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.

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The rae28 gene (rae28), also designated as mph1, is a mammalian ortholog of the Drosophila polyhomeotic gene, a member of Polycomb group genes (PcG). rae28 constitutes PcG complex 1 for maintaining transcriptional states which have been once initiated, presumably through modulation of the chromatin structure. Hematopoietic activity was impaired in the fetal liver of rae28-deficient animals (rae28 −/−), as demonstrated by progressive reduction of hematopoietic progenitors of multilineages and poor expansion of colony forming units in spleen (CFU-S12) during embryonic development. An in vitro long-term culture-initiating cell assay suggested a reduction in hematopoietic stem cells (HSCs), which was confirmed in vivo by reconstitution experiments in lethally irradiated congenic recipient mice. The competitive repopulating units (CRUs) reflect HSCs supporting multilineage blood-cell production. CRUs were generated, whereas the number of CRUs was reduced by a factor of 20 in the rae28 − / − fetal liver. We also performed serial transplantation experiments to semiquantitatively measure self-renewal activity of CRUs in vivo. Self-renewal activity of CRUs was 15-fold decreased in rae28 − / −. Thus the compromised HSCs were presumed to reduce hematopoietic activity in the rae28 − / − fetal liver. This is the first report to suggest that rae28 has a crucial role in sustaining the activity of HSCs to maintain hematopoiesis.

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TOL plasmid in Pseudomonas putida mt-2 has a series of genes for the degradation of xylene, toluene, and their derivatives to pyruvate and acetaldehyde (or propionaldehyde). Two operons, i.e., upper operon and meta operon, play indispensable roles for the digestion of xylene derivatives: When XyIR protein recognizes xylene derivatives, another controlling gene, xyIS, is activated, which results in the activation of meta operon. Therefore, we have constructed a fusion gene between TOL plasmid and the firefly luciferase gene under the control of XyIR and the promoter of xyIS gene; i.e., by using fusions of the meta operon with promotorless luciferase expression vector from firefly, we have constructed and tested biomonitors for benzene derivatives. Bioluminescence specified by Escherichia coli (pTSN316), carrying xyIR and xyIS promoters, Ampr and luc, was measured in either a benzene derivative-saturated or o-methylbenzyl alcohol-dissolved medium both in the case of cell suspension and in the case of immobilized cell form. The utility of the biosensing system for monitoring in chemical plant drainage was demonstrated with samples supplemented with benzene derivatives. The xyIR-xyIS promoter-lux fusion carried by pTSN316 responded to a benzene-related chemical in sample solutions. Immobilization of the transformed E. coli, at one end of fiber optic, bearing firefly luciferase gene fused to TOL plasmid, has been demonstrated to fabricate a luminescent remote biomonitoring device for the protection of environmental deterioration. Due to the luminescent detection, the detection limits for benzene-related aromatics that are recognized by a binding protein (XyIR) were parts-per-million. We had already submitted a preliminary report concerning the possibility of environmental monitoring based on the above idea by using the transformed E. coli in a cell-suspended solution. This paper describes mainly a fiber-optic-based biomonitoring device for the protection of environmental deterioration.

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