. In field tests, however, BR effects were unstable and not replicable. The biological activity of these BRs disappeared rapidly due to deactivation and was influenced by environmental conditions (Kamuro and Takatsuto, 1999).In addition to studies on agricultural applications of BRs, BR physiology has also been studied (Yokota, 1997; Altmann, 1999; Bishop and Yokota, 2001). After many BR-deficient and -insensitive mutants were identified in Arabidopsis, BR biosynthesis and signaling have been rapidly clarified. BR biosynthesis mutants such as deetiolated 2 (det2; Chory et...