The inositol 1,4,5-trisphosphate (IP(3)) receptor (IP(3)R) is an intracellular IP(3)-gated Ca(2+) channel that is located on intracellular Ca(2+) stores and modulates Ca(2+) signalling. Using the yeast two-hybrid system, we screened a mouse brain cDNA library with bait constructs for mouse IP(3)R type 1 (IP(3)R1) to identify IP(3)R1-associated proteins. In this way, we found that carbonic anhydrase-related protein (CARP) is a novel IP(3)R1-binding protein. Western blot analysis revealed that CARP is expressed exclusively in Purkinje cells of the cerebellum, in which IP(3)R1 is abundantly expressed. Immunohistochemical analysis showed that the subcellular localization of CARP in Purkinje cells is coincident with that of IP(3)R1. Biochemical analysis also showed that CARP is co-precipitated with IP(3)R1. Using deletion mutagenesis, we established that amino acids 45-291 of CARP are essential for its association with IP(3)R1, and that the CARP-binding site is located within the modulatory domain of IP(3)R1 amino acids 1387-1647. CARP inhibits IP(3) binding to IP(3)R1 by reducing the affinity of the receptor for IP(3). As reported previously, sensitivity to IP(3) for IP(3)-induced Ca(2+) release in Purkinje cells is low compared with that in other tissues. This could be due to co-expression of CARP with IP(3)R in Purkinje cells and its inhibitory effects on IP(3) binding.

In mice, Ϸ1,000 odorant receptor (OR) genes are expressed in olfactory sensory neurons (OSNs). Homeodomain sites can be recognized in the promoter and upstream regions of several OR genes. Here, using the yeast one-hybrid system and electrophoretic mobility shift assay, we report that Lhx2, a LIM-homeodomain protein, binds to the homeodomain site in the mouse M71 OR promoter region. In Lhx2-deficient mice, the morphology of the olfactory epithelium is grossly normal. However, expression of OMP is abolished and that of GAP43 is severely reduced, indicating that no mature and few immature OSNs are produced. M71 and other OR genes also are not expressed. OSN development appears to be arrested between the terminal differentiation into neurons and the transition to immature neurons. Thus, Lhx2 is required for complete development of OSNs in mice.I n the mammalian olfactory epithelium (OE), olfactory sensory neurons (OSNs) detect chemical stimuli in the external environment by expressing odorant receptor (OR) genes (1, 2). These genes encode proteins with a putative seven-transmembrane domain structure, a defining characteristic of G proteincoupled receptors. It is believed that an individual OSN expresses a single OR gene (3) from the Ϸ1,000 OR genes in the mouse genome (4), but the strength of the evidence for this one-neuron-one-receptor hypothesis has been questioned (5). An OR gene is expressed from a single allele in a given cell (6). The OE is thus a complex mosaic of Ϸ2,000 OSN populations, each defined as expressing one allele from a choice of 2 ϫ Ϸ1,000 genes. OSNs expressing the same OR gene typically reside within one of at least four zones in the OE (7,8), where they are interspersed with OSNs expressing other OR genes. By targeted mutagenesis, all OSNs expressing the same OR were shown to project their axons to the same glomeruli in a remarkably precise manner, and these OR-specific projections to the olfactory bulb are influenced by the specificity of the expressed OR (9, 10). The onset of OR expression occurs before the first contact between OSN axons and the forebrain in embryos, and OSNs express OR genes in the absence of the axonal target, the olfactory bulb (11).The mechanisms underlying OR gene choice and expression are not understood, but irreversible DNA rearrangements have been excluded (12, 13). Sequence analyses of human, mouse, and rat OR genes have revealed a variety of motifs upstream of the transcription start site, including O͞E-like, E-box, Ikaros, homeodomain, and methylation-sensitive vMYB motifs (14). However, an involvement in OR gene regulation has not been shown for any of these motifs. Short (9-kb) transgenes of two OR genes, MOR23 and M71, replicate most OR expression features (15). A region of 405 bp upstream of the MOR23 transcription start site is required for transgene expression. In this and other upstream OR regions, common sequence motifs of homeodomain and O͞E-like sites have been recognized (15).Here, we have conducted yeast one-hybrid screening (16) to identify transcr...

The vomeronasal organ (VNO) is a chemosensory organ specialized in the detection of pheromones in higher vertebrates. In mouse and rat, two gene superfamilies, V1r and V2r vomeronasal receptor genes, are expressed in sensory neurons whose cell bodies are located in, respectively, the apical and basal layers of the VNO epithelium. Here, we report that neurons of the basal layer express another multigene family, termed H2-Mv, representing nonclassical class I genes of the major histocompatibility complex. The nine H2-Mv genes are expressed differentially in subsets of neurons. More than one H2-Mv gene can be expressed in an individual neuron. In situ hybridization with probes for H2-Mv and V2r genes reveals complex and nonrandom combinations of coexpression. While neural expression of Mhc class I molecules is increasingly being appreciated, the H2-Mv family is distinguished by variegated expression across seemingly similar neurons and coexpression with a distinct multigene family encoding neural receptors. Our findings suggest that basal vomeronasal sensory neurons may consist of multiple lineages or compartments, defined by particular combinations of V2r and H2-Mv gene expression.

The dependency of purified mouse cerebellar type 1 inositol 1,4,5-trisphosphate receptor (IP3R1)/Ca2+ channel function on cytoplasmic Ca2+ was examined. In contrast to the channels in crude systems, the purified IP3R1 reconstituted into planar lipid bilayers did not show the bell-shaped dependence on Ca2+. It was activated with increasing Ca2+ sublinearly without inhibition even up to 200 microM. The addition of calmodulin to the cytoplasmic side inhibited the channel at high Ca2+ concentrations. Calmodulin antagonists reversed the Ca2+-dependent inactivation of the native channels in cerebellar microsomes. These results indicate that the bell-shaped dependence on cytoplasmic Ca2+ is not an intrinsic property of the IP3R1, and the Ca2+-dependent inactivation is directly mediated by calmodulin.

We report the construction of the mouse full-length cDNA encyclopedia, the most extensive view of a complex transcriptome, on the basis of preparing and sequencing 246 libraries. Before cloning, cDNAs were enriched in full-length by Cap-Trapper, and in most cases, aggressively subtracted/normalized. We have produced 1,442,236 successful 3Ј-end sequences clustered into 171,144 groups, from which 60,770 clones were fully sequenced cDNAs Cold Spring Harbor Laboratory Press on May 10, 2018 -Published by genome.cshlp.org Downloaded from annotated in the FANTOM-2 annotation. We have also produced 547,149 5Ј end reads, which clustered into 124,258 groups. Altogether, these cDNAs were further grouped in 70,000 transcriptional units (TU), which represent the best coverage of a transcriptome so far. By monitoring the extent of normalization/subtraction, we define the tentative equivalent coverage (TEC), which was estimated to be equivalent to >12,000,000 ESTs derived from standard libraries. High coverage explains discrepancies between the very large numbers of clusters (and TUs) of this project, which also include non-protein-coding RNAs, and the lower gene number estimation of genome annotations. Altogether, 5Ј-end clusters identify regions that are potential promoters for 8637 known genes and 5Ј-end clusters suggest the presence of almost 63,000 transcriptional starting points. An estimate of the frequency of polyadenylation signals suggests that at least half of the singletons in the EST set represent real mRNAs. Clones accounting for about half of the predicted TUs await further sequencing. The continued high-discovery rate suggests that the task of transcriptome discovery is not yet complete.[Supplemental material available online at www.genome.org.]One of the primary goals of genome sequencing projects is to identify the genome sequences that are transcribed into functional mRNAs, so that full-length cDNAs can be isolated to allow further downstream biology, and functional and structural genomics. The limitations of a priori genome annotation dictate that the transcriptome needs to be identified experimentally via cDNA cloning and sequencing. Although expressed sequence tags (ESTs) (Adams et al. 1991(Adams et al. , 1995Hillier et al. 1996;Marra et al. 1999;Kargul et al. 2001) and ORESTES (Camargo et al. 2001) have been extremely valuable for new gene discovery, these approaches have not allowed highthroughput recovering of full-length cDNA clones nor definition of protein sequence derived from actual cDNA clones. To overcome such problems, we undertook from the year 1995, a strategic project aimed at the comprehensive collection of at least one full-length cDNA derived from each mouse gene, a strategy that is recently becoming useful in similar projects to collect full-length gene collections (Stapleton et al. 2002;Strausberg et al. 2002).Because of the limited processivity of reverse transcriptase and other limitations, standard cDNA libraries generally contain a majority of truncated transcripts. The introductio...

The inositol 1,4,5-trisphosphate (IP 3 ) receptor (IP 3 R), an IP 3 -gated Ca 2؉ channel located on intracellular Ca 2؉ stores, modulates intracellular Ca 2؉ signaling. During apoptosis of the human T-cell line, Jurkat cells, as induced by staurosporine or Fas ligation, IP 3 R type 1 (IP 3 R1) was found to be cleaved. IP 3 R1 degradation during apoptosis was inhibited by pretreatment of Jurkat cells with the caspase-3 (-like protease) inhibitor, Ac-DEVD-CHO, and the caspases inhibitor, z-VAD-CH 2 DCB but not by the caspase-1 (-like protease) inhibitor, Ac-YVAD-CHO, suggesting that IP 3 R1 was cleaved by a caspase-3 (-like) protease. The recombinant caspase-3 cleaved IP 3 R1 in vitro to produce a fragmentation pattern consistent with that seen in Jurkat cells undergoing apoptosis. N-terminal amino acid sequencing revealed that the major cleavage site is 1888 DEVD* 1892 R (mouse IP 3 R1), which involves consensus sequence for caspase-3 cleavage (DEVD). To determine whether IP 3 R1 is cleaved by caspase-3 or is proteolyzed in its absence by other caspases, we examined the cleavage of IP 3 R1 during apoptosis in the MCF-7 breast carcinoma cell line, which has genetically lost caspase-3. Tumor necrosis factor-␣-or staurosporine-induced apoptosis in caspase-3-deficient MCF-7 cells failed to demonstrate cleavage of IP 3 R1. In contrast, MCF-7/Casp-3 cells stably expressing caspase-3 showed IP 3 R1 degradation upon apoptotic stimuli. Therefore IP 3 R1 is a newly identified caspase-3 substrate, and caspase-3 is essential for the cleavage of IP 3 R1 during apoptosis. This cleavage resulted in a decrease in the channel activity as IP 3 R1 was digested, indicating that caspase-3 inactivates IP 3 R1 channel functions.Apoptosis is an evolutionary conserved form of cell death by which normal cellular development and homeostasis are maintained. This programmed cell death is regulated by a series of biochemical events, namely activation of a family of cysteine proteases, caspases, which in turn cleave specific intracellular proteins resulting in an irreversible commitment to cell death.Among the caspase family, caspase-3 plays a crucial role in execution of apoptosis. Known substrates for caspase-3 (1) involve poly(ADP-ribose) polymerase, p21-activated kinase 2 (1, 2), gelsolin (3), DNA-dependent protein kinase catalytic subunit, DNA fragmentation factor 45 kDa subunit (4), and ␣-fodrin (5, 6). By analogy of the cleavage site of these substrates, amino acid sequence of DEXD is considered to be a recognition motif of caspase-3.Inositol 1,4,5-trisphosphate (IP 3 ) 1 receptor (IP 3 R), an IP 3 -gated Ca 2ϩ channel located on intracellular Ca 2ϩ stores, plays a crucial role in a variety of cell functions, including fertilization, cell proliferation, metabolism, secretion, contraction of smooth muscle, and neural signals (7,8). Molecular cloning studies revealed that there are three types of IP 3 R: IP 3 R type 1 (IP 3 R1), IP 3 R type 2 (IP 3 R2), and IP 3 R type 3 (IP 3 R3) (9 -12). The involvement of IP 3 Rs during apoptosis has b...

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The transcription factor Bcl11b/Ctip2 plays critical roles in the development of several systems and organs, including the immune system, central nervous system, skin and teeth. Here, we show that Bcl11b/Ctip2 is highly expressed in the developing vomeronasal system in mice and is required for its proper development. Bcl11b/Ctip2 is expressed in post-mitotic vomeronasal sensory neurons (VSNs) in the vomeronasal epithelium as well as projection neurons and GABAergic interneurons in the accessory olfactory bulb (AOB). In the absence of Bcl11b, these neurons are born in the correct number, but VSNs selectively die by apoptosis. The critical role of Bcl11b in vomeronasal system development is demonstrated by the abnormal phenotypes of Bcl11b-deficient mice: disorganization of layer formation of the AOB, impaired axonal projections of VSNs, a significant reduction in the expression of vomeronasal receptor genes, and defective mature differentiation of VSNs. VSNs can be classified into two major types of neurons, vomeronasal 1 receptor (V1r)/Gαi2-positive and vomeronasal 2 receptor (V2r)/Gαo-positive VSNs. We found that all Gαi2-positive cells co-expressed Gαo during embryogenesis. This co-expression is also observed in newly differentiated neurons in the adult VNE. Interestingly, loss of Bcl11b function resulted in an increased number of V1r/Gαi2-type VSNs and a decreased number of V2r/Gαo-type VSNs, suggesting that Bcl11b regulates the fate choice between these two VSN types. These results indicate that Bcl11b/Ctip2 is an essential regulator of the differentiation and dichotomy of VSNs.